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"datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 7, + "result_json": "experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 7, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } + } + ] +} \ No newline at end of file diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..ca2a15bdf735f79cebd3373bc61a034d7a8f97b6 --- /dev/null +++ b/README.md @@ -0,0 +1,58 @@ +# scFATE — NeurIPS 2026 + +Lie-algebraic conditional flow matching for zero-shot perturbation prediction in single cells. This repo contains all +checkpoints and configs behind Table 1 in the paper. Datasets are split out into a separate repo: +[`Angione-Lab/scFATE-datasets`](https://huggingface.co/datasets/Angione-Lab/scFATE-datasets). + +## Layout + +``` +backbones// — scFATE rotation autoencoders (load first) +flow_heads//seed{1,2,3}/ — pure-flow heads on the rotation latent +flow_heads/k562/base/ — K562 flow teacher (for reflow) +flow_heads/k562/reflow_K2_s1/ — K562 reflow K=2 student (paper headline 81.2 DA) +sciplex3_path_b/teachers/{priorkrr,priornone}/s{1..9}/ +sciplex3_path_b/students/mixed18_K16/s{1..7}/ — mixed-18 K=16 distilled student (paper headline 70.0 DA) +results/table1_inputs/ — saved eval JSONs for reviewer audit +REPRODUCE.md — paper reproduction guide +MANIFEST.json — machine-readable run inventory +``` + +## Quickstart + +```python +from huggingface_hub import snapshot_download +import torch + +# 1. Pull the K562 paper-headline checkpoint +ckpt_dir = snapshot_download("Angione-Lab/scFATE", allow_patterns="flow_heads/k562/reflow_K2_s1/*") +ckpt = torch.load(f"{ckpt_dir}/flow_heads/k562/reflow_K2_s1/flow_best.pt", map_location="cpu", weights_only=False) + +# 2. The ckpt has every hparam at top-level; the velocity-network state_dict is at ckpt["v_net_state_dict"] +print({k: v for k, v in ckpt.items() if not k.endswith("_state_dict") and not k.startswith("_")}) +``` + +For end-to-end reproduction (backbone → flow → reflow → eval), see [`REPRODUCE.md`](./REPRODUCE.md). + +## Caveat (important for paper integrity) + +Table 1 of the paper reports `cos=0.491 / PDE=0.483` for the SciPlex3 (Path B) row. **These two values are not in any +saved eval log on the original training machine.** Only the mean DA = 0.700 reproduces from +`results/table1_inputs/sciplex3_iter214_multi_metric_router_ensemble.json` +(`metric_da.tanimoto_morgan2048 = 0.7000`). The router pipeline only stored DA, not cos/PDE. We are re-running the +SciPlex3 Path-B eval to compute proper cos/PDE for camera-ready; until then, treat the SciPlex3 row's continuous metrics +as not-yet-reproduced. + +Norman cos/PDE in Table 1 differ from the saved JSONs by ~0.002 (rounding). K562 reflow cos/PDE differ by ~0.007 (likely +rounding/transcription). + +## Citation + +``` +@inproceedings{ahmad2026scfate, + title={scFATE: Zero-shot Perturbation Prediction via Lie-Algebraic Conditional Flow Matching}, + author={Ahmad, Farhan and Angione, Claudio and others}, + booktitle={NeurIPS}, + year={2026} +} +``` diff --git a/REPRODUCE.md b/REPRODUCE.md new file mode 100644 index 0000000000000000000000000000000000000000..a7ff436914051be23dd7e3626b604a11aa9ebd52 --- /dev/null +++ b/REPRODUCE.md @@ -0,0 +1,88 @@ +# scFATE NeurIPS 2026 — Reproduce the Paper + +This directory ships every checkpoint behind the paper's Table 1 + a `reproduce.sh` +for each run. All 31 paper-headline runs are listed below. + +## 0. Prerequisites + +```bash +git clone https://huggingface.co/Angione-Lab/scFATE +cd scFATE/code # source code is in scfate-code submodule +uv venv && uv pip install -e . # or pip install -r requirements.txt +``` + +Then download datasets: +```bash +huggingface-cli download Angione-Lab/scFATE-datasets --local-dir datasets/scFATE/processed --repo-type dataset +``` + +## 1. Dependency graph + +``` +backbone (rotation autoencoder) — hf-assets/checkpoints// + └─→ flow head (s1, s2, s3) — runs/_flow_*/flow_best.pt + └─→ reflow K=2 (K562) — runs/*_reflow_K2_*_s1/flow_best.pt + └─→ teachers ×18 (SciPlex3) — runs/*_priorkrr_V2B_s{1..9}, *_priornone_V2B_s{1..9} + └─→ student ×7 — runs/*_reflow_ensemble_mixed18_K16_V2B_s{1..7} +``` + +## 2. Per-run reproduction + +Each `runs//` contains: +- `flow_best.pt` — checkpoint with embedded hparams (load via `torch.load`, look at top-level keys or `ckpt['hparams']`) +- `config.json` — extracted hparams + result-JSON pointer + dataset path +- `reproduce.sh` — exact training command, ready to run +- `flow_metrics.jsonl` — training trajectory +- `krr_prior.pkl` — KRR-init prior (if `prior=krr`) + +## 3. Paper-headline runs + +| Paper row | Dataset | Run dir | Result JSON | Reproduce | +|---|---|---|---|---| +| Norman seed 1 | CRISPRa Norman | `runs/b200_norman_flow_e115_krrinit_s02_mask_30k` | `experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json` | `bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k/reproduce.sh` | +| Norman seed 2 | CRISPRa Norman | `runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2` | `experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed2.json` | `bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2/reproduce.sh` | +| Norman seed 3 | CRISPRa Norman | `runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3` | `experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed3.json` | `bash runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3/reproduce.sh` | +| RPE1 seed 1 | Replogle RPE1 | `runs/b200_rpe1_flow_block_krrinit_mask_30k_s1` | `experiments/results/fair_comparison/rpe1_rotation_vs_direct__flow__b200_rpe1_flow_block_krrinit_mask_30k_s1_rpe1_block_K128.json` | `bash runs/b200_rpe1_flow_block_krrinit_mask_30k_s1/reproduce.sh` | +| K562 base flow (teacher for reflow) | Replogle K562 | `runs/b200_k562_flow_bs2048_krrinit_mask_30k` | `experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_K128.json` | `bash runs/b200_k562_flow_bs2048_krrinit_mask_30k/reproduce.sh` | +| K562 reflow K=2 (paper headline 81.2) | Replogle K562 | `runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1` | `experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1_reflow_K2_bracket1p0_ens5seed_sigmainf0p15_antithetic_Kper128.json` | `bash runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1/reproduce.sh` | +| SciPlex3 priornone teacher s1 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/reproduce.sh` | +| SciPlex3 priorkrr teacher s1 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/reproduce.sh` | +| SciPlex3 priornone teacher s2 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/reproduce.sh` | +| SciPlex3 priorkrr teacher s2 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/reproduce.sh` | +| SciPlex3 priornone teacher s3 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/reproduce.sh` | +| SciPlex3 priorkrr teacher s3 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/reproduce.sh` | +| SciPlex3 priornone teacher s4 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/reproduce.sh` | +| SciPlex3 priorkrr teacher s4 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/reproduce.sh` | +| SciPlex3 priornone teacher s5 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/reproduce.sh` | +| SciPlex3 priorkrr teacher s5 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/reproduce.sh` | +| SciPlex3 priornone teacher s6 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/reproduce.sh` | +| SciPlex3 priorkrr teacher s6 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/reproduce.sh` | +| SciPlex3 priornone teacher s7 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/reproduce.sh` | +| SciPlex3 priorkrr teacher s7 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/reproduce.sh` | +| SciPlex3 priornone teacher s8 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/reproduce.sh` | +| SciPlex3 priorkrr teacher s8 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/reproduce.sh` | +| SciPlex3 priornone teacher s9 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/reproduce.sh` | +| SciPlex3 priorkrr teacher s9 | SciPlex3 | `runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9` | — | `bash runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s1 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1` | `experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s2 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2` | `experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s3 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3` | `experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s4 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4` | `experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s5 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5` | `experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s6 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6` | `experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6/reproduce.sh` | +| SciPlex3 mixed-18 K=16 student s7 (paper headline 70.0) | SciPlex3 | `runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7` | `experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json` | `bash runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7/reproduce.sh` | + +## 4. Eval pipeline + +```bash +.venv/bin/python scripts/eval_fair_comparison.py \\ + --dataset --flow_ckpt /flow_best.pt \\ + --multiview data/gene_embeddings/_multiview.pt --K_eval 128 +``` + +## 5. Known caveats + +- SciPlex3 paper-row cosine (0.491) and PDE (0.483) numbers in Table 1 are not in any saved + results JSON; only mean DA = 0.700 reproduces from `iter214_multi_metric_router_ensemble.json` + (`metric_da.tanimoto_morgan2048`). Re-eval needed before final submission. +- Norman cos/PDE in Table 1 differ by ~0.002 from `*_K128.json` (rounded). +- K562 reflow cos/PDE in Table 1 differ by ~0.007 from the saved ensemble JSON. diff --git a/backbones/k562/config.json b/backbones/k562/config.json new file mode 100644 index 0000000000000000000000000000000000000000..ea732ccb3cb14e5b1547328a5384d392d8b8f883 --- /dev/null +++ b/backbones/k562/config.json @@ -0,0 +1,6 @@ +{ + "checkpoint": "scFATE_epoch700_periodic.pt", + "type": "scFATE rotation autoencoder", + "dataset": "k562", + "source_path_in_b200_repo": "hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt" +} \ No newline at end of file diff --git a/backbones/k562/scFATE_epoch700_periodic.pt b/backbones/k562/scFATE_epoch700_periodic.pt new file mode 100644 index 0000000000000000000000000000000000000000..ae74c51b4f75ea6cff779c277afcd968379c5b43 --- /dev/null +++ b/backbones/k562/scFATE_epoch700_periodic.pt @@ -0,0 +1,3 @@ +version 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b/flow_heads/k562/base/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..3d8183c0b052149d56318ab0cf634bba8dca0130 --- /dev/null +++ b/flow_heads/k562/base/reproduce.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# Reproduce: K562 base flow (teacher for reflow) +# Run dir: runs/b200_k562_flow_bs2048_krrinit_mask_30k +# Result: experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_K128.json +# Original launch: runs/launch_tx_bch_combo.sh +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/replogle_k562/replogle_k562.h5ad" +BACKBONE="hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt" +RUN_DIR="runs/b200_k562_flow_bs2048_krrinit_mask_30k" + +.venv/bin/python -u scripts/train_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.05 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' diff --git a/flow_heads/k562/reflow_K2_s1/config.json b/flow_heads/k562/reflow_K2_s1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..d44624ee995b43d54df512922671c06ffbadeb0a --- /dev/null +++ b/flow_heads/k562/reflow_K2_s1/config.json @@ -0,0 +1,58 @@ +{ + "paper_row": "K562 reflow K=2 (paper headline 81.2)", + "dataset": "Replogle K562", + "run_dir": "runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1", + "backbone": "hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt", + "h5ad_rel": "datasets/scFATE/processed/replogle_k562/replogle_k562.h5ad", + "training_script": "scripts/reflow_k562_delta_flow.py", + "seed": 1, + "result_json": "experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1_reflow_K2_bracket1p0_ens5seed_sigmainf0p15_antithetic_Kper128.json", + "teacher": "runs/b200_k562_flow_bs2048_krrinit_mask_30k", + "teachers": null, + "launch_script": "runs/launch_iter174_ens5_Kper256_and_train_s6_s10.sh", + "checkpoint": { + "path": "runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1/flow_best.pt", + "size_mb": 46.5, + "files_in_dir": [ + "config.json", + "flow_best.pt", + "flow_metrics.jsonl", + "krr_prior.pkl", + "reproduce.sh" + ] + }, + "hparams_top": { + "_v_net_state_dict_present": true, + "theta_dim": 192, + "d_embed": 1824, + "d_hidden": 512, + "n_blocks": 4, + "sigma": 0.05, + "n_steps": 20, + "epoch": 21000, + "loss": 0.002288587740622461, + "pert_names": "", + "mv_gene_names": "", + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 1.0, + "head_kind": "flat", + "d_block_head": 16, + "velocity_arch": "mlp", + "teacher_arch": "mlp", + "tx_d_token": 128, + "tx_n_layers": 4, + "tx_n_heads": 4, + "tx_mlp_mult": 4.0, + "cfg_drop": 0.0, + "rectified_from": "runs/b200_k562_flow_bs2048_krrinit_mask_30k/flow_best.pt", + "rectified_K": 2, + "rectified_teacher_n_steps": 20, + "target_noise_sigma": 0.0, + "t_sampling": "uniform", + "bch_aug_rate": 0.0, + "bch_embed_mode": "mean", + "bracket_reg": 1.0 + }, + "hparams_nested": {} +} \ No newline at end of file diff --git a/flow_heads/k562/reflow_K2_s1/flow_best.pt b/flow_heads/k562/reflow_K2_s1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..8331b459c13a73317fce516e2f3dd8215f21950e --- /dev/null +++ b/flow_heads/k562/reflow_K2_s1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0b1c30fef5a275d495aea10c63a8418d059076910fe15a26bbdcd678d8fe2395 +size 48808267 diff --git a/flow_heads/k562/reflow_K2_s1/flow_metrics.jsonl b/flow_heads/k562/reflow_K2_s1/flow_metrics.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..55cbcb91b825bab8620d7184b4bfa7a8ebe1fe52 --- /dev/null +++ b/flow_heads/k562/reflow_K2_s1/flow_metrics.jsonl @@ -0,0 +1,31 @@ +{"epoch": 0, "loss": 0.012353552505373955, "recon_cos": 0.26796600222587585, "recon_mse": 0.007586885243654251, "lr": 0.00029999999918575764, "elapsed": 0.22760009765625} +{"epoch": 1000, "loss": 0.004366907058283687, "recon_cos": 0.3213195502758026, "recon_mse": 0.007488366682082415, "lr": 0.000299184875142442, "elapsed": 9.939256191253662} +{"epoch": 2000, "loss": 0.00322694331407547, "recon_cos": 0.3219950497150421, "recon_mse": 0.007425216026604176, "lr": 0.00029675168470201714, "elapsed": 19.642594575881958} +{"epoch": 3000, "loss": 0.0030198460444808006, "recon_cos": 0.3225366175174713, "recon_mse": 0.007321089506149292, "lr": 0.00029272708640812903, "elapsed": 29.34191346168518} +{"epoch": 4000, "loss": 0.0029479566728696227, 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b/flow_heads/k562/reflow_K2_s1/krr_prior.pkl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:04466eddd84193b892d70eab064ad29222aee31ec8fa6aa33f770f26044ac147 +size 6581197 diff --git a/flow_heads/k562/reflow_K2_s1/reproduce.sh b/flow_heads/k562/reflow_K2_s1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..1e0fe7ac5aba2104b3f7c72096c8a149a95d96df --- /dev/null +++ b/flow_heads/k562/reflow_K2_s1/reproduce.sh @@ -0,0 +1,45 @@ +#!/bin/bash +# Reproduce: K562 reflow K=2 (paper headline 81.2) +# Run dir: runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1 +# Result: experiments/results/fair_comparison/replogle_rotation_vs_direct__flow__b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1_reflow_K2_bracket1p0_ens5seed_sigmainf0p15_antithetic_Kper128.json +# Original launch: runs/launch_iter174_ens5_Kper256_and_train_s6_s10.sh +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/replogle_k562/replogle_k562.h5ad" +BACKBONE="hf-assets/checkpoints/crispri_k562/scFATE_epoch700_periodic.pt" +RUN_DIR="runs/b200_k562_flow_bs2048_krrinit_mask_30k_reflow_K2_nomask_bracket1ep0_s1" + +.venv/bin/python -u scripts/reflow_k562_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.05 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --head_kind 'flat' \ + --velocity_arch 'mlp' \ + --t_sampling 'uniform' \ + --target_noise_sigma 0.0 \ + --rectified_K 2 \ + --rectified_from 'runs/b200_k562_flow_bs2048_krrinit_mask_30k/flow_best.pt' \ + --rectified_teacher_n_steps 20 \ + --bracket_reg 1.0 \ + --cfg_drop 0.0 \ + --bch_aug_rate 0.0 \ + --bch_embed_mode 'mean' \ + --tx_d_token 128 \ + --tx_n_layers 4 \ + --tx_n_heads 4 \ + --tx_mlp_mult 4.0 \ + --d_block_head 16 \ + --teacher_arch 'mlp' diff --git a/flow_heads/norman/seed1/config.json b/flow_heads/norman/seed1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..d19b8355c10d52702b13d146f917217b7cf8f362 --- /dev/null +++ b/flow_heads/norman/seed1/config.json @@ -0,0 +1,41 @@ +{ + "paper_row": "Norman seed 1", + "dataset": "CRISPRa Norman", + "run_dir": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k", + "backbone": "hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt", + "h5ad_rel": "datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad", + "training_script": "scripts/train_flow.py", + "seed": 1, + "result_json": "experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json", + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k/flow_best.pt", + "size_mb": 46.5, + "files_in_dir": [ + "config.json", + "flow_best.pt", + "flow_metrics.jsonl", + "krr_prior.pkl", + "reproduce.sh" + ] + }, + "hparams_top": { + "_v_net_state_dict_present": true, + "theta_dim": 192, + "d_embed": 1824, + "d_hidden": 512, + "n_blocks": 4, + "sigma": 0.02, + "n_steps": 20, + "epoch": 28500, + "loss": 0.000217468106711749, + "pert_names": "", + "mv_gene_names": "", + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 1.0 + }, + "hparams_nested": {} +} \ No newline at end of file diff --git a/flow_heads/norman/seed1/flow_best.pt b/flow_heads/norman/seed1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..83529d06868c85b8905093264ba55299d8c2c699 --- /dev/null +++ b/flow_heads/norman/seed1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8321a5e46a8f0e07082a110a6522846d4fd7416eec9975f7c73fa56db5002211 +size 48778123 diff --git a/flow_heads/norman/seed1/flow_metrics.jsonl b/flow_heads/norman/seed1/flow_metrics.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..b3d2db7976e95307ba673223b28bdb88a9847c52 --- /dev/null +++ b/flow_heads/norman/seed1/flow_metrics.jsonl @@ -0,0 +1,61 @@ +{"epoch": 0, "loss": 0.01003973837941885, "recon_cos": 0.5566251277923584, "recon_cos_legacy": 0.5566251277923584, "n_nonzero": 76, "recon_mse": 0.011273065581917763, "lr": 0.00029999999918575764, "elapsed": 0.3872981071472168} +{"epoch": 500, "loss": 0.0007567266584374011, "recon_cos": 0.946628987789154, "recon_cos_legacy": 0.946628987789154, "n_nonzero": 76, "recon_mse": 0.0012348232557997108, "lr": 0.0002997956712275646, "elapsed": 4.166512489318848} +{"epoch": 1000, "loss": 0.000545473478268832, "recon_cos": 0.9728690981864929, "recon_cos_legacy": 0.9728690981864929, "n_nonzero": 76, "recon_mse": 0.000774765620008111, "lr": 0.000299184875142442, "elapsed": 7.958467721939087} 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+{"epoch": 29000, "loss": 0.00022093609732110053, "recon_cos": 0.9930673241615295, "recon_cos_legacy": 0.9930673241615295, "n_nonzero": 76, "recon_mse": 0.000183222015039064, "lr": 3.8118738376273407e-06, "elapsed": 247.22252988815308} +{"epoch": 29500, "loss": 0.00021909073257120326, "recon_cos": 0.9930500388145447, "recon_cos_legacy": 0.9930500388145447, "n_nonzero": 76, "recon_mse": 0.00018282099335920066, "lr": 3.2027010317082486e-06, "elapsed": 251.35426783561707} +{"epoch": 29999, "loss": 0.0002226803990197368, "recon_cos": 0.9930833578109741, "recon_cos_legacy": 0.9930833578109741, "n_nonzero": 76, "recon_mse": 0.00018210829875897616, "lr": 2.9999999999999997e-06, "elapsed": 255.48506379127502} diff --git a/flow_heads/norman/seed1/krr_prior.pkl b/flow_heads/norman/seed1/krr_prior.pkl new file mode 100644 index 0000000000000000000000000000000000000000..f6df7424359fefff337c6af4e736767e3859c4e2 --- /dev/null +++ b/flow_heads/norman/seed1/krr_prior.pkl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ed54b2612b50268760dc710e28dc0eca0f26b9162bfd5ab3c309af3e855f9c1a +size 613987 diff --git a/flow_heads/norman/seed1/reproduce.sh b/flow_heads/norman/seed1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..d2eae248bda92209c9b760ca66eefe8130de539f --- /dev/null +++ b/flow_heads/norman/seed1/reproduce.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# Reproduce: Norman seed 1 +# Run dir: runs/b200_norman_flow_e115_krrinit_s02_mask_30k +# Result: experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad" +BACKBONE="hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt" +RUN_DIR="runs/b200_norman_flow_e115_krrinit_s02_mask_30k" + +.venv/bin/python -u scripts/train_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.02 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' diff --git a/flow_heads/norman/seed2/config.json b/flow_heads/norman/seed2/config.json new file mode 100644 index 0000000000000000000000000000000000000000..699f0b6a8f4f4f9adecb64e6a9d397526153a781 --- /dev/null +++ b/flow_heads/norman/seed2/config.json @@ -0,0 +1,41 @@ +{ + "paper_row": "Norman seed 2", + "dataset": "CRISPRa Norman", + "run_dir": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2", + "backbone": "hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt", + "h5ad_rel": "datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad", + "training_script": "scripts/train_flow.py", + "seed": 2, + "result_json": "experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed2.json", + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2/flow_best.pt", + "size_mb": 46.5, + "files_in_dir": [ + "config.json", + "flow_best.pt", + "flow_metrics.jsonl", + "krr_prior.pkl", + "reproduce.sh" + ] + }, + "hparams_top": { + "_v_net_state_dict_present": true, + "theta_dim": 192, + "d_embed": 1824, + "d_hidden": 512, + "n_blocks": 4, + "sigma": 0.02, + "n_steps": 20, + "epoch": 29000, + "loss": 0.0001306741796724964, + "pert_names": "", + "mv_gene_names": "", + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 1.0 + }, + "hparams_nested": {} +} \ No newline at end of file diff --git a/flow_heads/norman/seed2/flow_best.pt b/flow_heads/norman/seed2/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..307aec9edaeb78a31b941b9c18671a11fc330ef6 --- /dev/null +++ b/flow_heads/norman/seed2/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4dab56cc4286ae62302f9f63d6d5a517b946885f49805d8942b5c2d8a994c16c +size 48778123 diff --git a/flow_heads/norman/seed2/flow_metrics.jsonl b/flow_heads/norman/seed2/flow_metrics.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..cd44de12821f96740a1e03d7ccb659e31a46a1e9 --- /dev/null +++ b/flow_heads/norman/seed2/flow_metrics.jsonl @@ -0,0 +1,61 @@ +{"epoch": 0, "loss": 0.011453788727521896, "recon_cos": 0.5006781220436096, "recon_cos_legacy": 0.5006781220436096, "n_nonzero": 76, "recon_mse": 0.010992382653057575, "lr": 0.00029999999918575764, "elapsed": 0.3346214294433594} +{"epoch": 500, "loss": 0.0007259499980136752, "recon_cos": 0.9239220023155212, 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0.9962025880813599, "n_nonzero": 76, "recon_mse": 0.00010019737965194508, "lr": 2.9999999999999997e-06, "elapsed": 243.26091957092285} diff --git a/flow_heads/norman/seed2/krr_prior.pkl b/flow_heads/norman/seed2/krr_prior.pkl new file mode 100644 index 0000000000000000000000000000000000000000..f6df7424359fefff337c6af4e736767e3859c4e2 --- /dev/null +++ b/flow_heads/norman/seed2/krr_prior.pkl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ed54b2612b50268760dc710e28dc0eca0f26b9162bfd5ab3c309af3e855f9c1a +size 613987 diff --git a/flow_heads/norman/seed2/reproduce.sh b/flow_heads/norman/seed2/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..70d70b5a2779c945bf143a5a1ffcf3524115cedb --- /dev/null +++ b/flow_heads/norman/seed2/reproduce.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# Reproduce: Norman seed 2 +# Run dir: runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2 +# Result: experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed2.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad" +BACKBONE="hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt" +RUN_DIR="runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed2" + +.venv/bin/python -u scripts/train_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 2 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.02 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' diff --git a/flow_heads/norman/seed3/config.json b/flow_heads/norman/seed3/config.json new file mode 100644 index 0000000000000000000000000000000000000000..7bb4273f4e32cac03275a802513f88bfcba3bf02 --- /dev/null +++ b/flow_heads/norman/seed3/config.json @@ -0,0 +1,41 @@ +{ + "paper_row": "Norman seed 3", + "dataset": "CRISPRa Norman", + "run_dir": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3", + "backbone": "hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt", + "h5ad_rel": "datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad", + "training_script": "scripts/train_flow.py", + "seed": 3, + "result_json": "experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed3.json", + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3/flow_best.pt", + "size_mb": 46.5, + "files_in_dir": [ + "config.json", + "flow_best.pt", + "flow_metrics.jsonl", + "krr_prior.pkl", + "reproduce.sh" + ] + }, + "hparams_top": { + "_v_net_state_dict_present": true, + "theta_dim": 192, + "d_embed": 1824, + "d_hidden": 512, + "n_blocks": 4, + "sigma": 0.02, + "n_steps": 20, + "epoch": 29500, + "loss": 0.0001756271449266933, + "pert_names": "", + "mv_gene_names": "", + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 1.0 + }, + "hparams_nested": {} +} \ No newline at end of file diff --git a/flow_heads/norman/seed3/flow_best.pt b/flow_heads/norman/seed3/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..1993edb0d2193f2fdcf48257f30f818eb4775248 --- /dev/null +++ b/flow_heads/norman/seed3/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9348ed5dfcbf59ac2a99463d64f006ac9287f4845ea6a2cef6ddc7495c747192 +size 48778123 diff --git a/flow_heads/norman/seed3/flow_metrics.jsonl b/flow_heads/norman/seed3/flow_metrics.jsonl new file mode 100644 index 0000000000000000000000000000000000000000..1c8509e70d61bf243adeef18f2ac9402b7507181 --- /dev/null +++ b/flow_heads/norman/seed3/flow_metrics.jsonl @@ -0,0 +1,61 @@ +{"epoch": 0, "loss": 0.010685030836611986, "recon_cos": 0.47311341762542725, "recon_cos_legacy": 0.47311341762542725, "n_nonzero": 76, "recon_mse": 0.01180971972644329, "lr": 0.00029999999918575764, "elapsed": 0.5167660713195801} +{"epoch": 500, "loss": 0.0007356101705227047, "recon_cos": 0.9160396456718445, "recon_cos_legacy": 0.9160396456718445, "n_nonzero": 76, "recon_mse": 0.001977349631488323, "lr": 0.0002997956712275646, "elapsed": 4.302055597305298} +{"epoch": 1000, "loss": 0.0005432900215964764, "recon_cos": 0.9728785157203674, "recon_cos_legacy": 0.9728785157203674, "n_nonzero": 76, "recon_mse": 0.0006862425361759961, "lr": 0.000299184875142442, "elapsed": 8.045132875442505} +{"epoch": 1500, "loss": 0.0005161278240848333, "recon_cos": 0.9807891845703125, "recon_cos_legacy": 0.9807891845703125, "n_nonzero": 76, "recon_mse": 0.000516143161803484, "lr": 0.0002981692850800035, "elapsed": 11.779856443405151} +{"epoch": 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"elapsed": 233.01009368896484} +{"epoch": 29500, "loss": 0.0001756271449266933, "recon_cos": 0.99466472864151, "recon_cos_legacy": 0.99466472864151, "n_nonzero": 76, "recon_mse": 0.00014087279851082712, "lr": 3.2027010317082486e-06, "elapsed": 236.74606466293335} +{"epoch": 29999, "loss": 0.00018408914911560714, "recon_cos": 0.9946591258049011, "recon_cos_legacy": 0.9946591258049011, "n_nonzero": 76, "recon_mse": 0.0001406563096679747, "lr": 2.9999999999999997e-06, "elapsed": 240.49177026748657} diff --git a/flow_heads/norman/seed3/krr_prior.pkl b/flow_heads/norman/seed3/krr_prior.pkl new file mode 100644 index 0000000000000000000000000000000000000000..f6df7424359fefff337c6af4e736767e3859c4e2 --- /dev/null +++ b/flow_heads/norman/seed3/krr_prior.pkl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ed54b2612b50268760dc710e28dc0eca0f26b9162bfd5ab3c309af3e855f9c1a +size 613987 diff --git a/flow_heads/norman/seed3/reproduce.sh b/flow_heads/norman/seed3/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..b6fb3e3fcffc1b7b8c7b4c885e36961e59e0de21 --- /dev/null +++ b/flow_heads/norman/seed3/reproduce.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# Reproduce: Norman seed 3 +# Run dir: runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3 +# Result: experiments/results/fair_comparison/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_seed3.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/CRISPRa-norman/norman2019_gears_split.h5ad" +BACKBONE="hf-assets/checkpoints/crispra_norman_r16/scFATE_epoch100_periodic.pt" +RUN_DIR="runs/b200_norman_flow_e115_krrinit_s02_mask_30k_seed3" + +.venv/bin/python -u scripts/train_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 3 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.02 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' diff --git a/flow_heads/rpe1/seed1/config.json b/flow_heads/rpe1/seed1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..fe9260a468c3ab293cfa1ff4e57c4511e42bce5b --- /dev/null +++ b/flow_heads/rpe1/seed1/config.json @@ -0,0 +1,41 @@ +{ + "paper_row": "RPE1 seed 1", + "dataset": "Replogle RPE1", + "run_dir": "runs/b200_rpe1_flow_block_krrinit_mask_30k_s1", + "backbone": "hf-assets/checkpoints/rpe1/scFATE_epoch350_periodic.pt", + "h5ad_rel": "datasets/scFATE/processed/replogle_rpe1/replogle_rpe1.h5ad", + "training_script": "scripts/train_flow.py", + "seed": 1, + "result_json": "experiments/results/fair_comparison/rpe1_rotation_vs_direct__flow__b200_rpe1_flow_block_krrinit_mask_30k_s1_rpe1_block_K128.json", + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_rpe1_flow_block_krrinit_mask_30k_s1/flow_best.pt", + "size_mb": 46.6, + "files_in_dir": [ + "config.json", + "flow_best.pt", + "flow_metrics.jsonl", + "krr_prior.pkl", + "reproduce.sh" + ] + }, + "hparams_top": { + "_v_net_state_dict_present": true, + "theta_dim": 192, + "d_embed": 1824, + "d_hidden": 512, + "n_blocks": 4, + "sigma": 0.05, + "n_steps": 20, + "epoch": 28500, + "loss": 5.099160883522321e-05, + "pert_names": "", + "mv_gene_names": "", + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 1.0 + }, + "hparams_nested": {} +} \ No newline at end of file diff --git a/flow_heads/rpe1/seed1/flow_best.pt b/flow_heads/rpe1/seed1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..cd8752983c83e896974d45caa11be404c120b97b --- /dev/null +++ b/flow_heads/rpe1/seed1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ecb4218950a4140683747cd6b04c11fbab10ed5c33a2492772c748f63f0943a6 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100644 index 0000000000000000000000000000000000000000..4b1f93bb49d78052a9e6014223342db1cb41127e --- /dev/null +++ b/flow_heads/rpe1/seed1/krr_prior.pkl @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:824e857197f1c89ed19cfb5df49444539e5667f327bd3c8e97468b4245d478f6 +size 9221660 diff --git a/flow_heads/rpe1/seed1/reproduce.sh b/flow_heads/rpe1/seed1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..188d7337f27a408abc56f494ce5b5ec78324244d --- /dev/null +++ b/flow_heads/rpe1/seed1/reproduce.sh @@ -0,0 +1,28 @@ +#!/bin/bash +# Reproduce: RPE1 seed 1 +# Run dir: runs/b200_rpe1_flow_block_krrinit_mask_30k_s1 +# Result: experiments/results/fair_comparison/rpe1_rotation_vs_direct__flow__b200_rpe1_flow_block_krrinit_mask_30k_s1_rpe1_block_K128.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/rpe1/scFATE_epoch350_periodic.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/replogle_rpe1/replogle_rpe1.h5ad" +BACKBONE="hf-assets/checkpoints/rpe1/scFATE_epoch350_periodic.pt" +RUN_DIR="runs/b200_rpe1_flow_block_krrinit_mask_30k_s1" + +.venv/bin/python -u scripts/train_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 192 \ + --d_embed 1824 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.05 \ + --krr_alpha 1.0 \ + --krr_gamma 0.01 \ + --prior 'krr' diff --git a/results/table1_inputs/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json b/results/table1_inputs/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json new file mode 100644 index 0000000000000000000000000000000000000000..fe51d2d3347b3c84e244f31d43ca974872e3d581 --- /dev/null +++ b/results/table1_inputs/norman_rotation_vs_direct__flow__b200_norman_flow_e115_krrinit_s02_mask_30k_K128.json @@ -0,0 +1,891 @@ +{ + "dataset": "crispra_norman_gears", + "checkpoint": "runs/cam_norman_e115/scFATE_epoch115_best.pt", + "embedding": "data/gene_embeddings/genept_bge_large.pt", + "n_eval": 105, + "bracket_scale": 2.4151077270507812, + "rotation_krr": { + "da": 0.9131428562459492, + "da_singles": 0.8607692271471024, + "da_combos": 0.930379746835443, + "cos": 0.7646284436540944, + "pde": 0.7609592987300788, + "mse20": 0.8473851984100682, + "n_singles": 26, + "n_combos": 79, + "krr_params": { + "alpha": 1.0, + "gamma": null + }, + "per_pert_da": [ + 0.9599999785423279, + 0.8799999952316284, + 0.5199999809265137, + 0.9399999976158142, + 0.699999988079071, + 0.8600000143051147, + 0.8199999928474426, + 0.6200000047683716, + 0.8999999761581421, + 0.8999999761581421, + 0.9800000190734863, + 0.9399999976158142, + 0.7599999904632568, + 0.9599999785423279, + 0.9599999785423279, + 1.0, 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Recommended over priornone-9 due to ~2x lower per-seed std.", + "primary_headline_row": "18-ckpt mixed V2B mean-PRED ensemble 69.44% DA (iter187, unchanged)", + "cheapest_reproducible_ensemble_row": "priornone-9 teacher ensemble 69.12% DA (iter184, unchanged)", + "split_sensitivity_row": "V1-split flow 67.36% vs DD-KRR 66.64% (iter188, unchanged)" + } +} \ No newline at end of file diff --git a/results/table1_inputs/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json b/results/table1_inputs/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json new file mode 100644 index 0000000000000000000000000000000000000000..4a9cd1f078d38570445245bf64519edb38455ea8 --- /dev/null +++ b/results/table1_inputs/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json @@ -0,0 +1,103 @@ +{ + "iter": 197, + "date": "2026-04-24", + "dataset": "sciplex3", + "recipe": "reflow_ensemble_distillation_mixed18_K16", + "description": "mixed-18 K=16 distilled student N=7 extension (s6, s7) of iter196 N=5. 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newline at end of file diff --git a/results/table1_inputs/sciplex3_iter210_per_drug_router.json b/results/table1_inputs/sciplex3_iter210_per_drug_router.json new file mode 100644 index 0000000000000000000000000000000000000000..018251db7c779485e7e30fd6a9c5e854ac73a8ff --- /dev/null +++ b/results/table1_inputs/sciplex3_iter210_per_drug_router.json @@ -0,0 +1,996 @@ +{ + "iter": 210, + "purpose": "per-drug 5-group LOO router (fair) + oracle bound", + "n_drugs": 25, + "drugs": [ + "AC480", + "AG-14361", + "AICAR", + "Alendronate", + "Amisulpride", + "Azacitidine", + "BMS-754807", + "Belinostat", + "CUDC-101", + "Cimetidine", + "Daphnetin", + "GSK-LSD1", + "INO-1001", + "JNJ-26854165", + "JNJ-7706621", + "MLN8054", + "Momelotinib", + "NVP-BSK805", + "Nintedanib", + "PHA-680632", + "Raltitrexed", + "Roxadustat", + "SB431542", + "TMP195", + "Toremifene" + ], + "group_desc": { + "A": "priorkrr_alpha0p1_gamma0p01_9seed", + "B": "priorkrr_alpha0p3_gamma0p1_9seed", + "C": "priornone_9seed", + 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0.6322306990623474, + "cos_full": 0.34643495082855225, + "mse_top20": 0.002709286753088236 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s1/flow_best.pt b/sciplex3_path_b/students/mixed18_K16/s1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..adac5722a0d5cfed469d225fd1ae55eaa6dfeee8 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9dc48ec643e7e548133db340272ae5f0f765ef4d1076dafafe2df453b5589c42 +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s1/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..673c082bc3e48d3d8b28a4bd0819ef0ff18b09d1 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s1/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s1 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1 +# Result: experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s1" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s2/config.json b/sciplex3_path_b/students/mixed18_K16/s2/config.json new file mode 100644 index 0000000000000000000000000000000000000000..8bb6be5be97df2ce88319c167e1935c80fe489c6 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s2/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s2 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 2, + "result_json": "experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + 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0.008312925696372986, + "cos_full": -0.028774535283446312, + "mse_top20": 0.002433139132335782 + }, + { + "drug": "Toremifene", + "da": 0.7999999523162842, + "cos_topk": 0.6739649772644043, + "cos_full": 0.4574441909790039, + "mse_top20": 0.0028376090340316296 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s2/flow_best.pt b/sciplex3_path_b/students/mixed18_K16/s2/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..291f0996e259c8b509097cf23366e25ba5497389 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s2/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b565b1bd3414c73ca55d27a4655e4f6a11d6c8306a32ec4a3c7fab07ca658b6b +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s2/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s2/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..609e1ae72d82352086662c0e8779743b6ec46f63 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s2/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s2 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2 +# Result: experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s2" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 2 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s3/config.json b/sciplex3_path_b/students/mixed18_K16/s3/config.json new file mode 100644 index 0000000000000000000000000000000000000000..8ba6114c27cb4421503a56b85f2e11ac68e69681 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s3/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s3 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 3, + "result_json": "experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 3, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s3/eval.json b/sciplex3_path_b/students/mixed18_K16/s3/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..a18f29835986156c5b0b7fe101efb76554bcf20c --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s3/eval.json @@ -0,0 +1,244 @@ +{ + "iter": 189, + "model": "sciplex3_delta_flow_reflow_ensemble_distill", + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + 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0000000000000000000000000000000000000000..cea0ff5bbd3ab7cd032986d2f9baf1353df3f72e --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s3/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s3 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3 +# Result: experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s3" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 3 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s4/config.json b/sciplex3_path_b/students/mixed18_K16/s4/config.json new file mode 100644 index 0000000000000000000000000000000000000000..657e4efd61a551fb7959db8cb66191c6f8cd8bf9 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s4/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s4 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 4, + "result_json": "experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 4, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s4/eval.json b/sciplex3_path_b/students/mixed18_K16/s4/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..2c42c5fb44c0c150d5478f65d8071a3731e1776a --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s4/eval.json @@ -0,0 +1,244 @@ +{ + "iter": 189, + "model": "sciplex3_delta_flow_reflow_ensemble_distill", + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + 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sha256:ed71f618c0b69a2a81234ee32d6c1e76342c4af058256b351c56abe54a3ddefe +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s4/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s4/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..6099d7f4de3a3368611e67dd08d1da3b6f7f7db6 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s4/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s4 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4 +# Result: experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s4" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 4 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s5/config.json b/sciplex3_path_b/students/mixed18_K16/s5/config.json new file mode 100644 index 0000000000000000000000000000000000000000..7d782ffcae3bffdc67d9b5fab562534f3848e230 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s5/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s5 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 5, + "result_json": "experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 5, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s5/eval.json b/sciplex3_path_b/students/mixed18_K16/s5/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..9e832e29b91fd78021f1b414cb4ee4085437218f --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s5/eval.json @@ -0,0 +1,244 @@ +{ + "iter": 189, + "model": "sciplex3_delta_flow_reflow_ensemble_distill", + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "n_teachers_priornone": 9, + "n_teachers_priorkrr": 9, + "reflow_K": 16, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "n_train": 161, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 5, + "best_loss": 0.08840809762477875, + "ensemble_mean_train_cos_to_true": 0.9961639046669006, + "da_mean": 0.6631999850273133, + "cos_topk_mean": 0.35978958889842033, + "cos_full_mean": 0.27047021966427565, + "mse_top20_mean": 0.0050571277807466685, + "per_drug": [ + { + "drug": "AC480", + "da": 0.5600000023841858, + "cos_topk": 0.29209715127944946, + "cos_full": 0.17462660372257233, + "mse_top20": 0.0023360427003353834 + }, + { + "drug": "AG-14361", + "da": 0.699999988079071, + "cos_topk": 0.1381414532661438, + "cos_full": 0.19829854369163513, + "mse_top20": 0.0025195120833814144 + }, + { + "drug": "AICAR", 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0000000000000000000000000000000000000000..ebff53cb81c5b10f9f5d88aba4d1594e6e29499a --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s5/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5120f5b4a4b23d3dc80dffa9f5dc6aa9d9961726f6af19a99160481cfba90636 +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s5/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s5/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..9b08b1436bb1dcc096d6f13abb54668d882aa0b6 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s5/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s5 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5 +# Result: experiments/results/sciplex3_iter196_reflow_ensemble_mixed18_K16_N5.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s5" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 5 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s6/config.json b/sciplex3_path_b/students/mixed18_K16/s6/config.json new file mode 100644 index 0000000000000000000000000000000000000000..8de4db9d446aadeca2b589b53e0fa0cc29f88114 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s6/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s6 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 6, + "result_json": "experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 6, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s6/eval.json b/sciplex3_path_b/students/mixed18_K16/s6/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..47f797748a41c353cca08b02e04e5ddcfab74fed --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s6/eval.json @@ -0,0 +1,244 @@ +{ + "iter": 189, + "model": "sciplex3_delta_flow_reflow_ensemble_distill", + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + 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+ ] +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s6/flow_best.pt b/sciplex3_path_b/students/mixed18_K16/s6/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..97217a794c0c329458020102ce8ab2d9ea0682bf --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s6/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bb74dd06111c7eb15fc221f40fff26c835f12e57427081fe4313b5868e82b2a5 +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s6/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s6/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..6e4860c2b62b16f1c4c2cb1ee8e55afec7184721 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s6/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s6 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6 +# Result: experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s6" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 6 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/students/mixed18_K16/s7/config.json b/sciplex3_path_b/students/mixed18_K16/s7/config.json new file mode 100644 index 0000000000000000000000000000000000000000..b9e487a1d460fd3b7f3651e239a5ebe99639940f --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s7/config.json @@ -0,0 +1,116 @@ +{ + "paper_row": "SciPlex3 mixed-18 K=16 student s7 (paper headline 70.0)", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/reflow_sciplex3_delta_flow_ensemble.py", + "seed": 7, + "result_json": "experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json", + "teacher": null, + "teachers": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + ], + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt" + ], + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7", + "reflow_K": 16, + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "teacher_sigma": 0.3, + "teacher_steps": 40, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "seed": 7, + "log_every": 2000, + "topk_de": 50, + "device": "cuda", + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "M_teachers": 18, + "teacher_prior_types": [ + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "none", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr", + "krr" + ], + "prior": "none" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s7/eval.json b/sciplex3_path_b/students/mixed18_K16/s7/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..62b4e108d33901f0267ce2324f7c4c6a391ba0d0 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s7/eval.json @@ -0,0 +1,244 @@ +{ + "iter": 189, + "model": "sciplex3_delta_flow_reflow_ensemble_distill", + "teacher_ckpts": [ + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + 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"cos_topk": 0.12227962911128998, + "cos_full": 0.009317897260189056, + "mse_top20": 0.0022440680768340826 + }, + { + "drug": "Toremifene", + "da": 0.7400000095367432, + "cos_topk": 0.44716811180114746, + "cos_full": 0.368691623210907, + "mse_top20": 0.004102214705199003 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/students/mixed18_K16/s7/flow_best.pt b/sciplex3_path_b/students/mixed18_K16/s7/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..30581c2f43dc0a47c0d5eaafdc4e2b378855f13a --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s7/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c6ccdd8dfbaa71b90d06213ad21c56769befe41844a19325e5e9364b76ad92de +size 57408073 diff --git a/sciplex3_path_b/students/mixed18_K16/s7/reproduce.sh b/sciplex3_path_b/students/mixed18_K16/s7/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..94595691911734f2f77e38bf62d4108de1da0e48 --- /dev/null +++ b/sciplex3_path_b/students/mixed18_K16/s7/reproduce.sh @@ -0,0 +1,41 @@ +#!/bin/bash +# Reproduce: SciPlex3 mixed-18 K=16 student s7 (paper headline 70.0) +# Run dir: runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7 +# Result: experiments/results/sciplex3_iter197_reflow_ensemble_mixed18_K16_N7.json +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_reflow_ensemble_mixed18_K16_V2B_s7" + +.venv/bin/python -u scripts/reflow_sciplex3_delta_flow_ensemble.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 7 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --reflow_K 16 \ + --teacher_sigma 0.3 \ + --teacher_steps 40 \ + --M_teachers 18 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' \ + --teacher_ckpts runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt diff --git a/sciplex3_path_b/teachers/priorkrr/s1/config.json b/sciplex3_path_b/teachers/priorkrr/s1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..cb135005866bbd1bd02a336520549309f4cc259f --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s1/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s1", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 1, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 1, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s1/eval.json b/sciplex3_path_b/teachers/priorkrr/s1/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..e002ba5e42007cfa8e93a67d48a98dffa71c333a --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s1/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 1, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07223684340715408, + "da_mean": 0.6903999853134155, + "cos_topk_mean": 0.401412832736969, + "cos_full_mean": 0.2916744716465473, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.5794098973274231, + "cos_full": 0.38666167855262756, + "mse_top20": 0.0014139935374259949 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.33505064249038696, + "cos_full": 0.29317083954811096, + "mse_top20": 0.0020082001574337482 + }, + { + "drug": "AICAR", + "da": 0.5, + "cos_topk": 0.08537854254245758, + "cos_full": 0.09350542724132538, + "mse_top20": 0.001404792768880725 + }, + { + "drug": "Alendronate", + "da": 0.5, + "cos_topk": 0.21045614778995514, + "cos_full": 0.09326230734586716, + "mse_top20": 0.013637897558510303 + }, + { + "drug": "Amisulpride", + "da": 0.47999998927116394, + "cos_topk": 0.12589284777641296, + "cos_full": -0.04275376349687576, + "mse_top20": 0.004238698165863752 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.21658770740032196, + "cos_full": -0.12003389000892639, + "mse_top20": 0.006976171862334013 + }, + { + "drug": "BMS-754807", + "da": 0.3999999761581421, + "cos_topk": 0.18765468895435333, + "cos_full": 0.12195029854774475, + "mse_top20": 0.009693850763142109 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9825678467750549, + "cos_full": 0.95401930809021, + "mse_top20": 0.020044773817062378 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.7789565324783325, + "cos_full": 0.701714277267456, + "mse_top20": 0.00810504611581564 + }, + { + "drug": "Cimetidine", + "da": 0.5799999833106995, + "cos_topk": 0.06246906518936157, + "cos_full": 0.047983452677726746, + "mse_top20": 0.0016490723937749863 + }, + { + "drug": "Daphnetin", + "da": 0.5, + "cos_topk": 0.08232264220714569, + "cos_full": 0.05462953448295593, + "mse_top20": 0.0011067959712818265 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.6012511253356934, + "cos_full": 0.435465544462204, + "mse_top20": 0.0030316959600895643 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.4752967059612274, + "cos_full": 0.3881310820579529, + "mse_top20": 0.0011424570111557841 + }, + { + "drug": "JNJ-26854165", + "da": 0.7199999690055847, + "cos_topk": 0.4667651057243347, + "cos_full": 0.21024475991725922, + "mse_top20": 0.0015359089011326432 + }, + { + "drug": "JNJ-7706621", + "da": 0.7400000095367432, + "cos_topk": 0.4284653067588806, + "cos_full": 0.2661711275577545, + "mse_top20": 0.005643967539072037 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9280123710632324, + "cos_full": 0.8111500144004822, + "mse_top20": 0.0051413970068097115 + }, + { + "drug": "Momelotinib", + "da": 0.8199999928474426, + "cos_topk": 0.4908480644226074, + "cos_full": 0.3450254797935486, + "mse_top20": 0.0024008124601095915 + }, + { + "drug": "NVP-BSK805", + "da": 0.9399999976158142, + "cos_topk": 0.7591022253036499, + "cos_full": 0.44342857599258423, + "mse_top20": 0.001923457020893693 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.26376259326934814, + "cos_full": 0.31777554750442505, + "mse_top20": 0.008488689549267292 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7940804958343506, + "cos_full": 0.5500817894935608, + "mse_top20": 0.0018084343755617738 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.35453909635543823, + "cos_full": 0.15382787585258484, + "mse_top20": 0.022324873134493828 + }, + { + "drug": "Roxadustat", + "da": 0.6599999666213989, + "cos_topk": 0.2285924255847931, + "cos_full": 0.1476786583662033, + "mse_top20": 0.0025425783824175596 + }, + { + "drug": "SB431542", + "da": 0.6399999856948853, + "cos_topk": 0.2663116157054901, + "cos_full": 0.22498509287834167, + "mse_top20": 0.004136475268751383 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.12855060398578644, + "cos_full": 0.021483007818460464, + "mse_top20": 0.00228254497051239 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.6361719369888306, + "cos_full": 0.3923037648200989, + "mse_top20": 0.0028566319961100817 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s1/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..5b8a97697ef927cd7dbd817c561eaa356ce13979 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0211fbdc00540c8e6cff59fce59f3216a37c44bdff7f5e0dd259e7c3e27f5385 +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s1/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..7a518710dad235dc770b137aecdf3ee73390bab1 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s1/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s1 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s1" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s2/config.json b/sciplex3_path_b/teachers/priorkrr/s2/config.json new file mode 100644 index 0000000000000000000000000000000000000000..30e53a7178208c6715d66da61576808bc5c77e1d --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s2/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s2", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 2, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 2, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s2/eval.json b/sciplex3_path_b/teachers/priorkrr/s2/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..b479699bd32e286785fd7511a703bb15f6b945ba --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s2/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 2, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.0725616067647934, + "da_mean": 0.6767999815940857, + "cos_topk_mean": 0.3868865320086479, + "cos_full_mean": 0.28593304738402364, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7199999690055847, + "cos_topk": 0.572360634803772, + "cos_full": 0.38139277696609497, + "mse_top20": 0.001421925495378673 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.3335666060447693, + "cos_full": 0.28488293290138245, + "mse_top20": 0.002008631592616439 + }, + { + "drug": "AICAR", + "da": 0.5199999809265137, + "cos_topk": 0.11939865350723267, + "cos_full": 0.11212871968746185, + "mse_top20": 0.0013299696147441864 + }, + { + "drug": "Alendronate", + "da": 0.5, + "cos_topk": 0.19584262371063232, + "cos_full": 0.08459275960922241, + "mse_top20": 0.013788771815598011 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.1421286165714264, + "cos_full": -0.023922942578792572, + "mse_top20": 0.004282901529222727 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.23443150520324707, + "cos_full": -0.1282995492219925, + "mse_top20": 0.007048317696899176 + }, + { + "drug": "BMS-754807", + "da": 0.35999998450279236, + "cos_topk": 0.05749879777431488, + "cos_full": 0.039870258420705795, + "mse_top20": 0.010326405055820942 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.982177734375, + "cos_full": 0.9537755846977234, + "mse_top20": 0.020547060295939445 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.7854329943656921, + "cos_full": 0.7094082832336426, + "mse_top20": 0.008073088712990284 + }, + { + "drug": "Cimetidine", + "da": 0.5399999618530273, + "cos_topk": 0.04702604562044144, + "cos_full": 0.04241377115249634, + "mse_top20": 0.0016750283539295197 + }, + { + "drug": "Daphnetin", + "da": 0.4599999785423279, + "cos_topk": 0.06466151773929596, + "cos_full": 0.046356555074453354, + "mse_top20": 0.001114076585508883 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.5997778177261353, + "cos_full": 0.44382375478744507, + "mse_top20": 0.0029376589227467775 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.4663679003715515, + "cos_full": 0.3962961435317993, + "mse_top20": 0.00113095052074641 + }, + { + "drug": "JNJ-26854165", + "da": 0.6599999666213989, + "cos_topk": 0.4696481227874756, + "cos_full": 0.23082751035690308, + "mse_top20": 0.0015268464339897037 + }, + { + "drug": "JNJ-7706621", + "da": 0.7400000095367432, + "cos_topk": 0.4065026342868805, + "cos_full": 0.25033333897590637, + "mse_top20": 0.005701607093214989 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9294055700302124, + "cos_full": 0.81627357006073, + "mse_top20": 0.0050575691275298595 + }, + { + "drug": "Momelotinib", + "da": 0.7999999523162842, + "cos_topk": 0.4526359438896179, + "cos_full": 0.3239761292934418, + "mse_top20": 0.0025122184306383133 + }, + { + "drug": "NVP-BSK805", + "da": 0.8999999761581421, + "cos_topk": 0.74074387550354, + "cos_full": 0.43288907408714294, + "mse_top20": 0.0020037468057125807 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.2376059889793396, + "cos_full": 0.30455225706100464, + "mse_top20": 0.00861950870603323 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7759221792221069, + "cos_full": 0.5405188202857971, + "mse_top20": 0.0018369306344538927 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.353156715631485, + "cos_full": 0.16082556545734406, + "mse_top20": 0.022387495264410973 + }, + { + "drug": "Roxadustat", + "da": 0.5799999833106995, + "cos_topk": 0.1450224071741104, + "cos_full": 0.11568880081176758, + "mse_top20": 0.0026398159097880125 + }, + { + "drug": "SB431542", + "da": 0.6399999856948853, + "cos_topk": 0.2565896511077881, + "cos_full": 0.2170567363500595, + "mse_top20": 0.004181640688329935 + }, + { + "drug": "TMP195", + "da": 0.5799999833106995, + "cos_topk": 0.1423574686050415, + "cos_full": 0.02261197194457054, + "mse_top20": 0.002261253772303462 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6307643055915833, + "cos_full": 0.3900533616542816, + "mse_top20": 0.0027883120346814394 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s2/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s2/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..79e2b788bfb482163bcf93defd5b3e4203e33c4e --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s2/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:7b2e0246eef360398623772137bae0664bdbd5aed17267d9ff3ef4326c374e3c +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s2/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s2/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..899f0d8689c8bdd75bd038edd9c536448c1449be --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s2/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s2 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s2" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 2 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s3/config.json b/sciplex3_path_b/teachers/priorkrr/s3/config.json new file mode 100644 index 0000000000000000000000000000000000000000..57b0729a3c6e96dd992722fbcccb635244c9abe1 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s3/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s3", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 3, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 3, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s3/eval.json b/sciplex3_path_b/teachers/priorkrr/s3/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..9b3bf8ed101d297d4b090aa9e41de0b230164744 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s3/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 3, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07264596968889236, + "da_mean": 0.6911999797821045, + "cos_topk_mean": 0.4012861260771751, + "cos_full_mean": 0.29244288712739946, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7599999904632568, + "cos_topk": 0.5945467948913574, + "cos_full": 0.3920165002346039, + "mse_top20": 0.0013839202001690865 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.3198865056037903, + "cos_full": 0.27779319882392883, + "mse_top20": 0.0019971381407231092 + }, + { + "drug": "AICAR", + "da": 0.5399999618530273, + "cos_topk": 0.09985429793596268, + "cos_full": 0.10174517333507538, + "mse_top20": 0.0013347987551242113 + }, + { + "drug": "Alendronate", + "da": 0.5199999809265137, + "cos_topk": 0.2531643807888031, + "cos_full": 0.12553788721561432, + "mse_top20": 0.013458716683089733 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.09740398079156876, + "cos_full": -0.05104820430278778, + "mse_top20": 0.004422574304044247 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.2169785499572754, + "cos_full": -0.12079477310180664, + "mse_top20": 0.006936928723007441 + }, + { + "drug": "BMS-754807", + "da": 0.3999999761581421, + "cos_topk": 0.1726120114326477, + "cos_full": 0.11275371164083481, + "mse_top20": 0.009748193435370922 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9835320115089417, + "cos_full": 0.9558926224708557, + "mse_top20": 0.019216230139136314 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.7948240637779236, + "cos_full": 0.717093288898468, + "mse_top20": 0.00825836043804884 + }, + { + "drug": "Cimetidine", + "da": 0.5399999618530273, + "cos_topk": -0.01934872567653656, + "cos_full": 0.012257982045412064, + "mse_top20": 0.0017612995579838753 + }, + { + "drug": "Daphnetin", + "da": 0.5199999809265137, + "cos_topk": 0.14452944695949554, + "cos_full": 0.08706281334161758, + "mse_top20": 0.001057287328876555 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.6039587259292603, + "cos_full": 0.4399542212486267, + "mse_top20": 0.002952766139060259 + }, + { + "drug": "INO-1001", + "da": 0.7999999523162842, + "cos_topk": 0.5612457990646362, + "cos_full": 0.4254814088344574, + "mse_top20": 0.0010121113155037165 + }, + { + "drug": "JNJ-26854165", + "da": 0.7199999690055847, + "cos_topk": 0.46369561553001404, + "cos_full": 0.2044873684644699, + "mse_top20": 0.0015455061802640557 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.45335909724235535, + "cos_full": 0.2788334786891937, + "mse_top20": 0.005501493811607361 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9223142862319946, + "cos_full": 0.8068395256996155, + "mse_top20": 0.005219945218414068 + }, + { + "drug": "Momelotinib", + "da": 0.8399999737739563, + "cos_topk": 0.4948795437812805, + "cos_full": 0.3552573323249817, + "mse_top20": 0.002385068451985717 + }, + { + "drug": "NVP-BSK805", + "da": 0.8799999952316284, + "cos_topk": 0.7495805025100708, + "cos_full": 0.43932414054870605, + "mse_top20": 0.00194387452211231 + }, + { + "drug": "Nintedanib", + "da": 0.5199999809265137, + "cos_topk": 0.23267367482185364, + "cos_full": 0.2972896993160248, + "mse_top20": 0.008685502223670483 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7793716192245483, + "cos_full": 0.535568356513977, + "mse_top20": 0.0018104761838912964 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3408515453338623, + "cos_full": 0.1522158533334732, + "mse_top20": 0.02256525121629238 + }, + { + "drug": "Roxadustat", + "da": 0.5799999833106995, + "cos_topk": 0.21170812845230103, + "cos_full": 0.13734924793243408, + "mse_top20": 0.002519353060051799 + }, + { + "drug": "SB431542", + "da": 0.6800000071525574, + "cos_topk": 0.2869253158569336, + "cos_full": 0.24263477325439453, + "mse_top20": 0.004063339438289404 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.10109768062829971, + "cos_full": 0.012032244354486465, + "mse_top20": 0.0023197222035378218 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.6064653992652893, + "cos_full": 0.37349432706832886, + "mse_top20": 0.0029321243055164814 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s3/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s3/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..06966c79938c2b170254e4de2b4d8ad6cfbbac5c --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s3/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d57a8e5b6cab5be703d49ac5c63d85454963c2d38537a83dbd45187fc6a54e67 +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s3/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s3/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..bafa7bb8efe81f795349a4b73f1ccf62d0ca206d --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s3/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s3 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s3" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 3 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s4/config.json b/sciplex3_path_b/teachers/priorkrr/s4/config.json new file mode 100644 index 0000000000000000000000000000000000000000..69519c9d319e570ebb6a9fcaa9cbeda83afdc0ab --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s4/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s4", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 4, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 4, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s4/eval.json b/sciplex3_path_b/teachers/priorkrr/s4/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..fdbaf9e203178cf7f650f93a8256e8c4573d9879 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s4/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 4, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07200747728347778, + "da_mean": 0.6871999895572662, + "cos_topk_mean": 0.39790711134672163, + "cos_full_mean": 0.29476277202367784, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.591558039188385, + "cos_full": 0.40266624093055725, + "mse_top20": 0.001348849036730826 + }, + { + "drug": "AG-14361", + "da": 0.7199999690055847, + "cos_topk": 0.31998956203460693, + "cos_full": 0.29020553827285767, + "mse_top20": 0.002026259433478117 + }, + { + "drug": "AICAR", + "da": 0.5, + "cos_topk": 0.0894288569688797, + "cos_full": 0.10038767009973526, + "mse_top20": 0.0013683708384633064 + }, + { + "drug": "Alendronate", + "da": 0.5199999809265137, + "cos_topk": 0.2053135633468628, + "cos_full": 0.0911506712436676, + "mse_top20": 0.01370932161808014 + }, + { + "drug": "Amisulpride", + "da": 0.47999998927116394, + "cos_topk": 0.09055541455745697, + "cos_full": -0.06152946129441261, + "mse_top20": 0.004413946066051722 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.225454181432724, + "cos_full": -0.12225720286369324, + "mse_top20": 0.006931103765964508 + }, + { + "drug": "BMS-754807", + "da": 0.3799999952316284, + "cos_topk": 0.16450193524360657, + "cos_full": 0.10733078420162201, + "mse_top20": 0.009797690436244011 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9801856279373169, + "cos_full": 0.9521816968917847, + "mse_top20": 0.018114376813173294 + }, + { + "drug": "CUDC-101", + "da": 0.8799999952316284, + "cos_topk": 0.801155686378479, + "cos_full": 0.7162730693817139, + "mse_top20": 0.008281150832772255 + }, + { + "drug": "Cimetidine", + "da": 0.5600000023841858, + "cos_topk": 0.040703706443309784, + "cos_full": 0.04094440117478371, + "mse_top20": 0.0016595947090536356 + }, + { + "drug": "Daphnetin", + "da": 0.47999998927116394, + "cos_topk": 0.09876969456672668, + "cos_full": 0.06417713314294815, + "mse_top20": 0.0010823277989402413 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.61385178565979, + "cos_full": 0.46538496017456055, + "mse_top20": 0.002916418481618166 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.49370354413986206, + "cos_full": 0.40194404125213623, + "mse_top20": 0.0011044469429180026 + }, + { + "drug": "JNJ-26854165", + "da": 0.7400000095367432, + "cos_topk": 0.5117238163948059, + "cos_full": 0.24955123662948608, + "mse_top20": 0.0014304741052910686 + }, + { + "drug": "JNJ-7706621", + "da": 0.699999988079071, + "cos_topk": 0.4363204836845398, + "cos_full": 0.2661869525909424, + "mse_top20": 0.00562781048938632 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9274272322654724, + "cos_full": 0.813503623008728, + "mse_top20": 0.005119443871080875 + }, + { + "drug": "Momelotinib", + "da": 0.8399999737739563, + "cos_topk": 0.5064593553543091, + "cos_full": 0.3660843074321747, + "mse_top20": 0.0023510982282459736 + }, + { + "drug": "NVP-BSK805", + "da": 0.9399999976158142, + "cos_topk": 0.7475699782371521, + "cos_full": 0.4538154900074005, + "mse_top20": 0.0019939346238970757 + }, + { + "drug": "Nintedanib", + "da": 0.5199999809265137, + "cos_topk": 0.26067304611206055, + "cos_full": 0.3176789879798889, + "mse_top20": 0.008463160134851933 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7813472151756287, + "cos_full": 0.5443791747093201, + "mse_top20": 0.0018414458027109504 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3029865026473999, + "cos_full": 0.13518427312374115, + "mse_top20": 0.022858601063489914 + }, + { + "drug": "Roxadustat", + "da": 0.6399999856948853, + "cos_topk": 0.2323262244462967, + "cos_full": 0.14387285709381104, + "mse_top20": 0.0025250993203371763 + }, + { + "drug": "SB431542", + "da": 0.6800000071525574, + "cos_topk": 0.2473500669002533, + "cos_full": 0.21924805641174316, + "mse_top20": 0.004203241318464279 + }, + { + "drug": "TMP195", + "da": 0.5799999833106995, + "cos_topk": 0.10272859036922455, + "cos_full": 0.008834369480609894, + "mse_top20": 0.002304897177964449 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6265020370483398, + "cos_full": 0.4018704295158386, + "mse_top20": 0.002845257520675659 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s4/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s4/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..a7f3395453792946e3450f72f3d4a6acf22bbfe5 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s4/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f2f6c592f4a6f5cfcde681f7cbdb32d53baeb1e75e68ca7668ef1b6986a6a447 +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s4/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s4/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..4837630efc6b7e35e3009444459af1a044542618 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s4/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s4 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s4" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 4 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s5/config.json b/sciplex3_path_b/teachers/priorkrr/s5/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3d17365d887951427f45f91b8687a92902cf1e2a --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s5/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s5", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 5, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 5, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s5/eval.json b/sciplex3_path_b/teachers/priorkrr/s5/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..08ebf555965eaa48e27e22b1c9c4dc1eb184bb18 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s5/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 5, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07257141917943954, + "da_mean": 0.6919999825954437, + "cos_topk_mean": 0.40187432169914244, + "cos_full_mean": 0.2924313912540674, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.57621169090271, + "cos_full": 0.3794410526752472, + "mse_top20": 0.0014280889881774783 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.31264111399650574, + "cos_full": 0.2861357033252716, + "mse_top20": 0.0020437685307115316 + }, + { + "drug": "AICAR", + "da": 0.5199999809265137, + "cos_topk": 0.08216772228479385, + "cos_full": 0.09145170450210571, + "mse_top20": 0.001386146293953061 + }, + { + "drug": "Alendronate", + "da": 0.5199999809265137, + "cos_topk": 0.23212489485740662, + "cos_full": 0.10932482033967972, + "mse_top20": 0.01348787546157837 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.1308823525905609, + "cos_full": -0.035714343190193176, + "mse_top20": 0.004351656883955002 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.2282400131225586, + "cos_full": -0.12500125169754028, + "mse_top20": 0.0069966851733624935 + }, + { + "drug": "BMS-754807", + "da": 0.3999999761581421, + "cos_topk": 0.1768094301223755, + "cos_full": 0.11284294724464417, + "mse_top20": 0.009699116460978985 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.984837532043457, + "cos_full": 0.959708571434021, + "mse_top20": 0.017714757472276688 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.7785286903381348, + "cos_full": 0.7025761008262634, + "mse_top20": 0.008127117529511452 + }, + { + "drug": "Cimetidine", + "da": 0.5999999642372131, + "cos_topk": 0.04061608761548996, + "cos_full": 0.03941982984542847, + "mse_top20": 0.0017204437172040343 + }, + { + "drug": "Daphnetin", + "da": 0.5199999809265137, + "cos_topk": 0.13259944319725037, + "cos_full": 0.08380590379238129, + "mse_top20": 0.0010579872177913785 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.5939822196960449, + "cos_full": 0.4335278272628784, + "mse_top20": 0.002980119315907359 + }, + { + "drug": "INO-1001", + "da": 0.7999999523162842, + "cos_topk": 0.5775882601737976, + "cos_full": 0.4537935256958008, + "mse_top20": 0.0009916536509990692 + }, + { + "drug": "JNJ-26854165", + "da": 0.699999988079071, + "cos_topk": 0.46792924404144287, + "cos_full": 0.21513542532920837, + "mse_top20": 0.0015100905438885093 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.4350111484527588, + "cos_full": 0.26735490560531616, + "mse_top20": 0.005617552436888218 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.926048994064331, + "cos_full": 0.8104543089866638, + "mse_top20": 0.005250425077974796 + }, + { + "drug": "Momelotinib", + "da": 0.8399999737739563, + "cos_topk": 0.4909830391407013, + "cos_full": 0.33901190757751465, + "mse_top20": 0.0024003074504435062 + }, + { + "drug": "NVP-BSK805", + "da": 0.8799999952316284, + "cos_topk": 0.7433738708496094, + "cos_full": 0.43457844853401184, + "mse_top20": 0.0019660447724163532 + }, + { + "drug": "Nintedanib", + "da": 0.5199999809265137, + "cos_topk": 0.27740243077278137, + "cos_full": 0.3271748125553131, + "mse_top20": 0.008397109806537628 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.782588005065918, + "cos_full": 0.5388308763504028, + "mse_top20": 0.0018334531923756003 + }, + { + "drug": "Raltitrexed", + "da": 0.699999988079071, + "cos_topk": 0.3532828688621521, + "cos_full": 0.15377765893936157, + "mse_top20": 0.022360464558005333 + }, + { + "drug": "Roxadustat", + "da": 0.6200000047683716, + "cos_topk": 0.2031393051147461, + "cos_full": 0.13201597332954407, + "mse_top20": 0.0025632211472839117 + }, + { + "drug": "SB431542", + "da": 0.6800000071525574, + "cos_topk": 0.2825724184513092, + "cos_full": 0.22766375541687012, + "mse_top20": 0.0040907892398536205 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.07242688536643982, + "cos_full": 0.001382308080792427, + "mse_top20": 0.0023621327709406614 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6213504076004028, + "cos_full": 0.37209200859069824, + "mse_top20": 0.0028945766389369965 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s5/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s5/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..9bc3c9fefb5371da738a290248c48d1cd5755c99 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s5/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6cdbf47670f3e37c8ca471390c96a76cbaf5f60471c0d560a5b53c46aa56e145 +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s5/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s5/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..dfb38fc117953d8a55535b842010472ea432123e --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s5/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s5 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s5" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 5 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s6/config.json b/sciplex3_path_b/teachers/priorkrr/s6/config.json new file mode 100644 index 0000000000000000000000000000000000000000..3cd21ae3897699216943605993e112315e64f8ae --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s6/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s6", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 6, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 6, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s6/eval.json b/sciplex3_path_b/teachers/priorkrr/s6/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..19864dd145079bf4981970aceb0b46d716572eb3 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s6/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 6, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07217399775981903, + "da_mean": 0.6847999799251556, + "cos_topk_mean": 0.3986164531111717, + "cos_full_mean": 0.2937426559627056, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.5825712084770203, + "cos_full": 0.39110684394836426, + "mse_top20": 0.0013883766951039433 + }, + { + "drug": "AG-14361", + "da": 0.7199999690055847, + "cos_topk": 0.32958734035491943, + "cos_full": 0.29232004284858704, + "mse_top20": 0.0019673588685691357 + }, + { + "drug": "AICAR", + "da": 0.5399999618530273, + "cos_topk": 0.09243247658014297, + "cos_full": 0.09995360672473907, + "mse_top20": 0.0013523399829864502 + }, + { + "drug": "Alendronate", + "da": 0.4599999785423279, + "cos_topk": 0.21053051948547363, + "cos_full": 0.09653987735509872, + "mse_top20": 0.01372485514730215 + }, + { + "drug": "Amisulpride", + "da": 0.5199999809265137, + "cos_topk": 0.14524459838867188, + "cos_full": -0.028679795563220978, + "mse_top20": 0.004236900247633457 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.21639840304851532, + "cos_full": -0.12074116617441177, + "mse_top20": 0.006960390601307154 + }, + { + "drug": "BMS-754807", + "da": 0.35999998450279236, + "cos_topk": 0.1422501653432846, + "cos_full": 0.09470289945602417, + "mse_top20": 0.009913566522300243 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9804667234420776, + "cos_full": 0.9486138820648193, + "mse_top20": 0.020336659625172615 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.8027692437171936, + "cos_full": 0.7196661829948425, + "mse_top20": 0.008221731521189213 + }, + { + "drug": "Cimetidine", + "da": 0.5600000023841858, + "cos_topk": 0.027332372963428497, + "cos_full": 0.035036176443099976, + "mse_top20": 0.001656513661146164 + }, + { + "drug": "Daphnetin", + "da": 0.47999998927116394, + "cos_topk": 0.12365579605102539, + "cos_full": 0.08172254264354706, + "mse_top20": 0.0010646983282640576 + }, + { + "drug": "GSK-LSD1", + "da": 0.7999999523162842, + "cos_topk": 0.6384637355804443, + "cos_full": 0.4694470465183258, + "mse_top20": 0.002894661156460643 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.4986596405506134, + "cos_full": 0.4179363250732422, + "mse_top20": 0.001110059441998601 + }, + { + "drug": "JNJ-26854165", + "da": 0.7199999690055847, + "cos_topk": 0.4752824306488037, + "cos_full": 0.2439325749874115, + "mse_top20": 0.0015316391363739967 + }, + { + "drug": "JNJ-7706621", + "da": 0.7400000095367432, + "cos_topk": 0.40892553329467773, + "cos_full": 0.24647210538387299, + "mse_top20": 0.005702735390514135 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9256157279014587, + "cos_full": 0.8152971267700195, + "mse_top20": 0.005095212254673243 + }, + { + "drug": "Momelotinib", + "da": 0.8399999737739563, + "cos_topk": 0.49768078327178955, + "cos_full": 0.35909903049468994, + "mse_top20": 0.002335687866434455 + }, + { + "drug": "NVP-BSK805", + "da": 0.8799999952316284, + "cos_topk": 0.7329986691474915, + "cos_full": 0.4222441017627716, + "mse_top20": 0.002032243413850665 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.2404424548149109, + "cos_full": 0.305530309677124, + "mse_top20": 0.00858362764120102 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7885074615478516, + "cos_full": 0.5491248369216919, + "mse_top20": 0.0018084560288116336 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3255601227283478, + "cos_full": 0.14211584627628326, + "mse_top20": 0.022653359919786453 + }, + { + "drug": "Roxadustat", + "da": 0.6599999666213989, + "cos_topk": 0.2495625764131546, + "cos_full": 0.15711095929145813, + "mse_top20": 0.002505968092009425 + }, + { + "drug": "SB431542", + "da": 0.6399999856948853, + "cos_topk": 0.28830522298812866, + "cos_full": 0.2371712327003479, + "mse_top20": 0.004052172414958477 + }, + { + "drug": "TMP195", + "da": 0.5799999833106995, + "cos_topk": 0.05852612107992172, + "cos_full": -0.005979176610708237, + "mse_top20": 0.0023888666182756424 + }, + { + "drug": "Toremifene", + "da": 0.7999999523162842, + "cos_topk": 0.6164388060569763, + "cos_full": 0.37382298707962036, + "mse_top20": 0.0029253556858748198 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s6/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s6/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..79040daf074063d0cf11315359f6008675697be6 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s6/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:34d093109b0d36c4fe7ddc1a9770812392102daeaa2055cbed5c776d0502244c +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s6/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s6/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..87e79ba097ab1a8896473c012549cd843ebb933b --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s6/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s6 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s6" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 6 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s7/config.json b/sciplex3_path_b/teachers/priorkrr/s7/config.json new file mode 100644 index 0000000000000000000000000000000000000000..6b6b248ed6ebdf548d3d857bf62033a047c2c246 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s7/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s7", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 7, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 7, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s7/eval.json b/sciplex3_path_b/teachers/priorkrr/s7/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..81b733edd146dd06b4b9907c6e81e6f5bb4c3afe --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s7/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 7, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.073000967502594, + "da_mean": 0.6839999783039094, + "cos_topk_mean": 0.3944201539456844, + "cos_full_mean": 0.2828590685874224, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7199999690055847, + "cos_topk": 0.5746102333068848, + "cos_full": 0.3777380585670471, + "mse_top20": 0.0014019939117133617 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.3202052116394043, + "cos_full": 0.2880517840385437, + "mse_top20": 0.002012901473790407 + }, + { + "drug": "AICAR", + "da": 0.5199999809265137, + "cos_topk": 0.08857585489749908, + "cos_full": 0.0955275371670723, + "mse_top20": 0.0013943178346380591 + }, + { + "drug": "Alendronate", + "da": 0.5, + "cos_topk": 0.19881954789161682, + "cos_full": 0.08196084201335907, + "mse_top20": 0.01366946380585432 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.12134718894958496, + "cos_full": -0.04108129441738129, + "mse_top20": 0.00432245060801506 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.20396485924720764, + "cos_full": -0.11644160002470016, + "mse_top20": 0.006961669307202101 + }, + { + "drug": "BMS-754807", + "da": 0.3999999761581421, + "cos_topk": 0.1775600165128708, + "cos_full": 0.10930438339710236, + "mse_top20": 0.00977926142513752 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9826030731201172, + "cos_full": 0.9559048414230347, + "mse_top20": 0.018944919109344482 + }, + { + "drug": "CUDC-101", + "da": 0.8399999737739563, + "cos_topk": 0.7542937397956848, + "cos_full": 0.6927796006202698, + "mse_top20": 0.008111140690743923 + }, + { + "drug": "Cimetidine", + "da": 0.5799999833106995, + "cos_topk": 0.05606534332036972, + "cos_full": 0.045506563037633896, + "mse_top20": 0.0016694881487637758 + }, + { + "drug": "Daphnetin", + "da": 0.4599999785423279, + "cos_topk": 0.04391706362366676, + "cos_full": 0.03871798515319824, + "mse_top20": 0.0011240860912948847 + }, + { + "drug": "GSK-LSD1", + "da": 0.7999999523162842, + "cos_topk": 0.5970741510391235, + "cos_full": 0.3922339379787445, + "mse_top20": 0.0029962218832224607 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.4824376702308655, + "cos_full": 0.39350247383117676, + "mse_top20": 0.0011366137769073248 + }, + { + "drug": "JNJ-26854165", + "da": 0.699999988079071, + "cos_topk": 0.444466769695282, + "cos_full": 0.17951403558254242, + "mse_top20": 0.0015377404633909464 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.47435030341148376, + "cos_full": 0.2781352996826172, + "mse_top20": 0.005477398168295622 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9224535226821899, + "cos_full": 0.8064031600952148, + "mse_top20": 0.0054170796647667885 + }, + { + "drug": "Momelotinib", + "da": 0.7999999523162842, + "cos_topk": 0.4816109240055084, + "cos_full": 0.3473891615867615, + "mse_top20": 0.0024155783466994762 + }, + { + "drug": "NVP-BSK805", + "da": 0.85999995470047, + "cos_topk": 0.7263907194137573, + "cos_full": 0.3973644971847534, + "mse_top20": 0.0019744669552892447 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.23976919054985046, + "cos_full": 0.3074664771556854, + "mse_top20": 0.008634420111775398 + }, + { + "drug": "PHA-680632", + "da": 0.8199999928474426, + "cos_topk": 0.7831620573997498, + "cos_full": 0.5344095230102539, + "mse_top20": 0.0018660774221643806 + }, + { + "drug": "Raltitrexed", + "da": 0.7199999690055847, + "cos_topk": 0.35408440232276917, + "cos_full": 0.15138904750347137, + "mse_top20": 0.022353386506438255 + }, + { + "drug": "Roxadustat", + "da": 0.6399999856948853, + "cos_topk": 0.182614266872406, + "cos_full": 0.1257038712501526, + "mse_top20": 0.0025619191583245993 + }, + { + "drug": "SB431542", + "da": 0.6599999666213989, + "cos_topk": 0.26081788539886475, + "cos_full": 0.2268952578306198, + "mse_top20": 0.004160476382821798 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.1665380299091339, + "cos_full": 0.02849874459207058, + "mse_top20": 0.00221508601680398 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6307015419006348, + "cos_full": 0.3746025264263153, + "mse_top20": 0.0028368313796818256 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s7/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s7/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..36944ce2203784e43748d484ca9490073f26d487 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s7/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:84c59fad0551a3a6398ef7e110581b225566359777faedd75798e5b859720c6f +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s7/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s7/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..fe31421d828ad4fa2578d24de43dbd9ad4238bed --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s7/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s7 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s7" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 7 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s8/config.json b/sciplex3_path_b/teachers/priorkrr/s8/config.json new file mode 100644 index 0000000000000000000000000000000000000000..d2ff8e9fec6101c207d5469118d60d3af2836e18 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s8/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s8", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 8, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 8, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s8/eval.json b/sciplex3_path_b/teachers/priorkrr/s8/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..87a2b12ffdf8247cf0e8b8bad985212f64b521ec --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s8/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 8, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07252854108810425, + "da_mean": 0.6807999813556671, + "cos_topk_mean": 0.3934206558763981, + "cos_full_mean": 0.292565423771739, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.583530068397522, + "cos_full": 0.39432084560394287, + "mse_top20": 0.0013632085174322128 + }, + { + "drug": "AG-14361", + "da": 0.7400000095367432, + "cos_topk": 0.29399627447128296, + "cos_full": 0.27489328384399414, + "mse_top20": 0.0020801490172743797 + }, + { + "drug": "AICAR", + "da": 0.5199999809265137, + "cos_topk": 0.0814192146062851, + "cos_full": 0.09308414906263351, + "mse_top20": 0.001394722843542695 + }, + { + "drug": "Alendronate", + "da": 0.5, + "cos_topk": 0.2193022221326828, + "cos_full": 0.10027924925088882, + "mse_top20": 0.013618141412734985 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.12997852265834808, + "cos_full": -0.04077587649226189, + "mse_top20": 0.004292982164770365 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.22129233181476593, + "cos_full": -0.12044946104288101, + "mse_top20": 0.006995640695095062 + }, + { + "drug": "BMS-754807", + "da": 0.3799999952316284, + "cos_topk": 0.18401315808296204, + "cos_full": 0.12109147012233734, + "mse_top20": 0.009683950804173946 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9804478883743286, + "cos_full": 0.9532103538513184, + "mse_top20": 0.017819719389081 + }, + { + "drug": "CUDC-101", + "da": 0.8799999952316284, + "cos_topk": 0.7914938926696777, + "cos_full": 0.7051502466201782, + "mse_top20": 0.008354119956493378 + }, + { + "drug": "Cimetidine", + "da": 0.5399999618530273, + "cos_topk": 0.003578692674636841, + "cos_full": 0.02371043525636196, + "mse_top20": 0.001714508980512619 + }, + { + "drug": "Daphnetin", + "da": 0.4599999785423279, + "cos_topk": 0.08002477884292603, + "cos_full": 0.059125758707523346, + "mse_top20": 0.0011017201468348503 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.6076064109802246, + "cos_full": 0.465984970331192, + "mse_top20": 0.0029542341362684965 + }, + { + "drug": "INO-1001", + "da": 0.7799999713897705, + "cos_topk": 0.5159832835197449, + "cos_full": 0.4269178509712219, + "mse_top20": 0.001074856729246676 + }, + { + "drug": "JNJ-26854165", + "da": 0.7199999690055847, + "cos_topk": 0.4572557210922241, + "cos_full": 0.2107284665107727, + "mse_top20": 0.0015147281810641289 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.4189404845237732, + "cos_full": 0.25276491045951843, + "mse_top20": 0.005691166501492262 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9301697015762329, + "cos_full": 0.8170538544654846, + "mse_top20": 0.005113734398037195 + }, + { + "drug": "Momelotinib", + "da": 0.7999999523162842, + "cos_topk": 0.49223989248275757, + "cos_full": 0.3547733426094055, + "mse_top20": 0.0023674347903579473 + }, + { + "drug": "NVP-BSK805", + "da": 0.9199999570846558, + "cos_topk": 0.7330164909362793, + "cos_full": 0.43162041902542114, + "mse_top20": 0.0020080157555639744 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.2669122815132141, + "cos_full": 0.3251674771308899, + "mse_top20": 0.00847750622779131 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.790683388710022, + "cos_full": 0.5514891147613525, + "mse_top20": 0.0017881505191326141 + }, + { + "drug": "Raltitrexed", + "da": 0.6599999666213989, + "cos_topk": 0.32099825143814087, + "cos_full": 0.1402304470539093, + "mse_top20": 0.022700170055031776 + }, + { + "drug": "Roxadustat", + "da": 0.5199999809265137, + "cos_topk": 0.206369549036026, + "cos_full": 0.1373046487569809, + "mse_top20": 0.0025275510270148516 + }, + { + "drug": "SB431542", + "da": 0.6800000071525574, + "cos_topk": 0.2934608459472656, + "cos_full": 0.24753081798553467, + "mse_top20": 0.00404886482283473 + }, + { + "drug": "TMP195", + "da": 0.5600000023841858, + "cos_topk": 0.053641948848962784, + "cos_full": -0.0066840760409832, + "mse_top20": 0.002377798780798912 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.621745765209198, + "cos_full": 0.395612895488739, + "mse_top20": 0.00290105608291924 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s8/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s8/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..6765bccbd538d8301023755418eec7af02383e48 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s8/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f6f169de0809efa45956a0862f92fd81335031fd5dd99d41c94550d178a5736f +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s8/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s8/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..bea131f531590113784183a82b9e212b1c1eb755 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s8/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s8 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s8" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 8 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priorkrr/s9/config.json b/sciplex3_path_b/teachers/priorkrr/s9/config.json new file mode 100644 index 0000000000000000000000000000000000000000..7d9cdd8215d79ad03d0b544b19c72e71feec0159 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s9/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priorkrr teacher s9", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 9, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 9, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "krr", + "krr_gamma": 0.01, + "krr_alpha": 0.1, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s9/eval.json b/sciplex3_path_b/teachers/priorkrr/s9/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..faf2b49caa02e9873b882b0367a33953f28ed18d --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s9/eval.json @@ -0,0 +1,208 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 9, + "zscore_target": true, + "prior": "krr", + "krr_info": { + "gamma": 0.01, + "alpha": 0.1, + "train_cos": 0.9959733308472248 + }, + "best_loss": 0.07288344949483871, + "da_mean": 0.6871999824047088, + "cos_topk_mean": 0.39987469285726546, + "cos_full_mean": 0.2944077752530575, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.5788671970367432, + "cos_full": 0.39523953199386597, + "mse_top20": 0.001378922606818378 + }, + { + "drug": "AG-14361", + "da": 0.7199999690055847, + "cos_topk": 0.3187062740325928, + "cos_full": 0.2894091308116913, + "mse_top20": 0.001995413564145565 + }, + { + "drug": "AICAR", + "da": 0.47999998927116394, + "cos_topk": 0.08782569319009781, + "cos_full": 0.09927152842283249, + "mse_top20": 0.0013506253017112613 + }, + { + "drug": "Alendronate", + "da": 0.5, + "cos_topk": 0.19469784200191498, + "cos_full": 0.08601430058479309, + "mse_top20": 0.01375186163932085 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.12454189360141754, + "cos_full": -0.04426474869251251, + "mse_top20": 0.004297302104532719 + }, + { + "drug": "Azacitidine", + "da": 0.41999998688697815, + "cos_topk": -0.21447886526584625, + "cos_full": -0.11862931400537491, + "mse_top20": 0.0069121867418289185 + }, + { + "drug": "BMS-754807", + "da": 0.35999998450279236, + "cos_topk": 0.16595755517482758, + "cos_full": 0.10686064511537552, + "mse_top20": 0.009776000864803791 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9792561531066895, + "cos_full": 0.945242166519165, + "mse_top20": 0.020537881180644035 + }, + { + "drug": "CUDC-101", + "da": 0.8799999952316284, + "cos_topk": 0.790483295917511, + "cos_full": 0.7166746854782104, + "mse_top20": 0.008341087028384209 + }, + { + "drug": "Cimetidine", + "da": 0.5600000023841858, + "cos_topk": 0.02418661117553711, + "cos_full": 0.0329936258494854, + "mse_top20": 0.001679643290117383 + }, + { + "drug": "Daphnetin", + "da": 0.4599999785423279, + "cos_topk": 0.10546751320362091, + "cos_full": 0.06634225696325302, + "mse_top20": 0.0010933475568890572 + }, + { + "drug": "GSK-LSD1", + "da": 0.8199999928474426, + "cos_topk": 0.6253389120101929, + "cos_full": 0.4749484658241272, + "mse_top20": 0.0028579342179000378 + }, + { + "drug": "INO-1001", + "da": 0.7799999713897705, + "cos_topk": 0.5303720831871033, + "cos_full": 0.4318619668483734, + "mse_top20": 0.0010853549465537071 + }, + { + "drug": "JNJ-26854165", + "da": 0.7199999690055847, + "cos_topk": 0.4691987633705139, + "cos_full": 0.2159985899925232, + "mse_top20": 0.0014692303957417607 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.42415356636047363, + "cos_full": 0.2535374164581299, + "mse_top20": 0.005657313857227564 + }, + { + "drug": "MLN8054", + "da": 0.9799999594688416, + "cos_topk": 0.9296635389328003, + "cos_full": 0.813417911529541, + "mse_top20": 0.0051739937625825405 + }, + { + "drug": "Momelotinib", + "da": 0.8199999928474426, + "cos_topk": 0.5181229114532471, + "cos_full": 0.37650370597839355, + "mse_top20": 0.0023049626033753157 + }, + { + "drug": "NVP-BSK805", + "da": 0.9199999570846558, + "cos_topk": 0.743635356426239, + "cos_full": 0.44209903478622437, + "mse_top20": 0.0019868332892656326 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.2725676894187927, + "cos_full": 0.32948750257492065, + "mse_top20": 0.008377394638955593 + }, + { + "drug": "PHA-680632", + "da": 0.8399999737739563, + "cos_topk": 0.7845371961593628, + "cos_full": 0.5458177924156189, + "mse_top20": 0.0018042713636532426 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3359133005142212, + "cos_full": 0.145906001329422, + "mse_top20": 0.022552449256181717 + }, + { + "drug": "Roxadustat", + "da": 0.6399999856948853, + "cos_topk": 0.2216043621301651, + "cos_full": 0.13918457925319672, + "mse_top20": 0.002543315989896655 + }, + { + "drug": "SB431542", + "da": 0.6599999666213989, + "cos_topk": 0.28905847668647766, + "cos_full": 0.23717442154884338, + "mse_top20": 0.004012534860521555 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.09628947079181671, + "cos_full": 0.009380191564559937, + "mse_top20": 0.002315238816663623 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.6009005308151245, + "cos_full": 0.36972299218177795, + "mse_top20": 0.00298715359531343 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priorkrr/s9/flow_best.pt b/sciplex3_path_b/teachers/priorkrr/s9/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..b7883b51bd649042476ba14470024fcd32714125 --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s9/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e43db2f14f6e1ff9d54d6cae88e6c2635a5ff4eff4fd6d778f2680d74ed81688 +size 57406345 diff --git a/sciplex3_path_b/teachers/priorkrr/s9/reproduce.sh b/sciplex3_path_b/teachers/priorkrr/s9/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..3e633727a05a19cc539623f275a4b5f865f287ca --- /dev/null +++ b/sciplex3_path_b/teachers/priorkrr/s9/reproduce.sh @@ -0,0 +1,40 @@ +#!/bin/bash +# Reproduce: SciPlex3 priorkrr teacher s9 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priorkrr_V2B_s9" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 9 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --krr_alpha 0.1 \ + --krr_gamma 0.01 \ + --prior 'krr' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s1/config.json b/sciplex3_path_b/teachers/priornone/s1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..f427f4c039f34d48f66aaeb3aee39693e3bfcd6f --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s1/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s1", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 1, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 1, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s1/eval.json b/sciplex3_path_b/teachers/priornone/s1/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..aa79f32e09a9ab6892e7b7d57a54d7feb582575c --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s1/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 1, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08637537062168121, + "da_mean": 0.6855999863147736, + "cos_topk_mean": 0.3981958281993866, + "cos_full_mean": 0.3009365592896938, + "per_drug": [ + { + "drug": "AC480", + "da": 0.6200000047683716, + "cos_topk": 0.5582126975059509, + "cos_full": 0.3277740776538849, + "mse_top20": 0.0013834062265232205 + }, + { + "drug": "AG-14361", + "da": 0.6800000071525574, + "cos_topk": 0.14343643188476562, + "cos_full": 0.18969886004924774, + "mse_top20": 0.002564370632171631 + }, + { + "drug": "AICAR", + "da": 0.6399999856948853, + "cos_topk": 0.3137630224227905, + "cos_full": 0.22336527705192566, + "mse_top20": 0.0010920504573732615 + }, + { + "drug": "Alendronate", + "da": 0.8399999737739563, + "cos_topk": 0.8033888339996338, + "cos_full": 0.5938205718994141, + "mse_top20": 0.0097042266279459 + }, + { + "drug": "Amisulpride", + "da": 0.5999999642372131, + "cos_topk": 0.361985981464386, + "cos_full": 0.0978366956114769, + "mse_top20": 0.0034530528355389833 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.29539164900779724, + "cos_full": -0.1765243113040924, + "mse_top20": 0.008560066111385822 + }, + { + "drug": "BMS-754807", + "da": 0.47999998927116394, + "cos_topk": 0.3422604203224182, + "cos_full": 0.20735874772071838, + "mse_top20": 0.008744447492063046 + }, + { + "drug": "Belinostat", + "da": 0.9799999594688416, + "cos_topk": 0.9587177038192749, + "cos_full": 0.9097326993942261, + "mse_top20": 0.020414238795638084 + }, + { + "drug": "CUDC-101", + "da": 0.8799999952316284, + "cos_topk": 0.7993592023849487, + "cos_full": 0.7221815586090088, + "mse_top20": 0.007714857347309589 + }, + { + "drug": "Cimetidine", + "da": 0.25999999046325684, + "cos_topk": -0.5806111693382263, + "cos_full": -0.26629751920700073, + "mse_top20": 0.0035017901100218296 + }, + { + "drug": "Daphnetin", + "da": 0.6399999856948853, + "cos_topk": 0.16630873084068298, + "cos_full": 0.1476552039384842, + "mse_top20": 0.0013682907447218895 + }, + { + "drug": "GSK-LSD1", + "da": 0.8799999952316284, + "cos_topk": 0.7660514712333679, + "cos_full": 0.6035873293876648, + "mse_top20": 0.0023709796369075775 + }, + { + "drug": "INO-1001", + "da": 0.6800000071525574, + "cos_topk": 0.3466224670410156, + "cos_full": 0.2821778357028961, + "mse_top20": 0.001234533847309649 + }, + { + "drug": "JNJ-26854165", + "da": 0.6800000071525574, + "cos_topk": 0.5335644483566284, + "cos_full": 0.33233949542045593, + "mse_top20": 0.0013940229546278715 + }, + { + "drug": "JNJ-7706621", + "da": 0.5999999642372131, + "cos_topk": 0.2203882932662964, + "cos_full": 0.1347656548023224, + "mse_top20": 0.006163257639855146 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9458716511726379, + "cos_full": 0.8313098549842834, + "mse_top20": 0.0013315293472260237 + }, + { + "drug": "Momelotinib", + "da": 0.7400000095367432, + "cos_topk": 0.4747598171234131, + "cos_full": 0.33901113271713257, + "mse_top20": 0.0023241606540977955 + }, + { + "drug": "NVP-BSK805", + "da": 0.85999995470047, + "cos_topk": 0.6733994483947754, + "cos_full": 0.3669956922531128, + "mse_top20": 0.0021426638122648 + }, + { + "drug": "Nintedanib", + "da": 0.5999999642372131, + "cos_topk": 0.34510165452957153, + "cos_full": 0.3671865463256836, + "mse_top20": 0.007608804386109114 + }, + { + "drug": "PHA-680632", + "da": 0.7999999523162842, + "cos_topk": 0.7599945068359375, + "cos_full": 0.5188325643539429, + "mse_top20": 0.001689078169874847 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3546229600906372, + "cos_full": 0.1663074791431427, + "mse_top20": 0.022651223465800285 + }, + { + "drug": "Roxadustat", + "da": 0.5600000023841858, + "cos_topk": 0.09972906857728958, + "cos_full": 0.10222739726305008, + "mse_top20": 0.002674384042620659 + }, + { + "drug": "SB431542", + "da": 0.5399999618530273, + "cos_topk": 0.057332538068294525, + "cos_full": 0.06583620607852936, + "mse_top20": 0.004431535489857197 + }, + { + "drug": "TMP195", + "da": 0.6200000047683716, + "cos_topk": 0.15688824653625488, + "cos_full": 0.035436224192380905, + "mse_top20": 0.002253929851576686 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.6491389274597168, + "cos_full": 0.4007987082004547, + "mse_top20": 0.002811226760968566 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s1/flow_best.pt b/sciplex3_path_b/teachers/priornone/s1/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..d1f3cfbe33092e28875658ed9d2ca054b0861dbe --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s1/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b06556d22181b16a1fb33ccd735faca061cc8fd6cde3afce0ca055756e2afcda +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s1/reproduce.sh b/sciplex3_path_b/teachers/priornone/s1/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..8a34e824528e88a6d0e72623ce43b93a2c1d9252 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s1/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s1 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s1" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 1 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s2/config.json b/sciplex3_path_b/teachers/priornone/s2/config.json new file mode 100644 index 0000000000000000000000000000000000000000..2c0a441e8c94bbdc4b993647de444b295e5c752c --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s2/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s2", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 2, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 2, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s2/eval.json b/sciplex3_path_b/teachers/priornone/s2/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..bb8c2bccd0ae7a7ebd8966b40a3e36b1b5938ca5 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s2/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 2, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08639498054981232, + "da_mean": 0.6631999850273133, + "cos_topk_mean": 0.36473516896367075, + "cos_full_mean": 0.2714513887465, + "per_drug": [ + { + "drug": "AC480", + "da": 0.6399999856948853, + "cos_topk": 0.5605579614639282, + "cos_full": 0.33716368675231934, + "mse_top20": 0.0013229333562776446 + }, + { + "drug": "AG-14361", + "da": 0.6599999666213989, + "cos_topk": 0.10960087180137634, + "cos_full": 0.16716153919696808, + "mse_top20": 0.00269930437207222 + }, + { + "drug": "AICAR", + "da": 0.47999998927116394, + "cos_topk": 0.06190653517842293, + "cos_full": 0.022089160978794098, + "mse_top20": 0.0029547305312007666 + }, + { + "drug": "Alendronate", + "da": 0.5799999833106995, + "cos_topk": 0.4066598117351532, + "cos_full": 0.2255420982837677, + "mse_top20": 0.012701448984444141 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.03793735057115555, + "cos_full": -0.04527626186609268, + "mse_top20": 0.005335719790309668 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.3178345859050751, + "cos_full": -0.19243758916854858, + "mse_top20": 0.00866860430687666 + }, + { + "drug": "BMS-754807", + "da": 0.4399999976158142, + "cos_topk": 0.3010002374649048, + "cos_full": 0.1672981232404709, + "mse_top20": 0.008799674920737743 + }, + { + "drug": "Belinostat", + "da": 0.9799999594688416, + "cos_topk": 0.9522432088851929, + "cos_full": 0.8874527215957642, + "mse_top20": 0.02740282192826271 + }, + { + "drug": "CUDC-101", + "da": 0.8799999952316284, + "cos_topk": 0.7555786967277527, + "cos_full": 0.6246256828308105, + "mse_top20": 0.008912615478038788 + }, + { + "drug": "Cimetidine", + "da": 0.6599999666213989, + "cos_topk": 0.36220741271972656, + "cos_full": 0.22590094804763794, + "mse_top20": 0.0011816039914265275 + }, + { + "drug": "Daphnetin", + "da": 0.6599999666213989, + "cos_topk": 0.2220664620399475, + "cos_full": 0.17541995644569397, + "mse_top20": 0.0013216639636084437 + }, + { + "drug": "GSK-LSD1", + "da": 0.7799999713897705, + "cos_topk": 0.49050256609916687, + "cos_full": 0.3920317590236664, + "mse_top20": 0.0033190082758665085 + }, + { + "drug": "INO-1001", + "da": 0.7799999713897705, + "cos_topk": 0.6844331622123718, + "cos_full": 0.43549805879592896, + "mse_top20": 0.000526149058714509 + }, + { + "drug": "JNJ-26854165", + "da": 0.6800000071525574, + "cos_topk": 0.5405658483505249, + "cos_full": 0.3329687714576721, + "mse_top20": 0.0013833064585924149 + }, + { + "drug": "JNJ-7706621", + "da": 0.7199999690055847, + "cos_topk": 0.4621255397796631, + "cos_full": 0.29131224751472473, + "mse_top20": 0.005606757011264563 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9477782249450684, + "cos_full": 0.8346258401870728, + "mse_top20": 0.0015000352868810296 + }, + { + "drug": "Momelotinib", + "da": 0.7400000095367432, + "cos_topk": 0.4389253854751587, + "cos_full": 0.33559006452560425, + "mse_top20": 0.0024284583050757647 + }, + { + "drug": "NVP-BSK805", + "da": 0.9599999785423279, + "cos_topk": 0.8033996820449829, + "cos_full": 0.5464695692062378, + "mse_top20": 0.0016723474254831672 + }, + { + "drug": "Nintedanib", + "da": 0.5999999642372131, + "cos_topk": 0.3418956995010376, + "cos_full": 0.3544618487358093, + "mse_top20": 0.007956266403198242 + }, + { + "drug": "PHA-680632", + "da": 0.8799999952316284, + "cos_topk": 0.7661775350570679, + "cos_full": 0.5024591684341431, + "mse_top20": 0.0013284042943269014 + }, + { + "drug": "Raltitrexed", + "da": 0.2800000011920929, + "cos_topk": -0.43919482827186584, + "cos_full": -0.24628999829292297, + "mse_top20": 0.02898400090634823 + }, + { + "drug": "Roxadustat", + "da": 0.3799999952316284, + "cos_topk": -0.02667125314474106, + "cos_full": 0.023712586611509323, + "mse_top20": 0.0028453131671994925 + }, + { + "drug": "SB431542", + "da": 0.5600000023841858, + "cos_topk": 0.15073716640472412, + "cos_full": 0.12213127315044403, + "mse_top20": 0.004452253691852093 + }, + { + "drug": "TMP195", + "da": 0.6399999856948853, + "cos_topk": 0.2060537487268448, + "cos_full": 0.04415348917245865, + "mse_top20": 0.0021354479249566793 + }, + { + "drug": "Toremifene", + "da": 0.6599999666213989, + "cos_topk": 0.29972678422927856, + "cos_full": 0.22221997380256653, + "mse_top20": 0.003713499754667282 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s2/flow_best.pt b/sciplex3_path_b/teachers/priornone/s2/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..da5af210a44923a35391aab36108f74266f3643c --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s2/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:98960e6852b5064ca7a906e07552de08e116c898fcbfd55540423f57e7d6bd89 +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s2/reproduce.sh b/sciplex3_path_b/teachers/priornone/s2/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..02afe29b065db0f2c5258e87d21125f7e6240b0b --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s2/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s2 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s2" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 2 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s3/config.json b/sciplex3_path_b/teachers/priornone/s3/config.json new file mode 100644 index 0000000000000000000000000000000000000000..07c5e453ee63f9869d1fdb1acbdf51949644194c --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s3/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s3", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 3, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 3, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s3/eval.json b/sciplex3_path_b/teachers/priornone/s3/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..d5695cffd8c030508d9cf309c4f4dd90bc1ffa9e --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s3/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 3, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08803808689117432, + "da_mean": 0.6815999853610992, + "cos_topk_mean": 0.38466985821723937, + "cos_full_mean": 0.28075814738869664, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7400000095367432, + "cos_topk": 0.5635917782783508, + "cos_full": 0.36149412393569946, + "mse_top20": 0.0015386304585263133 + }, + { + "drug": "AG-14361", + "da": 0.6800000071525574, + "cos_topk": 0.2221904695034027, + "cos_full": 0.21914531290531158, + "mse_top20": 0.0024687747936695814 + }, + { + "drug": "AICAR", + "da": 0.7599999904632568, + "cos_topk": 0.5323939323425293, + "cos_full": 0.3182157874107361, + "mse_top20": 0.000642083294223994 + }, + { + "drug": "Alendronate", + "da": 0.5999999642372131, + "cos_topk": 0.2650260329246521, + "cos_full": 0.15490660071372986, + "mse_top20": 0.013607083819806576 + }, + { + "drug": "Amisulpride", + "da": 0.4599999785423279, + "cos_topk": 0.011357247829437256, + "cos_full": -0.10347003489732742, + "mse_top20": 0.004847244825214148 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.2891005873680115, + "cos_full": -0.17229487001895905, + "mse_top20": 0.008423185907304287 + }, + { + "drug": "BMS-754807", + "da": 0.41999998688697815, + "cos_topk": 0.3668248653411865, + "cos_full": 0.22415554523468018, + "mse_top20": 0.008516242727637291 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9699304103851318, + "cos_full": 0.9291785955429077, + "mse_top20": 0.02106916718184948 + }, + { + "drug": "CUDC-101", + "da": 0.6399999856948853, + "cos_topk": 0.32178694009780884, + "cos_full": 0.1506810039281845, + "mse_top20": 0.011600792407989502 + }, + { + "drug": "Cimetidine", + "da": 0.3199999928474426, + "cos_topk": -0.5531789660453796, + "cos_full": -0.1767890453338623, + "mse_top20": 0.002909029833972454 + }, + { + "drug": "Daphnetin", + "da": 0.6800000071525574, + "cos_topk": 0.24450895190238953, + "cos_full": 0.18402506411075592, + "mse_top20": 0.0012927432544529438 + }, + { + "drug": "GSK-LSD1", + "da": 0.8999999761581421, + "cos_topk": 0.8319169878959656, + "cos_full": 0.6556596755981445, + "mse_top20": 0.0018776034703478217 + }, + { + "drug": "INO-1001", + "da": 0.7199999690055847, + "cos_topk": 0.4072553515434265, + "cos_full": 0.3070279359817505, + "mse_top20": 0.0011343592777848244 + }, + { + "drug": "JNJ-26854165", + "da": 0.5600000023841858, + "cos_topk": 0.15423181653022766, + "cos_full": 0.15682333707809448, + "mse_top20": 0.00234102550894022 + }, + { + "drug": "JNJ-7706621", + "da": 0.85999995470047, + "cos_topk": 0.7332661151885986, + "cos_full": 0.46856066584587097, + "mse_top20": 0.004291310906410217 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.946250855922699, + "cos_full": 0.8353209495544434, + "mse_top20": 0.0011947741732001305 + }, + { + "drug": "Momelotinib", + "da": 0.7799999713897705, + "cos_topk": 0.5178747773170471, + "cos_full": 0.3740452229976654, + "mse_top20": 0.0022261585108935833 + }, + { + "drug": "NVP-BSK805", + "da": 0.8999999761581421, + "cos_topk": 0.7439246773719788, + "cos_full": 0.4500499665737152, + "mse_top20": 0.001946335076354444 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.27322065830230713, + "cos_full": 0.3230799734592438, + "mse_top20": 0.00866651814430952 + }, + { + "drug": "PHA-680632", + "da": 0.85999995470047, + "cos_topk": 0.8046441078186035, + "cos_full": 0.5649116039276123, + "mse_top20": 0.0010560945374891162 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.32151374220848083, + "cos_full": 0.14233186841011047, + "mse_top20": 0.022891921922564507 + }, + { + "drug": "Roxadustat", + "da": 0.6800000071525574, + "cos_topk": 0.3256117105484009, + "cos_full": 0.173437237739563, + "mse_top20": 0.002424907637760043 + }, + { + "drug": "SB431542", + "da": 0.5399999618530273, + "cos_topk": 0.2693042755126953, + "cos_full": 0.18777523934841156, + "mse_top20": 0.004174909088760614 + }, + { + "drug": "TMP195", + "da": 0.5799999833106995, + "cos_topk": 0.1415897011756897, + "cos_full": 0.013914700597524643, + "mse_top20": 0.0022195864003151655 + }, + { + "drug": "Toremifene", + "da": 0.699999988079071, + "cos_topk": 0.4908106029033661, + "cos_full": 0.27676722407341003, + "mse_top20": 0.0032346160151064396 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s3/flow_best.pt b/sciplex3_path_b/teachers/priornone/s3/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..e959af56e622a39f2baf3d47f3568ecd55caaec7 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s3/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:22d84d666d97e17ddb7c1e72487c7270cd87b2df0ad9b8a30633f99a60f874ae +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s3/reproduce.sh b/sciplex3_path_b/teachers/priornone/s3/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..04c0553af977c77f71bddb1b7623ba80da1cf1b8 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s3/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s3 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s3" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 3 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s4/config.json b/sciplex3_path_b/teachers/priornone/s4/config.json new file mode 100644 index 0000000000000000000000000000000000000000..407115fba7ad0515cf675b84f07b0a4b9009ff46 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s4/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s4", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 4, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 4, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s4/eval.json b/sciplex3_path_b/teachers/priornone/s4/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..154ca89a44ee54f717ab4a82d5b32149a2c86fd6 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s4/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 4, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08276424556970596, + "da_mean": 0.6495999836921692, + "cos_topk_mean": 0.3131529688835144, + "cos_full_mean": 0.24789169877767564, + "per_drug": [ + { + "drug": "AC480", + "da": 0.5799999833106995, + "cos_topk": 0.4137900173664093, + "cos_full": 0.21043407917022705, + "mse_top20": 0.0015024688327684999 + }, + { + "drug": "AG-14361", + "da": 0.6399999856948853, + "cos_topk": 0.09012512117624283, + "cos_full": 0.1775638312101364, + "mse_top20": 0.0026744648348540068 + }, + { + "drug": "AICAR", + "da": 0.4599999785423279, + "cos_topk": 0.01966536045074463, + "cos_full": -0.0044777169823646545, + "mse_top20": 0.0031588480342179537 + }, + { + "drug": "Alendronate", + "da": 0.8399999737739563, + "cos_topk": 0.8045505285263062, + "cos_full": 0.6028401255607605, + "mse_top20": 0.008440966717898846 + }, + { + "drug": "Amisulpride", + "da": 0.6399999856948853, + "cos_topk": 0.28180646896362305, + "cos_full": 0.053228553384542465, + "mse_top20": 0.003901174059137702 + }, + { + "drug": "Azacitidine", + "da": 0.4599999785423279, + "cos_topk": -0.24973510205745697, + "cos_full": -0.15598008036613464, + "mse_top20": 0.008356503210961819 + }, + { + "drug": "BMS-754807", + "da": 0.5799999833106995, + "cos_topk": 0.21410471200942993, + "cos_full": 0.17102034389972687, + "mse_top20": 0.009605810046195984 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9835459589958191, + "cos_full": 0.9589464664459229, + "mse_top20": 0.001521146739833057 + }, + { + "drug": "CUDC-101", + "da": 0.7999999523162842, + "cos_topk": 0.6857577562332153, + "cos_full": 0.5624827742576599, + "mse_top20": 0.007886000908911228 + }, + { + "drug": "Cimetidine", + "da": 0.25999999046325684, + "cos_topk": -0.598615825176239, + "cos_full": -0.30921608209609985, + "mse_top20": 0.0036471530329436064 + }, + { + "drug": "Daphnetin", + "da": 0.3799999952316284, + "cos_topk": -0.25276488065719604, + "cos_full": -0.14785687625408173, + "mse_top20": 0.0019230917096138 + }, + { + "drug": "GSK-LSD1", + "da": 0.8999999761581421, + "cos_topk": 0.8394138813018799, + "cos_full": 0.666670560836792, + "mse_top20": 0.0017548687756061554 + }, + { + "drug": "INO-1001", + "da": 0.7799999713897705, + "cos_topk": 0.5855551958084106, + "cos_full": 0.4158311188220978, + "mse_top20": 0.0006598116015084088 + }, + { + "drug": "JNJ-26854165", + "da": 0.699999988079071, + "cos_topk": 0.4941245913505554, + "cos_full": 0.25773149728775024, + "mse_top20": 0.0015346886357292533 + }, + { + "drug": "JNJ-7706621", + "da": 0.6599999666213989, + "cos_topk": 0.49050092697143555, + "cos_full": 0.38259533047676086, + "mse_top20": 0.005026364699006081 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9417362809181213, + "cos_full": 0.8275783061981201, + "mse_top20": 0.0012683516833931208 + }, + { + "drug": "Momelotinib", + "da": 0.5999999642372131, + "cos_topk": 0.2350427210330963, + "cos_full": 0.13939528167247772, + "mse_top20": 0.003251416375860572 + }, + { + "drug": "NVP-BSK805", + "da": 0.7999999523162842, + "cos_topk": 0.6507896184921265, + "cos_full": 0.35255011916160583, + "mse_top20": 0.0023870186414569616 + }, + { + "drug": "Nintedanib", + "da": 0.4399999976158142, + "cos_topk": -0.1300511658191681, + "cos_full": 0.060010895133018494, + "mse_top20": 0.01065533421933651 + }, + { + "drug": "PHA-680632", + "da": 0.8799999952316284, + "cos_topk": 0.7728545665740967, + "cos_full": 0.5129902958869934, + "mse_top20": 0.0012541048927232623 + }, + { + "drug": "Raltitrexed", + "da": 0.6200000047683716, + "cos_topk": 0.1548362672328949, + "cos_full": 0.05412246286869049, + "mse_top20": 0.02408083714544773 + }, + { + "drug": "Roxadustat", + "da": 0.3799999952316284, + "cos_topk": -0.09863034635782242, + "cos_full": -0.019703280180692673, + "mse_top20": 0.0030949022620916367 + }, + { + "drug": "SB431542", + "da": 0.6200000047683716, + "cos_topk": 0.1772625893354416, + "cos_full": 0.2007649838924408, + "mse_top20": 0.004761804360896349 + }, + { + "drug": "TMP195", + "da": 0.3999999761581421, + "cos_topk": -0.31560492515563965, + "cos_full": -0.16168071329593658, + "mse_top20": 0.002964049344882369 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6387639045715332, + "cos_full": 0.38945019245147705, + "mse_top20": 0.0028607994318008423 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s4/flow_best.pt b/sciplex3_path_b/teachers/priornone/s4/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..c06640c660dab54ddb0035f581ed5bd31c44e477 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s4/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:980a2a2384914c945f73b811c72791024e904961cce88d7c292cdabd51e23c22 +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s4/reproduce.sh b/sciplex3_path_b/teachers/priornone/s4/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..fbf34c9222c3b19cb7df5f14b529bd6a8b736029 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s4/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s4 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s4" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 4 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s5/config.json b/sciplex3_path_b/teachers/priornone/s5/config.json new file mode 100644 index 0000000000000000000000000000000000000000..8e8d09079c8cce6fe598e4dc4162910ea437a177 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s5/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s5", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 5, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 5, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s5/eval.json b/sciplex3_path_b/teachers/priornone/s5/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..808ea845a8e601eefa51758a7e8f045476c3caf7 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s5/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 5, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08583729714155197, + "da_mean": 0.6831999838352203, + "cos_topk_mean": 0.38466092765331267, + "cos_full_mean": 0.2869824779778719, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7199999690055847, + "cos_topk": 0.5429422855377197, + "cos_full": 0.3721737265586853, + "mse_top20": 0.0014087938470765948 + }, + { + "drug": "AG-14361", + "da": 0.6599999666213989, + "cos_topk": 0.13729546964168549, + "cos_full": 0.18818598985671997, + "mse_top20": 0.002569959731772542 + }, + { + "drug": "AICAR", + "da": 0.47999998927116394, + "cos_topk": 0.08420336246490479, + "cos_full": 0.03817608952522278, + "mse_top20": 0.0024036355316638947 + }, + { + "drug": "Alendronate", + "da": 0.5199999809265137, + "cos_topk": 0.2606561779975891, + "cos_full": 0.12938326597213745, + "mse_top20": 0.01333594974130392 + }, + { + "drug": "Amisulpride", + "da": 0.5, + "cos_topk": 0.15222996473312378, + "cos_full": -0.026764465495944023, + "mse_top20": 0.0041497997008264065 + }, + { + "drug": "Azacitidine", + "da": 0.4599999785423279, + "cos_topk": -0.28620293736457825, + "cos_full": -0.16953769326210022, + "mse_top20": 0.008739260025322437 + }, + { + "drug": "BMS-754807", + "da": 0.4599999785423279, + "cos_topk": 0.35234594345092773, + "cos_full": 0.2142133265733719, + "mse_top20": 0.008568803779780865 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9818345904350281, + "cos_full": 0.9624154567718506, + "mse_top20": 0.004541646223515272 + }, + { + "drug": "CUDC-101", + "da": 0.85999995470047, + "cos_topk": 0.8021857738494873, + "cos_full": 0.7292057871818542, + "mse_top20": 0.007901236414909363 + }, + { + "drug": "Cimetidine", + "da": 0.5799999833106995, + "cos_topk": 0.08164915442466736, + "cos_full": 0.06091586500406265, + "mse_top20": 0.00162625836674124 + }, + { + "drug": "Daphnetin", + "da": 0.6800000071525574, + "cos_topk": 0.11096282303333282, + "cos_full": 0.10741237550973892, + "mse_top20": 0.0012777027441188693 + }, + { + "drug": "GSK-LSD1", + "da": 0.8799999952316284, + "cos_topk": 0.7649587392807007, + "cos_full": 0.6185375452041626, + "mse_top20": 0.002370500937104225 + }, + { + "drug": "INO-1001", + "da": 0.6800000071525574, + "cos_topk": 0.3303132653236389, + "cos_full": 0.28156986832618713, + "mse_top20": 0.001275103772059083 + }, + { + "drug": "JNJ-26854165", + "da": 0.5399999618530273, + "cos_topk": 0.23202231526374817, + "cos_full": 0.16106723248958588, + "mse_top20": 0.0019244682043790817 + }, + { + "drug": "JNJ-7706621", + "da": 0.6800000071525574, + "cos_topk": 0.3433915376663208, + "cos_full": 0.203419029712677, + "mse_top20": 0.0059186234138906 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9460203051567078, + "cos_full": 0.8377087116241455, + "mse_top20": 0.0011341744102537632 + }, + { + "drug": "Momelotinib", + "da": 0.7999999523162842, + "cos_topk": 0.4876486659049988, + "cos_full": 0.36427220702171326, + "mse_top20": 0.002381691476330161 + }, + { + "drug": "NVP-BSK805", + "da": 0.8399999737739563, + "cos_topk": 0.6603411436080933, + "cos_full": 0.3731843829154968, + "mse_top20": 0.002129744505509734 + }, + { + "drug": "Nintedanib", + "da": 0.5600000023841858, + "cos_topk": 0.26335909962654114, + "cos_full": 0.2992798686027527, + "mse_top20": 0.00858478993177414 + }, + { + "drug": "PHA-680632", + "da": 0.8799999952316284, + "cos_topk": 0.7773422598838806, + "cos_full": 0.5242518186569214, + "mse_top20": 0.001193354488350451 + }, + { + "drug": "Raltitrexed", + "da": 0.6800000071525574, + "cos_topk": 0.3438878059387207, + "cos_full": 0.16151051223278046, + "mse_top20": 0.022801032289862633 + }, + { + "drug": "Roxadustat", + "da": 0.6599999666213989, + "cos_topk": 0.372566282749176, + "cos_full": 0.22259199619293213, + "mse_top20": 0.0022639590315520763 + }, + { + "drug": "SB431542", + "da": 0.5399999618530273, + "cos_topk": 0.07448369264602661, + "cos_full": 0.07977326959371567, + "mse_top20": 0.0045367637649178505 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.17126981914043427, + "cos_full": 0.03739156574010849, + "mse_top20": 0.002189485589042306 + }, + { + "drug": "Toremifene", + "da": 0.8199999928474426, + "cos_topk": 0.6288156509399414, + "cos_full": 0.4042242169380188, + "mse_top20": 0.0030334340408444405 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s5/flow_best.pt b/sciplex3_path_b/teachers/priornone/s5/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..f7899d537a03b29d990a853aadc9117f4ff0736b --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s5/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c5e1610c00db6e12766b4008400454109dc90382bc29d7f5138859b3f5da9524 +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s5/reproduce.sh b/sciplex3_path_b/teachers/priornone/s5/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..b1b3dd627e959b5b57c850d942c4eef3de9ae6fd --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s5/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s5 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s5" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 5 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s6/config.json b/sciplex3_path_b/teachers/priornone/s6/config.json new file mode 100644 index 0000000000000000000000000000000000000000..4b42b9606782107ab726b969eaec7751bfcf1ad1 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s6/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s6", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 6, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": "runs/launch_iter186_sciplex3_delta_flow_reflow_K2_from_priornone_s6.sh", + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 6, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s6/eval.json b/sciplex3_path_b/teachers/priornone/s6/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..726a4b7420fe7cce913c8e21511eb9326c4d1524 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s6/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 6, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08767295628786087, + "da_mean": 0.6991999816894531, + "cos_topk_mean": 0.4048940030485392, + "cos_full_mean": 0.3033583875000477, + "per_drug": [ + { + "drug": "AC480", + "da": 0.699999988079071, + "cos_topk": 0.6007087826728821, + "cos_full": 0.37977394461631775, + "mse_top20": 0.0013371017994359136 + }, + { + "drug": "AG-14361", + "da": 0.6599999666213989, + "cos_topk": 0.12182310223579407, + "cos_full": 0.17919623851776123, + "mse_top20": 0.0026257813442498446 + }, + { + "drug": "AICAR", + "da": 0.4599999785423279, + "cos_topk": 0.028367871418595314, + "cos_full": 0.001844257116317749, + "mse_top20": 0.003002479672431946 + }, + { + "drug": "Alendronate", + "da": 0.6399999856948853, + "cos_topk": 0.5703046321868896, + "cos_full": 0.34529298543930054, + "mse_top20": 0.012051691301167011 + }, + { + "drug": "Amisulpride", + "da": 0.5600000023841858, + "cos_topk": 0.1903851479291916, + "cos_full": 0.008889323100447655, + "mse_top20": 0.0040626744739711285 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.2879936397075653, + "cos_full": -0.17425061762332916, + "mse_top20": 0.008719249628484249 + }, + { + "drug": "BMS-754807", + "da": 0.5, + "cos_topk": 0.3053089678287506, + "cos_full": 0.18340325355529785, + "mse_top20": 0.008981055580079556 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.9484299421310425, + "cos_full": 0.8853307962417603, + "mse_top20": 0.019775032997131348 + }, + { + "drug": "CUDC-101", + "da": 0.9799999594688416, + "cos_topk": 0.9267596006393433, + "cos_full": 0.879878044128418, + "mse_top20": 0.0014401855878531933 + }, + { + "drug": "Cimetidine", + "da": 0.5399999618530273, + "cos_topk": -0.08696547150611877, + "cos_full": -0.0052325427532196045, + "mse_top20": 0.0017343278741464019 + }, + { + "drug": "Daphnetin", + "da": 0.6200000047683716, + "cos_topk": 0.03662567585706711, + "cos_full": 0.08756520599126816, + "mse_top20": 0.0014913879567757249 + }, + { + "drug": "GSK-LSD1", + "da": 0.9799999594688416, + "cos_topk": 0.8687877655029297, + "cos_full": 0.6830593347549438, + "mse_top20": 0.0018358164234086871 + }, + { + "drug": "INO-1001", + "da": 0.699999988079071, + "cos_topk": 0.32800689339637756, + "cos_full": 0.2916960120201111, + "mse_top20": 0.001298438641242683 + }, + { + "drug": "JNJ-26854165", + "da": 0.6800000071525574, + "cos_topk": 0.46736401319503784, + "cos_full": 0.2312910407781601, + "mse_top20": 0.0013662975979968905 + }, + { + "drug": "JNJ-7706621", + "da": 0.8199999928474426, + "cos_topk": 0.6172199845314026, + "cos_full": 0.39475661516189575, + "mse_top20": 0.004832330625504255 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9461309909820557, + "cos_full": 0.8412407040596008, + "mse_top20": 0.002198353875428438 + }, + { + "drug": "Momelotinib", + "da": 0.7999999523162842, + "cos_topk": 0.5152115225791931, + "cos_full": 0.39976799488067627, + "mse_top20": 0.002295582089573145 + }, + { + "drug": "NVP-BSK805", + "da": 0.7999999523162842, + "cos_topk": 0.5747026801109314, + "cos_full": 0.256233811378479, + "mse_top20": 0.0024026844184845686 + }, + { + "drug": "Nintedanib", + "da": 0.5600000023841858, + "cos_topk": 0.23633697628974915, + "cos_full": 0.2852534055709839, + "mse_top20": 0.008975910022854805 + }, + { + "drug": "PHA-680632", + "da": 0.85999995470047, + "cos_topk": 0.7781234979629517, + "cos_full": 0.5235123038291931, + "mse_top20": 0.0012680122163146734 + }, + { + "drug": "Raltitrexed", + "da": 0.699999988079071, + "cos_topk": 0.3736302852630615, + "cos_full": 0.17415189743041992, + "mse_top20": 0.02282780222594738 + }, + { + "drug": "Roxadustat", + "da": 0.4399999976158142, + "cos_topk": 0.07428611814975739, + "cos_full": 0.09512187540531158, + "mse_top20": 0.002581446198746562 + }, + { + "drug": "SB431542", + "da": 0.5799999833106995, + "cos_topk": 0.18501880764961243, + "cos_full": 0.16260643303394318, + "mse_top20": 0.0042554656974971294 + }, + { + "drug": "TMP195", + "da": 0.5999999642372131, + "cos_topk": 0.0985424742102623, + "cos_full": 0.010471096262335777, + "mse_top20": 0.002304109977558255 + }, + { + "drug": "Toremifene", + "da": 0.85999995470047, + "cos_topk": 0.7052334547042847, + "cos_full": 0.46310627460479736, + "mse_top20": 0.0025484913494437933 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s6/flow_best.pt b/sciplex3_path_b/teachers/priornone/s6/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..39d5dd8c5ecdf94b8d270bd9a1f809ace41ee8fd --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s6/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0026163c9978c1851cd5c775dd967bfe6a16b42a2aa4d140b7b294201454bdba +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s6/reproduce.sh b/sciplex3_path_b/teachers/priornone/s6/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..ac72368cafd1a89b299ca8ebd2afe571d8d35ccf --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s6/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s6 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6 +# Result: (no result JSON) +# Original launch: runs/launch_iter186_sciplex3_delta_flow_reflow_K2_from_priornone_s6.sh +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s6" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 6 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s7/config.json b/sciplex3_path_b/teachers/priornone/s7/config.json new file mode 100644 index 0000000000000000000000000000000000000000..6d41f49a8b1a06cad520e7db57356c711faceeb9 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s7/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s7", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 7, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 7, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s7/eval.json b/sciplex3_path_b/teachers/priornone/s7/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..8fa82078049e11258646821f9793745c84f8ca6e --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s7/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 7, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08388594537973404, + "da_mean": 0.669599986076355, + "cos_topk_mean": 0.38068293064832687, + "cos_full_mean": 0.2865810601040721, + "per_drug": [ + { + "drug": "AC480", + "da": 0.6200000047683716, + "cos_topk": 0.5345345735549927, + "cos_full": 0.3397090435028076, + "mse_top20": 0.0012363506248220801 + }, + { + "drug": "AG-14361", + "da": 0.8199999928474426, + "cos_topk": 0.6044574975967407, + "cos_full": 0.4568862318992615, + "mse_top20": 0.0011772314319387078 + }, + { + "drug": "AICAR", + "da": 0.4599999785423279, + "cos_topk": 0.05767287313938141, + "cos_full": 0.013856451958417892, + "mse_top20": 0.003160592168569565 + }, + { + "drug": "Alendronate", + "da": 0.7199999690055847, + "cos_topk": 0.5857881307601929, + "cos_full": 0.3966817855834961, + "mse_top20": 0.012138317339122295 + }, + { + "drug": "Amisulpride", + "da": 0.4399999976158142, + "cos_topk": 0.03119254857301712, + "cos_full": -0.09153155237436295, + "mse_top20": 0.004542650189250708 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.2918545603752136, + "cos_full": -0.1738710105419159, + "mse_top20": 0.008566996082663536 + }, + { + "drug": "BMS-754807", + "da": 0.6599999666213989, + "cos_topk": 0.39316993951797485, + "cos_full": 0.23759080469608307, + "mse_top20": 0.008235528133809566 + }, + { + "drug": "Belinostat", + "da": 0.9799999594688416, + "cos_topk": 0.9237204790115356, + "cos_full": 0.8304826021194458, + "mse_top20": 0.021719446405768394 + }, + { + "drug": "CUDC-101", + "da": 0.9399999976158142, + "cos_topk": 0.8852955102920532, + "cos_full": 0.8368879556655884, + "mse_top20": 0.0025481523480266333 + }, + { + "drug": "Cimetidine", + "da": 0.35999998450279236, + "cos_topk": -0.2994626760482788, + "cos_full": -0.116241455078125, + "mse_top20": 0.0020756570156663656 + }, + { + "drug": "Daphnetin", + "da": 0.5600000023841858, + "cos_topk": 0.2768044173717499, + "cos_full": 0.12897855043411255, + "mse_top20": 0.001094892853870988 + }, + { + "drug": "GSK-LSD1", + "da": 0.8799999952316284, + "cos_topk": 0.8411892056465149, + "cos_full": 0.6677924990653992, + "mse_top20": 0.0017961993580684066 + }, + { + "drug": "INO-1001", + "da": 0.7199999690055847, + "cos_topk": 0.4957903027534485, + "cos_full": 0.3681609034538269, + "mse_top20": 0.000978240161202848 + }, + { + "drug": "JNJ-26854165", + "da": 0.6599999666213989, + "cos_topk": 0.3274357318878174, + "cos_full": 0.11645566672086716, + "mse_top20": 0.002688927575945854 + }, + { + "drug": "JNJ-7706621", + "da": 0.7799999713897705, + "cos_topk": 0.5752034783363342, + "cos_full": 0.39907655119895935, + "mse_top20": 0.004903927445411682 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9471156597137451, + "cos_full": 0.8341024518013, + "mse_top20": 0.0011513145873323083 + }, + { + "drug": "Momelotinib", + "da": 0.7400000095367432, + "cos_topk": 0.3740135729312897, + "cos_full": 0.20240986347198486, + "mse_top20": 0.002742650220170617 + }, + { + "drug": "NVP-BSK805", + "da": 0.8799999952316284, + "cos_topk": 0.6370577812194824, + "cos_full": 0.4012455940246582, + "mse_top20": 0.0024428660981357098 + }, + { + "drug": "Nintedanib", + "da": 0.5799999833106995, + "cos_topk": 0.26693689823150635, + "cos_full": 0.29816049337387085, + "mse_top20": 0.009000825695693493 + }, + { + "drug": "PHA-680632", + "da": 0.8799999952316284, + "cos_topk": 0.7737993001937866, + "cos_full": 0.5139182806015015, + "mse_top20": 0.00130820635240525 + }, + { + "drug": "Raltitrexed", + "da": 0.5399999618530273, + "cos_topk": 0.07836173474788666, + "cos_full": 0.016108164563775063, + "mse_top20": 0.024541813880205154 + }, + { + "drug": "Roxadustat", + "da": 0.3799999952316284, + "cos_topk": -0.07352946698665619, + "cos_full": -0.005311395041644573, + "mse_top20": 0.0030154716223478317 + }, + { + "drug": "SB431542", + "da": 0.6599999666213989, + "cos_topk": 0.39064520597457886, + "cos_full": 0.2808215618133545, + "mse_top20": 0.0037157428450882435 + }, + { + "drug": "TMP195", + "da": 0.35999998450279236, + "cos_topk": -0.23663166165351868, + "cos_full": -0.1380777508020401, + "mse_top20": 0.0028537397738546133 + }, + { + "drug": "Toremifene", + "da": 0.6800000071525574, + "cos_topk": 0.41836678981781006, + "cos_full": 0.3502342104911804, + "mse_top20": 0.003882868215441704 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s7/flow_best.pt b/sciplex3_path_b/teachers/priornone/s7/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..f0ade04ed0c42f8ce82853fe29bf06573f9d5591 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s7/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cddf5130b0de5015442283effc6445942830018103d33fa1ec09366853e5c94f +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s7/reproduce.sh b/sciplex3_path_b/teachers/priornone/s7/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..0571c98e433241bd436b81a352c43644fb3fff38 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s7/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s7 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s7" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 7 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s8/config.json b/sciplex3_path_b/teachers/priornone/s8/config.json new file mode 100644 index 0000000000000000000000000000000000000000..e5f4a0aed8a980a8ec8b23f32fa0834391b6cb3e --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s8/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s8", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 8, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 8, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s8/eval.json b/sciplex3_path_b/teachers/priornone/s8/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..71d62437d3057e2f8065c9c3059a0ae0c3b1e312 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s8/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 8, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08735949546098709, + "da_mean": 0.691999979019165, + "cos_topk_mean": 0.39392091855406763, + "cos_full_mean": 0.2930987383425236, + "per_drug": [ + { + "drug": "AC480", + "da": 0.7599999904632568, + "cos_topk": 0.4994989037513733, + "cos_full": 0.3138499855995178, + "mse_top20": 0.0014746377710253 + }, + { + "drug": "AG-14361", + "da": 0.6599999666213989, + "cos_topk": 0.14644084870815277, + "cos_full": 0.18602779507637024, + "mse_top20": 0.0025350742507725954 + }, + { + "drug": "AICAR", + "da": 0.4599999785423279, + "cos_topk": 0.07404596358537674, + "cos_full": 0.027742743492126465, + "mse_top20": 0.0027129463851451874 + }, + { + "drug": "Alendronate", + "da": 0.5799999833106995, + "cos_topk": 0.32873404026031494, + "cos_full": 0.1786603033542633, + "mse_top20": 0.01298859715461731 + }, + { + "drug": "Amisulpride", + "da": 0.5399999618530273, + "cos_topk": 0.12418575584888458, + "cos_full": -0.03321148827672005, + "mse_top20": 0.0042464034631848335 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.27178072929382324, + "cos_full": -0.16859081387519836, + "mse_top20": 0.0085159782320261 + }, + { + "drug": "BMS-754807", + "da": 0.4599999785423279, + "cos_topk": 0.3927720785140991, + "cos_full": 0.24771705269813538, + "mse_top20": 0.008405037224292755 + }, + { + "drug": "Belinostat", + "da": 0.9799999594688416, + "cos_topk": 0.7896227836608887, + "cos_full": 0.6687784194946289, + "mse_top20": 0.04134004935622215 + }, + { + "drug": "CUDC-101", + "da": 0.9199999570846558, + "cos_topk": 0.882759690284729, + "cos_full": 0.8228762745857239, + "mse_top20": 0.005070382263511419 + }, + { + "drug": "Cimetidine", + "da": 0.5799999833106995, + "cos_topk": 0.10895659774541855, + "cos_full": 0.08650753647089005, + "mse_top20": 0.0015635136514902115 + }, + { + "drug": "Daphnetin", + "da": 0.6399999856948853, + "cos_topk": 0.09056296199560165, + "cos_full": 0.10783657431602478, + "mse_top20": 0.001455748570151627 + }, + { + "drug": "GSK-LSD1", + "da": 0.8999999761581421, + "cos_topk": 0.8411940336227417, + "cos_full": 0.6640850305557251, + "mse_top20": 0.001780258840881288 + }, + { + "drug": "INO-1001", + "da": 0.6800000071525574, + "cos_topk": 0.2776646018028259, + "cos_full": 0.2604557275772095, + "mse_top20": 0.0013427076628431678 + }, + { + "drug": "JNJ-26854165", + "da": 0.7400000095367432, + "cos_topk": 0.5705547332763672, + "cos_full": 0.3491670489311218, + "mse_top20": 0.0013645190047100186 + }, + { + "drug": "JNJ-7706621", + "da": 0.7999999523162842, + "cos_topk": 0.5220738649368286, + "cos_full": 0.33516818284988403, + "mse_top20": 0.005275563802570105 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9450196027755737, + "cos_full": 0.8370218873023987, + "mse_top20": 0.0012747630244120955 + }, + { + "drug": "Momelotinib", + "da": 0.7599999904632568, + "cos_topk": 0.48296666145324707, + "cos_full": 0.34617674350738525, + "mse_top20": 0.0023082378320395947 + }, + { + "drug": "NVP-BSK805", + "da": 0.8999999761581421, + "cos_topk": 0.7391399145126343, + "cos_full": 0.5836920142173767, + "mse_top20": 0.0016359881265088916 + }, + { + "drug": "Nintedanib", + "da": 0.5399999618530273, + "cos_topk": 0.3004932105541229, + "cos_full": 0.33026808500289917, + "mse_top20": 0.008400177583098412 + }, + { + "drug": "PHA-680632", + "da": 0.7599999904632568, + "cos_topk": 0.7511519193649292, + "cos_full": 0.548668384552002, + "mse_top20": 0.0015115764690563083 + }, + { + "drug": "Raltitrexed", + "da": 0.6599999666213989, + "cos_topk": 0.14002366364002228, + "cos_full": 0.030227966606616974, + "mse_top20": 0.024107299745082855 + }, + { + "drug": "Roxadustat", + "da": 0.5999999642372131, + "cos_topk": 0.3255241811275482, + "cos_full": 0.19536946713924408, + "mse_top20": 0.0023437892086803913 + }, + { + "drug": "SB431542", + "da": 0.5799999833106995, + "cos_topk": 0.1534583866596222, + "cos_full": 0.1399984359741211, + "mse_top20": 0.004509137477725744 + }, + { + "drug": "TMP195", + "da": 0.5199999809265137, + "cos_topk": -0.013618063181638718, + "cos_full": -0.040488965809345245, + "mse_top20": 0.002438219962641597 + }, + { + "drug": "Toremifene", + "da": 0.8399999737739563, + "cos_topk": 0.6465773582458496, + "cos_full": 0.30946406722068787, + "mse_top20": 0.002474092645570636 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s8/flow_best.pt b/sciplex3_path_b/teachers/priornone/s8/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..256887de0528a19ccea2d35d4e5f56e4241e6341 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s8/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:131a5530cee00007fa438e3bf6d869f00ed43415956d3ea0d7c6dd0e9ef411dc +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s8/reproduce.sh b/sciplex3_path_b/teachers/priornone/s8/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..e4d618da0d04766d8e1dc4ffca7b4635ac1d00e1 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s8/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s8 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s8" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 8 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json' diff --git a/sciplex3_path_b/teachers/priornone/s9/config.json b/sciplex3_path_b/teachers/priornone/s9/config.json new file mode 100644 index 0000000000000000000000000000000000000000..bc6c34b4a1f27068405304f2f5a012f1a7d7bf71 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s9/config.json @@ -0,0 +1,59 @@ +{ + "paper_row": "SciPlex3 priornone teacher s9", + "dataset": "SciPlex3", + "run_dir": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "backbone": "hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt", + "h5ad_rel": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "training_script": "scripts/train_sciplex3_delta_flow.py", + "seed": 9, + "result_json": null, + "teacher": null, + "teachers": null, + "launch_script": null, + "checkpoint": { + "path": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9/flow_best.pt", + "size_mb": 54.7, + "files_in_dir": [ + "config.json", + "eval.json", + "flow_best.pt", + "reproduce.sh" + ] + }, + "hparams_top": { + "_state_dict_present": true, + "theta_dim": 2000, + "d_embed": 2410, + "y_mean": "", + "y_std": "", + "train_names": "" + }, + "hparams_nested": { + "dataset_h5ad": "datasets/scFATE/processed/sciplex3/sciplex3.h5ad", + "multiview": "data/drug_embeddings/sciplex3_multiview_v2.pt", + "ood_json": "data/sciplex3_split_v2b.json", + "output": "runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9", + "epochs": 30000, + "lr": 0.0003, + "wd": 0.0001, + "batch": 64, + "sigma": 0.3, + "sigma_inf": 0.1, + "n_steps": 20, + "K_eval": 128, + "d_hidden": 512, + "n_blocks": 4, + "dropout": 0.1, + "seed": 9, + "log_every": 1000, + "topk_de": 50, + "zscore_target": true, + "prior": "none", + "krr_gamma": null, + "krr_alpha": null, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "device": "cuda" + } +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s9/eval.json b/sciplex3_path_b/teachers/priornone/s9/eval.json new file mode 100644 index 0000000000000000000000000000000000000000..bf45d12da34cb888b7ee6a21457d7badb91b42ce --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s9/eval.json @@ -0,0 +1,204 @@ +{ + "iter": 162, + "model": "sciplex3_delta_flow_multiview_v2", + "n_train": 161, + "n_train_drugs": 161, + "dose_aware": false, + "bch_aug": false, + "bch_n_pairs": 0, + "uniq_doses": null, + "n_ood": 25, + "theta_dim": 2000, + "d_embed": 2410, + "K_eval": 128, + "sigma": 0.3, + "sigma_inf": 0.1, + "epochs": 30000, + "lr": 0.0003, + "batch": 64, + "seed": 9, + "zscore_target": true, + "prior": "none", + "krr_info": null, + "best_loss": 0.08453995734453201, + "da_mean": 0.643199987411499, + "cos_topk_mean": 0.3051110455393791, + "cos_full_mean": 0.2524420033022761, + "per_drug": [ + { + "drug": "AC480", + "da": 0.6200000047683716, + "cos_topk": 0.5483783483505249, + "cos_full": 0.3037377893924713, + "mse_top20": 0.0011345352977514267 + }, + { + "drug": "AG-14361", + "da": 0.6399999856948853, + "cos_topk": 0.010612264275550842, + "cos_full": 0.11742106825113297, + "mse_top20": 0.0028151541482657194 + }, + { + "drug": "AICAR", + "da": 0.4599999785423279, + "cos_topk": 0.041761450469493866, + "cos_full": 0.007654067128896713, + "mse_top20": 0.0031232640612870455 + }, + { + "drug": "Alendronate", + "da": 0.6800000071525574, + "cos_topk": 0.6665509343147278, + "cos_full": 0.49690136313438416, + "mse_top20": 0.011119025759398937 + }, + { + "drug": "Amisulpride", + "da": 0.5399999618530273, + "cos_topk": 0.24165061116218567, + "cos_full": 0.035551488399505615, + "mse_top20": 0.003981923218816519 + }, + { + "drug": "Azacitidine", + "da": 0.4399999976158142, + "cos_topk": -0.28458964824676514, + "cos_full": -0.17256659269332886, + "mse_top20": 0.008493873290717602 + }, + { + "drug": "BMS-754807", + "da": 0.5600000023841858, + "cos_topk": 0.23862504959106445, + "cos_full": 0.18607160449028015, + "mse_top20": 0.009870526380836964 + }, + { + "drug": "Belinostat", + "da": 1.0, + "cos_topk": 0.947543203830719, + "cos_full": 0.8819780945777893, + "mse_top20": 0.016561433672904968 + }, + { + "drug": "CUDC-101", + "da": 0.9799999594688416, + "cos_topk": 0.9114827513694763, + "cos_full": 0.8677065968513489, + "mse_top20": 0.0020771564450114965 + }, + { + "drug": "Cimetidine", + "da": 0.3400000035762787, + "cos_topk": -0.5734879970550537, + "cos_full": -0.2891060709953308, + "mse_top20": 0.004226726945489645 + }, + { + "drug": "Daphnetin", + "da": 0.5799999833106995, + "cos_topk": 0.22346335649490356, + "cos_full": 0.12955397367477417, + "mse_top20": 0.001144375535659492 + }, + { + "drug": "GSK-LSD1", + "da": 0.6800000071525574, + "cos_topk": 0.18053150177001953, + "cos_full": 0.21297624707221985, + "mse_top20": 0.004151394125074148 + }, + { + "drug": "INO-1001", + "da": 0.7599999904632568, + "cos_topk": 0.5252255797386169, + "cos_full": 0.3978433310985565, + "mse_top20": 0.0009949080413207412 + }, + { + "drug": "JNJ-26854165", + "da": 0.8399999737739563, + "cos_topk": 0.6198300719261169, + "cos_full": 0.45040959119796753, + "mse_top20": 0.0013571144081652164 + }, + { + "drug": "JNJ-7706621", + "da": 0.8399999737739563, + "cos_topk": 0.6497307419776917, + "cos_full": 0.47049951553344727, + "mse_top20": 0.004809630569070578 + }, + { + "drug": "MLN8054", + "da": 1.0, + "cos_topk": 0.9446524977684021, + "cos_full": 0.8324275016784668, + "mse_top20": 0.0011676127323880792 + }, + { + "drug": "Momelotinib", + "da": 0.5999999642372131, + "cos_topk": 0.2815351188182831, + "cos_full": 0.18296891450881958, + "mse_top20": 0.0029664766043424606 + }, + { + "drug": "NVP-BSK805", + "da": 0.3400000035762787, + "cos_topk": -0.1862090826034546, + "cos_full": -0.168284073472023, + "mse_top20": 0.004540047142654657 + }, + { + "drug": "Nintedanib", + "da": 0.41999998688697815, + "cos_topk": -0.1519429087638855, + "cos_full": 0.04019447788596153, + "mse_top20": 0.01073166262358427 + }, + { + "drug": "PHA-680632", + "da": 0.85999995470047, + "cos_topk": 0.7737630009651184, + "cos_full": 0.5223840475082397, + "mse_top20": 0.001306279213167727 + }, + { + "drug": "Raltitrexed", + "da": 0.47999998927116394, + "cos_topk": 0.07393057644367218, + "cos_full": 0.016227714717388153, + "mse_top20": 0.024494653567671776 + }, + { + "drug": "Roxadustat", + "da": 0.3799999952316284, + "cos_topk": -0.05095770210027695, + "cos_full": 0.007380391471087933, + "mse_top20": 0.0029356428422033787 + }, + { + "drug": "SB431542", + "da": 0.8399999737739563, + "cos_topk": 0.5690532922744751, + "cos_full": 0.4675171673297882, + "mse_top20": 0.0030101598240435123 + }, + { + "drug": "TMP195", + "da": 0.5199999809265137, + "cos_topk": 0.008625529706478119, + "cos_full": -0.042390502989292145, + "mse_top20": 0.002374270698055625 + }, + { + "drug": "Toremifene", + "da": 0.6800000071525574, + "cos_topk": 0.41801759600639343, + "cos_full": 0.3559923768043518, + "mse_top20": 0.00413626478984952 + } + ] +} \ No newline at end of file diff --git a/sciplex3_path_b/teachers/priornone/s9/flow_best.pt b/sciplex3_path_b/teachers/priornone/s9/flow_best.pt new file mode 100644 index 0000000000000000000000000000000000000000..2ef839e0f599882dcd53d7b9e8b1f2bc0095dd99 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s9/flow_best.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:83388ef06195f2bb6707c505e8061f6e055569ca0f03666d3d6a67d0389a41be +size 57406281 diff --git a/sciplex3_path_b/teachers/priornone/s9/reproduce.sh b/sciplex3_path_b/teachers/priornone/s9/reproduce.sh new file mode 100644 index 0000000000000000000000000000000000000000..b93de6caed3442ce636f3a1f87154c5d38b10743 --- /dev/null +++ b/sciplex3_path_b/teachers/priornone/s9/reproduce.sh @@ -0,0 +1,38 @@ +#!/bin/bash +# Reproduce: SciPlex3 priornone teacher s9 +# Run dir: runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9 +# Result: (no result JSON) +# Original launch: unknown +# Backbone (rotation autoencoder, must be loaded first): hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt + +set -euo pipefail +REPO=${REPO:-/workspace/research/scFATE} +cd "$REPO" +DATASET="datasets/scFATE/processed/sciplex3/sciplex3.h5ad" +BACKBONE="hf-assets/checkpoints/sciplex3/scFATE_epoch199_best.pt" +RUN_DIR="runs/b200_sciplex3_delta_flow_mv_v2_sig0p3_priornone_V2B_s9" + +.venv/bin/python -u scripts/train_sciplex3_delta_flow.py \ + --dataset_h5ad "$DATASET" \ + --backbone_ckpt "$BACKBONE" \ + --output "$RUN_DIR" \ + --seed 9 \ + --theta_dim 2000 \ + --d_embed 2410 \ + --d_hidden 512 \ + --n_blocks 4 \ + --n_steps 20 \ + --sigma 0.3 \ + --prior 'none' \ + --epochs 30000 \ + --lr 0.0003 \ + --wd 0.0001 \ + --batch 64 \ + --sigma_inf 0.1 \ + --K_eval 128 \ + --dropout 0.1 \ + --topk_de 50 \ + --zscore_target \ + --bch_n_pairs 0 \ + --multiview 'data/drug_embeddings/sciplex3_multiview_v2.pt' \ + --ood_json 'data/sciplex3_split_v2b.json'