Add files using upload-large-folder tool

.gitattributes

@@ -58,3 +58,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+benchmark_payloads/RRUFF_option1_473_with_buckets_maxnorm.hdf5 filter=lfs diff=lfs merge=lfs -text
+benchmark_payloads/RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5 filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1,4 @@
+# Local scratch files
+.DS_Store
+*.tmp
+*.log

README.md

@@ -1,3 +1,65 @@
----
-license: mit
----
+---
+language: en
+license: cc-by-4.0
+task_categories:
+  - classification
+tags:
+  - materials-science
+  - x-ray-diffraction
+  - crystallography
+  - benchmark
+  - neurips
+---
+
+# InformedXRD Benchmarks
+
+This staging directory is the draft Hugging Face dataset card for the NeurIPS Evaluations & Datasets artifact release associated with *InformedXRD*.
+
+## Contents
+
+The intended dataset repo contains:
+
+- the frozen `RRUFF-473` benchmark payload
+- the frozen `RRUFF-325` benchmark payload
+- a small reviewer subset with compact precomputed inference outputs
+- manifests and metadata needed to reproduce the benchmark definition
+
+It does **not** contain:
+
+- training code
+- the broader PRX archival release
+- model checkpoints
+
+## Why these benchmarks exist
+
+The paper's main benchmark contribution is not raw scale. It is a reproducible, auditable evaluation surface for real PXRD symmetry classification:
+
+- `RRUFF-473` retains hard real-data cases and supports broad robustness analysis
+- `RRUFF-325` is the cleaner downstream subset used for controlled calibration and error-structure analysis
+
+Both benchmarks are tied to explicit curation logic and frozen artifact manifests.
+
+## Intended use
+
+These datasets are intended for:
+
+- extinction-group evaluation on real powder diffraction patterns
+- hierarchy-aware rescoring of model predictions
+- benchmarking Top-k, prior-baseline, and stratified evaluation claims
+
+They are not intended as general-purpose training corpora.
+
+## Companion assets
+
+The associated code, manifests, and reviewer notebooks live in the separate GitHub reproducibility repo:
+
+- `scattering/neurips-ai-diffraction`
+
+The associated model checkpoints live in the separate Hugging Face model repo.
+
+## Publication plan
+
+1. Create a private Hugging Face dataset repo.
+2. Upload the benchmark payloads, reviewer subset, and metadata.
+3. Verify the benchmark manifests against the uploaded filenames.
+4. Switch visibility when the review/release posture is decided.

benchmark_payloads/RRUFF_option1_473_with_buckets_maxnorm.hdf5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:836d30a81879a56afab635cea149d405fb7e2174f972514804f85b470791a5d8
+size 6794891

benchmark_payloads/RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b3dfbc266120668b53bed0db91e9b02a518264ef40061beabd389999c8d9d7f3
+size 22193796

metadata/ARTIFACT_PLAN.md

@@ -0,0 +1,13 @@
+## Dataset Artifact Plan
+
+Candidate contents:
+- frozen `RRUFF-473` benchmark files
+- frozen `RRUFF-325` benchmark files
+- benchmark ID lists / checksums
+- reviewer subset matching the GitHub reviewer docs
+- dataset card text
+
+Candidate exclusions:
+- files already kept only for the PRX archival release
+- large unrelated training corpora
+- private intermediate curation outputs

metadata/MANIFEST.csv

@@ -0,0 +1,60 @@
+path,kind,description,status,expected_local_path,checkpoint_role
+src/paper_ai_diffraction/core/model.py,source,Core model definition,copied,,
+src/paper_ai_diffraction/core/dataset.py,source,Dataset loading including mixed dual-source support,copied,,
+src/paper_ai_diffraction/core/train.py,source,Training entrypoint,copied,,
+src/paper_ai_diffraction/core/inference.py,source,Inference helpers,copied,,
+src/paper_ai_diffraction/core/streaming_dataset.py,source,Streaming dataset helper retained because train.py imports it,copied,,
+src/paper_ai_diffraction/utils/extinction_multilabel.py,source,Extinction-group multilabel utilities,copied,,
+src/paper_ai_diffraction/eval/evaluate_calibration_metrics.py,source,Calibration metrics evaluation,copied,,
+src/paper_ai_diffraction/eval/evaluate_split_head_validity.py,source,Split-head validity evaluation,copied,,
+src/paper_ai_diffraction/topology/compare_325_failure_modes.py,source,Topology/failure-mode comparison,copied,,
+src/paper_ai_diffraction/topology/plot_extinction_topology_flow.py,source,Topology-flow figure generation,copied,,
+src/paper_ai_diffraction/topology/analyze_topological_error_distance.py,source,Topology distance summary analysis,copied,,
+src/paper_ai_diffraction/topology/plot_topological_error_distance.py,source,Topology distance plotting,copied,,
+src/paper_ai_diffraction/eval/plot_calibration_sweep.py,source,Calibration sweep plotting,copied,,
+assets/figure_data/stage2c_r325_temp_sweep.json,asset,Compact Stage-2c temperature sweep used for the calibration figure,copied,,
+assets/figure_data/physics_pe_curve_82ept35h.json,asset,Compact checkpoint curve used for the physics-PE supplementary figure,copied,,
+configs/final_mixed_2500k_dualsource.json,config,Final champion dual-source config,copied,,
+configs/mixed_200k_pilot.json,config,Mixed-200k pilot config,copied,,
+configs/po_1epoch.json,config,PO 1-epoch config,copied,,
+configs/po_resume2.json,config,PO continuation config,copied,,
+configs/mixed_2500k_merged_reference.json,config,Merged-HDF5 mixed config retained for reference,copied,,
+scripts/train_final_mixed.sh,script,Canonical portable wrapper for final champion training,authored,,
+scripts/train_mixed_200k.sh,script,Canonical portable wrapper for mixed-200k pilot training,authored,,
+scripts/train_po_1epoch.sh,script,Canonical portable wrapper for PO 1-epoch training,authored,,
+scripts/train_po_resume2.sh,script,Canonical portable wrapper for PO continuation training,authored,,
+scripts/tacc_archive/train_final_mixed_2500k_dualsource_tacc.sh,script,Historical TACC launcher for final champion,archived,,
+scripts/tacc_archive/train_mixed_200k_pilot_tacc.sh,script,Historical TACC launcher for mixed-200k pilot,archived,,
+scripts/tacc_archive/train_po_1epoch_tacc.sh,script,Historical TACC launcher for PO 1-epoch run,archived,,
+scripts/tacc_archive/train_po_resume2_tacc.sh,script,Historical TACC launcher for PO continuation,archived,,
+scripts/tacc_archive/eval_final_mixed_rruff_tacc.sh,script,Historical TACC launcher for final benchmark evaluation,archived,,
+scripts/tacc_archive/eval_mixed200k_topology_tacc.sh,script,Historical TACC launcher for mixed-200k topology eval,archived,,
+scripts/tacc_archive/eval_wiseft_r325_tacc.sh,script,Historical TACC launcher for WiSE-FT R325 eval,archived,,
+scripts/eval_rruff_325_473.sh,script,Paper-facing benchmark evaluation wrapper,authored,,
+scripts/make_topology_flow_figure.sh,script,Paper-facing topology-flow wrapper,authored,,
+scripts/make_topology_distance_figure.sh,script,Paper-facing topology-distance wrapper,authored,,
+scripts/make_calibration_figure.sh,script,Paper-facing calibration sweep wrapper,authored,,
+scripts/make_curriculum_real_holdout.py,script,Paper-facing Figure 2 generator from bundled benchmark values,adapted,,
+scripts/make_stage_decoder_tradeoffs_rruff473.py,script,Paper-facing Figure 3 generator from bundled benchmark values,adapted,,
+scripts/make_physics_pe_q2_ruler.py,script,Paper-facing S8 generator from bundled checkpoint-curve JSON,authored,,
+scripts/reconstruct_rruff_473.py,script,Public algorithm for reconstructing the frozen RRUFF-473 benchmark from upstream manifest and XY data,adapted,,
+scripts/build_rruff_325_from_473.py,script,Public deterministic builder for RRUFF-325 from frozen RRUFF-473,adapted,,
+scripts/make_main_tables.py,script,Paper-facing table-generation script,authored,,
+results/,directory,Compact JSON outputs used in paper; generated figures are intentionally excluded from git,copied,,
+docs/TRAINING.md,doc,Paper-facing training instructions,authored,,
+docs/EVALUATION.md,doc,Paper-facing evaluation instructions,authored,,
+docs/FIGURES.md,doc,Paper-facing figure instructions,authored,,
+docs/BENCHMARKS.md,doc,Benchmark-construction and non-redistribution notes for RRUFF-473 and RRUFF-325,authored,,
+assets/topology/extinction_group_adjacency.json,asset,Condensed extinction-group topology graph,copied,,
+reproducibility/checkpoint_manifest.csv,metadata,Checkpoint linkage manifest,generated,,
+reproducibility/dataset_manifest.csv,metadata,Dataset and external-asset manifest,generated,,
+notebooks/provenance/wandb_confusion_matrix_from_table.ipynb,notebook,Provenance notebook for the supplemental ViT confusion matrix from a W&B table artifact,adapted,,
+notebooks/provenance/supplemental_vit_inference.ipynb,notebook,Supplemental ViT batch inference — runs any of the 11 supplemental checkpoints against a RRUFF benchmark HDF5 and reports top-1/3/5 accuracy,authored,,
+notebooks/provenance/csv_to_db_with_bravais_vit_model.ipynb,notebook,Supplemental Fig S5 — VIT attention overlay with HKL annotations using checkpoint pi7r8pah,adapted,,
+assets/figure_data/1k_structures.csv,asset,1000 crystal structures (structure_id/space group/unit cell/atoms); source for runtime-generated intrep_crystal_xrd.db,copied,,
+assets/figure_data/interp_metadata_clean.csv,asset,Maps HDF5 index to structure_id for the interpretability subset; used by csv_to_db notebook,copied,,
+assets/figure_data/conf_mat_top5_copper-sweep-1_table_103_ff53214644fd32c50e63.table.json,asset,99x99 W&B confusion matrix table artifact (run 76zuzb4h); full artifact filename; primary backing Fig S3; used by wandb_confusion_matrix_from_table.ipynb,copied,,
+src/paper_ai_diffraction/core/rt_model.py,source,Regular Transformer (RT) model definition for supplemental checkpoints,adapted,,
+notebooks/provenance/supplemental_rt_inference.ipynb,notebook,Supplemental RT batch inference — runs an RT checkpoint against a RRUFF benchmark HDF5 and reports top-1/3/5 accuracy (tab:real_ablation),adapted,,
+notebooks/provenance/supplemental_rt_cross_test.ipynb,notebook,Supplemental RT 4x4 training-distribution cross-test (tab:rt_distribution),adapted,,
+notebooks/provenance/supplemental_rt_attention.ipynb,notebook,Supplemental RT attention overlay with HKL annotations (fig:rt_attention),adapted,,

metadata/STAGED_INVENTORY.json

@@ -0,0 +1,32 @@
+{
+  "staged_model_files": [
+    "pxrd_cnn_control_checkpoint.pt",
+    "xrd_model_82ept35h_best.pth",
+    "xrd_model_9rwv1qly_best.pth",
+    "xrd_model_cscjfdwk_best.pth",
+    "xrd_model_wwuvp1kj_best.pth"
+  ],
+  "staged_dataset_benchmark_payloads": [
+    "RRUFF_option1_473_with_buckets_maxnorm.hdf5",
+    "RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5"
+  ],
+  "staged_dataset_reviewer_subset": [
+    "correct_case_015_Arsenopyrite__R050071-1__6130.csv",
+    "correct_case_015_Arsenopyrite__R050071-1__6130.json",
+    "ext_group_priors.csv",
+    "ext_group_priors.json",
+    "failure_case_000_Actinolite__R050336-1__5330.csv",
+    "failure_case_000_Actinolite__R050336-1__5330.json",
+    "manifest.json",
+    "reviewer_case_metadata.csv",
+    "rruff325_precomputed_inference.json"
+  ],
+  "staged_dataset_metadata": [
+    "ARTIFACT_PLAN.md",
+    "MANIFEST.csv",
+    "STAGED_INVENTORY.json",
+    "checkpoint_manifest.csv",
+    "dataset_manifest.csv"
+  ],
+  "missing_expected_candidates": []
+}

metadata/checkpoint_manifest.csv

@@ -0,0 +1,33 @@
+checkpoint_role,archive_status,archive_filename,expected_local_path,notes
+cnn_control,external_model_repo,pxrd_cnn_control_checkpoint.pt,external/checkpoints/pxrd_cnn_control_checkpoint.pt,1D residual CNN control from the validated in-house RRUFF bs128 lineage; selected public-facing artifact name for the NeurIPS evaluation release
+stage1_base,external_archive,xrd_model_ic6gfmvm_best.pth,external/checkpoints/xrd_model_ic6gfmvm_best.pth,base initialization for later realism runs
+stage2a_decoder_tradeoff,external_archive,xrd_model_h7dqlpfp_best.pth,external/checkpoints/xrd_model_h7dqlpfp_best.pth,Stage-2a checkpoint named in the manuscript decoder tradeoff analysis
+stage2b_decoder_tradeoff,external_archive,xrd_model_guvsasrs_best.pth,external/checkpoints/xrd_model_guvsasrs_best.pth,Stage-2b checkpoint named in the manuscript decoder tradeoff analysis
+legacy_replay_baseline,external_archive,xrd_model_wwuvp1kj_best.pth,external/checkpoints/xrd_model_wwuvp1kj_best.pth,Legacy replay-era baseline named in the supplementary checkpoint map
+baseline_350k,external_archive,xrd_model_7pv3pv3y_best.pth,external/checkpoints/xrd_model_7pv3pv3y_best.pth,350k baseline named in the supplementary checkpoint map
+stage2c_baseline,external_archive,xrd_model_9rwv1qly_best.pth,external/checkpoints/xrd_model_9rwv1qly_best.pth,non-PO baseline used in paper
+stage2c_aux025_ablation,external_archive,xrd_model_0879pvmm_best.pth,external/checkpoints/xrd_model_0879pvmm_best.pth,Stage-2c auxiliary-loss ablation named in the supplement
+po_1epoch,external_archive,xrd_model_cscjfdwk_best.pth,external/checkpoints/xrd_model_cscjfdwk_best.pth,best Top-1 PO ablation
+po_resume2,external_archive,xrd_model_dsi7ehiv_best.pth,external/checkpoints/xrd_model_dsi7ehiv_best.pth,PO continuation comparison
+mixed_200k_pilot,external_archive,xrd_model_eeru8svx_best.pth,external/checkpoints/xrd_model_eeru8svx_best.pth,small mixed pilot
+final_mixed_champion,external_archive,xrd_model_82ept35h_best.pth,external/checkpoints/xrd_model_82ept35h_best.pth,final large mixed champion
+late_uniform_precursor,external_archive,xrd_model_xgy3h6uw_best.pth,external/checkpoints/xrd_model_xgy3h6uw_best.pth,exploratory larger-uniform precursor named in the supplement
+late_stage2_continuation,external_archive,xrd_model_2vegisf1_best.pth,external/checkpoints/xrd_model_2vegisf1_best.pth,exploratory larger-uniform continuation named in the supplement
+wiseft_a03_optional,external_archive,xrd_model_wiseft_9rwv1qly_cscjfdwk_a03_best.pth,external/checkpoints/xrd_model_wiseft_9rwv1qly_cscjfdwk_a03_best.pth,optional WiSE-FT ablation described as exploratory rather than part of the main manuscript lineage
+wiseft_a05_optional,external_archive,xrd_model_wiseft_9rwv1qly_cscjfdwk_a05_best.pth,external/checkpoints/xrd_model_wiseft_9rwv1qly_cscjfdwk_a05_best.pth,optional WiSE-FT ablation described as exploratory rather than part of the main manuscript lineage
+supplemental_vt_balanced,external_archive,xrd_model_tite66yo.pth,external/checkpoints/xrd_model_tite66yo.pth,Table S7 VT-Balanced; wandb_run_id=tite66yo; trained on 10M PyXtal balanced label distribution (5–90°)
+supplemental_vt_icsd,external_archive,xrd_model_k0it6fz2.pth,external/checkpoints/xrd_model_k0it6fz2.pth,Table S7 VT-ICSD; wandb_run_id=k0it6fz2; trained on 10M PyXtal ICSD label distribution (5–90°)
+supplemental_vt_rruff,external_archive,xrd_model_l0yy9wv9.pth,external/checkpoints/xrd_model_l0yy9wv9.pth,Table S7 VT-RRUFF; wandb_run_id=l0yy9wv9; trained on 10M PyXtal RRUFF label distribution (5–90°)
+supplemental_vt_augmented,external_archive,xrd_model_cpv8k8ha.pth,external/checkpoints/xrd_model_cpv8k8ha.pth,Table S7 VT-Augmented; wandb_run_id=cpv8k8ha; trained on 10M PyXtal augmented RRUFF-type distribution (5–90°)
+supplemental_vt_reduced_reflection,external_archive,xrd_model_smqmqi14.pth,external/checkpoints/xrd_model_smqmqi14.pth,Tables S4/S5 VT-Reduced Reflection and Fig S3 confusion matrix source; wandb_run_id=smqmqi14; spec_length=701 (10–80°); crashed run
+supplemental_vt_full_reflection,external_archive,xrd_model_mth7zg2w.pth,external/checkpoints/xrd_model_mth7zg2w.pth,Tables S3/S5 VT-Full Reflection; wandb_run_id=mth7zg2w; spec_length=1000; crashed run
+supplemental_vt_reduced_pyxtal,external_archive,xrd_model_bj1m83oz.pth,external/checkpoints/xrd_model_bj1m83oz.pth,Tables S4/S5 VT-Reduced PyXtal; wandb_run_id=bj1m83oz; spec_length=700 (10–80°)
+supplemental_vt_full_pyxtal,external_archive,xrd_model_3zmiyil8.pth,external/checkpoints/xrd_model_3zmiyil8.pth,Tables S3/S5 VT-Full PyXtal; wandb_run_id=3zmiyil8; spec_length=1000; use_rope=True
+supplemental_vt_biased_reflection,external_archive,xrd_model_f3sdux88.pth,external/checkpoints/xrd_model_f3sdux88.pth,Table S3 VT-Biased Reflection; wandb_run_id=f3sdux88; ICSD-biased label distribution; spec_length=1000; crashed run
+supplemental_vt_biased_pyxtal,external_archive,xrd_model_kd1znx23.pth,external/checkpoints/xrd_model_kd1znx23.pth,Table S3 VT-Biased PyXtal; wandb_run_id=kd1znx23; ICSD-biased label distribution; spec_length=1000
+supplemental_vt_fig_s5_attention,external_archive,xrd_model_pi7r8pah.pth,external/checkpoints/xrd_model_pi7r8pah.pth,Fig S5 VIT attention overlay with HKL annotations; wandb_run_id=pi7r8pah; trained on augmented RRUFF-type distribution; spec_length=8501
+rt_distribution_balanced,external_archive,xrd_model_yv1m76u6.pth,external/checkpoints/xrd_model_yv1m76u6.pth,RT-Balanced checkpoint for tab:rt_distribution; depth=8 num_heads=4 spec_length=8501
+rt_distribution_icsd,external_archive,xrd_model_4hv17ttu.pth,external/checkpoints/xrd_model_4hv17ttu.pth,RT-ICSD checkpoint for tab:rt_distribution and real-RRUFF ablation notebook; depth=6 num_heads=4 spec_length=8501
+rt_distribution_rruff,external_archive,xrd_model_hwixtnv7.pth,external/checkpoints/xrd_model_hwixtnv7.pth,RT-RRUFF checkpoint for tab:rt_distribution and fig:rt_attention; depth=6 num_heads=4 spec_length=8501
+rt_distribution_augmented,external_archive,xrd_model_mq1l94p7.pth,external/checkpoints/xrd_model_mq1l94p7.pth,RT-Augmented checkpoint for tab:rt_distribution and real-RRUFF ablation notebook; depth=6 num_heads=4 spec_length=8501
+rt_real_ablation_16heads,external_archive,xrd_model_7brb1pir.pth,external/checkpoints/xrd_model_7brb1pir.pth,RT 16-head ablation checkpoint for the supplemental real-RRUFF ablation notebook; depth=6 num_heads=16 spec_length=8501

metadata/dataset_manifest.csv

@@ -0,0 +1,42 @@
+logical_name,asset_class,redistributed_in_repo,expected_env_var,example_filename,expected_local_path_or_source,required_for,notes
+cnn_control_checkpoint,external_checkpoint,no,,pxrd_cnn_control_checkpoint.pt,external/checkpoints/pxrd_cnn_control_checkpoint.pt,baseline comparison,Public-facing CNN control checkpoint for the NeurIPS evaluation release; selected from the validated in-house RRUFF bs128 lineage.
+stage1_base_checkpoint,external_checkpoint,no,CHECKPOINT_PATH,xrd_model_ic6gfmvm_best.pth,external/checkpoints/xrd_model_ic6gfmvm_best.pth,training and ablation lineage,Download from external archive. This repo does not bundle checkpoints.
+stage2a_checkpoint,external_checkpoint,no,,xrd_model_h7dqlpfp_best.pth,external/checkpoints/xrd_model_h7dqlpfp_best.pth,decoder tradeoff reproduction,Named manuscript checkpoint for the Stage-2a decoder comparison.
+stage2b_checkpoint,external_checkpoint,no,,xrd_model_guvsasrs_best.pth,external/checkpoints/xrd_model_guvsasrs_best.pth,decoder tradeoff reproduction,Named manuscript checkpoint for the Stage-2b decoder comparison.
+legacy_replay_checkpoint,external_checkpoint,no,,xrd_model_wwuvp1kj_best.pth,external/checkpoints/xrd_model_wwuvp1kj_best.pth,supplementary baselines,Named supplementary replay-era baseline checkpoint.
+baseline_350k_checkpoint,external_checkpoint,no,,xrd_model_7pv3pv3y_best.pth,external/checkpoints/xrd_model_7pv3pv3y_best.pth,supplementary baselines,Named supplementary 350k baseline checkpoint.
+stage2c_baseline_checkpoint,external_checkpoint,no,,xrd_model_9rwv1qly_best.pth,external/checkpoints/xrd_model_9rwv1qly_best.pth,baseline comparison,Download from external archive if reproducing the Stage-2c baseline comparison.
+stage2c_aux025_checkpoint,external_checkpoint,no,,xrd_model_0879pvmm_best.pth,external/checkpoints/xrd_model_0879pvmm_best.pth,supplementary ablation,Named supplementary Stage-2c-aux025 ablation checkpoint.
+po_1epoch_checkpoint,external_checkpoint,no,,xrd_model_cscjfdwk_best.pth,external/checkpoints/xrd_model_cscjfdwk_best.pth,PO ablation,Download from external archive if reproducing the PO-only ablation.
+po_resume2_checkpoint,external_checkpoint,no,,xrd_model_dsi7ehiv_best.pth,external/checkpoints/xrd_model_dsi7ehiv_best.pth,PO continuation,Download from external archive if reproducing the continuation comparison.
+mixed200k_checkpoint,external_checkpoint,no,,xrd_model_eeru8svx_best.pth,external/checkpoints/xrd_model_eeru8svx_best.pth,mixed pilot,Download from external archive if rerunning mixed-200k checkpoint evaluation.
+final_mixed2500k_checkpoint,external_checkpoint,no,CHECKPOINT_PATH,xrd_model_82ept35h_best.pth,external/checkpoints/xrd_model_82ept35h_best.pth,main paper evaluation and figures,Default checkpoint path expected by the paper-facing evaluation wrapper.
+late_uniform_precursor_checkpoint,external_checkpoint,no,,xrd_model_xgy3h6uw_best.pth,external/checkpoints/xrd_model_xgy3h6uw_best.pth,exploratory supplement continuation family,Named supplementary larger-uniform precursor checkpoint.
+late_stage2_continuation_checkpoint,external_checkpoint,no,,xrd_model_2vegisf1_best.pth,external/checkpoints/xrd_model_2vegisf1_best.pth,exploratory supplement continuation family,Named supplementary continuation checkpoint.
+standard_trainready_h5,external_dataset,no,STANDARD_TRAINREADY_H5,rruff_conditioned_2346k_v1_trainready.hdf5,/scratch/.../rruff_conditioned_2346k_v1_trainready.hdf5,training only,External trainready dataset not redistributed in this repo.
+po_trainready_h5,external_dataset,no,PO_TRAINREADY_H5,rruff_conditioned_500k_po_v1_trainready.hdf5,/scratch/.../rruff_conditioned_500k_po_v1_trainready.hdf5,training only,External trainready dataset not redistributed in this repo.
+rruff325_h5,external_dataset,no,RRUFF_325_H5,RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5,/work2/.../RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5,evaluation,Primary harsh real-data benchmark. Required by `scripts/eval_rruff_325_473.sh`.
+rruff473_h5,external_dataset,no,RRUFF_473_H5,RRUFF_option1_473_with_buckets_maxnorm.hdf5,/work2/.../RRUFF_option1_473_with_buckets_maxnorm.hdf5,evaluation,Broader curated real-data benchmark. Required by `scripts/eval_rruff_325_473.sh`.
+prior_h5,external_dataset,no,PRIOR_H5,rruff_conditioned_2346k_v1_trainready.hdf5,/scratch/.../rruff_conditioned_2346k_v1_trainready.hdf5,evaluation,External prior/train HDF5 used for prior-derived calibration in the evaluation wrapper.
+canonical_extinction_csv,external_dataset,no,CANONICAL_CSV,canonical_extinction_to_space_group.csv,/scratch/.../ai-diffraction/Code/Post_Processing/canonical_extinction_to_space_group.csv,topology figures,External canonical extinction-group table required by `scripts/make_topology_flow_figure.sh`. The validated Stampede example lived in an `ai-diffraction` checkout on scratch.
+topology_graph_json,bundled_asset,yes,GRAPH_JSON,extinction_group_adjacency.json,assets/topology/extinction_group_adjacency.json,topology figures,Bundled in this repo.
+mixed200k_failure_json,bundled_result_json,yes,MIXED200K_FAILURE_JSON,mixed200k_compare_325_failure_modes_eeru8svx.json,results/mixed200k_compare_325_failure_modes_eeru8svx.json,topology figures,Bundled compact paper result artifact.
+mixed2500k_failure_json,bundled_result_json,yes,FAILURE_JSON,mixed2500k_compare_325_failure_modes_655279.json,results/mixed2500k_compare_325_failure_modes_655279.json,topology figures,Bundled compact paper result artifact.
+calibration_sweep_json,bundled_result_json,yes,CAL_SWEEP_JSON,stage2c_r325_temp_sweep.json,assets/figure_data/stage2c_r325_temp_sweep.json,calibration figure,Bundled compact Stage-2c sweep JSON used by `scripts/make_calibration_figure.sh` by default.
+physics_pe_curve_json,bundled_result_json,yes,PHYSICS_PE_CURVE_JSON,physics_pe_curve_82ept35h.json,assets/figure_data/physics_pe_curve_82ept35h.json,S8 physics PE figure,Bundled compact checkpoint-curve JSON used by `scripts/make_physics_pe_q2_ruler.py`.
+supplemental_train_pyxtal_balanced,external_dataset,no,,10Million_pyxtal_RRUFFF-type_repacked.hdf5,/scratch/<USER>/Data/10Million_pyxtal_RRUFFF-type_repacked.hdf5,supplemental Table S7 (tite66yo),10M PyXtal balanced label distribution; 5–90°; spec_length=8501
+supplemental_train_pyxtal_icsd,external_dataset,no,,10mil_pyxtal_rruff-type_icsd_distrib_repacked.hdf5,/scratch/<USER>/Data/10mil_pyxtal_rruff-type_icsd_distrib_repacked.hdf5,supplemental Table S7 (k0it6fz2),10M PyXtal ICSD label distribution; 5–90°; spec_length=8501
+supplemental_train_pyxtal_rruff,external_dataset,no,,10mil_pyxtal_rruff-type_rruff_distrib_repacked.hdf5,/scratch/<USER>/Data/10mil_pyxtal_rruff-type_rruff_distrib_repacked.hdf5,supplemental Table S7 (l0yy9wv9),10M PyXtal RRUFF label distribution; 5–90°; spec_length=8501
+supplemental_train_pyxtal_aug,external_dataset,no,,rruff_aug_10M_trainready_repacked.hdf5,/scratch/<USER>/Data/rruff_aug_10M_trainready_repacked.hdf5,supplemental Table S7 (cpv8k8ha) and Fig S5 (pi7r8pah),10M PyXtal augmented RRUFF-type distribution; 5–90°; spec_length=8501
+supplemental_train_reflection_highres,external_dataset,no,,10Million_ref_ext_highres.h5,/scratch/<USER>/Data/10Million_ref_ext_highres.h5,supplemental Tables S3/S4/S5 (smqmqi14 spec_length=701; mth7zg2w spec_length=1000),10M reflection high-res
+supplemental_train_pyxtal_cleaned,external_dataset,no,,10million_pyxtal_repacked_cleaned.hdf5,/scratch/<USER>/Data/10million_pyxtal_repacked_cleaned.hdf5,supplemental Tables S4/S5 (bj1m83oz spec_length=700; 3zmiyil8 spec_length=1000),10M PyXtal cleaned
+supplemental_train_reflection_icsd_bias,external_dataset,no,,10M_W_ICSD_Bias_reflection_repack.hdf5,/scratch/<USER>/Data/10M_W_ICSD_Bias_reflection_repack.hdf5,supplemental Table S3 (f3sdux88),10M reflection ICSD-biased label distribution
+supplemental_train_pyxtal_icsd_bias,external_dataset,no,,10M_W_ICSD_Bias_pyxtal_repack.hdf5,/scratch/<USER>/Data/10M_W_ICSD_Bias_pyxtal_repack.hdf5,supplemental Table S3 (kd1znx23),10M PyXtal ICSD-biased label distribution
+supplemental_test_rruff_reduced_700,external_dataset,no,,RRUFF_norm_reduced_range_10_80_deg_700_intensity.hdf5,/scratch/<USER>/Data/RRUFF_norm_reduced_range_10_80_deg_700_intensity.hdf5,supplemental Table S5 inference run e0sq2tus (bj1m83oz),Reduced range RRUFF; 700 pts; 10–80°
+supplemental_test_rruff_reduced_701,external_dataset,no,,RRUFF_norm_reduced_range_10_80_deg_701_intensity.hdf5,/scratch/<USER>/Data/RRUFF_norm_reduced_range_10_80_deg_701_intensity.hdf5,supplemental Table S5 inference runs njur2oso/x9ye2mrx (smqmqi14),Reduced range RRUFF; 701 pts; 10–80°
+supplemental_test_rruff_full_1000,external_dataset,no,,RRUFF_norm_uniform_sampling_5_90_deg_1000_intensity.hdf5,/scratch/<USER>/Data/RRUFF_norm_uniform_sampling_5_90_deg_1000_intensity.hdf5,supplemental Table S5 inference runs hrhk538h (mth7zg2w) and ollqf5gm (3zmiyil8),Full range RRUFF; 1000 pts; 5–90°
+supplemental_test_rruff_low_bkg_8501,external_dataset,no,,RRUFF_low_bkg_full_intensity.hdf5,/scratch/<USER>/Data/RRUFF_low_bkg_full_intensity.hdf5,supplemental Table S7 inference runs,Full RRUFF low background; 8501 pts; 5–90°
+supplemental_test_rruff_interp,external_dataset,no,,RRUFF_interp_data.hdf5,/scratch/<USER>/Data/RRUFF_interp_data.hdf5,supplemental Fig S5 attention overlay inference,RRUFF interpretability set with structure_id dataset
+supplemental_1k_structures_csv,bundled_asset,yes,,1k_structures.csv,assets/figure_data/1k_structures.csv,supplemental Fig S5 (csv_to_db_with_bravais_vit_model.ipynb),1000 crystal structures with structure_id/space group/unit cell/atoms; source for intrep_crystal_xrd.db
+supplemental_interp_metadata_csv,bundled_asset,yes,,interp_metadata_clean.csv,assets/figure_data/interp_metadata_clean.csv,supplemental Fig S5 (csv_to_db_with_bravais_vit_model.ipynb),Maps HDF5 index to structure_id for interpretability subset
+supplemental_confusion_matrix_json,bundled_asset,yes,,conf_mat_top5_copper-sweep-1_table_103_ff53214644fd32c50e63.table.json,assets/figure_data/conf_mat_top5_copper-sweep-1_table_103_ff53214644fd32c50e63.table.json,supplemental Fig S3 (wandb_confusion_matrix_from_table.ipynb),99x99 W&B confusion matrix table artifact from run 76zuzb4h; columns: Actual/Predicted/nPredictions

reviewer_subset/correct_case_015_Arsenopyrite__R050071-1__6130.json

@@ -0,0 +1,27 @@
+{
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+  "case_id": "Arsenopyrite__R050071-1__6130",
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+  "paper_model_summary": {
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+  "csv_path": "assets/reviewer_examples/correct_case_015_Arsenopyrite__R050071-1__6130.csv"
+}

reviewer_subset/ext_group_priors.csv

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reviewer_subset/ext_group_priors.json

@@ -0,0 +1,601 @@
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reviewer_subset/failure_case_000_Actinolite__R050336-1__5330.json

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+{
+  "tag": "failure_case",
+  "benchmark_index": 0,
+  "case_id": "Actinolite__R050336-1__5330",
+  "mineral": "Actinolite",
+  "severity": "recoverable",
+  "fit_bucket": "fail",
+  "rwp": 0.16142818331718445,
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+  "true_space_group": 12,
+  "true_space_group_symbol": "C2/m",
+  "true_space_group_source": "rruff_fit_dif",
+  "paper_model_summary": {
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+    "pred_eg": 4,
+    "top5_eg": [
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+    "correct": false
+  },
+  "csv_path": "assets/reviewer_examples/failure_case_000_Actinolite__R050336-1__5330.csv"
+}

reviewer_subset/manifest.json

@@ -0,0 +1,20 @@
+{
+  "benchmark_h5_basename": "RRUFF_usable_plus_recoverable_325_with_labels_maxnorm.hdf5",
+  "failure_json": "results/mixed2500k_compare_325_failure_modes_655279.json",
+  "model_key": null,
+  "metadata_csv": "reviewer_case_metadata.csv",
+  "examples": {
+    "correct_case": {
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+      "json_path": "assets/reviewer_examples/correct_case_015_Arsenopyrite__R050071-1__6130.json",
+      "case_id": "Arsenopyrite__R050071-1__6130",
+      "true_eg": 99
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+    "failure_case": {
+      "csv_path": "assets/reviewer_examples/failure_case_000_Actinolite__R050336-1__5330.csv",
+      "json_path": "assets/reviewer_examples/failure_case_000_Actinolite__R050336-1__5330.json",
+      "case_id": "Actinolite__R050336-1__5330",
+      "true_eg": 5
+    }
+  }
+}

reviewer_subset/reviewer_case_metadata.csv

@@ -0,0 +1,3 @@
+case_id,dif_filename,space_group_symbol,space_group_number,mapped_extinction_group,space_group_source
+Arsenopyrite__R050071-1__6130,Arsenopyrite__R050071-1__Powder__DIF_File__6130.txt,P-1,2,99,rruff_fit_dif
+Actinolite__R050336-1__5330,Actinolite__R050336-1__Powder__DIF_File__5330.txt,C2/m,12,5,rruff_fit_dif