WSI_Embedding

Patch and slide embeddings for whole-slide images, plus the run records used to produce them.

Original WSIs are not in this repo. They stay on HPC / the source dataset remotes. Do not expect .svs / .tif here.

Repo: thanminh01/WSI_Embedding

Top-level layout

Path	What it is	Download when
embeddings/<dataset>/<model>/<mag>x_<patch>px_<overlap>px_overlap/	Encoder tensors (.h5 / .pt / WSI-LLaVA json) and per-model TRIDENT _config_ / _logs_	You need features
Run-Information/runs-report/<dataset>/	Job logs, VALIDATION, SLURM, perf, TRIDENT runs/*.json, cohort CSVs	You need provenance
Run-Information/prep/<dataset>/	Contours, geojson, thumbnails, wsi_states, patch-coord h5 (N,2), overlay jpgs	You need QC / failed-mask / tiny-slide evidence
Run-Information/parked/<dataset>/	Encoder files for slides excluded from the official cohort	You need the parked cases

Selective download: pull only embeddings/DHMC-LUAD/titan/... or only Run-Information/prep/TCGA-LUAD.

Datasets

DHMC-LUAD (encoder cohort 143)

There are two HPC job directories. They are not duplicates of the same run:

Hub name	HPC folder	Role
DHMC-LUAD	runs-information/full-int-DHMC-LUAD/	Canonical shared coords + later encoders (Virchow/PRISM/KEEP/MUSK/WSI-LLaVA/PRISM2, MUSK 1024-d redo)
DHMC-LUAD-TITAN-CONCH	runs-information/full-int-DHMC-LUAD (TITAN CONCH)/	First encoder pack: TITAN + CONCH v1.5 / v1 at 20×/512

Use DHMC-LUAD for current coords, masks, and later-model logs. Use DHMC-LUAD-TITAN-CONCH for the original TITAN/CONCH job (SLURM 15450381 / 15450382).

Kept encoders (see per-model folders under embeddings/DHMC-LUAD/): TITAN 768, CONCH v1.5 768, CONCH v1 512, Virchow 2560, PRISM 1280, Virchow2 2560, Virchow2 CLS 1280, PRISM2, KEEP 768, MUSK 1024-d vision CLS (ms_aug=False, no CLIP head in the stored tensor), WSI-LLaVA captions + case-bank. GigaPath tiles at 512 exist only as the WSI-LLaVA tile encoder, not as an official GigaPath product.

TCGA-LUAD (encoder cohort 531)

531 diagnostic slides after parking 10 TCGA-05 DX1 cases (tiny GDC canvas + failed tissue mask). Those 10 are not in embeddings/ tensors (except leftovers under parked/). Their wsi_states, thumbnails, contours, and coords are in Run-Information/prep/TCGA-LUAD/ so the failure stays inspectable.

Tensors for TCGA-LUAD may still be landing on HPC; this Run-Information tree is uploaded independently.

TCGA-LUSC

Not in this Run-Information snapshot: prep was still writing on the cluster at upload time. Encoder tensors are not published yet.

Canonical mag / patch

Models	Setting
TITAN, CONCH v1.5, CONCH v1, WSI-LLaVA	20× / 512
PRISM, Virchow, Virchow2, Virchow2 CLS, PRISM2	20× / 224
KEEP	20× / 256
MUSK	20× / 384

How to download

# tensors only, one model
huggingface-cli download thanminh01/WSI_Embedding \
  --repo-type dataset \
  --include "embeddings/DHMC-LUAD/titan/**"

# QC / logs only
huggingface-cli download thanminh01/WSI_Embedding \
  --repo-type dataset \
  --include "Run-Information/**"

What is intentionally absent

• Original whole-slide images
• HPC runs-information/full-int-*/features_* trees (those tensors live under embeddings/ so they are not uploaded twice)
• TCGA-LUSC run snapshot while segmentation/coords were still in flight