reversely/tcga-ucec-embedding
TCGA-UCEC endometrial pathology: page images + ColPali embeddings Read-only serving assets for an endometrial pathology report review tool, derived from the public TCGA / GDC endometrial (UCEC) corpus. All source data is public and de-identified; embeddings come from the open-weight ColPali model. Contents <patient_filename>/page_NNN.png -- rendered report page images at 200 DPI (545 cases, 1921 pages), one folder per case. <patient_filename>.npz -- ColPali page… See the full description on the dataset page: https://huggingface.co/datasets/reversely/tcga-ucec-embedding.
TCGA-UCEC endometrial pathology: page images + ColPali embeddings
Read-only serving assets for an endometrial pathology report review tool, derived from the public TCGA / GDC endometrial (UCEC) corpus. All source data is public and de-identified; embeddings come from the open-weight ColPali model.
Contents
<patient_filename>/page_NNN.png-- rendered report page images at 200 DPI (545 cases, 1921 pages), one folder per case.<patient_filename>.npz-- ColPali page embeddings for that case: one float16 array per page, keyedpage_000,page_001, ...query_embeddings.npz-- ColPali embeddings for the 9 CAP/ICCR field queries (histologictype, histologicgrade, myometrialinvasionpercent, cervicalstromalinvasion, lymphovascularspaceinvasion, margins, regionallymphnodestatus, pathologicstage, molecular_classification).ocr/TCGA_Reports.csv-- OCR text for the reports.
Page and query vectors are scored with late-interaction MaxSim (ColBERT-style) on CPU, no GPU needed at serve time.
Provenance
- Page images: GDC pathology-report PDFs (files-API lookup by case barcode +
data_type="Pathology Report"), rendered to PNG at 200 DPI (PyMuPDF). - OCR text: tatonetti-lab/tcga-path-reports (Kefeli et al. 2024, Patterns).
- Embeddings:
vidore/colpali-v1.3, multi-vector, bf16 inference, stored float16.