Datasets:
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json
Languages:
English
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Tags:
histopathology
computational-pathology
survival-analysis
multiple-instance-learning
hypergraph-learning
graph-learning
Keep dataset card focused on data contents and usage
Browse files
README.md
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This dataset provides **pre-extracted patch features, aligned patch coordinates, and precomputed graph and group representations** for 1,344 diagnostic whole-slide images (WSIs) from four TCGA cancer cohorts. It supports survival prediction with multiple-instance learning, graph neural networks, and hypergraph neural networks.
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The data accompany
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## Cohorts
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`N` is the number of retained patches in a WSI and varies between slides. Features are stored once and shared across methods; graph files refer to that same patch ordering. PatchGCN graph files store connectivity without duplicating the feature arrays.
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### Directory layout
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python scripts/evaluate.py --config configs/hypermil.yaml --cohort STAD
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```
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Use `STAD`, `THCA`, `CHOL`, or `LIHC` to select a cohort. Omit `--cohort` from both download commands to obtain all four cohorts
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Methods are selected through YAML configurations within the same training and evaluation framework. Keep feature ordering, graph inputs, patient splits, and method configurations together when using the released checkpoints. See the [GitHub README](https://github.com/shannonchen37/HyperMIL#quick-start) for installation and evaluation details.
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This dataset provides **pre-extracted patch features, aligned patch coordinates, and precomputed graph and group representations** for 1,344 diagnostic whole-slide images (WSIs) from four TCGA cancer cohorts. It supports survival prediction with multiple-instance learning, graph neural networks, and hypergraph neural networks.
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The data accompany the [HyperMIL code repository](https://github.com/shannonchen37/HyperMIL). The supplied feature and graph files can be loaded directly by its training and evaluation scripts, without rerunning preprocessing.
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## Cohorts
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`N` is the number of retained patches in a WSI and varies between slides. Features are stored once and shared across methods; graph files refer to that same patch ordering. PatchGCN graph files store connectivity without duplicating the feature arrays.
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Both MGAS and PASG graph files are provided for **all four cohorts**.
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### Directory layout
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python scripts/evaluate.py --config configs/hypermil.yaml --cohort STAD
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```
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Use `STAD`, `THCA`, `CHOL`, or `LIHC` to select a cohort. Omit `--cohort` from both download commands to obtain all four cohorts. Downloads resume when the same command is rerun. The supplied layout requires no manual path edits or Hugging Face login.
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Methods are selected through YAML configurations within the same training and evaluation framework. Keep feature ordering, graph inputs, patient splits, and method configurations together when using the released checkpoints. See the [GitHub README](https://github.com/shannonchen37/HyperMIL#quick-start) for installation and evaluation details.
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