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Add H0-mini model. #96

Merged
merged 2 commits into from
Feb 27, 2025
Merged

Add H0-mini model. #96

merged 2 commits into from
Feb 27, 2025

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afilt
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@afilt afilt commented Feb 27, 2025

This PR integrates:

  • The implementation of H0-mini. The model is available on Hugging Face.
  • The implementation of Kaiko ViT B/8 and Hibou Large available respectively on Github and Hugging Face.

Note:

  • H0-mini is a ViT-B model with 768 output dimensions

To reproduce our results, you first need to be granted access to bioptimus/H0-mini on HF. Then, simply run python src/hest/bench/benchmark.py --config bench_config/custom_bench_config.yaml with custom_bench_config.yaml:

# directory containing the data for each task
bench_data_root: '/root_dir/HEST/bench_data'

# directory where benchmark results will be dumped
results_dir: '/root_dir/HEST/ST_pred_results'

# directory where the vision embeddings will be dumped
embed_dataroot: '/root_dir/HEST/ST_data_emb'

# directory to the model weights root
weights_root: '/root_dir/HEST/fm_v1'

# inference parameters
batch_size: 128
num_workers: 16

# encoders to benchmark
encoders: [
  "h0_mini"
]

# datasets contained in `bench_data_root` to benchmark
datasets: [
  "IDC",
  "PRAD",
  "PAAD",
  "SKCM",
  "COAD",
  "READ",
  "CCRCC",
  "HCC",
  "LUNG",
  "LYMPH_IDC",
]

dimreduce: "PCA" 

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@pauldoucet pauldoucet self-assigned this Feb 27, 2025
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Thank you for your additions! Everything looks good to me, ready to be merged

@afilt
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afilt commented Feb 27, 2025

Perfect ! Please go ahead :-)

@pauldoucet pauldoucet merged commit 568df6c into mahmoodlab:main Feb 27, 2025
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2 participants