removed GTEx and CPTAC, sorted rows
Browse files
README.md
CHANGED
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@@ -103,8 +103,6 @@ print(f"Embedding shape: {embedding[0].shape}")
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|---------|------|---------------|------------|
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| TCGA | 12k | Public | FFPE only |
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| NKI-80k | 80k | Proprietary | 10,141 patients, 31 organs |
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| GTEx | 25k | Public | Healthy subjects |
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| CPTAC | 7.2k | Public | Tumor samples from 13 cohorts |
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## Training Components
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@@ -129,14 +127,14 @@ Our best model **Midnight-92k/392** consistently outperforms or matches leading
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|-------|------|---------------|------|-------|----------|-----|---------|-------|------|---------------|---------------|--------|---------|------|
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| **[Midnight-92k/392](#usage)** | **0.778** | **0.900** | **0.904** | **0.646** | 0.802 | 0.966 | **0.807** | 0.828 | **0.951** | 0.868 | 0.651 | **0.662** | **0.708** | 0.415 |
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| [UNI-2](https://huggingface.co/MahmoodLab/UNI2-h) | **0.776** | **0.885** | **0.924** | **0.651** | **0.863** | **0.970** | 0.777 | 0.829 | **0.951** | **0.873** | **0.666** | 0.626 | 0.644 | **0.431** |
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| [Virchow2](https://huggingface.co/paige-ai/Virchow2) | 0.766 | 0.835 | 0.890 | 0.633 | 0.818 | 0.966 | 0.791 | **0.865** | 0.938 | 0.860 | 0.646 | 0.640 | 0.674 | 0.403 |
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| **[Midnight-92k](#usage)** | **0.767** | **0.882** | 0.889 | 0.615 | 0.793 | **0.967** | **0.823** | 0.831 | 0.948 | **0.872** | 0.643 | 0.629 | 0.656 | **0.425** |
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| [Kaiko-B8](https://github.com/kaiko-ai/towards_large_pathology_fms) | 0.757 | 0.799 | 0.876 | 0.641 | **0.842** | 0.960 | 0.761 | 0.830 | 0.920 | 0.836 | 0.650 | **0.644** | 0.686 | 0.391 |
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| [Prov_GigaPath](https://github.com/prov-gigapath/prov-gigapath) | 0.752 | 0.853 | 0.794 | 0.626 | **0.846** | 0.959 | 0.727 | 0.831 | 0.944 | 0.812 | 0.657 | 0.628 | **0.688** | 0.405 |
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| [Hibou-L](https://huggingface.co/histai/hibou-L) | 0.751 | 0.825 | 0.792 | **0.643** | 0.767 | 0.954 | 0.766 | **0.850** | **0.949** | 0.852 | 0.654 | **0.646** | 0.668 | 0.397 |
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| 139 |
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| [UNI](https://huggingface.co/MahmoodLab/UNI) | 0.749 | 0.833 | 0.797 | 0.613 | 0.808 | 0.954 | 0.759 | 0.841 | 0.937 | 0.854 | 0.662 | 0.627 | 0.662 | 0.391 |
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| [Phikon](https://huggingface.co/owkin/phikon) | 0.724 | 0.826 | 0.744 | 0.579 | 0.715 | 0.946 | 0.743 | 0.824 | 0.919 | 0.822 | 0.648 | 0.624 | 0.644 | 0.377 |
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| [Phikon-v2](https://huggingface.co/owkin/phikon-v2) | 0.718 | 0.756 | 0.737 | 0.607 | 0.725 | 0.953 | 0.753 | 0.796 | 0.900 | 0.807 | 0.634 | 0.626 | 0.645 | 0.391 |
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| [Lunit](https://github.com/lunit-io/benchmark-ssl-pathology) | 0.714 | 0.763 | 0.785 | 0.627 | 0.759 | 0.943 | 0.758 | 0.785 | 0.905 | 0.759 | 0.604 | 0.600 | 0.630 | 0.362 |
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|---------|------|---------------|------------|
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| TCGA | 12k | Public | FFPE only |
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| 105 |
| NKI-80k | 80k | Proprietary | 10,141 patients, 31 organs |
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## Training Components
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|-------|------|---------------|------|-------|----------|-----|---------|-------|------|---------------|---------------|--------|---------|------|
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| **[Midnight-92k/392](#usage)** | **0.778** | **0.900** | **0.904** | **0.646** | 0.802 | 0.966 | **0.807** | 0.828 | **0.951** | 0.868 | 0.651 | **0.662** | **0.708** | 0.415 |
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| [UNI-2](https://huggingface.co/MahmoodLab/UNI2-h) | **0.776** | **0.885** | **0.924** | **0.651** | **0.863** | **0.970** | 0.777 | 0.829 | **0.951** | **0.873** | **0.666** | 0.626 | 0.644 | **0.431** |
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| **[Midnight-92k](#usage)** | **0.767** | **0.882** | 0.889 | 0.615 | 0.793 | **0.967** | **0.823** | 0.831 | 0.948 | **0.872** | 0.643 | 0.629 | 0.656 | **0.425** |
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| 131 |
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| [Virchow2](https://huggingface.co/paige-ai/Virchow2) | 0.766 | 0.835 | 0.890 | 0.633 | 0.818 | 0.966 | **0.791** | **0.865** | 0.938 | 0.860 | 0.646 | 0.640 | 0.674 | 0.403 |
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| **[Midnight-12k](#usage)** | 0.763 | 0.803 | **0.907** | 0.639 | 0.840 | **0.967** | 0.790 | 0.815 | 0.931 | **0.869** | 0.656 | 0.625 | 0.664 | 0.412 |
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| [Kaiko-B8](https://github.com/kaiko-ai/towards_large_pathology_fms) | 0.757 | 0.799 | 0.876 | 0.641 | **0.842** | 0.960 | 0.761 | 0.830 | 0.920 | 0.836 | 0.650 | **0.644** | 0.686 | 0.391 |
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| [H-Optimus-0](https://huggingface.co/bioptimus/H-optimus-0) | 0.755 | 0.831 | 0.752 | 0.620 | 0.813 | 0.962 | 0.769 | **0.850** | 0.943 | 0.847 | **0.672** | **0.644** | **0.687** | **0.425** |
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| [Prov_GigaPath](https://github.com/prov-gigapath/prov-gigapath) | 0.752 | 0.853 | 0.794 | 0.626 | **0.846** | 0.959 | 0.727 | 0.831 | 0.944 | 0.812 | 0.657 | 0.628 | **0.688** | 0.405 |
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| [Hibou-L](https://huggingface.co/histai/hibou-L) | 0.751 | 0.825 | 0.792 | **0.643** | 0.767 | 0.954 | 0.766 | **0.850** | **0.949** | 0.852 | 0.654 | **0.646** | 0.668 | 0.397 |
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| 137 |
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| [UNI](https://huggingface.co/MahmoodLab/UNI) | 0.749 | 0.833 | 0.797 | 0.613 | 0.808 | 0.954 | 0.759 | 0.841 | 0.937 | 0.854 | **0.662** | 0.627 | 0.662 | 0.391 |
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| [Phikon](https://huggingface.co/owkin/phikon) | 0.724 | 0.826 | 0.744 | 0.579 | 0.715 | 0.946 | 0.743 | 0.824 | 0.919 | 0.822 | 0.648 | 0.624 | 0.644 | 0.377 |
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| [Phikon-v2](https://huggingface.co/owkin/phikon-v2) | 0.718 | 0.756 | 0.737 | 0.607 | 0.725 | 0.953 | 0.753 | 0.796 | 0.900 | 0.807 | 0.634 | 0.626 | 0.645 | 0.391 |
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| [Lunit](https://github.com/lunit-io/benchmark-ssl-pathology) | 0.714 | 0.763 | 0.785 | 0.627 | 0.759 | 0.943 | 0.758 | 0.785 | 0.905 | 0.759 | 0.604 | 0.600 | 0.630 | 0.362 |
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