| # AutoMSC Baseline Models |
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| Baseline models for **MICCAI FLARE 2026 Task 2 — AutoMSC: Automated Medical Image Segmentation and Classification**. |
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| **Codebase:** [github.com/medfm-flare/AutoMSC-Baseline](https://github.com/medfm-flare/AutoMSC-Baseline) |
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| Each model jointly performs organ/lesion segmentation and case-level classification using a multi-task learning nnUNet framework (`nnUNetCLSTrainerMTL`). Models are trained with 5-fold cross-validation; this repository contains the best-checkpoint weights (`checkpoint_best.pth`) for each fold. |
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| ## Datasets |
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| | Dataset | Modality | Cases | Segmentation Labels | Classification Labels (cases per class) | License | |
| |---|---|---:|---|---|---| |
| | [Dataset001_BrainMets](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset001_BrainMets/README.md) | T1, T1c, T2, FLAIR, CT, RTP | 166 | Necrotic Core (1), Enhancing Tumor (2), Edema (3) | Primary Tumor Origin: NSCLC (102), Breast carcinoma (64) | CC BY 4.0 | |
| | [Dataset002_MU_Glioma](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset002_MU_Glioma/README.md) | T1c, T1, FLAIR, T2 | 591 | Non-Enhancing Tumor Core (1), Surrounding Non-Enhancing FLAIR Hyperintensity (2), Enhancing Tumor (3), Resection Cavity (4) | Primary Diagnosis: GBM (446), Astrocytoma (87), Others (58) | CC-BY-NC 4.0 | |
| | [Dataset003_UCSD_PTGB](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset003_UCSD_PTGB/README.md) | T1c, FLAIR, ADC | 184 | Tumor (1) | IDH Mutation Status: Wild-Type (169), Mutant (15) | CC-BY-NC 4.0 | |
| | [Dataset004_PICAI](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset004_PICAI/README.md) | T2, ADC, HBV | 1500 | Prostate (1), Tumor (2) | ISUP Grade: Benign/Indolent (847), ISUP 1 (228), ISUP 2 (234), ISUP 3 (99), ISUP 4 (40), ISUP 5 (52) | CC-BY-NC 4.0 | |
| | [Dataset005_LUNA25](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset005_LUNA25/README.md) | CT | 6132 | Nodule (1) | Malignancy: Benign (5,589), Malignant (543) | CC BY 4.0 | |
| | [Dataset061_PETWB_Lung](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset061_PETWB_Lung/README.md) | CT, PET | 490 | Lung (1) | Cancer type: Other (42), Lung Cancer (448) | CC BY 4.0 | |
| | [Dataset062_PETWB_Liver](https://huggingface.co/cyyu96/AutoMSC-Baselines/blob/main/Dataset062_PETWB_Liver/README.md) | CT, PET | 490 | Liver (1) | Cancer type: Other (242), Liver Cancer (248) | CC BY 4.0 | |
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| ## Repository Structure |
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| ``` |
| DatasetXXX_<name>/ |
| ├── README.md # per-fold results and figures |
| ├── figures/ # box plots, ROC/PRC, confusion matrix, case samples |
| └── nnUNetCLSTrainerMTL__nnUNetPlans__3d_fullres/ |
| ├── dataset.json |
| ├── dataset_fingerprint.json |
| ├── plans.json |
| ├── fold_0/ |
| │ └── checkpoint_best.pth |
| ├── ... |
| └── fold_4/ |
| └── checkpoint_best.pth |
| ``` |
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