# AutoMSC Baseline Models

Baseline models for **MICCAI FLARE 2026 Task 2 — AutoMSC: Automated Medical Image Segmentation and Classification**.

**Codebase:** [github.com/medfm-flare/AutoMSC-Baseline](https://github.com/medfm-flare/AutoMSC-Baseline)

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.

## Datasets

| 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 |

## Repository Structure

```
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
```