├── LICENSE ├── README.md ├── assets └── fig1.png ├── demo ├── __init__.py ├── demo_GRG.py ├── demo_GVQA.py ├── demo_Medtrinity.py ├── demo_RegionCap.py ├── demo_disease.py ├── demo_seg2D.py ├── demo_seg3D.py └── eval_utils │ ├── __init__.py │ ├── cal_3d_metrics.py │ ├── eval_seg2D.py │ ├── eval_seg3D.py │ ├── metrics_grg.py │ ├── metrics_grounded_disease.py │ ├── metrics_gvqa.py │ ├── metrics_medtrinity.py │ ├── metrics_region_cap.py │ └── utils │ ├── __init__.py │ ├── dist.py │ ├── refcoco_refer.py │ └── utils_refcoco.py ├── demo_RegionCap.sh ├── demo_disease.sh ├── demo_seg.sh ├── environment.yml ├── example.py ├── examples ├── CT_abdomen.png ├── CT_lung.png └── pathology_multiple.png ├── projects └── unibiomed │ ├── configs │ ├── biomed.py │ └── biomed_subset.py │ ├── datasets │ ├── Biomed3d_Dataset.py │ ├── BiomedDisease_Dataset.py │ ├── BiomedGRG_Dataset.py │ ├── BiomedGVQA_Dataset.py │ ├── BiomedMedtrinity_Dataset.py │ ├── BiomedRegionDescribe_Dataset.py │ ├── BiomedRegionUnderstand_Dataset.py │ ├── Biomed_Dataset.py │ ├── __init__.py │ ├── collect_fns.py │ ├── encode_fn.py │ └── utils.py │ ├── deepspeed_zero2_sam2.json │ ├── hf │ ├── convert_to_hf.py │ └── models │ │ ├── configuration_intern_vit.py │ │ ├── configuration_internlm2.py │ │ ├── configuration_phi3.py │ │ ├── configuration_sa2va_chat.py │ │ ├── flash_attention.py │ │ ├── modeling_intern_vit.py │ │ ├── modeling_internlm2.py │ │ ├── modeling_phi3.py │ │ ├── modeling_sa2va_chat.py │ │ ├── sam2.py │ │ ├── templates.py │ │ ├── tokenization_internlm2.py │ │ └── tokenization_internlm2_fast.py │ └── models │ ├── __init__.py │ ├── extension │ ├── __init__.py │ └── sam2_base.py │ ├── internvl.py │ ├── lisa.py │ ├── llava_sam2.py │ ├── predictor │ ├── __init__.py │ └── sam2_predictor.py │ ├── preprocess │ └── image_resize.py │ ├── sam2.py │ ├── sam2_train.py │ └── utils.py ├── requirements.txt ├── third_parts ├── __init__.py ├── mmdet │ ├── datasets │ │ ├── __pycache__ │ │ │ └── refcoco.cpython-310.pyc │ │ └── refcoco.py │ └── models │ │ ├── losses │ │ ├── __init__.py │ │ ├── accuracy.py │ │ ├── cross_entropy_loss.py │ │ ├── dice_loss.py │ │ └── utils.py │ │ └── utils │ │ ├── __init__.py │ │ └── point_sample.py ├── sam2 │ ├── __init__.py │ ├── automatic_mask_generator.py │ ├── build_sam.py │ ├── csrc │ │ └── connected_components.cu │ ├── modeling │ │ ├── __init__.py │ │ ├── backbones │ │ │ ├── __init__.py │ │ │ ├── hieradet.py │ │ │ ├── image_encoder.py │ │ │ └── utils.py │ │ ├── memory_attention.py │ │ ├── memory_encoder.py │ │ ├── position_encoding.py │ │ ├── sam │ │ │ ├── __init__.py │ │ │ ├── mask_decoder.py │ │ │ ├── prompt_encoder.py │ │ │ └── transformer.py │ │ ├── sam2_base.py │ │ └── sam2_utils.py │ ├── sam2_configs │ │ ├── __init__.py │ │ ├── sam2_hiera_b+.yaml │ │ ├── sam2_hiera_l.yaml │ │ ├── sam2_hiera_s.yaml │ │ └── sam2_hiera_t.yaml │ ├── sam2_image_predictor.py │ ├── sam2_video_predictor.py │ └── utils │ │ ├── __init__.py │ │ ├── amg.py │ │ ├── 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