| --- |
| license: cc-by-nc-4.0 |
| task_categories: |
| - visual-question-answering |
| - object-detection |
| language: |
| - en |
| - zh |
| tags: |
| - pathology |
| - medical-imaging |
| - benchmark |
| - vqa |
| - grounding |
| size_categories: |
| - 1K<n<10K |
| pretty_name: PathBind |
| configs: |
| - config_name: PathBind-VQA |
| data_files: |
| - split: manifest |
| path: PathBind-VQA/manifest.tsv |
| - config_name: PathBind-PTA |
| data_files: |
| - split: eval |
| path: PathBind-PTA/pathbind_pta_600.tsv |
| - config_name: PathBind-Grounding |
| data_files: |
| - split: manifest |
| path: PathBind-Grounding/manifest.jsonl |
| extra_gated_prompt: >- |
| PathBind is released for non-commercial research use only. It is NOT |
| certified for clinical diagnostic use. By requesting access you agree to |
| (1) non-commercial use, (2) no redistribution of the manifest, images, or |
| derivatives, (3) citing the PathBind paper in any publication that uses |
| the dataset, (4) obtaining the underlying source datasets (PathMMU, |
| Path-VQA, Quilt-VQA, MedXpert-Path, OmniMed-Bright, PathVG) under their |
| own licenses when using the VQA / Grounding manifests, and (5) not using |
| PathBind-PTA to inform patient care. Fill in the fields below; we aim to |
| review within five business days. |
| extra_gated_fields: |
| Full name: text |
| Affiliation: text |
| Email (institutional preferred): text |
| Country: country |
| Intended use: text |
| I agree to use PathBind for non-commercial research only: checkbox |
| I agree not to redistribute the manifest, images, or derivatives: checkbox |
| I understand PathBind-PTA is not for clinical use: checkbox |
| extra_gated_button_content: Request access |
| --- |
| |
| # PathBind |
|
|
| **A diagnostic benchmark for evaluating pathology vision-language models.** |
|
|
| PathBind bundles 2,600 samples across three components — each filtered by |
| an automated pipeline and finalized under expert pathologist review — to |
| jointly probe visual dependence, cross-domain replication, and |
| entity-level visual-semantic binding. |
|
|
| | Config | # samples | Format | |
| |------------------------|----------:|-----------------------------------------| |
| | `PathBind-VQA` | 1,500 | sample-ID manifest (TSV) | |
| | `PathBind-PTA` | 600 | self-contained TSV, base64 JPEGs inline | |
| | `PathBind-Grounding` | 500 | sample-ID manifest (JSONL) | |
|
|
| ## Diagnostic dimensions |
|
|
| | Dim. | Name | Definition | |
| |:----:|---------------------------------|------------------------------------------------------------------| |
| | D1 | Coarse tissue/organ recognition | Broad tissue type, organ context, general histologic category. | |
| | D2 | Cellular morphology | Nuclear atypia, cytoplasm, mitotic figures, necrosis. | |
| | D3 | Cell–stroma interaction | Infiltration pattern, inflammatory distribution, desmoplasia. | |
| | D4 | Spatial localization | Spatial position, arrangement, or distribution of structures. | |
| | D5 | Diagnostic reasoning | Integrated visual evidence for diagnosis, grading, staging. | |
| | D6 | Staining & IHC interpretation | Staining patterns, IHC positivity, intensity/distribution. | |
|
|
| ## Repository layout |
|
|
| ``` |
| PathBind/ |
| ├── PathBind-VQA/ # 1,500 sample IDs (D1–D6 × 250) |
| │ └── manifest.tsv |
| ├── PathBind-PTA/ # 600 self-contained samples (D1–D5 × 120) |
| │ └── pathbind_pta_600.tsv |
| └── PathBind-Grounding/ # 500 sample IDs (testA 380 + testB 120) |
| └── manifest.jsonl |
| ``` |
|
|
| ## Usage |
|
|
| ### PathBind-VQA |
|
|
| We ship only sample IDs. Obtain the five source benchmarks yourself, then |
| materialize the full TSV with the PathBind evaluation repo: |
|
|
| ```bash |
| git clone https://github.com/<org>/PathBind |
| python pathbind/data/PathBind-VQA/build.py \ |
| --pathmmu_dir /path/to/PathMMU \ |
| --pathvqa_dir /path/to/Path-VQA \ |
| --quiltvqa_dir /path/to/Quilt-VQA \ |
| --omnimed_dir /path/to/OmniMed-Bright \ |
| --medxpert_dir /path/to/MedXpert-Path |
| ``` |
|
|
| Fields: `index`, `dimension`, `source_dataset`, `source_sample_id`, `answer_type`. |
|
|
| Composition: PathMMU 1,311 · OmniMed-Bright 102 · Path-VQA 37 · Quilt-VQA 25 · MedXpert-Path 25. |
|
|
| ### PathBind-Grounding |
|
|
| Similarly, obtain PathVG and materialize: |
|
|
| ```bash |
| python pathbind/data/PathBind-Grounding/build.py --pathvg_dir /path/to/PathVG |
| ``` |
|
|
| Fields: `split`, `image_id`, `bbox_id`, `expression`, `bbox`, `width`, `height`. |
|
|
| ### PathBind-PTA |
|
|
| Self-contained — no external download needed. Follows the PathoSage TSV |
| convention: the `image` column contains **base64-encoded JPEG** data (long |
| side ≤ 1024 px, quality 85). |
|
|
| Balanced across five diagnostic dimensions (D1–D5, 120 each) and answer |
| options (A–D, 150 each). |
|
|
| ## Running an evaluation |
|
|
| ```bash |
| git clone https://github.com/<org>/PathBind |
| cd PathBind |
| python -m pathbind.eval_a1 \ |
| --data PathBind-VQA/pathbind_vqa_1500.tsv \ |
| --model_module pathbind.models.patho_r1 --ckpt /path/to/Patho-R1 \ |
| --out results/vqa.jsonl |
| ``` |
|
|
| Replace `--data` with the PTA or Grounding materialized file for the |
| other two components. See the PathBind code repo README for the full API |
| and how to port a new model. |
|
|
| ## Citation |
|
|
| Coming soon. |
|
|
| ## License |
|
|
| - `PathBind-VQA` and `PathBind-Grounding` manifests: MIT. Referenced source |
| datasets remain under their **original licenses** — please follow the |
| terms of PathMMU / Path-VQA / Quilt-VQA / MedXpert-Path / OmniMed-Bright / |
| PathVG when using them. |
| - `PathBind-PTA` component: **CC BY-NC 4.0** (non-commercial research use |
| only, not for clinical use). |
|
|
