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| license: cc-by-nc-nd-4.0 |
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| # CASE: Clinical Agents for Seeking Evidence — Agent Trajectories & Benchmarks (De-identified) |
|
|
| **Partial, de-identified release** — companion data for the paper |
| *From Given to Gathered Evidence: Agentic Learning for Longitudinal Medical |
| Reasoning*: recorded agent trajectories, RL training prompts, benchmark banks |
| and example preview images for longitudinal medical imaging. Full imaging data |
| is not included (UK Biobank controlled); participant identifiers have been |
| replaced by uniform anonymous IDs (`case0001`–`case4739`); the ID mapping exists |
| but is not publicly disclosed, in accordance with UK Biobank requirements. |
| Rendered example/preview images are provided in `images_examples/` (figure |
| headers cropped). |
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|
|
| The CASE project trains three cooperating clinical-agent personas on |
| longitudinal medical imaging through an agentic harness (multi-turn tool |
| calling; the model plans, calls tools, reads observations and answers): |
|
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| - **Anatomist** — organ segmentation / volumetry across body stations |
| - **Radiologist** — cross-visit image comparison (multi-modality, multi-sequence) |
| - **Consultant** — report-grounded synthesis and claim verification |
|
|
| ## Contents |
|
|
| | Path | What | |
| |---|---| |
| | `trajectories/{Anatomist_agent,Radiologist_agent,Consultant_agent}/` | recorded agent trajectories (`agent_caseNNNN.jsonl`) and per-patient annotations (`dense_caseNNNN.json`); Consultant additionally ships `skills_caseNNNN.jsonl` | |
| | `rl/verl_train_tool.parquet` | reinforcement-learning prompts (verl parquet, one row per patient-question; 30,604 rows) | |
| | `benchmark/` | evaluation question banks: `benchmark.parquet` = current bank (14,795 rows / 482 patients); `test.parquet` and `unified.parquet` = earlier banks; each bank ships its participant ID list | |
| | `images_examples/` | rendered preview slices for the benchmark set: per participant × six body stations × baseline/follow-up visits (4,938 images; figure headers cropped) | |
|
|
| ## Formats |
|
|
| - **Trajectories** — JSONL, one question instance per line with the full message |
| list. Image content appears only as relative path references |
| (`images/<caseNNNN>/img_*.png`); the image files themselves are **not** included. |
|
|
| - **Parquet** (`rl/`, `benchmark/`) — one row per (patient, question); columns: |
| - `data_source` — task origin: `vista3d_opsd` (Anatomist), `medpanel_v2_opsd` |
| (Radiologist), `medboard_opsd` (Consultant) |
| - `prompt` — full chat template: system message (persona, tool definitions, |
| output-format rules) + user message (question, options, tool-use |
| instructions) |
| - `reward_model` — answer key, e.g. `{"ground_truth": "D"}` |
| - `extra_info` — JSON string with `patient_id` (anonymous case ID), |
| `question_idx`, `question`, `options`, `ground_truth`, `tools_kwargs` |
| (patient-scoped tool arguments) and `teacher_insight` (teacher reasoning |
| notes used for the OPSD distillation signal) |
| - `agent_name` — `tool_agent` (multi-turn tool-calling loop) |
| |
| Row counts — `rl/verl_train_tool.parquet`: 30,604 (vista3d 9,788 / medpanel |
| 10,408 / medboard 10,408); `benchmark.parquet`: 14,795. |
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|
| **No images are embedded** in any parquet: image observations are served to |
| the tools at run time and are not part of this release. |
|
|
| ## Licensing / data access |
|
|
| Built on UK Biobank-derived data under an access-controlled research agreement. |
|
|
| - **Participant IDs** — all participant references use uniform anonymous IDs |
| (`case0001`–`case4739`). An ID mapping to the original identifiers exists but |
| is **not disclosed on this platform**, in accordance with UK Biobank |
| requirements. |
| - **Images** (`images_examples/`) — rendered preview images are |
| provided for **academic display only**; redistribution and commercial use are |
| **prohibited**. |
| - **Complete dataset** — the full dataset is not redistributed here; access |
| must be requested through the **UK Biobank Access Management System (AMS)** |
| to obtain access permission for the returned data. |
