Improve dataset card: add task categories, license, and project links

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  1. README.md +59 -323
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@@ -1,47 +1,60 @@
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  ---
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- license: other
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  language:
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  - en
 
 
 
 
 
 
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  tags:
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  - clinical
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  - ehr
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  - medical
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  - multimodal
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  - benchmark
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- pretty_name: ClinSeek-Bench
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- size_categories:
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- - 1K<n<10K
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  configs:
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  - config_name: text_tasks
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- data_files: "ClinSeek-Bench_text.json"
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  - config_name: multimodal_tasks
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- data_files: "ClinSeek-Bench_multimodal.jsonl"
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  ---
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  # ClinSeek-Bench
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- ClinSeek-Bench is the evaluation suite introduced in
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- [ClinSeekAgent: Automating Multimodal Evidence Seeking for Agentic Clinical
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- Reasoning](https://arxiv.org/abs/2605.20176). It evaluates clinical reasoning
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- under two paired settings with the same task definitions and answer labels:
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- - **Curated Input**: the model answers from the evidence package provided by
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- the source benchmark.
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- - **Automated Evidence-Seeking**: the curated context is removed, and the model
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- must retrieve evidence from raw clinical data using ClinSeekAgent tools.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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- This Hugging Face dataset release provides the metadata needed to reconstruct
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- ClinSeek-Bench. It is not a fully materialized benchmark package.
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- To rebuild the full benchmark locally from this released metadata, see
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- [Reconstructing The Full Benchmark](#reconstructing-the-full-benchmark).
 
 
 
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  ## Why This Release Contains Metadata Only
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- ClinSeek-Bench is built from credentialed clinical datasets, including MIMIC-IV,
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- MIMIC-IV-Note, MIMIC-IV-ED, MIMIC-CXR, MIMIC-CXR-JPG, EHRXQA, and MedMod. These
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- sources contain protected clinical information and must be obtained under each
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- user's own credentialed access and data-use agreements.
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  For privacy and licensing reasons, this repository does **not** redistribute:
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@@ -51,8 +64,7 @@ For privacy and licensing reasons, this repository does **not** redistribute:
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  - radiology report text;
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  - experiment logs or model trajectories.
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- Instead, this repository releases the metadata needed to rebuild the complete
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- runtime benchmark locally from the official source datasets.
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  ## Released Metadata
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@@ -61,276 +73,30 @@ runtime benchmark locally from the official source datasets.
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  | Text-only | `ClinSeek-Bench_text.json` | 1,800 | EHR | `qid`, `subject_id`, `hadm_id`, prediction-time metadata, task names, questions, labels, candidates | patient SQLite DBs and raw MIMIC rows |
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  | Multimodal | `ClinSeek-Bench_multimodal.jsonl` | 989 | EHR + CXR | released `qid`s, questions, normalized labels, patient/time metadata, CXR image references, report references | CXR JPG files, report text, rendered EHR contexts, patient SQLite DBs |
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- The metadata files are the source of truth for reconstruction and evaluation.
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- During local reconstruction, the ClinSeekAgent scripts materialize protected
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- runtime assets such as patient databases, rendered EHR contexts, linked CXR
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- files, and radiology reports from the official source datasets.
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69
  ## Benchmark Composition
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71
  ### Text-only EHR tasks
72
 
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- The text-only split is derived from EHR-Bench in
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- [EHR-R1](https://github.com/MAGIC-AI4Med/EHR-R1). It contains 45 EHR subtasks
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- covering risk-prediction and decision-making scenarios. We sample 40 examples
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- per subtask, resulting in 1,800 text-only examples. The released metadata
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- contains 1,563 unique patients.
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79
  ### Multimodal tasks
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81
- The multimodal split adapts EHRXQA and MedMod, both grounded in MIMIC-IV EHRs
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- and MIMIC-CXR chest radiographs. It contains 989 image-grounded examples:
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  - 497 EHRXQA-derived CXR question-answering rows;
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  - 492 MedMod-derived ICU/CXR prediction rows.
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- The six multimodal task groups are CXR finding presence, CXR finding
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- enumeration, CXR temporal change comparison, 24-hour decompensation prediction,
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- in-hospital mortality prediction, and phenotype prediction.
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-
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- ## Experimental Results
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-
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- We evaluate ClinSeekAgent under the **Automated Evidence-Seeking** setting and
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- compare it with the paired **Curated Input** setting. All numbers below are F1
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- scores in percentage points. `Δ` is Automated Evidence-Seeking minus
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- Curated Input.
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-
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- ### Text-only EHR tasks
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-
100
- <table>
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- <thead>
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- <tr>
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- <th rowspan="2">Model</th>
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- <th colspan="3">Risk Prediction</th>
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- <th colspan="3">Decision Making</th>
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- <th colspan="3">Overall</th>
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- </tr>
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- <tr>
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- <th>ClinSeekAgent</th>
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- <th>Curated<br>Input</th>
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- <th>Δ</th>
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- <th>ClinSeekAgent</th>
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- <th>Curated<br>Input</th>
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- <th>Δ</th>
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- <th>ClinSeekAgent</th>
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- <th>Curated<br>Input</th>
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- <th>Δ</th>
118
- </tr>
119
- </thead>
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- <tbody>
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- <tr><td colspan="10"><em>Closed-source models</em></td></tr>
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- <tr>
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- <td>Claude Opus 4.6</td>
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- <td align="right">90.7</td><td align="right">81.0</td><td align="right"><strong>+9.7</strong></td>
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- <td align="right">44.8</td><td align="right">45.9</td><td align="right"><strong>-1.1</strong></td>
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- <td align="right">63.2</td><td align="right">60.0</td><td align="right"><strong>+3.2</strong></td>
127
- </tr>
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- <tr>
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- <td>Claude Sonnet 4.6</td>
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- <td align="right">90.0</td><td align="right">77.5</td><td align="right"><strong>+12.5</strong></td>
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- <td align="right">35.9</td><td align="right">42.6</td><td align="right"><strong>-6.7</strong></td>
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- <td align="right">57.5</td><td align="right">56.6</td><td align="right"><strong>+0.9</strong></td>
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- </tr>
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- <tr><td colspan="10"><em>Open-source models</em></td></tr>
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- <tr>
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- <td>EHR-R1-72B</td>
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- <td align="right">--</td><td align="right">67.1</td><td align="right">--</td>
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- <td align="right">--</td><td align="right">45.2</td><td align="right">--</td>
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- <td align="right">--</td><td align="right">53.9</td><td align="right">--</td>
140
- </tr>
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- <tr>
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- <td>GLM-4.7</td>
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- <td align="right">75.1</td><td align="right">70.4</td><td align="right"><strong>+4.7</strong></td>
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- <td align="right">23.1</td><td align="right">38.6</td><td align="right"><strong>-15.5</strong></td>
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- <td align="right">43.9</td><td align="right">51.3</td><td align="right"><strong>-7.4</strong></td>
146
- </tr>
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- <tr>
148
- <td>Qwen3.5-35B-A3B</td>
149
- <td align="right">84.4</td><td align="right">73.6</td><td align="right"><strong>+10.8</strong></td>
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- <td align="right">22.0</td><td align="right">29.0</td><td align="right"><strong>-7.0</strong></td>
151
- <td align="right">47.0</td><td align="right">46.8</td><td align="right"><strong>+0.1</strong></td>
152
- </tr>
153
- <tr>
154
- <td>Gemma-4-26B-A4B-it</td>
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- <td align="right">83.5</td><td align="right">78.6</td><td align="right"><strong>+4.9</strong></td>
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- <td align="right">17.3</td><td align="right">27.8</td><td align="right"><strong>-10.5</strong></td>
157
- <td align="right">43.8</td><td align="right">48.1</td><td align="right"><strong>-4.3</strong></td>
158
- </tr>
159
- <tr>
160
- <td>MiniMax M2.5</td>
161
- <td align="right">86.7</td><td align="right">68.4</td><td align="right"><strong>+18.3</strong></td>
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- <td align="right">21.0</td><td align="right">26.3</td><td align="right"><strong>-5.3</strong></td>
163
- <td align="right">47.3</td><td align="right">43.1</td><td align="right"><strong>+4.2</strong></td>
164
- </tr>
165
- <tr>
166
- <td>Kimi K2.5</td>
167
- <td align="right">65.0</td><td align="right">79.9</td><td align="right"><strong>-14.9</strong></td>
168
- <td align="right">19.8</td><td align="right">28.8</td><td align="right"><strong>-9.0</strong></td>
169
- <td align="right">37.9</td><td align="right">49.2</td><td align="right"><strong>-11.3</strong></td>
170
- </tr>
171
- <tr>
172
- <td>Qwen3-VL-235B</td>
173
- <td align="right">67.9</td><td align="right">71.0</td><td align="right"><strong>-3.1</strong></td>
174
- <td align="right">19.1</td><td align="right">33.4</td><td align="right"><strong>-14.3</strong></td>
175
- <td align="right">38.6</td><td align="right">48.4</td><td align="right"><strong>-9.8</strong></td>
176
- </tr>
177
- <tr>
178
- <td>gpt-oss-120b</td>
179
- <td align="right">75.4</td><td align="right">74.0</td><td align="right"><strong>+1.4</strong></td>
180
- <td align="right">16.6</td><td align="right">22.3</td><td align="right"><strong>-5.7</strong></td>
181
- <td align="right">40.1</td><td align="right">43.0</td><td align="right"><strong>-2.9</strong></td>
182
- </tr>
183
- <tr>
184
- <td>MedGemma-27B-it</td>
185
- <td align="right">--</td><td align="right">65.0</td><td align="right">--</td>
186
- <td align="right">--</td><td align="right">25.2</td><td align="right">--</td>
187
- <td align="right">--</td><td align="right">41.1</td><td align="right">--</td>
188
- </tr>
189
- <tr>
190
- <td>EHR-R1-8B</td>
191
- <td align="right">--</td><td align="right">64.0</td><td align="right">--</td>
192
- <td align="right">--</td><td align="right">23.4</td><td align="right">--</td>
193
- <td align="right">--</td><td align="right">39.7</td><td align="right">--</td>
194
- </tr>
195
- </tbody>
196
- </table>
197
-
198
- ### Multimodal tasks
199
-
200
- <table>
201
- <thead>
202
- <tr>
203
- <th>Model</th>
204
- <th>Method</th>
205
- <th>CXR:<br>finding<br>presence</th>
206
- <th>CXR:<br>finding<br>enumeration</th>
207
- <th>CXR:<br>change<br>comparison</th>
208
- <th>Mortality<br>(24 h)</th>
209
- <th>Inpatient<br>mortality</th>
210
- <th>Phenotype<br>(CCS groups)</th>
211
- <th>Multimodal<br>overall</th>
212
- </tr>
213
- </thead>
214
- <tbody>
215
- <tr>
216
- <td rowspan="3">Claude Opus 4.6</td>
217
- <td>ClinSeekAgent</td>
218
- <td align="right">78.3</td><td align="right">43.6</td><td align="right">54.8</td><td align="right">92.0</td><td align="right">74.4</td><td align="right">45.5</td><td align="right"><strong>62.6</strong></td>
219
- </tr>
220
- <tr>
221
- <td>Curated Input</td>
222
- <td align="right">55.2</td><td align="right">31.6</td><td align="right">38.0</td><td align="right">93.6</td><td align="right">69.6</td><td align="right">11.5</td><td align="right"><strong>47.5</strong></td>
223
- </tr>
224
- <tr>
225
- <td>Δ</td>
226
- <td align="right"><strong>+23.2</strong></td><td align="right"><strong>+12.0</strong></td><td align="right"><strong>+16.8</strong></td><td align="right"><strong>-1.6</strong></td><td align="right"><strong>+4.8</strong></td><td align="right"><strong>+34.0</strong></td><td align="right"><strong>+15.1</strong></td>
227
- </tr>
228
- <tr>
229
- <td rowspan="3">Claude Sonnet 4.6</td>
230
- <td>ClinSeekAgent</td>
231
- <td align="right">79.5</td><td align="right">41.3</td><td align="right">51.5</td><td align="right">64.0</td><td align="right">68.8</td><td align="right">26.1</td><td align="right"><strong>54.9</strong></td>
232
- </tr>
233
- <tr>
234
- <td>Curated Input</td>
235
- <td align="right">64.8</td><td align="right">29.7</td><td align="right">34.7</td><td align="right">90.4</td><td align="right">70.4</td><td align="right">13.8</td><td align="right"><strong>48.0</strong></td>
236
- </tr>
237
- <tr>
238
- <td>Δ</td>
239
- <td align="right"><strong>+14.7</strong></td><td align="right"><strong>+11.6</strong></td><td align="right"><strong>+16.8</strong></td><td align="right"><strong>-26.4</strong></td><td align="right"><strong>-1.6</strong></td><td align="right"><strong>+12.3</strong></td><td align="right"><strong>+6.9</strong></td>
240
- </tr>
241
- <tr>
242
- <td rowspan="3">Qwen3.5-35B-A3B</td>
243
- <td>ClinSeekAgent</td>
244
- <td align="right">73.8</td><td align="right">34.2</td><td align="right">44.4</td><td align="right">91.2</td><td align="right">74.4</td><td align="right">0.3</td><td align="right"><strong>51.7</strong></td>
245
- </tr>
246
- <tr>
247
- <td>Curated Input</td>
248
- <td align="right">59.1</td><td align="right">34.1</td><td align="right">30.7</td><td align="right">90.4</td><td align="right">81.6</td><td align="right">0.5</td><td align="right"><strong>46.9</strong></td>
249
- </tr>
250
- <tr>
251
- <td>Δ</td>
252
- <td align="right"><strong>+14.7</strong></td><td align="right"><strong>+0.2</strong></td><td align="right"><strong>+13.7</strong></td><td align="right"><strong>+0.8</strong></td><td align="right"><strong>-7.2</strong></td><td align="right"><strong>-0.2</strong></td><td align="right"><strong>+4.8</strong></td>
253
- </tr>
254
- <tr>
255
- <td rowspan="3">Kimi K2.5</td>
256
- <td>ClinSeekAgent</td>
257
- <td align="right">61.4</td><td align="right">34.9</td><td align="right">43.8</td><td align="right">71.2</td><td align="right">62.4</td><td align="right">12.3</td><td align="right"><strong>46.9</strong></td>
258
- </tr>
259
- <tr>
260
- <td>Curated Input</td>
261
- <td align="right">56.3</td><td align="right">24.7</td><td align="right">35.0</td><td align="right">91.2</td><td align="right">87.2</td><td align="right">12.4</td><td align="right"><strong>47.5</strong></td>
262
- </tr>
263
- <tr>
264
- <td>Δ</td>
265
- <td align="right"><strong>+5.1</strong></td><td align="right"><strong>+10.2</strong></td><td align="right"><strong>+8.8</strong></td><td align="right"><strong>-20.0</strong></td><td align="right"><strong>-24.8</strong></td><td align="right"><strong>-0.1</strong></td><td align="right"><strong>-0.6</strong></td>
266
- </tr>
267
- <tr>
268
- <td rowspan="3">Qwen3-VL-235B</td>
269
- <td>ClinSeekAgent</td>
270
- <td align="right">70.4</td><td align="right">35.7</td><td align="right">47.8</td><td align="right">79.2</td><td align="right">61.6</td><td align="right">6.0</td><td align="right"><strong>49.8</strong></td>
271
- </tr>
272
- <tr>
273
- <td>Curated Input</td>
274
- <td align="right">60.3</td><td align="right">21.1</td><td align="right">32.8</td><td align="right">87.2</td><td align="right">72.8</td><td align="right">6.6</td><td align="right"><strong>43.9</strong></td>
275
- </tr>
276
- <tr>
277
- <td>Δ</td>
278
- <td align="right"><strong>+10.1</strong></td><td align="right"><strong>+14.6</strong></td><td align="right"><strong>+15.0</strong></td><td align="right"><strong>-8.0</strong></td><td align="right"><strong>-11.2</strong></td><td align="right"><strong>-0.6</strong></td><td align="right"><strong>+5.9</strong></td>
279
- </tr>
280
- <tr>
281
- <td rowspan="3">Gemma-4-26B-A4B-it</td>
282
- <td>ClinSeekAgent</td>
283
- <td align="right">78.9</td><td align="right">21.6</td><td align="right">38.4</td><td align="right">65.6</td><td align="right">71.2</td><td align="right">0.4</td><td align="right"><strong>44.9</strong></td>
284
- </tr>
285
- <tr>
286
- <td>Curated Input</td>
287
- <td align="right">56.9</td><td align="right">21.4</td><td align="right">25.4</td><td align="right">79.2</td><td align="right">60.0</td><td align="right">0.0</td><td align="right"><strong>38.2</strong></td>
288
- </tr>
289
- <tr>
290
- <td>Δ</td>
291
- <td align="right"><strong>+22.0</strong></td><td align="right"><strong>+0.2</strong></td><td align="right"><strong>+13.0</strong></td><td align="right"><strong>-13.6</strong></td><td align="right"><strong>+11.2</strong></td><td align="right"><strong>+0.4</strong></td><td align="right"><strong>+6.7</strong></td>
292
- </tr>
293
- </tbody>
294
- </table>
295
-
296
- These results show that active evidence acquisition is most helpful when the
297
- answer depends on sparse, longitudinal, or multimodal signals that may be missed
298
- by fixed curated inputs. The gains are especially clear for risk prediction in
299
- the text-only split and for CXR-related multimodal tasks, where models can
300
- combine EHR retrieval, image-tool outputs, and task-relevant medical knowledge.
301
-
302
- ## Files
303
-
304
- ```text
305
- ClinSeek-Bench/
306
- +-- README.md
307
- +-- ClinSeek-Bench_text.json
308
- +-- ClinSeek-Bench_multimodal.jsonl
309
- ```
310
-
311
- The paths above are the released metadata paths in this dataset repository. If
312
- you clone this dataset next to the ClinSeekAgent repository, reference the
313
- metadata as:
314
-
315
- ```text
316
- ClinSeek-Bench/ClinSeek-Bench_text.json
317
- ClinSeek-Bench/ClinSeek-Bench_multimodal.jsonl
318
- ```
319
-
320
- If you use ClinSeekAgent's default local data layout, you may copy or symlink
321
- the text manifest to `data/text/ClinSeek-Bench_text.json`. That location is a
322
- local workspace convenience, not a released metadata path.
323
 
324
  ## Reconstructing The Full Benchmark
325
 
326
- Reconstruction code and detailed instructions are maintained in the
327
- ClinSeekAgent GitHub repository:
328
 
329
  - Code: https://github.com/UCSC-VLAA/ClinSeekAgent
330
- - Text data preparation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_text_data_prepare.md
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- - Automated Evidence-Seeking text evaluation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_text_evaluation.md
332
- - Curated Input text evaluation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_text_curated_input_evaluation.md
333
- - Multimodal data preparation: https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_multimodal_data_prepare.md
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335
  At a high level:
336
 
@@ -339,13 +105,9 @@ git clone https://huggingface.co/datasets/UCSC-VLAA/ClinSeek-Bench
339
  git clone https://github.com/UCSC-VLAA/ClinSeekAgent.git
340
  ```
341
 
342
- Then obtain the required official source datasets, prepare local paths, and
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- follow the text and multimodal reconstruction guides above.
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-
345
  ## Required Source Data
346
 
347
- Download clinical source data only from official sources under your own
348
- credentialed access and data-use agreements.
349
 
350
  | Dataset or source | Official source | Used for |
351
  | --- | --- | --- |
@@ -358,46 +120,20 @@ credentialed access and data-use agreements.
358
  | MedMod | https://github.com/nyuad-cai/MedMod | source-aligned ICU/CXR prediction rows |
359
  | EHR-R1 / EHR-Bench | https://github.com/MAGIC-AI4Med/EHR-R1 | source benchmark for text-only EHR tasks |
360
 
361
- ## Validation
362
-
363
- After cloning ClinSeekAgent, validate the released multimodal metadata without
364
- requiring protected assets:
365
-
366
- ```bash
367
- python ClinSeekAgent/scripts/data_build/validate_multimodal_release.py \
368
- --bench-root ClinSeek-Bench \
369
- --input ClinSeek-Bench/ClinSeek-Bench_multimodal.jsonl \
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- --manifest-only
371
- ```
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-
373
- Expected released metadata counts:
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-
375
- - 1,800 text-only rows;
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- - 45 text-only EHR subtasks;
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- - 1,563 unique text-only patients;
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- - 989 multimodal rows;
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- - 497 EHRXQA-derived multimodal rows;
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- - 492 MedMod-derived multimodal rows;
381
- - 350 unique EHRXQA linked CXR JPG paths;
382
- - 477 unique MedMod linked CXR JPG paths;
383
- - 356 unique EHRXQA linked CXR report paths.
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-
385
- After local reconstruction, the same validation script can also check the
386
- materialized runtime assets, including patient DBs, image paths, and report
387
- paths. See the ClinSeekAgent reconstruction documentation for the full commands.
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-
389
- ## Evaluation
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-
391
- Evaluation code and instructions are maintained in the ClinSeekAgent repository:
392
- https://github.com/UCSC-VLAA/ClinSeekAgent.
393
-
394
- After reconstructing the protected runtime assets locally, follow the
395
- ClinSeekAgent documentation for Automated Evidence-Seeking evaluation, Curated
396
- Input evaluation, and scoring.
397
-
398
  ## Responsible Use
399
 
400
- ClinSeek-Bench is for research on clinical evidence seeking. It is not a
401
- medical device and must not be used for clinical diagnosis, treatment, triage,
402
- or patient management without separate validation, governance, and regulatory
403
- review.
 
 
 
 
 
 
 
 
 
 
 
 
1
  ---
 
2
  language:
3
  - en
4
+ license: apache-2.0
5
+ size_categories:
6
+ - 1K<n<10K
7
+ pretty_name: ClinSeek-Bench
8
+ task_categories:
9
+ - image-text-to-text
10
  tags:
11
  - clinical
12
  - ehr
13
  - medical
14
  - multimodal
15
  - benchmark
 
 
 
16
  configs:
17
  - config_name: text_tasks
18
+ data_files: ClinSeek-Bench_text.json
19
  - config_name: multimodal_tasks
20
+ data_files: ClinSeek-Bench_multimodal.jsonl
21
  ---
22
 
23
  # ClinSeek-Bench
24
 
25
+ [**Project Page**](https://ucsc-vlaa.github.io/ClinSeekAgent/) | [**Paper**](https://arxiv.org/abs/2605.20176) | [**Code**](https://github.com/UCSC-VLAA/ClinSeekAgent)
 
 
 
26
 
27
+ ClinSeek-Bench is the evaluation suite introduced in [ClinSeekAgent: Automating Multimodal Evidence Seeking for Agentic Clinical Reasoning](https://arxiv.org/abs/2605.20176). It evaluates clinical reasoning under two paired settings with the same task definitions and answer labels:
28
+
29
+ - **Curated Input**: the model answers from the evidence package provided by the source benchmark.
30
+ - **Automated Evidence-Seeking**: the curated context is removed, and the model must retrieve evidence from raw clinical data using ClinSeekAgent tools.
31
+
32
+ This Hugging Face dataset release provides the metadata needed to reconstruct ClinSeek-Bench. It is not a fully materialized benchmark package.
33
+
34
+ ## Sample Usage
35
+
36
+ ### Metadata Validation
37
+ After cloning the [ClinSeekAgent repository](https://github.com/UCSC-VLAA/ClinSeekAgent), you can validate the released multimodal metadata without requiring protected assets:
38
+
39
+ ```bash
40
+ python ClinSeekAgent/scripts/data_build/validate_multimodal_release.py \
41
+ --bench-root ClinSeek-Bench \
42
+ --input ClinSeek-Bench/ClinSeek-Bench_multimodal.jsonl \
43
+ --manifest-only
44
+ ```
45
 
46
+ ### Quick Start Evaluation
47
+ To run a smoke test on text-only evaluation (using synthetic examples provided in the code repo):
48
 
49
+ ```bash
50
+ DATA_PATH=examples/synthetic_text_sample.jsonl \
51
+ OUTPUT_DIR=outputs/text_smoke \
52
+ bash scripts/run_text_eval.sh
53
+ ```
54
 
55
  ## Why This Release Contains Metadata Only
56
 
57
+ ClinSeek-Bench is built from credentialed clinical datasets, including MIMIC-IV, MIMIC-IV-Note, MIMIC-IV-ED, MIMIC-CXR, MIMIC-CXR-JPG, EHRXQA, and MedMod. These sources contain protected clinical information and must be obtained under each user's own credentialed access and data-use agreements.
 
 
 
58
 
59
  For privacy and licensing reasons, this repository does **not** redistribute:
60
 
 
64
  - radiology report text;
65
  - experiment logs or model trajectories.
66
 
67
+ Instead, this repository releases the metadata needed to rebuild the complete runtime benchmark locally from the official source datasets.
 
68
 
69
  ## Released Metadata
70
 
 
73
  | Text-only | `ClinSeek-Bench_text.json` | 1,800 | EHR | `qid`, `subject_id`, `hadm_id`, prediction-time metadata, task names, questions, labels, candidates | patient SQLite DBs and raw MIMIC rows |
74
  | Multimodal | `ClinSeek-Bench_multimodal.jsonl` | 989 | EHR + CXR | released `qid`s, questions, normalized labels, patient/time metadata, CXR image references, report references | CXR JPG files, report text, rendered EHR contexts, patient SQLite DBs |
75
 
76
+ The metadata files are the source of truth for reconstruction and evaluation. During local reconstruction, the ClinSeekAgent scripts materialize protected runtime assets such as patient databases, rendered EHR contexts, linked CXR files, and radiology reports from the official source datasets.
 
 
 
77
 
78
  ## Benchmark Composition
79
 
80
  ### Text-only EHR tasks
81
 
82
+ The text-only split is derived from EHR-Bench in [EHR-R1](https://github.com/MAGIC-AI4Med/EHR-R1). It contains 45 EHR subtasks covering risk-prediction and decision-making scenarios. We sample 40 examples per subtask, resulting in 1,800 text-only examples. The released metadata contains 1,563 unique patients.
 
 
 
 
83
 
84
  ### Multimodal tasks
85
 
86
+ The multimodal split adapts EHRXQA and MedMod, both grounded in MIMIC-IV EHRs and MIMIC-CXR chest radiographs. It contains 989 image-grounded examples:
 
87
 
88
  - 497 EHRXQA-derived CXR question-answering rows;
89
  - 492 MedMod-derived ICU/CXR prediction rows.
90
 
91
+ The six multimodal task groups are CXR finding presence, CXR finding enumeration, CXR temporal change comparison, 24-hour decompensation prediction, in-hospital mortality prediction, and phenotype prediction.
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
92
 
93
  ## Reconstructing The Full Benchmark
94
 
95
+ Reconstruction code and detailed instructions are maintained in the ClinSeekAgent GitHub repository:
 
96
 
97
  - Code: https://github.com/UCSC-VLAA/ClinSeekAgent
98
+ - Text data preparation: [Guide](https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_text_data_prepare.md)
99
+ - Multimodal data preparation: [Guide](https://github.com/UCSC-VLAA/ClinSeekAgent/blob/main/docs/ClinSeek-Bench_multimodal_data_prepare.md)
 
 
100
 
101
  At a high level:
102
 
 
105
  git clone https://github.com/UCSC-VLAA/ClinSeekAgent.git
106
  ```
107
 
 
 
 
108
  ## Required Source Data
109
 
110
+ Download clinical source data only from official sources under your own credentialed access and data-use agreements.
 
111
 
112
  | Dataset or source | Official source | Used for |
113
  | --- | --- | --- |
 
120
  | MedMod | https://github.com/nyuad-cai/MedMod | source-aligned ICU/CXR prediction rows |
121
  | EHR-R1 / EHR-Bench | https://github.com/MAGIC-AI4Med/EHR-R1 | source benchmark for text-only EHR tasks |
122
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
123
  ## Responsible Use
124
 
125
+ ClinSeek-Bench is for research on clinical evidence seeking. It is not a medical device and must not be used for clinical diagnosis, treatment, triage, or patient management without separate validation, governance, and regulatory review.
126
+
127
+ ## Citation
128
+
129
+ ```bibtex
130
+ @misc{wu2026clinseekagent,
131
+ title = {ClinSeekAgent: Automating Multimodal Evidence Seeking for Agentic Clinical Reasoning},
132
+ author = {Wu, Juncheng and Zhang, Letian and Wang, Yuhan and Tu, Haoqin and Chen, Hardy and Wang, Zijun and Xie, Cihang and Zhou, Yuyin},
133
+ year = {2026},
134
+ eprint = {2605.20176},
135
+ archivePrefix = {arXiv},
136
+ primaryClass = {cs.CL},
137
+ url = {https://arxiv.org/abs/2605.20176}
138
+ }
139
+ ```