Datasets:
Add CT-RATE findings + 137 leaf-label dataset (deduped splits, radiologist-validated test)
1976d8c verified | license: cc-by-nc-sa-4.0 | |
| language: | |
| - en | |
| task_categories: | |
| - text-classification | |
| tags: | |
| - radiology | |
| - chest-ct | |
| - ct-rate | |
| - multi-label | |
| - report-labeling | |
| size_categories: | |
| - 10K<n<100K | |
| dataset_info: | |
| features: | |
| - name: original_report | |
| dtype: string | |
| - name: refined_report | |
| dtype: string | |
| - name: split | |
| dtype: string | |
| - name: Consolidation | |
| dtype: int8 | |
| - name: Ground-glass opacity (GGO) | |
| dtype: int8 | |
| - name: Crazy-paving pattern | |
| dtype: int8 | |
| - name: Mosaic attenuation / air-trapping | |
| dtype: int8 | |
| - name: Tree-in-bud | |
| dtype: int8 | |
| - name: Centrilobular nodules / bronchiolitis pattern | |
| dtype: int8 | |
| - name: Pulmonary nodule (solid / PSN / GGN) | |
| dtype: int8 | |
| - name: Pulmonary mass (>3 cm) | |
| dtype: int8 | |
| - name: Cavitary nodule / mass | |
| dtype: int8 | |
| - name: Emphysema | |
| dtype: int8 | |
| - name: Bullae / giant bulla | |
| dtype: int8 | |
| - name: Pulmonary cysts / cystic lung disease | |
| dtype: int8 | |
| - name: Reticulation / intralobular thickening | |
| dtype: int8 | |
| - name: Interlobular septal thickening | |
| dtype: int8 | |
| - name: Traction bronchiectasis / bronchiolectasis | |
| dtype: int8 | |
| - name: Honeycombing | |
| dtype: int8 | |
| - name: Parenchymal scarring / fibrotic band | |
| dtype: int8 | |
| - name: Tracheal stenosis / malacia | |
| dtype: int8 | |
| - name: Tracheal / bronchial wall thickening | |
| dtype: int8 | |
| - name: Bronchiectasis | |
| dtype: int8 | |
| - name: Mucoid impaction / plugging | |
| dtype: int8 | |
| - name: Tracheal diverticulum | |
| dtype: int8 | |
| - name: Endotracheal tube | |
| dtype: int8 | |
| - name: Tracheostomy tube | |
| dtype: int8 | |
| - name: Lobar / segmental atelectasis | |
| dtype: int8 | |
| - name: Subsegmental / linear atelectasis | |
| dtype: int8 | |
| - name: Post-lobectomy / segmentectomy | |
| dtype: int8 | |
| - name: Post-pneumonectomy | |
| dtype: int8 | |
| - name: Lung transplant | |
| dtype: int8 | |
| - name: Lungs & Airways_others | |
| dtype: int8 | |
| - name: Pleural effusion | |
| dtype: int8 | |
| - name: Loculated pleural effusion | |
| dtype: int8 | |
| - name: Hemothorax | |
| dtype: int8 | |
| - name: Chest tube / pleural drain | |
| dtype: int8 | |
| - name: Pneumothorax | |
| dtype: int8 | |
| - name: Tension pneumothorax | |
| dtype: int8 | |
| - name: Pleural thickening | |
| dtype: int8 | |
| - name: Pleural plaques | |
| dtype: int8 | |
| - name: Pleural nodule / mass | |
| dtype: int8 | |
| - name: Pleura_others | |
| dtype: int8 | |
| - name: Mediastinal lymphadenopathy | |
| dtype: int8 | |
| - name: Hilar lymphadenopathy | |
| dtype: int8 | |
| - name: Calcified mediastinal / hilar lymph nodes | |
| dtype: int8 | |
| - name: Anterior mediastinal mass | |
| dtype: int8 | |
| - name: Middle / posterior mediastinal mass or cyst | |
| dtype: int8 | |
| - name: Thymic remnant / hyperplasia | |
| dtype: int8 | |
| - name: Esophageal wall thickening / mass | |
| dtype: int8 | |
| - name: Hiatal hernia | |
| dtype: int8 | |
| - name: Esophageal dilation | |
| dtype: int8 | |
| - name: Nasogastric / orogastric tube | |
| dtype: int8 | |
| - name: Pneumomediastinum | |
| dtype: int8 | |
| - name: Mediastinal hematoma / fluid collection | |
| dtype: int8 | |
| - name: Mediastinum & Hila_others | |
| dtype: int8 | |
| - name: Cardiomegaly | |
| dtype: int8 | |
| - name: Pericardial effusion | |
| dtype: int8 | |
| - name: Pericardial thickening / calcification | |
| dtype: int8 | |
| - name: Coronary artery calcification | |
| dtype: int8 | |
| - name: Coronary stent or bypass graft | |
| dtype: int8 | |
| - name: Thoracic aortic calcification | |
| dtype: int8 | |
| - name: Thoracic aortic ectasia / dilation (non-aneurysmal) | |
| dtype: int8 | |
| - name: Thoracic aortic aneurysm | |
| dtype: int8 | |
| - name: Aortic dissection / intramural hematoma | |
| dtype: int8 | |
| - name: Main pulmonary artery enlargement | |
| dtype: int8 | |
| - name: Pulmonary embolism | |
| dtype: int8 | |
| - name: Aortic valve calcification | |
| dtype: int8 | |
| - name: Mitral annular calcification | |
| dtype: int8 | |
| - name: Pacemaker / ICD leads | |
| dtype: int8 | |
| - name: Central venous catheter / PICC | |
| dtype: int8 | |
| - name: LVAD / other cardiac assist device | |
| dtype: int8 | |
| - name: Cardiovascular_others | |
| dtype: int8 | |
| - name: Chest wall soft tissue edema / hematoma | |
| dtype: int8 | |
| - name: Subcutaneous emphysema | |
| dtype: int8 | |
| - name: Chest wall mass | |
| dtype: int8 | |
| - name: Post-thoracotomy change | |
| dtype: int8 | |
| - name: Chest wall tumor invasion | |
| dtype: int8 | |
| - name: Chest Wall_others | |
| dtype: int8 | |
| - name: Acute rib fracture | |
| dtype: int8 | |
| - name: Non-acute / healed rib fracture | |
| dtype: int8 | |
| - name: Sternal fracture | |
| dtype: int8 | |
| - name: Vertebral compression fracture | |
| dtype: int8 | |
| - name: Degenerative spine changes | |
| dtype: int8 | |
| - name: Osteolytic bone lesion | |
| dtype: int8 | |
| - name: Osteosclerotic bone lesion | |
| dtype: int8 | |
| - name: Mixed osteolytic-osteosclerotic lesion | |
| dtype: int8 | |
| - name: Osteopenia | |
| dtype: int8 | |
| - name: Scoliosis / kyphosis | |
| dtype: int8 | |
| - name: Vertebral hemangioma | |
| dtype: int8 | |
| - name: Postoperative spine change / hardware | |
| dtype: int8 | |
| - name: Bones / Spine_others | |
| dtype: int8 | |
| - name: Hepatic steatosis | |
| dtype: int8 | |
| - name: Focal liver lesion (nodule / mass) | |
| dtype: int8 | |
| - name: Hepatomegaly | |
| dtype: int8 | |
| - name: Liver contour irregularity / cirrhosis features | |
| dtype: int8 | |
| - name: Hepatic calcification | |
| dtype: int8 | |
| - name: Cholelithiasis / gallstones | |
| dtype: int8 | |
| - name: Post-cholecystectomy (gallbladder operated / absent) | |
| dtype: int8 | |
| - name: Gallbladder wall thickening | |
| dtype: int8 | |
| - name: Hydropic gallbladder / distension | |
| dtype: int8 | |
| - name: Biliary sludge | |
| dtype: int8 | |
| - name: Biliary stent / catheter / drain | |
| dtype: int8 | |
| - name: Splenomegaly | |
| dtype: int8 | |
| - name: Accessory spleen / splenule / polysplenia | |
| dtype: int8 | |
| - name: Focal splenic lesion (nodule / mass) | |
| dtype: int8 | |
| - name: Pancreatic mass / focal lesion | |
| dtype: int8 | |
| - name: Pancreatic lipomatosis | |
| dtype: int8 | |
| - name: Adrenal nodule / mass | |
| dtype: int8 | |
| - name: Adrenal thickening / hyperplasia | |
| dtype: int8 | |
| - name: Adrenal calcification | |
| dtype: int8 | |
| - name: Simple renal cyst | |
| dtype: int8 | |
| - name: Complex renal cyst / solid renal mass | |
| dtype: int8 | |
| - name: Hydronephrosis | |
| dtype: int8 | |
| - name: Renal calculi / nephrolithiasis | |
| dtype: int8 | |
| - name: Renal atrophy / decreased renal size | |
| dtype: int8 | |
| - name: Nephrectomy (kidney absent / operated) | |
| dtype: int8 | |
| - name: Ascites | |
| dtype: int8 | |
| - name: Pneumoperitoneum | |
| dtype: int8 | |
| - name: Bowel wall thickening / inflammation | |
| dtype: int8 | |
| - name: Diverticulosis | |
| dtype: int8 | |
| - name: Omental caking / peritoneal carcinomatosis | |
| dtype: int8 | |
| - name: Abdominal lymphadenopathy | |
| dtype: int8 | |
| - name: Abdominal aortic aneurysm (partially imaged) | |
| dtype: int8 | |
| - name: Abdominal aortic calcification / atherosclerosis (partially imaged) | |
| dtype: int8 | |
| - name: IVC filter | |
| dtype: int8 | |
| - name: Upper Abdomen_others | |
| dtype: int8 | |
| - name: Thyroid enlargement (goiter) | |
| dtype: int8 | |
| - name: Thyroid nodule | |
| dtype: int8 | |
| - name: Cervical / supraclavicular lymphadenopathy | |
| dtype: int8 | |
| - name: Neck soft tissue mass | |
| dtype: int8 | |
| - name: Lower Neck_others | |
| dtype: int8 | |
| - name: Breast mass / focal asymmetry | |
| dtype: int8 | |
| - name: Post-lumpectomy / post-mastectomy change | |
| dtype: int8 | |
| - name: Breast implant (intact or present) | |
| dtype: int8 | |
| - name: Axillary lymphadenopathy | |
| dtype: int8 | |
| - name: Motion artifact / suboptimal study | |
| dtype: int8 | |
| - name: Study limitation / limited evaluation (non-motion) | |
| dtype: int8 | |
| - name: No significant intrathoracic abnormality | |
| dtype: int8 | |
| - name: Others_others | |
| dtype: int8 | |
| splits: | |
| - name: train | |
| num_bytes: 58124167 | |
| num_examples: 20648 | |
| - name: valid | |
| num_bytes: 4525829 | |
| num_examples: 1483 | |
| - name: test | |
| num_bytes: 4196521 | |
| num_examples: 1483 | |
| download_size: 18881153 | |
| dataset_size: 66846517 | |
| configs: | |
| - config_name: default | |
| data_files: | |
| - split: train | |
| path: data/train-* | |
| - split: valid | |
| path: data/valid-* | |
| - split: test | |
| path: data/test-* | |
| # CT-RATE Findings — Chest Imaging Leaf Labels | |
| Chest-CT **findings** from the [CT-RATE](https://huggingface.co/datasets/ibrahimhamamci/CT-RATE) | |
| dataset. Each row maps an **original findings report → a section-structured refined | |
| version**, plus a **137-label** ternary multi-label annotation over a chest-imaging taxonomy. | |
| - **Rows:** 23,614 unique CT-RATE findings reports (one row per report) | |
| - **Splits (report-text-level de-duplicated):** train 20,648 / valid 1,483 / test 1,483 | |
| - **Labels:** 137 leaf labels (106 clinical + 31 other). Full taxonomy, definitions and per-split counts in **[`LABEL_HIERARCHY.md`](./LABEL_HIERARCHY.md)**. | |
| ## Columns | |
| | Column | Type | Description | | |
| |---|---|---| | |
| | `original_report` | string | Original CT-RATE findings text (input) | | |
| | `refined_report` | string | Section-structured / cleaned findings (target; empty for 281 rows) | | |
| | `split` | string | `train` / `valid` / `test` | | |
| | *137 label columns* | int8 | Per-label status — see encoding below | | |
| ### Label encoding (ternary) | |
| | Value | Meaning | | |
| |---:|---| | |
| | `1` | positive | | |
| | `0` | negative | | |
| | `-1` | uncertain | | |
| | `null` | not assessed for this report | | |
| ## Notes | |
| - Splits are **de-duplicated across each other at the report-text level**: no | |
| `original_report` or `refined_report` text appears in more than one split. | |
| - **Breast & Axilla** were originally intended as their own top-level section, but because | |
| such findings are relatively infrequent in CT-RATE they were folded into the **Others** | |
| section. The individual breast/axilla leaf labels are still present (under `Others`). | |
| - 281 rows have an empty `refined_report` (labels are still provided). | |
| - 601 reports (2.5%) have no positive on any label. | |
| - `IVC filter` is present for taxonomy completeness but is **entirely unlabeled** (all `null` — no positive, negative, or uncertain in any row). | |
| - Label names exactly match the hierarchy in **[`LABEL_HIERARCHY.md`](./LABEL_HIERARCHY.md)**. | |
| ## Radiologist validation (test set) | |
| A radiologist manually reviewed **966 of the 1,483 test reports** (65.1%), comparing the | |
| assigned labels against the report: | |
| | Verdict | Reports | Share | | |
| |---|---:|---:| | |
| | Fully accepted | 857 | 88.7% | | |
| | Imperfect / uncertain but acceptable | 60 | 6.2% | | |
| | Failed | 49 | 5.1% | | |
| | **Reviewed** | **966** | **100%** | | |
| **Acceptable (accepted + borderline): 917 / 966 = 94.9%.** This is a spot-check of the | |
| weak-label quality on the held-out test split, not a re-annotation — the published labels are | |
| the original pipeline output, unchanged. | |
| ## Provenance & caveats | |
| - **Weak labels, not radiologist ground truth.** Labels were generated by an LLM labeling | |
| pipeline from the report text (not from images), then validated against the fixed taxonomy. | |
| - `refined_report` is an LLM-cleaned, section-structured rewrite of `original_report`. | |
| ## License & attribution | |
| This dataset is a **derivative of [CT-RATE](https://huggingface.co/datasets/ibrahimhamamci/CT-RATE)** | |
| and is released under **CC-BY-NC-SA-4.0**, the same license as CT-RATE. The report text | |
| (`original_report`) originates from CT-RATE; the `refined_report` rewrite and the 137 leaf | |
| labels are added by this work. | |
| **If you use this dataset you must cite the original CT-RATE paper** (a requirement of the | |
| CC-BY-NC-SA attribution terms), in addition to this dataset: | |
| ```bibtex | |
| @misc{hamamci2024ctrate, | |
| title = {A foundation model utilizing chest CT volumes and radiology reports | |
| for supervised-level zero-shot detection of abnormalities}, | |
| author = {Hamamci, Ibrahim Ethem and others}, | |
| year = {2024}, | |
| eprint = {2403.17834}, | |
| archivePrefix = {arXiv}, | |
| primaryClass = {cs.CV} | |
| } | |
| ``` | |
| Please confirm the canonical CT-RATE citation on the | |
| [official CT-RATE page](https://huggingface.co/datasets/ibrahimhamamci/CT-RATE). | |
| ## Usage | |
| ```python | |
| from datasets import load_dataset | |
| ds = load_dataset("chest2vec/chest2vec_labels") | |
| ds["test"][0]["original_report"] | |
| [k for k, v in ds["test"][0].items() if v == 1] # positive labels for the first test report | |
| ``` | |