README.md

---
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
```