Datasets:

chest2vec
/

chest2vec_labels

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 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.

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.

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 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:

@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.

Usage

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