LABEL_HIERARCHY.md

Final Chest Imaging Label Hierarchy with Clinical vs Other Counts

Source: refined from the uploaded chest imaging label hierarchy.

Counting definitions

• Top-level sections are the major anatomy/global sections. They are not counted as upper/container labels.
• Upper/container labels are the first-level labels under each top-level section.
• Assignable leaf labels are the actual model labels/findings under each upper/container label.
• Every *_others label is counted twice structurally:
  • once as an upper/container label, and
  • once as an assignable leaf label under itself.
• Clinical finding leaf labels are radiologic/pathologic/anatomic findings that can be clinically interpreted from chest CT.
• Other leaf labels are non-primary clinical findings: *_others catch-all labels, study-quality/global labels, support devices/procedural hardware, and post-surgical/transplant/absent-organ status labels.
• Some upper/container labels are mixed because they contain both clinical and other leaf labels. I keep these separate instead of forcing a misleading binary upper-label count.

Overall count summary

Count type	Count
Top-level sections	9
Upper/container labels, total	46
Clinical-only upper/container labels	24
Other-only upper/container labels	11
Mixed clinical/other upper/container labels	11
Assignable leaf labels, total	137
Clinical finding leaf labels	106
Other leaf labels	31

Other leaf-label breakdown

Other leaf type	Count	Labels
*_others catch-all labels	9	Lungs & Airways_others, Pleura_others, Mediastinum & Hila_others, Cardiovascular_others, Chest Wall_others, Bones / Spine_others, Upper Abdomen_others, Lower Neck_others, Others_others
Study quality / global labels	3	Motion artifact / suboptimal study; Study limitation / limited evaluation (non-motion); No significant intrathoracic abnormality
Support / device / procedural-status labels	12	Endotracheal tube; Tracheostomy tube; Chest tube / pleural drain; Nasogastric / orogastric tube; Coronary stent or bypass graft; Pacemaker / ICD leads; Central venous catheter / PICC; LVAD / other cardiac assist device; Biliary stent / catheter / drain; IVC filter; Breast implant (intact or present); Postoperative spine change / hardware
Post-surgical / transplant / absent-organ status labels	7	Post-lobectomy / segmentectomy; Post-pneumonectomy; Lung transplant; Post-thoracotomy change; Post-cholecystectomy (gallbladder operated / absent); Nephrectomy (kidney absent / operated); Post-lumpectomy / post-mastectomy change
Total other leaf labels	31	—

Section-wise count table

Section	Upper total	Clinical-only upper	Mixed upper	Other-only upper	Leaf total	Clinical leaf	Other leaf
Lungs & Airways	8	5	1	2	30	24	6
Pleura	4	2	1	1	10	8	2
Mediastinum & Hila	5	3	1	1	13	11	2
Cardiovascular	6	3	2	1	17	12	5
Chest Wall	3	1	1	1	6	4	2
Bones / Spine	3	1	1	1	13	11	2
Upper Abdomen	10	6	3	1	35	30	5
Lower Neck	3	2	0	1	5	4	1
Others	4	1	1	2	8	2	6
Total	46	24	11	11	137	106	31

Dataset & split coverage (CT-RATE findings)

One row per unique CT-RATE findings report; labels are ternary (1=positive, 0=negative, -1=uncertain, NaN=not assessed). "Positive" below = value 1. Splits are de-duplicated across each other at the report-text level (no original_report / refined_report appears in more than one split).

Findings counts by split

Split	Findings	No positive (any of 137 labels)	No clinical positive (of 106 clinical labels)
train	20,648	545 (2.6%)	1,330 (6.4%)
valid	1,483	16 (1.1%)	37 (2.5%)
test	1,483	40 (2.7%)	101 (6.8%)
All	23,614	601 (2.5%)	1,468 (6.2%)

• No positive (any label): the report has no 1 across all 137 leaf labels.
• No clinical positive: no 1 among the 106 clinical finding labels — the report may still be positive on an other label (*_others, study-quality, support/device, or post-surgical/status). Of the 1,468 such reports, 867 carry ≥1 other-type positive (e.g. normal-study / device-only) and the remaining 601 have no positive on any label.

Positive cells by clinical/other group

Total positive label-assignments (1s), split across the 106 clinical vs 31 other leaf labels.

Split	Clinical positives (106)	Other positives (31)	Total
train	90,866	29,845	120,711
valid	8,449	2,700	11,149
test	6,942	1,976	8,918
All	106,257	34,521	140,778

Note: valid was stratified to match test per-label positive counts, so it runs slightly denser in positives — its all-negative/normal share (1.1%) is lower than test's (2.7%).

Mixed upper/container labels

These upper labels contain both clinical and other leaf labels:

• Lungs & Airways → Trachea & Airways
• Pleura → Pleural fluid / drain-related findings
• Mediastinum & Hila → Esophagus / hiatus / enteric tube
• Cardiovascular → Coronary arteries
• Cardiovascular → Valves, vascular lines, and cardiac devices
• Chest Wall → Post-surgical / tumor invasion
• Bones / Spine → Degenerative / osseous lesions
• Upper Abdomen → Gallbladder & biliary
• Upper Abdomen → Kidneys / urinary tract
• Upper Abdomen → Upper abdominal vessels
• Others → Breast

Hierarchy

Lungs & Airways

• Parenchymal / small-airways patterns
  • Consolidation
  • Ground-glass opacity (GGO)
  • Crazy-paving pattern
  • Mosaic attenuation / air-trapping
  • Tree-in-bud
  • Centrilobular nodules / bronchiolitis pattern
• Nodules and masses
  • Pulmonary nodule (solid / PSN / GGN)
  • Pulmonary mass (>3 cm)
  • Cavitary nodule / mass
• Emphysema & cystic lung disease
  • Emphysema
  • Bullae / giant bulla
  • Pulmonary cysts / cystic lung disease
• Interstitial / fibrotic lung disease
  • Reticulation / intralobular thickening
  • Interlobular septal thickening
  • Traction bronchiectasis / bronchiolectasis
  • Honeycombing
  • Parenchymal scarring / fibrotic band
• Trachea & Airways
  • Tracheal stenosis / malacia
  • Tracheal / bronchial wall thickening
  • Bronchiectasis
  • Mucoid impaction / plugging
  • Tracheal diverticulum
  • Endotracheal tube
  • Tracheostomy tube
• Volume loss / hyperinflation
  • Lobar / segmental atelectasis
  • Subsegmental / linear atelectasis
• Post-surgical / transplant status
  • Post-lobectomy / segmentectomy
  • Post-pneumonectomy
  • Lung transplant
• Lungs & Airways_others
  • Lungs & Airways_others

Pleura

• Pleural fluid / drain-related findings
  • Pleural effusion
  • Loculated pleural effusion
  • Hemothorax
  • Chest tube / pleural drain
• Pleural air
  • Pneumothorax
  • Tension pneumothorax
• Pleural thickening / masses
  • Pleural thickening
  • Pleural plaques
  • Pleural nodule / mass
• Pleura_others
  • Pleura_others

Mediastinum & Hila

• Lymph nodes
  • Mediastinal lymphadenopathy
  • Hilar lymphadenopathy
  • Calcified mediastinal / hilar lymph nodes
• Mediastinal masses / cysts
  • Anterior mediastinal mass
  • Middle / posterior mediastinal mass or cyst
  • Thymic remnant / hyperplasia
• Esophagus / hiatus / enteric tube
  • Esophageal wall thickening / mass
  • Hiatal hernia
  • Esophageal dilation
  • Nasogastric / orogastric tube
• Air / fluid in mediastinum
  • Pneumomediastinum
  • Mediastinal hematoma / fluid collection
• Mediastinum & Hila_others
  • Mediastinum & Hila_others

Cardiovascular

• Cardiac size and morphology
  • Cardiomegaly
• Pericardium
  • Pericardial effusion
  • Pericardial thickening / calcification
• Coronary arteries
  • Coronary artery calcification
  • Coronary stent or bypass graft
• Aorta / pulmonary artery
  • Thoracic aortic calcification
  • Thoracic aortic ectasia / dilation (non-aneurysmal)
  • Thoracic aortic aneurysm
  • Aortic dissection / intramural hematoma
  • Main pulmonary artery enlargement
  • Pulmonary embolism
• Valves, vascular lines, and cardiac devices
  • Aortic valve calcification
  • Mitral annular calcification
  • Pacemaker / ICD leads
  • Central venous catheter / PICC
  • LVAD / other cardiac assist device
• Cardiovascular_others
  • Cardiovascular_others

Chest Wall

• Chest wall soft tissues
  • Chest wall soft tissue edema / hematoma
  • Subcutaneous emphysema
  • Chest wall mass
• Post-surgical / tumor invasion
  • Post-thoracotomy change
  • Chest wall tumor invasion
• Chest Wall_others
  • Chest Wall_others

Bones / Spine

• Fractures
  • Acute rib fracture
  • Non-acute / healed rib fracture
  • Sternal fracture
  • Vertebral compression fracture
• Degenerative / osseous lesions
  • Degenerative spine changes
  • Osteolytic bone lesion
  • Osteosclerotic bone lesion
  • Mixed osteolytic-osteosclerotic lesion
  • Osteopenia
  • Scoliosis / kyphosis
  • Vertebral hemangioma
  • Postoperative spine change / hardware
• Bones / Spine_others
  • Bones / Spine_others

Upper Abdomen

• Liver
  • Hepatic steatosis
  • Focal liver lesion (nodule / mass)
  • Hepatomegaly
  • Liver contour irregularity / cirrhosis features
  • Hepatic calcification
• Gallbladder & biliary
  • Cholelithiasis / gallstones
  • Post-cholecystectomy (gallbladder operated / absent)
  • Gallbladder wall thickening
  • Hydropic gallbladder / distension
  • Biliary sludge
  • Biliary stent / catheter / drain
• Spleen
  • Splenomegaly
  • Accessory spleen / splenule / polysplenia
  • Focal splenic lesion (nodule / mass)
• Pancreas
  • Pancreatic mass / focal lesion
  • Pancreatic lipomatosis
• Adrenals
  • Adrenal nodule / mass
  • Adrenal thickening / hyperplasia
  • Adrenal calcification
• Kidneys / urinary tract
  • Simple renal cyst
  • Complex renal cyst / solid renal mass
  • Hydronephrosis
  • Renal calculi / nephrolithiasis
  • Renal atrophy / decreased renal size
  • Nephrectomy (kidney absent / operated)
• GI & peritoneum
  • Ascites
  • Pneumoperitoneum
  • Bowel wall thickening / inflammation
  • Diverticulosis
  • Omental caking / peritoneal carcinomatosis
• Lymph nodes
  • Abdominal lymphadenopathy
• Upper abdominal vessels
  • Abdominal aortic aneurysm (partially imaged)
  • Abdominal aortic calcification / atherosclerosis (partially imaged)
  • IVC filter
• Upper Abdomen_others
  • Upper Abdomen_others

Lower Neck

• Thyroid
  • Thyroid enlargement (goiter)
  • Thyroid nodule
• Neck nodes and soft tissues
  • Cervical / supraclavicular lymphadenopathy
  • Neck soft tissue mass
• Lower Neck_others
  • Lower Neck_others

Others

Breast & Axilla were originally intended as a separate top-level section. Because such findings are relatively infrequent in CT-RATE, they were merged into Others rather than kept as their own section. The individual breast/axilla leaf labels are retained below.

• Breast
  • Breast mass / focal asymmetry
  • Post-lumpectomy / post-mastectomy change
  • Breast implant (intact or present)
• Axilla
  • Axillary lymphadenopathy
• Study quality / global
  • Motion artifact / suboptimal study
  • Study limitation / limited evaluation (non-motion)
  • No significant intrathoracic abnormality
• Others_others
  • Others_others