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 (`1`s), 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