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mxslrmxslr/mlcraft/skills/domain-medical-imaging/SKILL.md

domain-medical-imaging

Skill8 starsChanged 4 months agoMITView on GitHub

Use for medical-image AI: tumor/cancer detection & classification, brain tumor MRI, mammography (benign vs malignant), chest X-ray, CT, histopathology, retinal/fundus, ultrasound, dermoscopy. Encodes hard-won rigor: patient-level splits (no leakage), medical preprocessing (CLAHE, ROI/organ cropping, artifact/pectoral removal), clinical operating points (high sensitivity), probability calibration, and skepticism toward inflated ROI-crop/leaky benchmark numbers. Triggers on 'detect cancer/tumor', 'MRI/CT/X-ray/mammogram/histopathology classification', 'benign vs malignant', 'medical images'.

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    PATIENT-LEVEL split: All images/views/slices of one patient in ONE split.

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Files
SKILL.md

Medical Imaging - Method Selection & Rigor

High stakes + small, leaky-prone datasets. Rigor matters more than architecture.

Decision table

Sub-taskRecommendedNotes
2D scan classification (mammo, X-ray, derm, fundus)EfficientNet(-B3..B5) / ConvNeXt, ImageNet-pretrainedModern-but-not-huge backbones win on low/medium-quality medical data; giant models often don't transfer better.
Whole-image with tiny lesionsWeakly-supervised localization (GMIC-style) or patch-pretrain then whole-image (Shen-style)Best whole-image ceiling; also yields saliency maps for clinicians.
Multi-view study (e.g., CC+MLO mammo)Two-view / multi-input fusionBiggest research-backed lever over single view.
3D volumes (CT/MRI)3D U-Net / nnU-Net (seg), 2.5D or 3D CNN (classify)nnU-Net is a very strong segmentation default.
Histopathology WSIMIL / CLAM on tilesGigapixel images, so tile them and use multiple-instance learning.
Lesion/organ segmentationU-Net / nnU-Net / SegFormerDice/IoU.

Non-negotiable rigor (this is where most medical ML fails)

  • PATIENT-LEVEL split. All images/views/slices of one patient in ONE split. Use the dataset's official split when it exists (often encoded in the ID). Add asserts (data-rigor-and-leakage). Random per-image splitting is the classic fake-accuracy trap.
  • Whole-image vs ROI-crop honesty. Cropped-lesion ROI classification is an easier, different problem; ~98-99% papers are usually ROI-crop and/or leaky. Report which one you are doing and never conflate.
  • Medical preprocessing: CLAHE for contrast; crop to the organ/breast (largest connected component) to drop background/labels/tape; remove confounders (e.g., pectoral muscle on mammogram MLO - verify the model isn't attending to it via Grad-CAM); intensity normalization (windowing for CT, z-score for MRI). Apply identically at inference (parity).
  • Clinical operating point: report sensitivity AND specificity; prefer a high-sensitivity threshold (recall ≥ ~0.90) chosen on validation - missing cancer >> a false alarm. Don't ship a 0.5 or Youden threshold blindly.
  • Calibration: temperature-scale probabilities so "78% malignant" is trustworthy for decision support.
  • Framing: decision-support / second-reader, NOT autonomous diagnosis; prototype needs clinical + regulatory validation (deployment-explainability).

Realistic ceilings (whole-image, rigorous)

State honest targets from literature-review rather than chasing leaderboard peaks (e.g., CBIS-DDSM whole-image benign-vs-malignant ≈ 0.83 AUC single-view, ~0.86 two-view; higher numbers are typically ROI/leaky). Use accuracy-improvement-loop to push toward the ceiling.

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