@research-copilot/plugin 1.1.16 → 1.1.18

package/dist/skills/medical-imaging-review/references/DOMAINS.md

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+# Domain-Specific Method Taxonomies (3-Axis Grouping)
+
+**This file replaces the v2 "flat 10-subsection list" approach.** For each medical imaging domain, methods are organized along **3 thematic axes**, not as a long flat list. These axes are **subsection structure** (the H3 organization in §Methods), with **bold lead-ins** for individual method families inside each axis.
+
+The 3 axes are universal:
+1. **Architectural priors** — what kind of network (CNN, Transformer, Mamba, etc.)
+2. **Inductive priors** — what kind of geometric / structural / multi-task bias is built in (topology, multi-task, graph, etc.)
+3. **Data regime** — how data is used / pre-trained / federated (self-supervised, foundation models, federated, etc.)
+
+**Critical:** These 3 axes are how the §Methods section is structured. Do NOT bullet 10 method categories as 10 H3 subsections. Use 3 axis subsections, with bold lead-ins inside each axis for the method families.
+
+---
+
+## How to use this file
+
+When writing the §Methods section:
+
+1. Open this file to find your domain.
+2. Use the 3-axis grouping as your H3 structure.
+3. Inside each axis subsection, use bold lead-ins for the individual method families.
+4. End each axis subsection with a verdict sentence.
+
+Example for coronary segmentation §Methods:
+
+```markdown
+## Methods
+
+### Architectural priors
+
+**CNN-based design.** ... 2-3 paragraphs ...
+**Transformer-based design.** ... 2-3 paragraphs ...
+**Mamba and state-space design.** ... 1-2 paragraphs ...
+
+Verdict: CNN-based design remains the operational default; transformer
+hybrids are starting to show convincing gains in centerline-vs-mask hybrid
+problems but have yet to displace U-Net on pure segmentation.
+
+### Inductive priors
+
+**Topology-aware design.** ... 2-3 paragraphs ...
+**Multi-task design.** ... 2-3 paragraphs ...
+**Graph neural network design.** ... 1-2 paragraphs ...
+
+Verdict: Topology-aware losses are the single most cost-effective design
+choice for coronary segmentation when paired with any decent backbone.
+
+### Data regime
+
+**Self-supervised pre-training.** ... 2-3 paragraphs ...
+**Foundation models.** ... 2-3 paragraphs ...
+**Federated learning.** ... 1-2 paragraphs ...
+**Physics-informed models.** ... 1 paragraph ...
+
+Verdict: Foundation models are the next 2-3 years' wild card; their gap to
+domain-tuned specialists has narrowed substantially but is not yet closed.
+```
+
+---
+
+## Coronary Artery / Cardiovascular CT (CCTA)
+
+### Axis 1: Architectural priors
+- **CNN-based**: U-Net, V-Net, nnU-Net variants
+- **Transformer-based**: ViT, SwinUNETR, TransUNet, TransCC, FocusUNETR
+- **Mamba / state-space**: VM-UNet, U-Mamba for vessels
+- **Hybrid CNN-Transformer**: nnFormer, hybrid encoders
+
+### Axis 2: Inductive priors
+- **Topology-aware**: clDice loss, VCP loss, persistent-homology losses
+- **Multi-task**: joint segmentation + centerline, joint segmentation + bifurcation detection
+- **Graph neural network**: vessel graph extraction, GNN-based labeling
+
+### Axis 3: Data regime
+- **Self-supervised pre-training**: contrastive, masked-image-modeling for vessels
+- **Foundation models**: SAM-Med, vesselFM, generalist segmentation models
+- **Semi-supervised**: pseudo-labeling for CCTA datasets
+- **Federated learning**: multi-center coronary segmentation without data sharing
+- **Physics-informed**: PDE-constrained losses for vessel topology
+
+### Downstream tasks (separate section, not part of methods axis structure)
+- Centerline extraction
+- Vessel labeling (SCCT 18-segment / AHA 17-segment myocardium)
+- Stenosis detection
+- CT-FFR computation
+- Plaque analysis
+- Calcium scoring
+- Pericoronary fat analysis (FAI)
+
+### Key datasets
+- CAT08 (32 cases, centerline)
+- ASOCA (40 cases, segmentation)
+- ImageCAS (1000 cases, single-center, segmentation)
+- PCCTA120 (120 cases, artery + plaque)
+
+---
+
+## Lung Imaging (CT / X-ray)
+
+### Axis 1: Architectural priors
+- **Anchor-based detection**: Faster R-CNN, RetinaNet
+- **Anchor-free detection**: CenterNet, FCOS, YOLO variants
+- **Transformer-based detection**: DETR family
+- **3D detection**: 3D nodule detection networks
+- **U-Net variants for segmentation**
+
+### Axis 2: Inductive priors
+- **Multi-scale feature pyramids**: FPN-based, PSP
+- **Attention mechanisms**: SE blocks, CBAM, axial attention
+- **Boundary-aware**: edge-loss formulations
+- **Uncertainty quantification**: MC dropout, ensembles
+
+### Axis 3: Data regime
+- **Self-supervised**: contrastive learning on chest CT
+- **Weakly-supervised**: from radiology reports
+- **Foundation models**: chest X-ray foundation models
+
+### Tasks
+- Nodule detection / segmentation / malignancy classification
+- COVID-19 detection
+- Interstitial lung disease characterization
+
+### Key datasets
+- LUNA16 (888 CT scans)
+- LIDC-IDRI (1018 cases)
+- ChestX-ray14 (112,120 X-rays)
+
+---
+
+## Brain Imaging (MRI / CT)
+
+### Axis 1: Architectural priors
+- **CNN-based**: U-Net, V-Net
+- **Transformer-based**: SwinUNETR, UNETR for BraTS
+- **Hybrid**
+
+### Axis 2: Inductive priors
+- **Attention mechanisms**: spatial, channel, self-attention
+- **Graph neural networks**: brain connectivity GNNs
+- **Multi-atlas-informed**: deep atlas registration
+
+### Axis 3: Data regime
+- **Self-supervised pre-training**: masked-image-modeling on MRI
+- **Foundation models**: medSAM, BrainSAM
+- **Multi-modal fusion**: T1/T2/FLAIR fusion strategies
+- **Federated learning**: cross-institutional MRI federation
+
+### Tasks
+- Brain tissue segmentation
+- Tumor segmentation (BraTS)
+- Lesion detection (stroke, MS)
+- Cerebrovascular segmentation
+- Age / disease estimation
+
+### Key datasets
+- BraTS (brain tumor)
+- ADNI (Alzheimer's)
+- IXI (healthy brains)
+- ISLES (stroke lesions)
+
+---
+
+## Cardiac Imaging (MRI / CT / Echo)
+
+### Axis 1: Architectural priors
+- **CNN-based**: nnU-Net, V-Net cine MRI
+- **Temporal modeling**: RNN, 3D CNN, transformer-based temporal
+- **Multi-view fusion**: SA + LA cine fusion
+
+### Axis 2: Inductive priors
+- **Shape priors**: SSM-constrained networks
+- **Anatomical loss formulations**
+- **Uncertainty estimation**: ensembles, MC dropout
+
+### Axis 3: Data regime
+- **Multi-modal fusion**: cine + LGE + perfusion
+- **Foundation models**: cardiac generalists
+- **Self-supervised pre-training**
+
+### Tasks
+- Chamber segmentation
+- Wall motion analysis
+- Scar / fibrosis detection (LGE)
+- Valve assessment
+- Strain analysis
+
+### Key datasets
+- ACDC (100 patients)
+- M&Ms (320 subjects)
+- CAMUS (500 patients, echo)
+
+---
+
+## Pathology (Whole Slide Images)
+
+### Axis 1: Architectural priors
+- **Patch-based CNN**: ResNet, EfficientNet
+- **Transformer-based**: ViT, hierarchical transformers
+- **Graph neural networks**: nuclei-level graphs
+
+### Axis 2: Inductive priors
+- **Multiple Instance Learning (MIL)**: attention-MIL, max-pooling
+- **Attention-based aggregation**: TransMIL
+- **Topology-aware**: persistent homology of histological structures
+
+### Axis 3: Data regime
+- **Self-supervised pre-training**: SimCLR / MoCo / DINO on patches
+- **Foundation models**: PathLM, CONCH, UNI, Virchow
+- **Weakly-supervised**: from slide-level labels
+
+### Tasks
+- Cancer detection / grading / staging
+- Biomarker prediction
+- Survival prediction
+
+### Key datasets
+- CAMELYON (lymph node)
+- TCGA (multi-cancer)
+- PANDA (prostate)
+
+---
+
+## Retinal Imaging (Fundus / OCT)
+
+### Axis 1: Architectural priors
+- **CNN-based**: multi-scale networks
+- **Transformer-based**: ViT for fundus
+- **Hybrid**
+
+### Axis 2: Inductive priors
+- **Attention mechanisms**: dual-attention for vessels
+- **Domain adaptation**: between fundus camera types
+
+### Axis 3: Data regime
+- **Self-supervised**: on large unlabeled fundus image sets
+- **Foundation models**: RETFound, FLAIR
+- **Federated learning**: privacy-preserving DR screening
+
+### Tasks
+- Diabetic retinopathy grading
+- Glaucoma detection
+- Age-related macular degeneration
+- Vessel segmentation
+
+### Key datasets
+- EyePACS (88,702 images)
+- DRIVE (40 images, vessels)
+- REFUGE (1200 images, glaucoma)
+
+---
+
+## Universal Medical Image Segmentation (Fallback Axis Structure)
+
+When the domain is generic or your topic spans multiple modalities, use this universal 3-axis grouping:
+
+### Axis 1: Architectural priors
+- Encoder-Decoder (U-Net, V-Net, nnU-Net)
+- Transformer-based (SwinUNETR, UNETR, TransUNet)
+- Mamba / state-space
+- Hybrid CNN-Transformer
+
+### Axis 2: Inductive priors
+- Attention mechanisms (SE, CBAM, axial, deformable)
+- Multi-scale processing (FPN, PSP, ASPP)
+- Boundary-aware (active contours, edge losses)
+- Topology-preserving (clDice, persistent homology)
+- Uncertainty quantification (MC Dropout, ensembles)
+
+### Axis 3: Data regime
+- Self-supervised pre-training (contrastive, masked)
+- Foundation models (SAM, MedSAM)
+- Few-shot / zero-shot (prototypical, foundation models)
+- Domain adaptation (adversarial, self-training)
+- Federated learning
+- Efficient architectures (MobileNet, EfficientNet, Mamba — when efficiency is the focus)
+
+### Universal evaluation metrics (Box 1 content)
+- **Overlap**: Dice, IoU / Jaccard
+- **Distance**: Hausdorff (HD, HD95), ASSD
+- **Topology**: clDice, Betti numbers
+- **Clinical**: Sensitivity, Specificity, AUC, PPV / NPV
+
+---
+
+## What to do when a method family doesn't fit cleanly into 3 axes
+
+Some methods span axes (e.g., a foundation-model-based topology-aware Mamba would touch all 3). In such cases:
+
+- Place the method in the axis it's most centrally about.
+- Cross-reference from the other 2 axes ("see also: this method type combines architectural and data-regime innovations").
+- Don't create a 4th axis to accommodate it. Three axes is the structural commitment.
+
+If 30%+ of your methods don't fit, you may be in a sub-domain where the 3-axis structure needs adaptation. In that case, document the alternative structure in PARADIGM.md and use it consistently — but stay disciplined to 3 axes.
+
+---
+
+## Why 3 axes, not 10 flat subsections
+
+The v2 skill's coronary section listed 10 flat method categories. The resulting draft had a §3 with 10 nearly-equal H3 subsections, each ~500 words. The effect on the reader: **a textbook chapter, not a flagship review**.
+
+Flagship reviews compress 10+ method variants into 3 thematic axes. The 3-axis structure also forces explicit comparison ("CNN-based vs Transformer-based vs Mamba-based architectures all aim to capture spatial inductive bias differently") which is what a real review reader wants — synthesis, not catalogue.
+
+If your editor / reviewer feedback says "the methods section reads as a flat list", this file's structure is the fix.

package/dist/skills/medical-imaging-review/references/HALLUCINATION_PATTERNS.md

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+# 9 Patterns of LLM Hallucination in Medical Imaging Reviews
+
+Use this as a checklist during Phase 4 (writing) and Phase 5 (peer review). Every paragraph should be self-scanned against these patterns. The 9 patterns are derived from the actual failure modes observed in the `coronary-cta-paper` v2 draft.
+
+Examples are drawn from coronary imaging but the patterns are domain-general.
+
+---
+
+## Pattern 1: Real paper, fabricated author list
+
+**Most common.** The paper exists, but the author list is a generic 4-name pattern (or only includes 1-2 real authors mixed with fabricated co-authors).
+
+### Detection signals
+
+- Author list looks like "Liu Y, Zhang H, Chen X, Wang J" — 4 of the most common surnames in a language paired with most common initials.
+- First-author initial doesn't match real first author (e.g., "Wittmann F" vs. real Bastian Wittmann).
+- Author count obviously wrong for the journal (Nature paper with 3 authors is unusual; methods paper with 12 authors is unusual).
+- Author list looks suspiciously "alphabetical" or "rhythmic" — real lists are messy.
+
+### Example from coronary-cta-paper
+
+- v2 reference [30]: "Liu Y, Zhang H, Chen X, Wang J. TransCC..."
+- Reality: Chenchu Xu, Meng Li, Xue Wu (3 actual authors of the real TransCC paper)
+
+### Fix
+
+Replace entire author list with verbatim from arXiv / PubMed / Crossref / Zotero.
+
+---
+
+## Pattern 2: Inflated performance numbers
+
+The cited paper is real, the topic is right, but the specific Dice / sensitivity / specificity / HR is fabricated and typically inflated.
+
+### Detection signals
+
+- Dice values ending in `.891`, `.917`, `.943` — suspiciously specific 3-decimal numbers
+- Performance numbers consistently above field benchmarks
+- Round-looking numbers when papers usually report messier values
+- Multiple methods all reporting "Dice 0.89" when the real distribution should span 0.70-0.85
+
+### Example from coronary-cta-paper
+
+- v2: "TransCC achieves Dice 0.891 / HD95 1.72 mm on 120 cases"
+- Reality: Dice 0.730 / IoU 0.582 on ImageCAS (not "120 cases")
+
+### Fix
+
+Open the actual paper. Quote the actual numbers from abstract or results table. If the paper isn't accessible, drop the specific numeric claim and only cite the contribution level ("first to apply X to Y").
+
+---
+
+## Pattern 3: Conclusion-direction flip
+
+Most pernicious. Real paper, real authors, real finding — but the direction (higher/lower, increased/decreased) is reversed.
+
+### Detection signals
+
+- Look for any body sentence with directional language: "higher", "lower", "increased", "decreased", "better", "worse", "more", "less"
+- These all need explicit verification against the source
+
+### Example from coronary-cta-paper
+
+- v2: "Lv et al. showed collateral circulation is associated with **higher** FAI"
+- Reality: collaterals associated with **lower** FAI
+
+### Fix
+
+Always quote directional claims verbatim from the source abstract. Don't paraphrase quantitative directional language.
+
+---
+
+## Pattern 4: Vendor / agency material cited as peer-reviewed
+
+Vendor white papers, FDA clearance letters, NHS reports cited with fabricated journal attribution.
+
+### Detection signals
+
+- References that look like: "Company X. Product Y Whitepaper. Major Journal. 2024"
+- "Study Investigators. Findings. BMJ Open. 2024" (when no such BMJ Open paper exists)
+- Citations of clinical findings backed by a regulatory document rather than a peer-reviewed trial
+
+### Example from coronary-cta-paper
+
+- v2: "NHS England. FISH&CHIPS Study Implementation Report. BMJ Open. 2024"
+- Reality: real publication is Fairbairn TA, et al. Nat Med. 2025;31(6):1903-1910
+
+### Fix
+
+Search PubMed for the actual peer-reviewed publication of the study. Use vendor materials only for regulatory / programmatic facts (clearance dates, indications), never for clinical claims.
+
+---
+
+## Pattern 5: Placeholder DOIs
+
+`xxx`, `[TBD]`, `x):xxx-xxx` stubs left in the bibliography.
+
+### Detection
+
+```bash
+grep -nE "xxx|\[TBD\]|x\):xxx|doi:10\.[a-z]+/x" manuscript_draft.md
+```
+
+### Example from coronary-cta-paper
+
+- v2 had 17 entries like: `Eur Radiol. 2026;36(x):xxx-xxx. doi:10.1007/s00330-025-xxx`
+- Reality: each has a real DOI resolvable via PubMed by PMID
+
+### Fix
+
+For each placeholder, WebFetch on PubMed by PMID to extract real metadata. If the paper genuinely doesn't have a DOI yet (true preprint), use the arXiv ID or accept the "online ahead of print" notation — but never `xxx`.
+
+---
+
+## Pattern 6: Generic 4-author hallucination (subset of pattern 1, called out separately)
+
+Specifically the "4 common surnames + common initials" pattern. So distinctive it deserves its own watch.
+
+### Examples
+
+- "Zhang H, Wang L, Chen Y, Liu Q" (Chinese)
+- "Smith J, Johnson A, Williams M, Brown D" (English)
+- "Patel R, Kumar A, Singh P, Sharma N" (Indian)
+- "Sato K, Tanaka T, Suzuki M, Watanabe H" (Japanese)
+
+### Fix
+
+Any time you see exactly 4 authors with this pattern, verify all 4 against the source. Real 4-author papers usually have at least one less-common name.
+
+---
+
+## Pattern 7: Citation number drift
+
+Body says "[43]" but bibliography [43] is the wrong paper. The correct paper is at [10] (or wherever).
+
+### Detection
+
+For every paragraph, check 1-2 random `[N]` against bibliography:
+- Is the body sentence's topic congruent with bibliography [N]'s title?
+- Is the body sentence's author name (if mentioned) the bibliography [N] author?
+
+### Example from coronary-cta-paper
+
+- v2: "Shit et al. [43] introduced clDice"
+- v2 bibliography [43]: a centerline DRL paper (unrelated)
+- v2 bibliography [10]: Shit S, Paetzold JC. clDice — CVPR 2021 (correct)
+- Total drift instances in v2: 30-40
+
+### Fix
+
+For each affected `[N]`, grep for the correct number and edit body in place.
+
+---
+
+## Pattern 8: Metric formula errors
+
+Definitions of standard metrics are wrong. Often: clDice written as "sum-divided-by", actually defined as "harmonic mean".
+
+### Common confusions
+
+- clDice: actually harmonic mean of topological precision and recall (HM(Tprec, Tsens)), often mis-written as "sum / 2" or "average"
+- Hausdorff distance: actually `max(d(A→B), d(B→A))`, often mis-written as "average distance"
+- IoU vs Dice: `|A∩B|/|A∪B|` vs `2|A∩B|/(|A|+|B|)` — sometimes swapped
+- FedAvg: weighted by client-data-size, often mis-described as simple averaging
+
+### Fix
+
+For every metric or method formula displayed, verify against the original paper. Don't rely on memory — these are textbook formulas with subtle precise definitions.
+
+---
+
+## Pattern 9: Internal inconsistency across sections
+
+The same paper is cited in §3.2 with one author list and in §3.5 with a different author list. Or the same dataset appears with different patient counts in different sections.
+
+### Detection
+
+Pick the 5 most-cited papers in the manuscript. For each, grep for every appearance:
+
+```bash
+grep -n "TransCC\|Wittmann\|FISH&CHIPS\|ORFAN\|<key-paper-name>" manuscript_draft.md
+```
+
+Check: every appearance of the same paper should attribute to the same author list with the same numbers.
+
+### Example from coronary-cta-paper
+
+- v2: ImageCAS described as "1000 cases" in §2, "multi-center 1500 cases" in §3.2, "single-center 1000 cases" in Table 3
+- Reality: ImageCAS is single-center, 1000 cases
+
+### Fix
+
+For each high-value paper or dataset, lock in a canonical description in CLAUDE.md terminology table. All sections must conform.
+
+---
+
+## Self-Check Workflow
+
+Every 5-6 paragraphs during writing:
+
+1. Scan the last block for direction language → verify pattern 3.
+2. Look at any new citations → verify patterns 1, 2, 5, 6.
+3. Cross-check any vendor/agency references → verify pattern 4.
+4. Random-sample 1-2 `[N]` body↔bib → verify pattern 7.
+5. Check any metric formula displayed → verify pattern 8.
+
+Every section completion:
+
+6. Search the section for the manuscript's top 5 cited papers → verify pattern 9 (internal consistency).
+
+This adds ~10-15% to writing time. Catches >90% of hallucinations before they leave the writer's desk.