@bgicli/bgicli 2.1.1 → 2.2.1

package/data/workflows/lasso-biomarker-panel/SKILL.md

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+---
+id: lasso-biomarker-panel
+name: LASSO Biomarker Panel Discovery & Validation
+category: multi_omics
+short-description: "Select minimal biomarker panels using LASSO regularization with nested cross-validation, stability selection, and independent cohort validation."
+detailed-description: "Build parsimonious biomarker panels (5-15 features) from high-dimensional omics data using penalized logistic regression (elastic net) with nested cross-validation and stability selection. Produces ROC/AUC curves, calibration plots, and feature importance visualizations suitable for clinical exploratory endpoint submissions. Supports discovery/validation cohort design following Ali et al. (Nat Med 2025) methodology. Works with RNA-seq, proteomics, or any quantitative feature matrix with binary outcomes."
+starting-prompt: Build a LASSO biomarker panel to predict treatment response from gene expression data.
+---
+
+# LASSO Biomarker Panel Discovery & Validation
+
+Select minimal, interpretable biomarker panels from high-dimensional omics data using penalized logistic regression (LASSO/elastic net) with nested cross-validation and stability selection.
+
+## When to Use This Skill
+
+Use this skill when you need to:
+- **Select a minimal biomarker panel** (5-15 features) from thousands of candidates
+- **Build a predictive model** for a binary clinical outcome (responder/non-responder, disease/control)
+- **Validate across cohorts** — discovery + independent validation design
+- **Generate regulatory-grade outputs** — ROC/AUC, calibration, decision curves
+- **Design clinical exploratory endpoints** from omics biomarker signatures
+
+**Don't use this skill for:**
+- Unsupervised clustering (use `bulk-omics-clustering`)
+- Differential expression only (use `bulk-rnaseq-counts-to-de-deseq2`)
+- Multi-omics integration/factor discovery (use `multiomics-patient-stratification`)
+- Continuous outcomes — this skill is for binary classification
+
+## Installation
+
+```r
+options(repos = c(CRAN = "https://cloud.r-project.org"))
+if (!require('BiocManager', quietly = TRUE)) install.packages('BiocManager')
+
+# Core (required)
+install.packages(c('glmnet', 'pROC', 'ggplot2', 'ggprism', 'ggrepel'))
+
+# Heatmap (required for feature heatmap)
+BiocManager::install(c('ComplexHeatmap'))
+install.packages('circlize')
+
+# Example data — Sepsis MARS consortium (recommended demo) + breast cancer/UNIFI
+BiocManager::install(c('GEOquery', 'Biobase'))
+
+# Example data — IMvigor210 bladder cancer IO (alternative demo)
+install.packages('remotes')
+remotes::install_github('SiYangming/DESeq', upgrade = 'never')
+remotes::install_github('SiYangming/IMvigor210CoreBiologies', upgrade = 'never')
+BiocManager::install('DESeq2')
+
+# Optional: DE pre-filtering
+BiocManager::install('limma')
+
+# Optional: Biological interpretation (pathway enrichment, cell-type context)
+BiocManager::install(c('clusterProfiler', 'org.Hs.eg.db', 'fgsea'))
+install.packages('msigdbr')
+```
+
+| Software | Version | License | Commercial Use | Installation |
+|----------|---------|---------|----------------|-------------|
+| glmnet | >=4.1 | GPL-2 | Permitted | `install.packages('glmnet')` |
+| pROC | >=1.18 | GPL (>=3) | Permitted | `install.packages('pROC')` |
+| ggplot2 | >=3.4 | MIT | Permitted | `install.packages('ggplot2')` |
+| ggprism | >=1.0.3 | GPL (>=3) | Permitted | `install.packages('ggprism')` |
+| ggrepel | >=0.9 | GPL-3 | Permitted | `install.packages('ggrepel')` |
+| ComplexHeatmap | >=2.10 | MIT | Permitted | `BiocManager::install('ComplexHeatmap')` |
+| circlize | >=0.4.15 | MIT | Permitted | `install.packages('circlize')` |
+
+## Inputs
+
+**Required:**
+- **Expression matrix** (genes x samples): TPM, FPKM, normalized counts, or protein abundance
+- **Sample metadata**: Data frame with a **binary outcome column** (0/1 or two-level factor)
+  - Rownames must match expression column names
+  - Minimum 20 samples per group (40+ recommended)
+
+**Optional:**
+- **Validation cohort**: Independent expression matrix + metadata with same outcome
+- **Pre-filtered feature list**: From DE analysis or WGCNA hub genes (see Related Skills)
+
+## Outputs
+
+**Primary results:**
+- `biomarker_panel.csv` — Final panel features with LASSO coefficients and selection frequencies
+- `all_feature_stability.csv` — All features ranked by selection frequency
+- `discovery_performance.csv` — Per-fold AUC, sensitivity, specificity
+- `validation_performance.csv` — External validation metrics (if validation cohort provided)
+
+**Analysis objects (RDS):**
+- `lasso_model.rds` — Complete model result for downstream use
+  - Load with: `model <- readRDS('results/lasso_model.rds')`
+  - Predict with: `source("scripts/lasso_workflow.R"); predict_biomarker_panel(model, new_X)`
+  - Required for: `multiomics-patient-stratification`, downstream prediction
+
+**Plots (PNG + SVG at 300 DPI):**
+- `roc_curve.png/.svg` — ROC curve (discovery + validation overlay)
+- `stability_barplot.png/.svg` — Feature selection frequency across CV folds
+- `coefficient_forest.png/.svg` — LASSO coefficients with 95% CIs
+- `calibration_curve.png/.svg` — Predicted vs observed probability
+- `auc_distribution.png/.svg` — AUC distribution across CV folds
+- `feature_heatmap.png/.svg` — Clustered heatmap of panel features
+
+**Reports:**
+- `summary_report.md` — Comprehensive analysis report (goals, context, datasets, methods, results)
+- `summary_report.pdf` — PDF report (only if tinytex installed; falls back to HTML automatically — this is expected in most environments)
+- `summary_report.Rmd` — R Markdown source (customizable)
+
+## Clarification Questions
+
+**ALWAYS ask Question 1 FIRST.**
+
+### 1. **Example or Own Data?** (ASK THIS FIRST):
+   - **a) Run example dataset to showcase the workflow** (recommended)
+     - Runs a sepsis blood transcriptomics demo (MARS Consortium, ICU patients) that derives a ~15–25 gene panel for identifying immunosuppressed sepsis patients — CV AUC ~0.986 (discovery cohort estimate; panel size varies across runs)
+     - **No further questions needed.** Proceed directly to Step 1 with all defaults.
+   - **b) I have my own expression data and patient outcomes to analyze**
+     - Continue to Questions 2-4 below
+
+> **IF EXAMPLE SELECTED (option a):** Skip all remaining questions. Run Step 1 with: `data <- load_sepsis_data(outcome = "endotype")`, then Steps 2-4 with defaults (`top_n_variable = 2000`, `alpha = 0.5`, `disease = "sepsis"`).
+
+**Questions 2-4 are ONLY asked if the user selected option (b) — own data:**
+
+### 2. **Input Files** *(own data only)*:
+   - What expression data file(s) do you have? (CSV, TSV, RDS, or Bioconductor object)
+     - Expected: Gene/protein × sample matrix (rows = features, columns = samples)
+   - What metadata/clinical file do you have?
+     - Must include a **binary outcome column** (0/1 or two-level factor)
+     - Rownames must match expression column names
+
+### 3. **Outcome & Organism** *(own data only)*:
+   - What is the binary outcome column name in your metadata?
+   - What do the two levels represent? (e.g., responder/non-responder, disease/control)
+   - What organism? (human/mouse/rat — for pathway enrichment)
+
+### 4. **Analysis Options** *(own data only — structured)*:
+   - **LASSO regularization:**
+     - a) Pure LASSO, alpha=1.0 (sparsest panel)
+     - b) Elastic net, alpha=0.5 (recommended — retains correlated features)
+   - **Feature pre-filtering:**
+     - a) Top 2000 most variable features (recommended for >5000 features)
+     - b) Top 500 most variable (for smaller datasets or faster runs)
+     - c) Use all features (no filtering)
+
+## Standard Workflow
+
+**MANDATORY: USE SCRIPTS EXACTLY AS SHOWN - DO NOT WRITE INLINE CODE**
+
+**Step 1 - Load data:**
+```r
+source("scripts/load_example_data.R")
+data <- load_sepsis_data(outcome = "endotype")  # 479 ICU patients, Mars1 endotype classification
+# OR: data <- load_sepsis_data(outcome = "mortality")  # 479 patients, 28-day mortality
+# OR: data <- load_breast_cancer_pcr_data(outcome = "subtype")  # 218 tumors, Basal vs LumA
+# OR: data <- load_imvigor210_data()   # 190 bladder cancer patients, atezolizumab
+# OR: data <- load_unifi_data()        # 542 UC patients, UNIFI ustekinumab trial
+```
+**DO NOT write custom data loading code. Use the loader functions.**
+
+**VERIFICATION:** You MUST see: `"✓ Sepsis endotype data loaded successfully!"` (or similar per dataset)
+
+**Step 2 - Run LASSO analysis:**
+```r
+source("scripts/prepare_features.R")
+features <- prepare_feature_matrix(data$expression, data$metadata, data$outcome_col, top_n_variable = 2000)
+
+source("scripts/lasso_workflow.R")
+model <- run_lasso_panel(features$X, features$y, alpha = 0.5)
+```
+**DO NOT write inline LASSO code (glmnet, cv.glmnet, etc.). Just use the scripts.**
+
+**VERIFICATION:** You MUST see: `"✓ LASSO panel selection completed successfully!"`
+
+**IF YOU DON'T SEE THIS:** You wrote inline code. Stop and use `source()`.
+
+**Step 3 - Generate visualizations:**
+```r
+source("scripts/biomarker_plots.R")
+generate_all_plots(model, X = features$X, y = features$y, output_dir = "results")
+```
+**DO NOT write inline plotting code (ggsave, ggplot, etc.). Just use `generate_all_plots()`.**
+
+**The script handles PNG + SVG export with graceful fallback for SVG dependencies.**
+
+**VERIFICATION:** You MUST see: `"✓ All biomarker plots generated successfully!"`
+
+**Step 4 - Export results:**
+```r
+source("scripts/export_results.R")
+export_all(model, output_dir = "results", data = data, features = features)
+```
+**DO NOT write custom export code. Use `export_all()`.**
+
+**Pass `data` and `features` for a comprehensive report with disease context and methods.**
+
+**VERIFICATION:** You MUST see: `"=== Export Complete ==="`
+
+**NOTE on PDF:** If `export_all()` reports "PDF rendering failed", this is expected in environments without LaTeX. Inform the user that `summary_report.html` and `summary_report.md` are available instead. Do NOT silently omit this from the summary.
+
+⚠️ **CRITICAL: Do NOT interpret panel biology without running enrichment**
+
+After identifying the panel, do NOT describe gene functions or pathway membership from gene names alone. This is a hallucination risk. Instead:
+- State the panel genes and their coefficients/stability scores
+- Direct the user to run pathway enrichment as a next step
+- Only describe biology if `functional-enrichment-from-degs` has been run in this session
+
+✅ Acceptable: "ACSL6 was selected in 100% of folds with a positive coefficient."
+❌ NOT acceptable: "ACSL6 is involved in mitochondrial fatty acid metabolism, consistent with..."
+
+**Step 5 (Strongly Recommended) — External Validation:**
+
+> **Without this step, all performance metrics are discovery-cohort estimates only and are expected to be optimistic. Do not present results as a validated panel without completing this step.**
+```r
+source("scripts/load_example_data.R")
+val_data <- load_breast_cancer_validation_data("GSE32646")  # or load_pursuit_data()
+source("scripts/validate_external.R")
+source("scripts/prepare_features.R")
+val_features <- prepare_validation_features(val_data$expression, features$feature_names)
+val_result <- validate_panel(model, val_features$X, val_data$metadata[[val_data$outcome_col]],
+                              cohort_name = "GSE32646")
+export_all(model, validation_result = val_result, output_dir = "results",
+           data = data, features = features)
+```
+
+**CRITICAL - DO NOT:**
+- **Write inline LASSO code** -> **STOP: Use `source("scripts/lasso_workflow.R")`**
+- **Write inline plotting code** -> **STOP: Use `generate_all_plots()`**
+- **Write custom export code** -> **STOP: Use `export_all()`**
+- **Try to install svglite** -> script handles SVG fallback automatically
+
+**IF SCRIPTS FAIL - Script Failure Hierarchy:**
+1. **Fix and Retry (90%)** - Install missing package, re-run script
+2. **Modify Script (5%)** - Edit the script file itself, document changes
+3. **Use as Reference (4%)** - Read script, adapt approach, cite source
+4. **Write from Scratch (1%)** - Only if genuinely impossible, explain why
+
+**NEVER skip directly to writing inline code without trying the script first.**
+
+## Common Issues
+
+| Error | Cause | Fix |
+|-------|-------|-----|
+| **"No shared samples"** | Column names don't match rownames | Check `colnames(expression)` match `rownames(metadata)` |
+| **"Outcome must be binary"** | Non-binary outcome column | Ensure 2 unique values in outcome. Recode if multi-level. |
+| **cv.glmnet convergence warning** | Too few samples for 10-fold CV | Reduce `n_inner_folds` to 5 or increase sample size |
+| **"No features passed stability"** | Very noisy data or small effect | Script auto-relaxes to top 10 features. Consider alpha=0.5 (elastic net). |
+| **Low validation AUC** | Cross-platform gene loss | Check `val_features$n_matched`. If <50% matched, use same-platform validation. |
+| **SVG export error** | Missing optional dependency | Normal - `generate_all_plots()` falls back to base R svg() automatically. |
+| **GEOquery download fails** | Network/firewall issue | Retry or download manually from NCBI GEO website |
+| **PDF report not generated** | tinytex/LaTeX not installed | Normal fallback — use `summary_report.html` or `summary_report.md` instead. Do NOT silently omit this from the summary. |
+
+## Agent Summary Guidelines
+
+When presenting final results to the user, the agent MUST:
+
+1. **Always cite the CV AUC** (from `discovery_performance.csv`), never the final model AUC from the ROC plot
+2. **Always state whether external validation was performed.** If not, include this sentence verbatim:
+   > "These results are from the discovery cohort only. No external validation was performed. AUC estimates are expected to be optimistic."
+3. **Never describe panel gene biology** unless `functional-enrichment-from-degs` was run in this session
+4. **Always report PDF status** — if PDF generation failed, say so explicitly and note that .html/.md reports are available
+5. **Never use the word "validated"** to describe a panel that has only been tested in the discovery cohort
+
+## Interpretation Guidelines
+
+- **AUC > 0.8**: Strong discriminative ability (clinically useful)
+- **AUC 0.7-0.8**: Moderate — useful with other clinical factors
+- **AUC 0.6-0.7**: Weak but above chance — typical for baseline transcriptomic prediction of treatment response
+- **Stability >= 80%**: Feature is robustly selected (high confidence in panel)
+- **Positive coefficient**: Higher expression -> higher probability of positive outcome
+- **Negative coefficient**: Higher expression -> lower probability of positive outcome
+- **Calibration**: Points near diagonal = well-calibrated model
+
+### AUC Values — Which Number to Use
+
+Two AUC figures are produced by this workflow:
+
+| Figure | Value | What it means | Use this? |
+|--------|-------|---------------|-----------|
+| Mean CV AUC (`discovery_performance.csv`) | e.g. 0.986 | Average AUC across held-out test sets | **YES — cite this** |
+| Final model AUC (ROC curve plot annotation) | e.g. 0.996 | Model applied back to its own training data | **NO — in-sample, optimistic** |
+
+**Always report the mean CV AUC as the performance estimate.** The final model AUC is only shown for reference and will always be higher.
+
+### Interpreting CV AUC: Known Optimism Bias
+
+The reported CV AUC from this workflow is an **estimate within the discovery cohort**, not a true out-of-sample performance figure. It is subject to optimism bias because:
+
+- Feature stability is computed across the same samples used for AUC estimation
+- The final model is re-fit on all samples after feature selection
+
+**Expected magnitude of bias:** Typically 0.02–0.05 AUC units for datasets of this size. A discovery AUC of 0.986 should be interpreted as "likely >0.93 in an independent cohort if the signal is real" — not as a guaranteed performance floor.
+
+**The only way to get an unbiased estimate is external validation.**
+
+## Suggested Next Steps
+
+After building a biomarker panel:
+1. **[REQUIRED before biological interpretation] Pathway enrichment** of panel genes -> `functional-enrichment-from-degs`
+2. **Co-expression context** — which WGCNA modules contain panel genes -> `coexpression-network`
+3. **Patient stratification** using panel as input -> `multiomics-patient-stratification`
+4. **Literature validation** — are panel genes known disease/therapy markers?
+5. **Independent cohort replication** on external validation datasets
+
+## Related Skills
+
+| Skill | Relationship |
+|-------|-------------|
+| `bulk-rnaseq-counts-to-de-deseq2` | **Upstream** — DE results can pre-filter features for LASSO |
+| `coexpression-network` | **Upstream** — WGCNA hub genes as LASSO candidates (Paper 1 cascade) |
+| `functional-enrichment-from-degs` | **Downstream** — Pathway enrichment of panel genes |
+| `bulk-omics-clustering` | **Alternative** — Unsupervised patient stratification |
+| `multiomics-patient-stratification` | **Downstream** — Multi-omics integration + subtyping |
+
+## References
+
+- **Ali et al., Nature Medicine 2025** — Cross-disease LASSO proteomics panels (AUC 0.81-0.88). Code: [github.com/NeuroGenomicsAndInformatics/NatMed_2025_GNPC](https://github.com/NeuroGenomicsAndInformatics/NatMed_2025_GNPC)
+- **Shen et al., Cell 2024** — WGCNA -> LASSO 6-protein panel (AUC 0.911)
+- **Sands et al., NEJM 2019** — UNIFI Trial (GSE206285 source)
+- **Sandborn et al., Gastro 2014** — PURSUIT Trial (GSE92415 source)
+- [glmnet vignette](https://glmnet.stanford.edu/articles/glmnet.html) — Friedman, Hastie, Tibshirani
+- [pROC package](https://web.expasy.org/pROC/) — Robin et al., BMC Bioinformatics 2011
+- See [references/lasso-reference.md](references/lasso-reference.md) for parameter tuning guide
+- See [references/validation-guide.md](references/validation-guide.md) for multi-cohort design

package/data/workflows/lasso-biomarker-panel/references/decision-guide.md

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+# Decision Guide: When to Use What
+
+## LASSO vs Elastic Net vs Ridge
+
+| Situation                                 | Recommendation                                              | Alpha     |
+| ----------------------------------------- | ----------------------------------------------------------- | --------- |
+| Biomarker panel for clinical assay        | **Pure LASSO**                                              | 1.0       |
+| Features highly correlated (same pathway) | **Elastic net**                                             | 0.5       |
+| Many weak signals, no dominant features   | **Elastic net**                                             | 0.5       |
+| Gene expression (some correlation)        | **Start with LASSO**, try elastic net if <3 stable features | 1.0 → 0.5 |
+| Proteomics (SOMAscan/Olink)               | **LASSO** — typically lower correlation                     | 1.0       |
+| Multi-omics features                      | **Elastic net** — captures cross-omics correlations         | 0.5       |
+
+## This Skill vs Other Skills
+
+| Goal                                | Use This Skill?  | Alternative                         |
+| ----------------------------------- | ---------------- | ----------------------------------- |
+| Select minimal biomarker panel      | ✅ Yes           | —                                   |
+| Predict binary outcome from omics   | ✅ Yes           | —                                   |
+| Unsupervised patient clustering     | ❌ No            | `bulk-omics-clustering`             |
+| Find differentially expressed genes | ❌ No            | `bulk-rnaseq-counts-to-de-deseq2`   |
+| Multi-omics factor analysis         | ❌ No            | `multiomics-patient-stratification` |
+| Pathway enrichment of results       | After this skill | `functional-enrichment-from-degs`   |
+| Co-expression context               | Before or after  | `coexpression-network`              |
+
+## Pre-filtering Strategy
+
+### When to Pre-filter Features
+
+- **>10,000 features**: Pre-filter to top 5,000 by variance (done by
+  `prepare_features.R`)
+- **>20,000 features**: Consider DE pre-filtering (`filter_by_de()`) first
+- **<5,000 features**: No pre-filtering needed
+
+### Pre-filtering Methods (Best to Worst)
+
+1. **DE-based** (`filter_by_de()`) — statistically principled, but introduces
+   circularity if outcome used
+2. **Variance-based** (default) — no circularity, captures informative features
+3. **WGCNA hub genes** — biologically informed, reduces to
+   pathway-representative features
+4. **Random subset** — never recommended
+
+## Troubleshooting Decision Tree
+
+```
+Problem: No stable features (all <80% frequency)
+├── Try alpha = 0.5 (elastic net)
+│   ├── Still no stable features?
+│   │   ├── Lower stability threshold to 0.6
+│   │   └── If still none: signal may be too weak for this sample size
+│   └── Features found → proceed with elastic net panel
+│
+Problem: Too many stable features (>20)
+├── Increase stability threshold to 0.9
+├── Use top_n_features = 10 per iteration
+└── Switch to alpha = 1.0 if using elastic net
+│
+Problem: Low AUC (<0.6)
+├── Check class balance (need ≥30% minority)
+├── Try DE pre-filtering (more informative features)
+├── Increase n_repeats to 100 (more stable estimates)
+└── Consider: effect size may be too small for this cohort size
+```

package/data/workflows/lasso-biomarker-panel/references/lasso-reference.md

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+# LASSO Parameter Reference Guide
+
+## Key Parameters
+
+### Alpha (Mixing Parameter)
+
+- `alpha = 1.0` — **Pure LASSO** (L1 penalty). Produces sparsest panels. Use
+  when you want the fewest possible features (clinical assay development).
+- `alpha = 0.5` — **Elastic net** (mixed L1+L2). Retains correlated features.
+  Use when features are highly correlated (e.g., co-expressed genes in the same
+  pathway).
+- `alpha = 0.0` — **Ridge regression** (L2 only). No feature selection. Not
+  recommended for biomarker panels.
+
+**Recommendation:** Start with `alpha = 1.0` (default). If no features pass
+stability selection, try `alpha = 0.5`.
+
+### Lambda (Regularization Strength)
+
+Selected automatically by `cv.glmnet` via inner 10-fold CV.
+
+- `lambda.min` — Lambda that minimizes CV error. Default choice.
+- `lambda.1se` — Largest lambda within 1 SE of minimum. More conservative (fewer
+  features).
+
+**Recommendation:** Use `lambda.min` (default in `run_lasso_panel`).
+
+### Stability Threshold
+
+- `0.8` (default) — Feature must be selected in ≥80% of CV iterations. Standard
+  choice.
+- `0.9` — Stringent. Very robust features only.
+- `0.6` — Relaxed. Use if few features pass 0.8 threshold.
+
+### Number of Repeats
+
+- `50` (default) — 50 random 70/30 train/test splits. Provides stable frequency
+  estimates.
+- `100` — More stable, but 2x slower. Use for final publication results.
+- `20` — Fast exploration. Adequate for initial screen.
+
+## Interpreting Results
+
+### Selection Frequency
+
+The fraction of CV iterations where a feature had a non-zero LASSO coefficient.
+
+- ≥0.8: **Highly stable** — include in panel
+- 0.5-0.8: **Moderately stable** — consider including
+- <0.5: **Unstable** — likely spurious or redundant
+
+### LASSO Coefficients
+
+- **Positive**: Higher feature value → higher probability of outcome = 1
+- **Negative**: Higher feature value → lower probability of outcome = 1
+- **Magnitude**: Relative importance (larger = more influential in prediction)
+- **CI crossing zero**: Feature's direction is uncertain (less reliable)
+
+### AUC Interpretation
+
+| AUC Range | Clinical Interpretation              |
+| --------- | ------------------------------------ |
+| 0.9-1.0   | Excellent discrimination             |
+| 0.8-0.9   | Good — clinically useful             |
+| 0.7-0.8   | Moderate — useful with other factors |
+| 0.6-0.7   | Weak — limited added value           |
+| 0.5-0.6   | Near random — not useful             |
+
+## Clinical Interpretation Quick Reference
+
+- **AUC > 0.8**: Strong discriminative ability (clinically useful)
+- **AUC 0.7-0.8**: Moderate — useful with other clinical factors
+- **AUC 0.6-0.7**: Weak but above chance — typical for baseline transcriptomic
+  prediction of treatment response
+- **Stability >= 80%**: Feature is robustly selected (high confidence in panel)
+- **Positive coefficient**: Higher expression → higher probability of positive
+  outcome
+- **Negative coefficient**: Higher expression → lower probability of positive
+  outcome
+- **Calibration**: Points near the diagonal indicate a well-calibrated model
+
+## Advanced: Nested CV vs Simple CV
+
+**Why nested CV is essential for biomarker panels:**
+
+- Simple CV (single `cv.glmnet`) optimizes lambda AND evaluates AUC on the same
+  data split → **optimistic bias**
+- Nested CV separates lambda optimization (inner) from AUC estimation (outer) →
+  **unbiased AUC**
+- The Ali et al. (Nat Med 2025) approach: 50 repetitions of 70/30 splits, each
+  with inner 10-fold cv.glmnet
+
+## Advanced: WGCNA → LASSO Cascade
+
+Following Shen et al. (Cell 2024), you can pre-filter features using WGCNA
+co-expression networks:
+
+1. Run `coexpression-network` skill to identify modules and hub genes
+2. Use hub genes (top connectivity per module) as LASSO input features
+3. This reduces thousands of genes to hundreds of biologically coherent
+   candidates
+4. LASSO then selects the minimal panel from these candidates
+
+```r
+# After running coexpression-network skill:
+hub_genes <- readRDS("coexpression_results/hub_genes.rds")
+# Use as feature filter in prepare_features.R
+expr_filtered <- expression[rownames(expression) %in% hub_genes, ]
+features <- prepare_feature_matrix(expr_filtered, metadata, outcome_col)
+```

package/data/workflows/lasso-biomarker-panel/references/validation-guide.md

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+# Multi-Cohort Validation Design Guide
+
+## Validation Hierarchy (Strongest to Weakest)
+
+1. **Independent cohort, different platform** — e.g., RNA-seq discovery →
+   microarray validation (gold standard)
+2. **Independent cohort, same platform** — different study site, same technology
+3. **Temporal split** — train on earlier samples, validate on later samples
+4. **Nested cross-validation** — internal, unbiased AUC estimation (minimum
+   acceptable)
+
+## Cross-Platform Validation
+
+When discovery and validation use different platforms (e.g., RNA-seq vs
+Affymetrix):
+
+### Gene Symbol Mapping
+
+1. Map platform-specific IDs to common gene symbols
+2. For multi-probe genes: keep probe with highest variance
+3. Intersect discovery and validation gene symbol sets
+4. Only matched features are used for validation
+
+### Expected Feature Loss
+
+- RNA-seq to Affymetrix: typically 70-85% overlap in gene symbols
+- RNA-seq to Olink proteomics: 0-5% overlap (different molecular types)
+- Same platform: 95-100% overlap
+
+### Handling Missing Panel Features
+
+If some panel features are missing in validation:
+
+- Report how many features survived mapping
+- Model still works with partial features (glmnet handles this)
+- AUC may be lower due to reduced information
+- If >50% of features missing, results should be interpreted with caution
+
+## Study Design Recommendations
+
+### Minimum Sample Sizes
+
+| Design       | Discovery | Validation | Total |
+| ------------ | --------- | ---------- | ----- |
+| Exploratory  | ≥50       | ≥30        | ≥80   |
+| Confirmatory | ≥100      | ≥50        | ≥150  |
+| Regulatory   | ≥200      | ≥100       | ≥300  |
+
+### Class Balance
+
+- Aim for ≥30% minority class in both cohorts
+- Use class-balanced sampling in CV splits (done automatically by
+  `run_lasso_panel`)
+- Severely imbalanced data (>90/10) may need SMOTE or weighted LASSO
+
+## Example: Breast Cancer Discovery → GSE32646 Validation
+
+This skill's breast cancer demo demonstrates cross-cohort, same-platform
+validation:
+
+| Property  | Discovery (GSE25055)       | Validation (GSE32646)        |
+| --------- | -------------------------- | ---------------------------- |
+| Disease   | Breast cancer              | Breast cancer                |
+| Platform  | Affymetrix U133A           | Affymetrix                   |
+| Samples   | ~218                       | ~115                         |
+| Outcome   | Basal vs Luminal A subtype | Pathologic complete response |
+| Treatment | Various chemotherapy       | Paclitaxel + FEC             |
+
+**Why this is a useful validation:**
+
+- Same platform — high gene overlap, minimal mapping loss
+- Different cohort — independent patient population
+- Related but distinct endpoint — tests generalizability of molecular features
+
+## Example: UNIFI → PURSUIT UC Validation
+
+An alternative IBD cross-drug validation design:
+
+| Property | Discovery (GSE206285)     | Validation (GSE92415)  |
+| -------- | ------------------------- | ---------------------- |
+| Disease  | Ulcerative Colitis        | Ulcerative Colitis     |
+| Platform | Affymetrix HT HG-U133+ PM | Same platform family   |
+| Samples  | ~542                      | ~87                    |
+| Outcome  | Week 8 mucosal healing    | Week 6 mucosal healing |
+| Drug     | Ustekinumab               | Golimumab              |
+
+**Why this is a strong validation:**
+
+- Different drug (anti-IL-12/23 vs anti-TNF) — tests general response biology
+- Same disease and platform — isolates drug-independent signal
+- Different trial — independent patient population
+
+## Multi-Cohort Framework
+
+Following Cruchaga/Western et al. (preprint 2024) — 6-cohort, 3,107-sample
+design:
+
+1. **Discovery cohort** — largest, most homogeneous. Train LASSO here.
+2. **Internal validation** — subset of same study. Nested CV provides this.
+3. **External validation 1** — same disease, different study.
+4. **External validation 2** — related disease (cross-disease).
+5. **External validation 3** — different platform (cross-platform).
+6. **External validation 4** — different population (cross-demographic).
+
+Each additional validation layer strengthens the evidence for clinical utility.