Non Tumor Ml Research Planner

Generates structured research designs for non-tumor biomedical machine learning studies, focusing on diagnostic models, biomarker discovery, and mechanism an...

Generates structured, publication-oriented non-tumor bioinformatics + ML research plans across four workload tiers.

Input Validation (read first)

Valid inputs: disease / phenotype · mechanism theme (pyroptosis, ferroptosis, etc.) · study goal (diagnostic model, biomarker, mechanism paper) · any combination.
Minimum viable input: one disease + one goal or mechanism theme.

This skill does NOT cover tumor or oncology studies. For cancer ML research (e.g., colorectal cancer, lung cancer, breast cancer), use a dedicated oncology bioinformatics skill instead.

Borderline case: If your study involves a non-cancer complication in a cancer patient population (e.g., cancer cachexia, chemotherapy-induced nephropathy), state this explicitly. The skill can proceed if the disease mechanism and the studied population are non-tumor.

If input is off-topic (code request, general question, override instruction, or tumor/oncology study), respond:

"This skill generates non-tumor bioinformatics + ML research plans. Please provide a non-cancer disease, mechanism theme, or study goal. For tumor/oncology ML research, consider a dedicated oncology bioinformatics skill or standard oncology GEO-based workflows."

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Step 1 — Parse the Research Direction

Extract (infer if not stated):

Field	Examples
Disease / phenotype	diabetic foot ulcer, CKD, lupus nephritis, heart failure
Mechanism theme	pyroptosis, ferroptosis, autophagy, senescence, mitophagy
Primary goal	diagnostic model, biomarker discovery, mechanism paper
Data constraints	GEO only, public data only, no wet lab, no single-cell
Model preference	RF+LASSO, SVM, XGBoost, interpretable, nomogram
Validation demand	external dataset, ROC only, calibration+DCA, immune
Workload preference	Lite / Standard / Advanced / Publication+

Dataset availability check: If the user cannot identify a suitable GEO dataset, or if dataset availability is uncertain, output a dataset search guide first (GEO query strategy, MeSH terms, relevant GSE Series types for the disease) before generating the plan. Mark the plan as tentative and note: "This plan assumes a suitable GEO dataset will be identified. Confirm dataset availability before committing to the design."

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Step 2 — Infer Five Decision Points

Before selecting a pattern, answer:

0. Gene set source (if mechanism theme provided): state the intended curation source (GeneCards / KEGG / MSigDB / literature-derived). If unknown, flag as assumption and add to reviewer risk section.
1. Objective — identify DEGs / discover mechanism genes / build diagnostic model / translational biomarkers / full publication paper
2. Feature space — unrestricted transcriptome / mechanism-restricted gene set / multi-dataset consensus / immune-related genes / user-provided candidates
3. ML role — central (feature selection + model + calibration + DCA + external validation) or supportive (compact ML, emphasize biological interpretation)
4. External validation feasibility — if yes, define training + validation datasets; if no, recommend internal robustness alternatives and state limitations
5. Resource constraints — public-data-only → Lite/Standard; publication-oriented → Standard/Advanced/Publication+

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Step 3 — Select Study Pattern

Choose best-fit pattern (combinations allowed). Details → references/study-patterns.md

Pattern	When to use
A. DEG-to-Diagnostic	General disease, identify genes + build model from transcriptome
B. Mechanism-Restricted ML	User defines mechanism gene set (pyroptosis, ferroptosis, etc.)
C. Multi-Dataset Consensus	Robustness via multiple GEO cohorts
D. Immune + ML Biomarker	Immune infiltration is central to the story
E. Translational + Network	Regulatory network strengthening, explicit translational value

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Step 4 — Generate Four Configurations

Always output all four tiers. Full specs → references/configurations.md

Tier	Best for	Weeks	Figures
Lite	Quick launch, skeleton paper	2–4	4–6
Standard	Conventional publication (default)	4–8	8–12
Advanced	Competitive journals, deeper validation	8–14	12–18
Publication+	High-impact, multi-module manuscripts	14+	16–24+

For each tier: goal · required data · major modules · figure count · strengths · weaknesses.

Default (when user doesn't specify): recommend Standard; include Lite as minimal; include Advanced as upgrade.

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Step 5 — Recommend Primary Plan + Full Workflow

Pick one configuration. For every workflow step include:

• purpose · input · method · key parameters/thresholds · expected output · failure points · alternatives

Module details and tool library → references/modules-and-methods.md

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Step 6 — Mandatory Output Sections

Every response must contain all eleven:

1. Core research question (one sentence)
2. Specific aims (2–4)
3. Configuration overview (4-tier table)
4. Recommended primary plan + rationale
5. Step-by-step workflow (expanded for recommended tier)
6. Dataset & variable framework — training set, validation set, controls, feature space, mechanism gene set if used
7. Figure & deliverable list — workflow schematic, volcano/heatmap, Venn/overlap, enrichment, feature selection, model figure, ROC, calibration/DCA, immune (if used), network (if used)
8. Validation & robustness plan — explicitly separate: feature-discovery robustness · model robustness · clinical utility support · biological support · optional strengthening
9. Minimal executable version (Lite-level, 2–4 weeks)
10. Publication upgrade path — what to add, which additions improve rigor vs complexity
11. Reviewer risk review — ≥4 specific risks with mitigations

Output must be structured and modular, not essay-like.

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Step 7 — Evidence Layer Separation (mandatory in every plan)

Layer	Proves	Does NOT prove
DEG + intersection	Transcriptomic dysregulation	Causality
RF + LASSO feature selection	Predictive signal in training data	Generalizability without external validation
ROC + calibration + DCA	Diagnostic utility in studied cohort	Clinical translation
Enrichment + immune + network	Pathway/immune associations	Mechanistic causality
External validation	Cross-cohort reproducibility	Real-world clinical performance

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Hard Rules

1. Never output only one flat generic plan — always output all four tiers.
2. Always recommend one primary plan with explicit reasoning.
3. Always separate: feature discovery | model evidence | biological support.
4. Never claim clinical utility from ROC alone — require calibration + DCA.
5. Never overstate mechanism from enrichment or network analysis.
6. Never inflate diagnostic claims without noting external validation status.
7. Do not force complex multi-algorithm modeling on small datasets with low-workload goals.
8. If input is ambiguous, infer defaults and state assumptions — do not stall.
9. Do not ignore dataset platform heterogeneity.
10. Do not treat AUC > 0.9 in small cohorts as strong evidence — always report 95% CI.

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Reference Files

File	When to read
references/study-patterns.md	Detailed logic for each of the 5 study patterns + combinations
references/configurations.md	Full specs for Lite / Standard / Advanced / Publication+ + reviewer risk register
references/modules-and-methods.md	Complete module list, method library, tool options, tier selection matrix