engineering/advanced-ml-engineering/skills/hyperparameter-optimization/SKILL.md
This skill should be used when the user asks about "hyperparameter tuning", "HPO", "Bayesian optimization", "Gaussian process", "acquisition function", "Expected Improvement", "Upper Confidence Bound", "Hyperband", "ASHA", "Optuna", "Ray Tune", "learning rate search", "grid search", "random search", "hyperparameter importance", "fANOVA", or when a model's validation loss is suboptimal and systematic tuning is needed.
npx skillsauth add harsh040506/claude-code-unified-skill-plugin-library hyperparameter-optimizationInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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Provides methodology for finding optimal hyperparameter configurations λ* in high-dimensional spaces using Gaussian Process surrogate modeling, acquisition function optimization, and compute-efficient pruning strategies.
For d ≥ 3 hyperparameters and a budget of < 200 trials, Bayesian optimization typically requires 5–10× fewer trials than random search to reach the same optimum.
The surrogate model f̂(λ) ~ GP(μ(λ), k(λ, λ')) encodes:
Kernel selection:
After n trials, the GP posterior provides: expected value μ_n(λ) and uncertainty σ_n(λ) at any new point λ.
See references/acquisition-functions.md for mathematical derivations.
Summary:
Hyperband extends SHA (Successive Halving Algorithm) to handle unknown budget:
ASHA (Asynchronous SHA): runs brackets in parallel without synchronization barriers — better GPU utilization.
Hyperband reduces wasted compute by 3–10× vs. running all trials to completion.
After HPO, estimate which hyperparameters most influence the objective using fANOVA:
See references/bayesian-optimization.md for full GP formulation, implementation details, and Optuna/Ray Tune integration patterns.
testing
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or following scverse/scanpy best practices for single-cell analysis.
tools
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers include mentions of scVI, scANVI, totalVI, PeakVI, MultiVI, DestVI, veloVI, sysVI, scArches, variational autoencoder, VAE, batch correction, data integration, multi-modal, CITE-seq, multiome, reference mapping, latent space.
testing
This skill should be used when scientists need help with research problem selection, project ideation, troubleshooting stuck projects, or strategic scientific decisions. Use this skill when users ask to pitch a new research idea, work through a project problem, evaluate project risks, plan research strategy, navigate decision trees, or get help choosing what scientific problem to work on. Typical requests include "I have an idea for a project", "I'm stuck on my research", "help me evaluate this project", "what should I work on", or "I need strategic advice about my research".
development
Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.