engineering/advanced-ml-engineering/skills/ml-theory/SKILL.md
This skill should be used when the user asks about "loss functions", "gradient descent", "backpropagation", "vanishing gradients", "regularization", "bias-variance tradeoff", "statistical learning theory", "PAC learning", "VC dimension", "overfitting", "underfitting", "cross-entropy loss", "KL divergence", "ELBO", "maximum likelihood estimation", "Bayesian inference", or any foundational mathematical concepts underlying machine learning models and optimization.
npx skillsauth add harsh040506/claude-code-unified-skill-plugin-library ml-theoryInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
3 of 9 scanners reported clean
Some scanners were skipped, did not run, or reported a non-clean status. Review each row below.
Provides the rigorous mathematical theory underlying all machine learning components in this plugin. Covers loss function derivation, optimization dynamics, and statistical learning guarantees that inform architectural and training decisions.
Loss functions define what a model is optimizing. The choice of loss encodes all assumptions about the output distribution:
See references/loss-functions.md for complete derivations and PyTorch implementations.
All training is an instance of empirical risk minimization: find θ* = argmin_θ (1/n) Σ L(f_θ(xᵢ), yᵢ).
Key optimization concepts:
See references/optimization-theory.md for convergence proofs, saddle point analysis, and loss landscape geometry.
Theory that bounds generalization error — the gap between training loss and test loss:
See references/statistical-learning.md for formal bounds, regularization theory, and empirical verification methods.
Apply ML theory concepts when:
| Symbol | Meaning | |---|---| | θ | Model parameters | | η | Learning rate | | L(·) | Loss function | | f_θ(x) | Model prediction | | μ, σ | Mean, standard deviation | | ∇_θ | Gradient with respect to θ | | ᾱ_t | Cumulative noise schedule product (diffusion) | | γ | Discount factor (RL) |
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.