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High-performance reinforcement learning framework optimized for speed and scale. Use when you need fast parallel training, vectorized environments, multi-agent systems, or integration with game environments (Atari, Procgen, NetHack). Achieves 2-10x speedups over standard implementations. For quick prototyping or standard algorithm implementations with extensive documentation, use stable-baselines3 instead.

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Parameter-efficient fine-tuning for LLMs using LoRA, QLoRA, and 25+ methods. Use when fine-tuning large models (7B-70B) with limited GPU memory, when you need to train <1% of parameters with minimal accuracy loss, or for multi-adapter serving. HuggingFace's official library integrated with transformers ecosystem.

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Post-training 4-bit quantization for LLMs with minimal accuracy loss. Use for deploying large models (70B, 405B) on consumer GPUs, when you need 4× memory reduction with <2% perplexity degradation, or for faster inference (3-4× speedup) vs FP16. Integrates with transformers and PEFT for QLoRA fine-tuning.

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Bayesian parameter estimation with MCMC (emcee) and probabilistic programming (PyMC). Posterior distributions, corner plots, model evidence, convergence diagnostics. Use when you need full posterior distributions, not just point estimates.

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Publication-quality physics plots — vector fields, streamlines, contour maps, 3D surfaces, phase space, spectrograms, and animations. Optimized for journal submission with LaTeX labels, proper colormaps, and multi-panel layouts.

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Train neural operators (FNO, DeepONet) to learn solution maps for parametric PDE families. Once trained, solve new PDE instances in milliseconds. Use when you need to solve many instances of the same PDE with different parameters/ICs/BCs.

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Fast structured generation and serving for LLMs with RadixAttention prefix caching. Use for JSON/regex outputs, constrained decoding, agentic workflows with tool calls, or when you need 5× faster inference than vLLM with prefix sharing. Powers 300,000+ GPUs at xAI, AMD, NVIDIA, and LinkedIn.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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Activation-aware weight quantization for 4-bit LLM compression with 3x speedup and minimal accuracy loss. Use when deploying large models (7B-70B) on limited GPU memory, when you need faster inference than GPTQ with better accuracy preservation, or for instruction-tuned and multimodal models. MLSys 2024 Best Paper Award winner.

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Patterns for loading PDE simulation datasets (PDEBench, PhiFlow, JAX-CFD) from HDF5 files. Handles layout detection (single tensor vs separate variables), spatial/temporal downsampling, multi-variable systems, HuggingFace and DaRUS data sources, and efficient PyTorch DataLoader creation. Use when preparing PDE data for neural operator training.

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Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.

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Optimizes LLM inference with NVIDIA TensorRT for maximum throughput and lowest latency. Use for production deployment on NVIDIA GPUs (A100/H100), when you need 10-100x faster inference than PyTorch, or for serving models with quantization (FP8/INT4), in-flight batching, and multi-GPU scaling.

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Facebook's library for efficient similarity search and clustering of dense vectors. Supports billions of vectors, GPU acceleration, and various index types (Flat, IVF, HNSW). Use for fast k-NN search, large-scale vector retrieval, or when you need pure similarity search without metadata. Best for high-performance applications.

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Language-independent tokenizer treating text as raw Unicode. Supports BPE and Unigram algorithms. Fast (50k sentences/sec), lightweight (6MB memory), deterministic vocabulary. Used by T5, ALBERT, XLNet, mBART. Train on raw text without pre-tokenization. Use when you need multilingual support, CJK languages, or reproducible tokenization.

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Generate the success criteria for a task or question, then review work against them. Given a task, goal, or open-ended question, decompose it into scenarios, evaluation perspectives, and fine-grained weighted YES/NO criteria using the Recursive Expansion Tree (RET) method; if work is supplied, score it criterion-by-criterion and surface what is missing or could be better. Use when asked to self-review or check your own work, judge whether a task is done well or completely, build a definition-of-done or completeness checklist, create an evaluation rubric or grading criteria, score or grade answers to a question, set up an LLM-as-judge rubric, or when the user mentions self-review, completeness check, success criteria, evaluation criteria, scoring rubric, Qworld, or the RET algorithm.

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ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.

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Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference. Best for econometrics, time series, rigorous inference with coefficient tables. For guided statistical test selection with APA reporting use statistical-analysis.

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Enzyme kinetics — Michaelis-Menten Km, Vmax, kcat (turnover), and kcat/Km (catalytic efficiency / specificity constant) from substrate-velocity data, plus inhibition-mechanism analysis (competitive / uncompetitive / non-competitive, Ki). Fits the MM equation by nonlinear regression (and reports Lineweaver-Burk for reference). Use when you have substrate concentrations and initial reaction velocities and need kinetic parameters or to classify an inhibitor. NOT for BRENDA database lookups of published constants (use the BRENDA tools).

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Pharmacokinetic (PK) analysis of concentration-time data — non-compartmental analysis (NCA) for Cmax, Tmax, AUC (0-t and 0-∞), terminal half-life, clearance (CL), volume of distribution (Vd), MRT, and absolute bioavailability (F). Also one-compartment fitting. Use when you have plasma/serum drug concentrations over time after a dose and need PK parameters, or to compute bioavailability from IV + oral AUCs. NOT for ADMET property prediction from structure (use tooluniverse-admet-prediction).

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Dose-response / concentration-response curve fitting — IC50, EC50, Hill slope, Emax/Emin efficacy, and relative potency from paired concentration vs response data (enzyme/cell assays, drug screening, agonist/antagonist pharmacology). Fits the 4-parameter logistic (Hill sigmoidal) model. Use when you have concentrations + responses and need a potency value, to compare two compounds' potency, or to judge curve quality. NOT for image-derived dose-response (use tooluniverse-image-analysis) and NOT for survival/regression (use tooluniverse-statistical-modeling).

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Drug-combination synergy analysis — quantify whether two drugs together are synergistic, additive, or antagonistic using the standard reference models (Bliss independence, HSA / highest single agent, Loewe additivity, ZIP, and the Chou-Talalay Combination Index). Use when you have measured single-drug and combination effects (inhibition/viability) and need a synergy score. Explains which model to use, what data each one needs, and how to read the score. NOT for looking up pre-computed synergy in a database (use the SYNERGxDB tool / cell-line-profiling skill).

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PyTorch library for audio generation including text-to-music (MusicGen) and text-to-sound (AudioGen). Use when you need to generate music from text descriptions, create sound effects, or perform melody-conditioned music generation.

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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.

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Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis). Combines literature insights with data-driven hypothesis testing. For manual hypothesis formulation use hypothesis-generation; for creative ideation use scientific-brainstorming.

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