Claude Skills by KalarisLabs

Adds PyTorch FSDP2 (fully_shard) to training scripts with correct init, sharding, mixed precision/offload config, and distributed checkpointing. Use when models exceed single-GPU memory or when you need DTensor-based sharding with DeviceMesh.

High-level PyTorch framework with Trainer class, automatic distributed training (DDP/FSDP/DeepSpeed), callbacks system, and minimal boilerplate. Scales from laptop to supercomputer with same code. Use when you want clean training loops with built-in best practices.

Organizes PyTorch training code with the lightning package (PyTorch Lightning): LightningModule, LightningDataModule, Trainer, callbacks such as ModelCheckpoint and EarlyStopping, loggers (TensorBoard, W&B, MLflow, Comet, CSV), and multi-GPU/TPU strategies (DDP, FSDP, DeepSpeed). Use when structuring a PyTorch model into training, validation and test steps. Use when configuring a Trainer for multi-GPU or TPU runs. Use when writing a LightningDataModule for data loading. Use when adding checkp...

Provides guidance for performing causal interventions on PyTorch models using pyvene's declarative intervention framework. Use when conducting causal tracing, activation patching, interchange intervention training, or testing causal hypotheses about model behavior.

Reads and writes Zotero libraries from Python with pyzotero 1.13.0 and the Zotero Web API v3: items, collections, tags, attachments, saved searches, full-text content, and BibTeX, CSL-JSON, and bibliography export. Also covers the pyzotero CLI and MCP server for a local Zotero 7. Use when fetching or searching library items programmatically; when creating, updating, or deleting references, collections, or tags; when uploading PDF attachments or downloading files; when exporting citations as B...

High-performance vector similarity search engine for RAG and semantic search. Use when building production RAG systems requiring fast nearest neighbor search, hybrid search with filtering, or scalable vector storage with Rust-powered performance.

Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages.

Quantizes LLMs to 8-bit or 4-bit for 50-75% memory reduction with minimal accuracy loss. Use when GPU memory is limited, need to fit larger models, or want faster inference. Supports INT8, NF4, FP4 formats, QLoRA training, and 8-bit optimizers. Works with HuggingFace Transformers.

Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.

Scalable data processing for ML workloads. Streaming execution across CPU/GPU, supports Parquet/CSV/JSON/images. Integrates with Ray Train, PyTorch, TensorFlow. Scales from single machine to 100s of nodes. Use for batch inference, data preprocessing, multi-modal data loading, or distributed ETL pipelines.

Distributed training orchestration across clusters. Scales PyTorch/TensorFlow/HuggingFace from laptop to 1000s of nodes. Built-in hyperparameter tuning with Ray Tune, fault tolerance, elastic scaling. Use when training massive models across multiple machines or running distributed hyperparameter sweeps.

Guides use of RDKit (Python) for reading and writing SMILES, MOL/SDF, and InChI, computing descriptors (MW, LogP, TPSA), generating Morgan/MACCS/atom-pair fingerprints, running SMARTS substructure searches, applying reaction SMARTS, and building 2D/3D coordinates with ETKDG. Use when parsing or sanitizing molecules that fail default sanitization, calculating Tanimoto similarity or clustering compounds, filtering libraries by substructure, embedding and optimizing conformers, or computing Murc...

Plan and write responses to peer review, including journal "response to reviewers" letters for revise-and-resubmit, conference rebuttals under strict length limits (OpenReview/ICLR, NeurIPS, ICML, ACL ARR, CVPR), author responses to meta-reviews, and appeals. Use when a user receives reviews, must triage reviewer comments, draft point-by-point replies, decide what new experiments to run, disagree respectfully with a reviewer, or track manuscript changes for a revision. For authors answering r...

Move and sync reference libraries between Zotero, Mendeley, EndNote, JabRef, Paperpile and writing tools (LaTeX/BibTeX, Word, Google Docs, Pandoc, Quarto, Overleaf). Use when converting RIS, BibTeX, BibLaTeX or CSL-JSON files, migrating a library, setting up auto-exported .bib files, choosing a citation style (CSL), or fixing citations lost between tools. Includes a zero-dependency BibTeX/RIS/CSL-JSON converter.

Multivariate severity assessment and humane endpoint prediction for laboratory animal studies using the RELSA (RELative Severity Assessment) score and ARIMA-based foRcast forecasting. Use when combining welfare readouts — body weight or weight loss, body temperature, clinical or nesting scores, biomarkers, activity, heart rate, burrowing, wheel running — into one severity score per animal per day, when asking which animals are at risk of reaching a humane endpoint or when one will be reached,...

Prepare the reproducibility, transparency and open-science parts of a paper, including data and code availability statements, reproducibility checklists (NeurIPS, ICML, ICLR, ACL Responsible NLP, Nature reporting summaries), research artifact packaging (Zenodo DOI, CITATION.cff, environment lockfiles, seeds), ethics/broader-impact statements, CRediT author contributions, competing interests and AI-use disclosures. Use when a venue requires any of these statements or checklists, or when prepar...

Navigate the Research Agent Skills collection by Kalaris Labs for academia across AI, machine learning, biology, chemistry, medicine, physics, and academic writing. Use when a researcher needs to choose a field of study, identify relevant specialist SKILL.md files, or coordinate a cross-disciplinary research workflow. For a narrow task with a matching specialist skill already available, use that skill directly.

Guides writing of competitive research grant proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Covers agency-specific formatting and review criteria, specific aims, project descriptions, significance and innovation narratives, broader impacts, budgets and justifications, timelines, biosketches, and the NSTC CM03 form. Use when drafting a proposal for one of these agencies. Use when writing specific aims or broader impacts statements. Use when preparing a budget justification or milestone p...

Turn a bibliography or literature corpus into a knowledge graph of papers, authors, venues, topics and citation links, then analyze it (citation clusters, key papers, bridging work, research gaps) or export it to Neo4j, Gephi, NetworkX, Obsidian or Markdown-graph tools such as graphify. Use when mapping a research field, building a citation network, finding influential or bridging papers, or visualizing how a literature connects. Zero-dependency builder with optional OpenAlex enrichment.

Compile current scholarly evidence for a scientific manuscript or research brief. Use when the user explicitly asks to gather literature, references, background evidence, competing findings, or a manuscript research packet. Uses Parallel Search by default, Parallel Extract for source verification, Parallel Research for explicitly deep/exhaustive work, optional explicit Parallel Chat, and optional Perplexity only when requested or allowed as a failure fallback.

Create, improve and test agent skills for research workflows (paper writing, lab protocols, analysis pipelines, domain databases) that meet the Agent Skills specification and this repository's quality and security bar. Use when turning a repeated research task into a reusable skill, contributing a new skill to Research Agent Skills, rewriting an existing skill, writing trigger-accurate descriptions, or adding evals. Works alongside Anthropic's official skill-creator.

Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue docking, protein-ligand cofolding, MSA generation, molecular dynamics, permeability, descriptor workflows, and related small-molecule or protein modeling tasks. Ideal for programmatic batch screening, multi-step chemistry pipelines, and workflows that would otherwise require maintaining local HPC/GPU...

Covers the RWKV (Receptance Weighted Key Value) architecture, an RNN/Transformer hybrid with O(n) inference and no KV cache, including RWKV-7, its parallel GPT-mode training and sequential RNN-mode inference, state passing, fine-tuning with DeepSpeed, and CUDA kernel setup. Use when generating text token by token with constant memory, processing very long contexts of 100K+ tokens, fine-tuning an RWKV model, comparing RWKV memory and speed against Transformers, or debugging RWKV state handling...

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.

Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.

Prepare manuscripts for Science and the Science family of journals (Science, Science Advances, Science Translational Medicine, Science Robotics, Science Immunology, Science Signaling), covering Research Article vs Report formats, abstracts and one-sentence summaries, reference and notes style, Supplementary Materials, data/code policies, figure requirements and the initial-submission vs revision workflow. Use when targeting a Science journal, converting a manuscript to Science style, or check...

Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. Use for early-stage research brainstorming or prioritizing candidate directions; hand off empirical validation, study design, ethics or regulatory review, and clinical questions to appropriate experts or skills.

Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best for understanding evidence quality, identifying flaws. For formal peer review writing use peer-review.

Generates publication-style scientific diagrams as raster PNG images from a natural-language prompt, using Nano Banana 2 via OpenRouter, then scores each image with Gemini 3.6 Flash against a document-type threshold (journal, conference, thesis, grant, preprint, poster, etc.) and regenerates up to twice. Writes versioned PNGs and a review_log.json. Use when drawing neural network architectures, CONSORT or PRISMA flowcharts, biological signaling pathways, system or block diagrams, or circuit s...

Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.

Create and audit truthful, accessible, publication-ready scientific figures with Matplotlib, Seaborn, or Plotly. Use for figure design, multi-panel layouts, uncertainty and missing-data displays, color/contrast review, image metadata validation, and journal export planning.

Draft, revise, and audit scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission preparation when scientific accuracy and traceability matter.

Python library scikit-bio for biological sequence and community-ecology analysis: DNA/RNA/protein sequences, pair_align alignment, phylogenetic trees (NJ, UPGMA, GME/BME, Newick), alpha/beta diversity including Faith''s PD and UniFrac, PCoA/CCA/RDA ordination, PERMANOVA/ANOSIM/Mantel tests, ancom and dirmult differential abundance, BIOM tables, and FASTA/FASTQ/GenBank I/O. Use when computing microbiome diversity from a BIOM or feature table. Use when running PCoA and PERMANOVA on a distance m...

Covers classical machine learning in Python with scikit-learn (sklearn): classification and regression estimators, clustering and dimensionality reduction, preprocessing, Pipeline and ColumnTransformer, cross-validation, metrics, and GridSearchCV hyperparameter tuning. Use when training or comparing classifiers and regressors on tabular or text data, clustering data and choosing the cluster count, building leakage-free preprocessing pipelines, evaluating models with cross-validation and metri...

Builds, evaluates, and audits right-censored survival analysis workflows with scikit-survival (sksurv): Cox PH, Coxnet, IPC ridge, survival trees, forests, boosting, and SVMs, plus nonparametric cumulative incidence for competing risks. Covers leakage-safe scikit-learn pipelines, nested CV, and censoring-aware metrics. Use when fitting survival models on time-to-event data, building structured outcome arrays, computing IPCW concordance, dynamic AUC, or Brier scores, estimating cause-specific ...

Performs RNA velocity analysis with scVelo on single-cell RNA-seq AnnData objects that have spliced and unspliced layers (from velocyto, STARsolo, kallisto|bustools, or alevin-fry). Covers stochastic and dynamical velocity models, velocity graphs and embedding arrows, latent time, PAGA trajectory graphs, and driver gene ranking. Use when inferring differentiation direction from snapshot data, estimating latent time from splicing kinetics, finding driver genes of a trajectory, or adding veloci...

Trains and applies scvi-tools probabilistic deep generative models (scVI, scANVI, totalVI, MultiVI, PeakVI, DestVI, Solo, CellAssign, MrVI and others) on AnnData or MuData single-cell data using PyTorch. Covers batch correction, integration, cell type annotation, probabilistic differential expression, and scRNA-seq, ATAC-seq, CITE-seq, spatial and methylation data. Use when integrating batches or datasets with scVI, annotating cells with scANVI, jointly modeling RNA and protein or ATAC, decon...

Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and categorical comparisons with attractive defaults. Best for box plots, violin plots, pair plots, heatmaps. Built on matplotlib. For interactive plots use plotly; for publication styling use scientific-visualization.

Foundation model for image segmentation with zero-shot transfer. Use when you need to segment any object in images using points, boxes, or masks as prompts, or automatically generate all object masks in an image.

Generates sentence, text, and image embeddings locally with the Python sentence-transformers (SBERT) library, using pre-trained Hugging Face models such as all-MiniLM-L6-v2, all-mpnet-base-v2, and multilingual variants. Covers encoding, cosine similarity, semantic search, batch encoding, fine-tuning, and LangChain/LlamaIndex integration. Use when building embeddings for RAG, running semantic search or similarity scoring, clustering or classifying text, embedding multilingual text without an A...

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.

Serves LLMs with high throughput using vLLM's PagedAttention and continuous batching. Use when deploying production LLM APIs, optimizing inference latency/throughput, or serving models with limited GPU memory. Supports OpenAI-compatible endpoints, quantization (GPTQ/AWQ/FP8), and tensor parallelism.

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.

Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producing local or global SHAP visualizations.

Simple Preference Optimization for LLM alignment. Reference-free alternative to DPO with better performance (+6.4 points on AlpacaEval 2.0). No reference model needed, more efficient than DPO. Use for preference alignment when want simpler, faster training than DPO/PPO.

Builds, tests, and analyzes bounded process-based discrete-event simulations in Python with SimPy 4.1.2: Environment, Timeout, Process, AnyOf/AllOf conditions, interrupts, Resource, PriorityResource, PreemptiveResource, Container, Store, time-weighted monitoring, and replication-based output analysis, plus bundled safe CLIs. Use when modeling queues, production lines, logistics, or service operations with generator processes; when contending entities need shared resources or preemption; when ...

Multi-cloud orchestration for ML workloads with automatic cost optimization. Use when you need to run training or batch jobs across multiple clouds, leverage spot instances with auto-recovery, or optimize GPU costs across providers.

Provides guidance for LLM post-training with RL using slime, a Megatron+SGLang framework. Use when training GLM models, implementing custom data generation workflows, or needing tight Megatron-LM integration for RL scaling.

Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.

Accelerate LLM inference using speculative decoding, Medusa multiple heads, and lookahead decoding techniques. Use when optimizing inference speed (1.5-3.6× speedup), reducing latency for real-time applications, or deploying models with limited compute. Covers draft models, tree-based attention, Jacobi iteration, parallel token generation, and production deployment strategies.