Machine Learning Skills

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

Comprehensive toolkit for developing with the CocoIndex library. Use when users need to create data transformation pipelines (flows), write custom functions, or operate flows via CLI or API. Covers building ETL workflows for AI data processing, including embedding documents into vector databases, building knowledge graphs, creating search indexes, or processing data streams with incremental updates.

| Query the Sequence Read Archive (SRA), retrieve scientific publications, and analyze genomics metadata using the SRAgent toolkit. Supports accession conversion (GSE→SRX→SRR), BigQuery metadata queries, manuscript downloads from multiple sources, and scRNA-seq technology identification. Use when working with SRA/GEO datasets, finding publications, or analyzing single-cell sequencing experiments.

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

Quantum computing framework for building, simulating, optimizing, and executing quantum circuits. Use this skill when working with quantum algorithms, quantum circuit design, quantum simulation (noiseless or noisy), running on quantum hardware (Google, IonQ, AQT, Pasqal), circuit optimization and compilation, noise modeling and characterization, or quantum experiments and benchmarking (VQE, QAOA, QPE, randomized benchmarking).

Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.

Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

Neuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess, motion correction, Kilosort4 spike sorting, quality metrics, Allen/IBL curation, AI-assisted visual analysis, for Neuropixels 1.0/2.0 extracellular electrophysiology. Use when working with neural recordings, spike sorting, extracellular electrophysiology, or when the user mentions Neuropixels, SpikeGLX, Open Ephys, Kilosort, quality metrics, or unit curation.

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

Guides security professionals in implementing defense-in-depth security architectures, achieving compliance with industry frameworks (SOC2, ISO27001, GDPR, HIPAA), conducting threat modeling and risk assessments, managing security operations and incident response, and embedding security throughout the SDLC.

Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.

Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.

將提示詞和程式碼從 Claude Sonnet 4.0、Sonnet 4.5 或 Opus 4.1 遷移至 Opus 4.5。當使用者想要更新其程式碼庫、提示詞或 API 呼叫以使用 Opus 4.5 時使用。處理模型字串更新和針對已知 Opus 4.5 行為差異的提示詞調整。不會遷移 Haiku 4.5。

Create and train AI learning plugins with AgentDB's 9 reinforcement learning algorithms. Includes Decision Transformer, Q-Learning, SARSA, Actor-Critic, and more. Use when building self-learning agents, implementing RL, or optimizing agent behavior through experience.

Train AI agents using AgentDB's 9 reinforcement learning algorithms including Q-Learning, DQN, PPO, and Actor-Critic. Build self-learning agents, implement RL training loops with experience replay, and deploy optimized models to production.

Build semantic vector search systems with AgentDB for intelligent document retrieval, RAG applications, and knowledge bases using embedding-based similarity matching

Implement semantic vector search with AgentDB for intelligent document retrieval, similarity matching, and context-aware querying. Use when building RAG systems, semantic search engines, or intelligent knowledge bases.

Automated coordination, formatting, and learning from Claude Code operations using intelligent hooks with MCP integration. Includes pre/post task hooks, session management, Git integration, memory coordination, and neural pattern training for enhanced development workflows.

Implement machine learning solutions including model architectures, training pipelines, optimization strategies, and performance improvements. This skill spawns a specialist ML implementation agent...

Diagnose machine learning training failures including loss divergence, mode collapse, gradient issues, architecture problems, and optimization failures. This skill spawns a specialist ML debugging ...

Implement ReasoningBank adaptive learning with AgentDB's 150x faster vector database. Includes trajectory tracking, verdict judgment, memory distillation, and pattern recognition. Use when building self-learning agents, optimizing decision-making, or implementing experience replay systems.

Debug ML training issues and optimize performance including loss divergence, overfitting, and slow convergence

Specialized ML model development, training, and deployment workflow

This SOP provides a systematic workflow for training and deploying neural networks using Flow Nexus platform with distributed E2B sandboxes. It covers architecture selection, distributed training, ...

Prevents 30+ critical AI/ML mistakes including data leakage, evaluation errors, training pitfalls, and deployment issues. Use when working with ML training, testing, model evaluation, or deployment.

Use Tavily Search API for optimized, real-time web search results for RAG. A pre-configured, cost-effective search tool.

Guide for benchmarking FlashInfer kernels with CUPTI timing

Web search and content extraction with Tavily and Exa via inference.sh CLI. Apps: Tavily Search, Tavily Extract, Exa Search, Exa Answer, Exa Extract. Capabilities: AI-powered search, content extraction, direct answers, research. Use for: research, RAG pipelines, fact-checking, content aggregation, agents. Triggers: web search, tavily, exa, search api, content extraction, research, internet search, ai search, search assistant, web scraping, rag, perplexity alternative

Build RAG (Retrieval Augmented Generation) pipelines with web search and LLMs. Tools: Tavily Search, Exa Search, Exa Answer, Claude, GPT-4, Gemini via OpenRouter. Capabilities: research, fact-checking, grounded responses, knowledge retrieval. Use for: AI agents, research assistants, fact-checkers, knowledge bases. Triggers: rag, retrieval augmented generation, grounded ai, search and answer, research agent, fact checking, knowledge retrieval, ai research, search + llm, web grounded, perplexity alternative, ai with sources, citation, research pipeline

Web search and content extraction with Tavily and Exa via inference.sh CLI. Apps: Tavily Search, Tavily Extract, Exa Search, Exa Answer, Exa Extract. Capabilities: AI-powered search, content extraction, direct answers, research. Use for: research, RAG pipelines, fact-checking, content aggregation, agents. Triggers: web search, tavily, exa, search api, content extraction, research, internet search, ai search, search assistant, web scraping, rag, perplexity alternative

| Build RAG (Retrieval Augmented Generation) pipelines with web search and LLMs. research agent, fact checking, knowledge retrieval, ai research, search + llm, web grounded, perplexity alternative, ai with sources, citation, research pipeline

| Run 150+ AI apps via inference.sh CLI - image generation, video creation, LLMs, search, 3D, Twitter automation. Use when running AI apps, generating images/videos, calling LLMs, web search, or automating Twitter. image generation, video generation, openrouter, tavily, exa search, twitter api, grok

| Automate Twitter/X with posting, engagement, and user management via inference.sh CLI. social media automation, x automation, tweet scheduler, twitter integration, post tweet, twitter post, x post, send tweet

| Web search and content extraction with Tavily and Exa via inference.sh CLI. internet search, ai search, search assistant, web scraping, rag, perplexity alternative

Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

Comprehensive Mastra framework guide. Teaches how to find current documentation, verify API signatures, and build agents and workflows. Covers documentation lookup strategies (embedded docs, remote docs), core concepts (agents vs workflows, tools, memory, RAG), TypeScript requirements, and common patterns. Use this skill for all Mastra development to ensure you're using current APIs from the installed version or latest documentation.

Testing and benchmarking LLM agents including behavioral testing, capability assessment, reliability metrics, and production monitoring—where even top agents achieve less than 50% on real-world benchmarks Use when: agent testing, agent evaluation, benchmark agents, agent reliability, test agent.

Build production-ready LLM applications, advanced RAG systems, and intelligent agents. Implements vector search, multimodal AI, agent orchestration, and enterprise AI integrations. Use PROACTIVELY for LLM features, chatbots, AI agents, or AI-powered applications.

Every product will be AI-powered. The question is whether you'll build it right or ship a demo that falls apart in production. This skill covers LLM integration patterns, RAG architecture, prompt engineering that scales, AI UX that users trust, and cost optimization that doesn't bankrupt you. Use when: keywords, file_patterns, code_patterns.

Select and optimize embedding models for semantic search and RAG applications. Use when choosing embedding models, implementing chunking strategies, or optimizing embedding quality for specific domains.

Execute Hugging Face Hub operations using the `hf` CLI. Use when the user needs to download models/datasets/spaces, upload files to Hub repositories, create repos, manage local cache, or run compute jobs on HF infrastructure. Covers authentication, file transfers, repository creation, cache operations, and cloud compute.

This skill should be used when users want to run any workload on Hugging Face Jobs infrastructure. Covers UV scripts, Docker-based jobs, hardware selection, cost estimation, authentication with tokens, secrets management, timeout configuration, and result persistence. Designed for general-purpose compute workloads including data processing, inference, experiments, batch jobs, and any Python-based tasks. Should be invoked for tasks involving cloud compute, GPU workloads, or when users mention running jobs on Hugging Face infrastructure without local setup.