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Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

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Universal LaTeX document skill: create, compile, and convert any document to professional PDF with PNG previews. Supports resumes, reports, cover letters, invoices, academic papers, theses/dissertations, academic CVs, presentations (Beamer), scientific posters, formal letters, exams/quizzes, books, cheat sheets, reference cards, exam formula sheets, fillable PDF forms (hyperref form fields), conditional content (etoolbox toggles), mail merge from CSV/JSON (Jinja2 templates), version diffing (latexdiff), charts (pgfplots + matplotlib), tables (booktabs + CSV import), images (TikZ), Mermaid diagrams, AI-generated images, watermarks, landscape pages, bibliography/citations (BibTeX/biblatex), multi-language/CJK (auto XeLaTeX), algorithms/pseudocode, colored boxes (tcolorbox), SI units (siunitx), Pandoc format conversion (Markdown/DOCX/HTML ↔ LaTeX), and PDF-to-LaTeX conversion of handwritten or printed documents (math, business, legal, general). Compile script supports pdflatex, xelatex, lualatex with auto-detection, latexmk backend, texfot log filtering, PDF/A output, and verbosity control (--verbose/--quiet). Empirically optimized scaling: single agent 1-10 pages, split 11-20, batch-7 pipeline 21+. Use when user asks to: (1) create a resume/CV/cover letter, (2) write a LaTeX document, (3) create PDF with tables/charts/images, (4) compile a .tex file, (5) make a report/invoice/presentation, (6) anything involving LaTeX or pdflatex, (7) convert/OCR a PDF to LaTeX, (8) convert handwritten notes, (9) create charts/graphs/diagrams, (10) create slides, (11) write a thesis or dissertation, (12) create an academic CV, (13) create a poster, (14) create an exam/quiz, (15) create a book, (16) convert between document formats (Markdown, DOCX, HTML to/from LaTeX), (17) generate Mermaid diagrams for LaTeX, (18) create a formal business letter, (19) create a cheat sheet or reference card, (20) create an exam formula sheet or crib sheet, (21) condense lecture notes/PDFs into a cheat sheet, (22) create a fillable PDF form with text fields/checkboxes/dropdowns, (23) create a document with conditional content/toggles (show/hide sections), (24) generate batch/mail-merge documents from CSV/JSON data, (25) create a version diff PDF (latexdiff) highlighting changes between documents, (26) create a homework or assignment submission with problems and solutions, (27) create a lab report with data tables, graphs, and error analysis, (28) encrypt or password-protect a PDF, (29) merge multiple PDFs into one, (30) optimize/compress a PDF for web or email, (31) lint or check a LaTeX document for common issues, (32) count words in a LaTeX document, (33) analyze document statistics (figures, tables, citations), (34) fetch BibTeX from a DOI, (35) convert a Graphviz .dot file to PDF/PNG, (36) convert a PlantUML .puml file to PDF/PNG, (37) create a one-pager/fact sheet/executive summary, (38) create a datasheet or product specification sheet, (39) extract pages from a PDF (page ranges, odd/even), (40) check LaTeX package availability before compiling, (41) analyze citations and cross-reference with .bib files, (42) debug LaTeX compilation errors, (43) make a document accessible (PDF/A, tagged PDF), (44) create lecture notes or course handouts, (45) fill an existing PDF form (fillable fields or non-fillable with annotations), (46) extract text or tables from a PDF (pdfplumber, pypdf), (47) OCR a scanned PDF to text (pytesseract), (48) create a PDF programmatically with reportlab (Canvas, Platypus), (49) rotate or crop PDF pages (pypdf), (50) add a watermark to an existing PDF, (51) extract metadata from a PDF (title, author, subject).

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SQL and NoSQL query optimization techniques, indexing strategies, execution plan analysis, JOIN algorithms, cardinality estimation, and database-specific query patterns

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Embedding strategies, ANN algorithms, hybrid search, RAG chunking strategies, and reranking for semantic search and retrieval.

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Design, implement, debug, and review industrial recommendation-system architecture or algorithms using released PDFs, curated examples, and runnable templates.

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Design, implement, debug, and review industrial recommendation-system architecture or algorithms using the released book PDFs, curated examples, and runnable templates.

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Use when you need to apply Java secure coding best practices — including validating untrusted inputs, defending against injection attacks with parameterized queries, minimizing attack surface via least privilege, applying strong cryptographic algorithms, handling exceptions securely without exposing sensitive data, managing secrets at runtime, avoiding unsafe deserialization, and encoding output to prevent XSS. This should trigger for requests such as Review Java code for secure coding; Find input validation risks in Java code; Review Java code for injection vulnerabilities; Improve secure error handling in Java services; Harden Java code against common security flaws. Part of Plinth Toolkit

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Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating synthetic networks, or visualizing network topologies. Applicable to social networks, biological networks, transportation systems, citation networks, and any domain involving pairwise relationships.

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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).

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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.

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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.

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Diagnose, fix, and improve IEEEtran LaTeX manuscripts using routed template, layout, float, equation, algorithm, table, bibliography, and PDF-compliance guidance. Use when fixing IEEE LaTeX compile errors, overfull boxes, float placement, two-column layout, figure sizing, tables, equations, algorithms, BibTeX, citation commands, template compliance, or final submission PDF checks.

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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.

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Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.

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PyTorch Geometric (PyG) for graph neural networks: node/graph classification, link prediction with GCN, GAT, GraphSAGE, GIN. Message passing, mini-batches, heterogeneous graphs, neighbor sampling, explainability. Supports molecules (QM9, MoleculeNet), social/knowledge graphs, 3D point clouds. For non-graph DL use PyTorch; for classical graph algorithms use NetworkX.

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Python framework for single- and multi-objective optimization with evolutionary algorithms. Define vectorized objectives and constraints; solve with NSGA-II, NSGA-III, MOEA/D, GAs, or differential evolution. Analyze Pareto fronts, visualize trade-offs, customize operators and callbacks. For engineering design, hyperparameter search, and conflicting objectives. Alternatives: scipy.optimize (single-objective, gradient), platypus, jMetalPy (Java).

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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.

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Detects time and space complexity hotspots via AST scan. Use when code feels slow, before performance-sensitive merges, or to find O(n²) regressions.

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Improves code quality across duplication, efficiency, and architectural fit. Use when code passes tests but quality is poor or before a major release.

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Use IBM AI Fairness 360 for tabular fairness datasets, metrics, bias mitigation algorithms, sklearn-compatible workflows, subgroup detectors, and explainers.

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Algorithmic philosophies are computational aesthetic movements that are then expressed through code. Output .md files (philosophy), .html files (interactive viewer), and .js files (generative algorithms).

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Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.

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Extract language-agnostic pseudocode from formally verified programs (Isabelle/HOL, Coq) while preserving verified control flow, data dependencies, and algorithmic logic. Use when: (1) Users have verified code and need readable pseudocode, (2) Documenting verified algorithms for broader audiences, (3) Translating verified implementations to other languages, (4) Creating algorithm specifications from verified code, (5) Preserving verification guarantees in pseudocode form, or (6) Abstracting proof-heavy code to essential logic. Maintains semantic faithfulness to verified implementation.

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Generate implementation code and tests from written specifications. Use when the user provides specifications (natural language descriptions, formal specs, requirements documents, API specs) and asks Claude to implement the described functionality. Supports data structures, algorithms, classes, functions, and includes automatic test generation to validate implementation against specification.

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