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lingzhi227Skilllingzhi227/agent-research-skills/skills/algorithm-design/SKILL.md
Design algorithms with LaTeX pseudocode and UML diagrams. Generate algorithmic environments, Mermaid class/sequence diagrams, and ensure consistency between pseudocode and implementation. Use when formalizing methods for a paper.
lingzhi227Skilllingzhi227/agent-research-skills/skills/atomic-decomposition/SKILL.md
Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping. For each concept, extract the math formula from papers and find code implementations. Use for complex system papers requiring formal grounding.
lingzhi227Skilllingzhi227/agent-research-skills/skills/backward-traceability/SKILL.md
Make every number in the final PDF traceable to the exact code line that produced it. Uses \hypertarget/\hyperlink LaTeX commands and \num{formula} evaluated at compile time. Use for reproducibility and data integrity verification.
lingzhi227Skilllingzhi227/agent-research-skills/skills/citation-management/SKILL.md
Manage BibTeX citations for LaTeX papers. Harvest missing citations from a draft using Semantic Scholar, validate cite keys against .bib files, deduplicate entries, and format bibliography. Use when working with references, BibTeX, or citations.
Often used withvenue-templatesstatistical-analysisscientific-critical-thinking
lingzhi227Skilllingzhi227/agent-research-skills/skills/code-debugging/SKILL.md
Debug experiment code with structured error analysis. Categorize errors, apply targeted fixes with retry logic, and use reflection to prevent recurring issues. Use when experiment code fails or produces incorrect results.
lingzhi227Skilllingzhi227/agent-research-skills/skills/data-analysis/SKILL.md
Generate statistical analysis code with 4-round review. Select appropriate statistical tests, interpret results, and produce analysis reports with p-values, effect sizes, and confidence intervals. Use when analyzing experimental data for a paper.
lingzhi227Skilllingzhi227/agent-research-skills/skills/deep-research/SKILL.md
Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Output is organized by phase for clarity.
Often used withcommunity-led-growthacademic-paper-revieweracademic-pipeline
lingzhi227Skilllingzhi227/agent-research-skills/skills/excalidraw-skill/SKILL.md
Programmatic canvas toolkit for creating, editing, and refining Excalidraw diagrams via MCP tools with real-time canvas sync. Use when an agent needs to (1) draw or lay out diagrams on a live canvas, (2) iteratively refine diagrams using describe_scene and get_canvas_screenshot to see its own work, (3) export/import .excalidraw files or PNG/SVG images, (4) save/restore canvas snapshots, (5) convert Mermaid to Excalidraw, or (6) perform element-level CRUD, alignment, distribution, grouping, duplication, and locking. Requires a running canvas server (EXPRESS_SERVER_URL, default http://localhost:3000).
lingzhi227Skilllingzhi227/agent-research-skills/skills/experiment-code/SKILL.md
Write ML experiment code with iterative improvement. Generate training/evaluation pipelines, debug errors, and optimize results through code reflection. Use when implementing experiments for a research paper.
lingzhi227Skilllingzhi227/agent-research-skills/skills/experiment-design/SKILL.md
Design experiment plans with progressive stages — initial implementation, baseline tuning, creative research, and ablation studies. Plan baselines, datasets, hyperparameter sweeps, and evaluation metrics. Use when planning experiments for a research paper.
lingzhi227Skilllingzhi227/agent-research-skills/skills/figure-generation/SKILL.md
Generate publication-quality scientific figures using matplotlib/seaborn with a three-phase pipeline (query expansion, code generation with execution, VLM visual feedback). Handles bar charts, line plots, heatmaps, training curves, ablation plots, and more. Use when the user needs figures, plots, or visualizations for a paper.
lingzhi227Skilllingzhi227/agent-research-skills/skills/github-research/SKILL.md
Explore and analyze GitHub repositories related to a research topic. Reads deep-research output, discovers repos from multiple sources, deeply analyzes code, and produces integration blueprints.
lingzhi227Skilllingzhi227/agent-research-skills/skills/idea-generation/SKILL.md
Generate novel research ideas with iterative refinement and novelty checking against literature. Score ideas on Interestingness, Feasibility, and Novelty. Use when brainstorming research directions or validating idea novelty.
lingzhi227Skilllingzhi227/agent-research-skills/skills/latex-formatting/SKILL.md
Handle LaTeX formatting, templates, and styling for academic papers. Set up conference templates (ICML, ICLR, NeurIPS, AAAI, ACL), fix formatting issues, manage packages, and ensure venue-specific compliance. Use when the user needs to set up a paper template, fix LaTeX formatting, or prepare for submission.
lingzhi227Skilllingzhi227/agent-research-skills/skills/literature-review/SKILL.md
Conduct comprehensive literature reviews using multi-perspective dialogue simulation. Generate diverse expert personas, conduct grounded Q&A conversations, and synthesize findings into structured knowledge. Use when starting a new research project or writing a survey section.
Often used withpdf-exploreresearch-lookupfigure-style
lingzhi227Skilllingzhi227/agent-research-skills/skills/literature-search/SKILL.md
Search academic literature using Semantic Scholar, arXiv, and OpenAlex APIs. Returns structured JSONL with title, authors, year, venue, abstract, citations, and BibTeX. Use when the user needs to find papers, check related work, or build a bibliography.
lingzhi227Skilllingzhi227/agent-research-skills/skills/math-reasoning/SKILL.md
Formal mathematical reasoning for research papers — derive equations, write proofs, formalize problem settings, select statistical tests, and generate LaTeX math notation. Use when the user needs mathematical derivations, theorem proofs, notation tables, or statistical analysis formalization.
lingzhi227Skilllingzhi227/agent-research-skills/skills/novelty-assessment/SKILL.md
Assess research idea novelty through systematic literature search. Multi-round search-evaluate loops with harsh critic persona. Binary novel/not-novel decision with justification. Use before committing to a research direction.
lingzhi227Skilllingzhi227/agent-research-skills/skills/paper-assembly/SKILL.md
Orchestrate the full paper pipeline end-to-end. Manage state propagation between phases (literature → plan → code → experiments → figures → tables → writing → review), support checkpointing and resumption. Use for assembling a complete paper from components.
lingzhi227Skilllingzhi227/agent-research-skills/skills/paper-compilation/SKILL.md
Compile LaTeX papers to PDF with automatic error detection, chktex style checking, and citation/reference validation. Runs the full pdflatex + bibtex pipeline. Use when the user wants to compile a paper, fix compilation errors, or debug LaTeX.
Plain text files in a repository that tell a coding agent how the project works: commands to run, conventions to follow and things to avoid. CLAUDE.md, AGENTS.md, cursor rules and skills are the common kinds.
CLAUDE.md is read by Claude Code. AGENTS.md is an open format that Codex, Cursor and other agents read. Many projects keep one and point the other at it.
A folder with a SKILL.md that describes one capability, such as filling PDFs or reviewing code. The agent loads it only when the task calls for it.
Your agents already can, over MCP, limited to the files you're allowed to read. Searching them from this page is coming.
