agent-research-skills

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Revise papers based on reviewer feedback. Map reviewer concerns to specific sections, apply targeted edits, run additional experiments if needed, and verify improvements. Use after receiving peer review with revision requests.

Write a specific section of an academic paper (Abstract, Introduction, Background, Related Work, Methods, Experiments, Results, Discussion/Conclusion) with section-specific guidance and two-pass refinement. Use when the user wants to write, draft, or improve a paper section.

Write Related Work sections that compare and contrast prior work with your approach. Organize by theme, cite broadly, and explain how your work differs. Use when writing or improving the Related Work section of a paper.

Generate publication-quality LaTeX tables from experimental results. Convert JSON/CSV data to booktabs-styled tables with bold best results, multi-row layouts, and proper captions. Use when creating result tables, comparison tables, or ablation tables for papers.

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.

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.

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.

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.

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.

Automatically review an academic paper using the NeurIPS review form with three reviewer personas, ensemble scoring, and reflection refinement. Extracts text from PDF, runs structured review, and outputs actionable feedback. Use when the user wants to review a paper before submission or get feedback on a draft.

Convert a completed paper into presentation slides (Beamer LaTeX) or poster. Extract key figures, tables, equations, and create a narrative flow for oral presentation. Identified gap in existing tools — designed from best practices.

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.

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.

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.

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).

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.

Convert an ML research paper into a complete, runnable code repository. 3-stage pipeline from Paper2Code — Planning (UML + dependency graph) → Analysis (per-file logic) → Coding (dependency-ordered generation). Use for reproducing paper methods.

Write point-by-point rebuttals to reviewer comments. Extract concerns from reviews, generate evidence-based responses, and format as a structured rebuttal document. Use after receiving peer review feedback.

Design research plans and paper architectures. Given a research topic or idea, generate structured plans with methodology outlines, paper structure, dependency-ordered task lists, UML diagrams, and experiment designs. Use when starting a new research project or paper.

Generate complete academic survey papers using multi-LLM parallel outline generation, RAG-based subsection writing, citation validation, and local coherence enhancement. Based on AutoSurvey pipeline. Use for writing comprehensive literature surveys.

Discover scientific equations from data using LLM-guided evolutionary search (LLM-SR). Multi-island algorithm with softmax-based cluster sampling, island reset, and LLM-proposed equation mutations. Use for symbolic regression and equation discovery.