By fcakyon
Audit ML/CV research papers against codebases, data, and experiments to verify claims, citations, numerical accuracy, and methodology. Design ablation studies with cost estimates, analyze datasets for bias, setup LaTeX environments, conduct literature gap analysis, and prepare repos for open-source release.
Verify BibTeX entries and cited claims against DBLP and web sources. Checks author names, venues, years, and specific numerical claims.
Select strongest ablations and anticipate reviewer questions. Reads paper and experiment results to prepare for peer review.
Literature gap analysis with web confirmation. Takes a research topic or question and maps existing work to find what's missing.
Show all phd-skills features, commands, skills, agents, and hooks at a glance. Use for in-session discoverability.
Interactive onboarding wizard — configure notifications, CLI allowlist, research-specific CLAUDE.md rules, and LaTeX environment.
Analyze experiment results from any tracking system. Use when asked to compare runs, generate reports, summarize training results, or monitor experiments. Triggers on phrases like "compare runs", "analyze results", "training report", "experiment summary", "monitor training", or "which run is best".
Autonomous paper consistency verification. Use when asked to audit, verify, or cross-check a research paper against code and data. Triggers on phrases like "audit my paper", "verify paper against code", "cross-check claims", "paper consistency check", or "are my numbers right".
Use when the user wants to analyze dataset bias, create stratified samples, evaluate fairness, or plan dataset collection. Triggers on phrases like "dataset bias", "stratified sample", "class imbalance", "data distribution", "fairness analysis", or "ethical review".
Use when the user wants to design experiments, plan ablation studies, structure baselines, or create incremental evaluation strategies. Triggers on phrases like "design ablation", "plan experiment", "what experiments should I run", "baseline comparison", or "experiment matrix".
Use when the user wants to set up or troubleshoot a LaTeX environment, choose between biber and bibtex, install packages for a specific venue template, or configure compilation. Triggers on phrases like "setup latex", "biber vs bibtex", "latex compilation error", "install latex packages", "venue template", or "texlive setup".
Use when the user wants to find related work, survey a research area, identify literature gaps, or discover open-source implementations. Triggers on phrases like "find papers on", "related work", "literature review", "what papers exist", "open source implementation", or "papers with code".
Use when the user wants to verify paper claims against code or data, audit numerical accuracy, check formula-code alignment, or validate citation accuracy. Triggers on phrases like "verify claims", "check numbers", "do the numbers match", "formula vs code", "audit the paper", or "cross-check results".
Executes bash commands
Hook triggers when Bash tool is used
Modifies files
Hook triggers on file write and edit operations
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Uses power tools
Uses Bash, Write, or Edit tools
Uses power tools
Uses Bash, Write, or Edit tools
Research integrity plugin for Claude Code — paper auditing, citation verification, experiment analysis, and methodology-first skills for academic workflows.
Built by Fatih Cagatay Akyon (1300+ citations, 7 patents) after 200+ Claude Code sessions, tens of critical AI mistakes caught the hard way, and thousands of hours of PhD research. Every guardrail in this plugin traces to a real mistake.
I use Claude Code daily for my PhD. It's powerful, but it makes research-specific mistakes that cost hours:
Other plugins give you more commands. This plugin gives you guardrails.
claude plugin marketplace add fcakyon/phd-skills
claude plugin install phd-skills@phd-skills
Then run /phd-skills:setup inside Claude Code to configure notifications, LaTeX, and allowlist.
Open Claude Code in your paper directory, then:
/phd-skills:xray — audit paper against code and data across 5 dimensions, get prioritized fixes/phd-skills:factcheck — verify all BibTeX entries and cited claims against DBLP/phd-skills:fortify CVPR — anticipate reviewer questions, rank ablations, and suggest paper improvements/phd-skills:gaps neural architecture search — find what's missing in the literature/loop 30m check experiment logs, notify me if metrics beat the baseline or if loss starts to diverge"check if my numbers match the code" — skills auto-trigger, no slash command needed"make code publish ready" — prepares code for open-source release with license, docs, and reproducibility checksAfter running /phd-skills:setup, all Claude Code notifications (task completion,
background agents) are forwarded to your configured service (ntfy/Slack/email).
| Command | What it does |
|---|---|
/phd-skills:xray | Audit paper against code and data (5 parallel dimensions) |
/phd-skills:factcheck | Verify BibTeX entries and cited claims against DBLP |
/phd-skills:gaps <topic> | Literature gap analysis with web confirmation |
/phd-skills:fortify [venue] | Select strongest ablations + anticipate reviewer questions |
/phd-skills:setup | Interactive onboarding (notifications, allowlist, LaTeX) |
/phd-skills:help | Show all features at a glance |
| When you say... | Skill activates |
|---|---|
| "design an ablation study" | Experiment Design |
| "find related papers on X" | Literature Research |
| "review my methods section for consistency" | Paper Verification |
| "check if my numbers match the code" | Paper Verification |
| "analyze dataset bias" | Dataset Curation |
| "prepare code for open-source release" | Research Publishing |
| "what will reviewers ask about this?" | Reviewer Defense |
| "setup latex for CVPR" | LaTeX Setup |
| Agent | What it does | Special |
|---|---|---|
paper-auditor | Cross-checks paper claims vs code and data | Runs in isolated worktree, remembers patterns across sessions |
experiment-analyzer | Analyzes results from wandb/neptune/local/any format | Can schedule monitoring via cron, sends SSH notifications |
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