Plugin
claude-codex-settings
Battle-tested Claude Code, OpenAI Codex, Cursor configs, plugins, hooks and agents with Kimi, MiniMax and GLM API support.
98 skills4 agents5 commands4 MCP+3+2+2+2+1+1+1+11.2k
@fcakyonResearch
Plugin
phd-skills
Catch AI mistakes before they cost weeks of compute. Reproduce papers from arxiv. Debug runs evidence-first. Compare experiments at the right epoch.
Plugin Signal81/100Strong
maintained97
capable63
documented100
adopted56
Install on Claude Code
> /plugin marketplace add fcakyon/phd-skills> /plugin install phd-skills@phd-skills
What's inside
Skill(12 skills)
/compareSame-epoch comparison of training runs across wandb, neptune, tensorboard, or mlflow. Aligns runs at the student's current step (never current-vs-final-of-baseline) and separates proxy metrics from downstream targets. Use when the user asks to compare runs, check if a run is/dataset-curationUse 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"./debugEvidence-before-action diagnosis of failing ML experiments. Probes the system before guessing causes, process list, dmesg, GPU stats, log scrollback, checkpoint state, then states a hypothesis as a hypothesis and runs a smoke before claiming a root cause. Use when the user asks
Command(6 commands)
/factcheckVerify BibTeX entries and cited claims against DBLP and web sources. Checks author names, venues, years, and specific numerical claims./fortifySelect strongest ablations and anticipate reviewer questions. Reads paper and experiment results to prepare for peer review./gapsLiterature gap analysis with web confirmation. Takes a research topic or question and maps existing work to find what's missing.
Agent(2 agents)
experiment-analyzerAnalyze 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", orpaper-auditorAutonomous 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".
README
phd-skills
Catch AI mistakes before they cost weeks of compute. Reproduce papers from arxiv. Debug runs evidence-first. Compare experiments at the right epoch. Launch with discipline.
Built by Fatih Cagatay Akyon (2000+ citations, 5 patents) after 300+ 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.
Paper search and acquisition use Paper Search CLI, installed with uv and Python 3.10+. See paper search setup. Other skills do not require it.
Why This Plugin Exists
Claude Code is powerful, but it makes research-specific mistakes that cost weeks of compute:
- It typed "done?" as "dont?" and launched an unwanted upload of thousands of files
- It analyzed my full dataset when I asked for a specific 4k/2k/2k split
- It claimed a test covered a bug it had never actually verified
- It never once looked at a figure it generated, just trusted the numbers
- It restarted a 50-hour training job without diffing the config against the reference run, lost three days
- It claimed an experiment was diverging based on a non-converged proxy metric, killed it before downstream eval would have shown the truth
- It ran
rm -rfon a path it had hallucinated from memory, lost local checkpoints
Other plugins give you more commands. This plugin gives you guardrails.
Install
claude plugin marketplace add fcakyon/phd-skills
claude plugin install phd-skills@phd-skills
The plugin works correctly the moment it is installed. Optional: run /phd-skills:setup for a 30-second tour of what was auto-detected and to opt into extras (notifications, allowlist, LaTeX).
Usage
Open Claude Code in your project directory, then:
/phd-skills:reproduce arxiv 2508.12345reproduce a paper from arxiv URL through replication runs"why is my loss diverging?"thedebugskill auto-triggers, runs evidence-first probes"compare run alpha to baseline"thecompareskill auto-triggers, aligns at the same epoch"launch the new training run"thelaunchskill auto-triggers, runs the pre-flight checklist/loop 30m check experiment logs, notify me if metrics beat the baseline or if loss starts to diverge
Notifications (task completion, background agents) forward to ntfy / Slack / email after /phd-skills:setup.
What You Get
Commands
| 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 | Auto-detection tour + optional extras |
/phd-skills:help | Show all features at a glance |
Skills (auto-trigger, just describe what you need)
| When you say... | Skill activates |
|---|---|
| "reproduce this arxiv paper" | Reproduce |
| "why is X failing / diverging / OOMing" | Debug |
| "compare run A to baseline" | Compare |
| "launch a new training run" / "kick off training" | Launch |
| "design an ablation study" | Experiment Design |
| "find related papers on X" | Literature Research |
| "check if my numbers match the code" | Paper Verification |
| "review my methods section for consistency" | Paper Writing |
| "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 |
Agents (Claude delegates automatically)
| 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 / tensorboard / mlflow / local | Hands off to compare and debug skills for discipline |
Research Guardrails (run silently, you never invoke these)
How It Compares
| phd-skills | flonat/claude-research | Others | |
|---|---|---|---|
| Commands to learn | 6 | 39 | 13-20 |
| Research integrity hooks | 11 (agent + 10 auto-detect) | 1 | 0 |
| Paper reproduction (arxiv to runs) | Yes (7-stage skill) | No | No |
| Paper-code consistency audit | 5-dimension parallel | Read-only, no code cross-ref | None |
| Experiment monitoring + SSH notifications | Yes (ntfy / slack / email) | No | No |
| External dependencies | Paper Search CLI for paper workflows | npm + pip + MCP servers | MCP required |
| Install time | 30 seconds | 10+ minutes | Varies |
Design Principles
- Methodology over scripts. Skills teach the approach, Claude generates code for your specific setup (wandb, neptune, local files, whatever)
- Human oversight first. Claude makes premature claims and jumps to conclusions. Every skill builds in verification checkpoints
- Actionable output. Ranked suggestions with specific fixes, never just a list of findings
License
MIT. Use it, fork it, adapt it to your research.
Thank you for the support!
Contributors
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More plugins by @fcakyon.
View @fcakyon’s profile@fcakyonFAQ
phd-skills is a Claude Code plugin with 12 hand-picked skills, indexed on Flowy in the Research category. Install it with the command on its page. It includes compare, dataset-curation, debug. Its skills do not fire on their own yet. Request auto-invocation to have Flowy route them as you prompt. Free and open source.
- What is phd-skills?
- Catch AI mistakes before they cost weeks of compute. Reproduce papers from arxiv. Debug runs evidence-first. Compare experiments at the right epoch. Launch with discipline.
- How do I install phd-skills?
- Run these in Claude Code: /plugin marketplace add fcakyon/phd-skills then /plugin install phd-skills@phd-skills. Then prompt normally.
- Does phd-skills auto-invoke its skills?
- Not yet. It is indexed on Flowy as a plain plugin. Request auto-invocation on its page and Flowy will route its skills for you as you prompt.
- Is phd-skills free?
- Yes. Flowy is free and open source, with nothing gated. You can read every skill in full before you install.
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