Academic Research Skills for Claude Code
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A comprehensive suite of Claude Code skills for academic research, covering the full pipeline from research to publication.
Install in 30 seconds (Claude Code CLI / VS Code / JetBrains, v3.7.0+):
/plugin marketplace add Imbad0202/academic-research-skills
/plugin install academic-research-skills
Then try /ars-plan to walk through your paper structure via Socratic dialogue, or jump to Quick install for prerequisites and the traditional symlink flow.
AI is your copilot, not the pilot. This tool won't write your paper for you. It handles the grunt work — hunting down references, formatting citations, verifying data, checking logical consistency — so you can focus on the parts that actually require your brain: defining the question, choosing the method, interpreting what the data means, and writing the sentence after "I argue that."
Unlike a humanizer, this tool doesn't help you hide the fact that you used AI. It helps you write better. Style Calibration learns your voice from past work. Writing Quality Check catches the patterns that make prose feel machine-generated. The goal is quality, not cheating.
Why human-in-the-loop, not full automation?
Lu et al. (2026, Nature 651:914-919) built The AI Scientist — the first fully autonomous AI research system to publish a paper through blind peer review at a top-tier ML venue (ICLR 2025 workshop, score 6.33/10 vs workshop average 4.87). Their Limitations section enumerates the failure modes that any fully-autonomous AI research pipeline inherits: implementation bugs, hallucinated results, shortcut reliance, bug-as-insight reframing, methodology fabrication, frame-lock, citation hallucinations.
ARS is built on the premise that a human researcher augmented by AI avoids these failure modes better than either alone. Stage 2.5 and Stage 4.5 integrity gates run a 7-mode blocking checklist (see academic-pipeline/references/ai_research_failure_modes.md); the reviewer offers an opt-in calibration mode that measures its own FNR/FPR against a user-supplied gold set.
Zhao et al. (2026-05) audited 111M references across 2.5M papers on arXiv, bioRxiv, SSRN, and PMC. Their conservative estimate is 146,932 hallucinated citations for 2025 alone, with an observed mid-2024 inflection; for the bioRxiv-to-PMC pairing they report 85.3% preprint-to-published persistence. The paper describes "real citations deployed to support claims the cited references do not actually make" as an open challenge. ARS v3.7.1 added trust-chain frontmatter for source provenance; v3.7.3 added locator infrastructure (three-layer citation anchors) for future claim-level audits and surfaces advisory risk signals at cite time (ARS labels the claim-faithfulness gap internally as "L3"; this is ARS terminology, not the paper's). v3.7.x is motivated by Zhao et al.'s corpus-scale findings; corpus-scale evaluation of ARS itself remains future work.
v3.8 closes the second half of the L3 gap. v3.7.3 made every citation carry a locator anchor; v3.8 adds an opt-in audit pass (ARS_CLAIM_AUDIT=1) that fetches the cited source against each anchor and judges whether the claim is actually supported. Five new HIGH-WARN classes (claim-not-supported, negative-constraint-violation, fabricated-reference, anchorless, constraint-violation-uncited) gate-refuse output through the formatter terminal hard gate. Calibration is shipped as a 20-tuple gold set with FNR<0.15 + FPR<0.10 acceptance thresholds; ramp-on plan is deferred to post-calibration evidence per v3.8 spec §5.
Ren et al. (2026, Self-Improvements in Modern Agentic Systems: A Survey) supplies a third, survey-level anchor. Its scientific-discovery synthesis (§7.4) concludes that discovery agents cannot easily verify novelty, correctness, or reproducibility on their own and may exploit weak proxies instead, must manage evidence across heterogeneous tools and literature, and raise governance issues — "scientific writing can also amplify misinformation when the evidence is weak." Its generation-loop chapters (§5.1–§5.2) list human auditing and retained human anchors among the practical safeguards for self-generated evaluation loops, and its historical chapter (§2.2) records the oldest form of the same lesson: the practical success of Lenat's EURISKO depended heavily on the user serving as the external evaluation signal, pruning unproductive heuristic drift — a limitation the survey notes persists in modern agentic systems. ARS cites the survey as design rationale for its human-in-the-loop stance, not as empirical proof that human-in-the-loop pipelines outperform autonomous ones; the survey's actionable deltas for ARS are tracked in #539–#541 and #547–#550.
Gartenberg et al. (2026, Organization Science 37(3):795-812, "More versus better") supplies a fourth anchor, and the first from the journal side. The Organization Science AI Task Force scored every first submission (6,957) and every text-format review (10,389) the journal received between January 2021 and February 2026 with a commercial AI-writing classifier and standard readability indices. Manuscripts scored as heavily AI-written read worse on those indices and were desk-rejected more often; reviews scored as more AI-written leaned toward theory and away from data; and the editors conclude that current AI tools, amplified by publish-or-perish incentives, "appear to be pushing the system toward an equilibrium of more rather than better research." Their §5 contrasts "cognitive surrender" (Shaw & Nave, 2026, as cited there) with human-first use and asks authors to disclose how a manuscript was produced. The evidence is observational, aggregate, and from one journal, and the classifier is a proprietary instrument. ARS cites the editorial as design rationale for recording volume as a non-goal (see POSITIONING.md) and for the Collaboration Depth Observer and the claim-strength ladder, not as evidence about ARS output; the actionable deltas are tracked in #829–#833.
v3.3 was inspired by PaperOrchestra (Song, Song, Pfister & Yoon, 2026, Google): Semantic Scholar API verification, anti-leakage protocol, VLM figure verification, and revision-trajectory tracking. ARS now implements that last idea through categorical, evidence-anchored criterion trajectories rather than score deltas.
Architecture & pipeline
👉 docs/ARCHITECTURE.md — the full pipeline view: flow diagram, stage-by-stage matrix, data-access flow, skill dependency graph, quality gates, and mode list.
The architecture doc supersedes the sprawling pipeline description that used to live here. Everything about what runs in which stage now lives in one place.
Quick install
Prerequisites
- Claude Code (latest; plugin packaging requires recent versions)
ANTHROPIC_API_KEY exported, or set on first claude run- Optional: Pandoc for DOCX, tectonic + Source Han Serif TC for APA 7.0 PDF (Markdown output works without either)
- Optional (real Python): The core skills (research / write / review) need no Python — they are prompt-driven. A real Python interpreter is needed only for: the
PreToolUse write-scope guard (optional subagent hardening — if no real Python is found it cleanly no-ops and the guard is simply inactive; core skills are unaffected), plus a few opt-in features that shell out to Python (revision-patch mode, the submission-package verifier, and the /ars-cache-invalidate / /ars-mark-read / /ars-unmark-read commands). On Windows, note that python3 is often a non-functional Microsoft Store placeholder rather than real Python; install Python from python.org (or via winget) so the launcher can find a real interpreter. The guard launcher is a POSIX shell script and hooks.json invokes it through bash, so on Windows it needs Git Bash (bundled with Git for Windows). With Git Bash present, a missing real Python degrades cleanly (the guard no-ops, silently). Without Git Bash, Claude Code falls back to PowerShell, which cannot run the .sh launcher at all: the guard is inactive and the PreToolUse hook will log an error per call rather than no-op quietly (accepted degradation — the guard is optional and never blocks your writes, but the hook noise is the trade-off until Git Bash is installed).
Which controls are active in your install channel? Availability varies by install channel. See the per-channel map: docs/CONTROL_AVAILABILITY.md.
Plugin install (v3.7.0+, recommended):
/plugin marketplace add Imbad0202/academic-research-skills
/plugin install academic-research-skills
Verify it works: run /ars-plan and describe a paper you're working on — ARS will start a Socratic dialogue to map out chapter structure. For a single-shot test instead, try /ars-lit-review "your topic".
👉 docs/SETUP.md — full guide: install Claude Code, set up API keys, optional Pandoc/tectonic for DOCX/PDF, cross-model verification (ARS_CROSS_MODEL), and six installation methods (Plugin, project skills, global skills, claude.ai Project, repo-cloned, Claude Science import).
👉 docs/DATA_FLOWS.md — what leaves your machine (bibliographic resolvers, optional consent-gated cross-model calls, the plugin update check), what is cached locally, for how long, and how to turn each path off.
👉 docs/RISK_REGISTER.md — the standing risks the suite knows about, which existing controls address each one, the evidence status behind those controls, and what remains open.
Using Claude Science? The four skills import directly: Skills → Import from GitHub, paste https://github.com/Imbad0202/academic-research-skills, Preview, then Import 4 skills (requires v3.14.0+ of this repo — the importer reads the explicit skill paths in the marketplace manifest). Imports are point-in-time snapshots: re-import after ARS updates. Imported skills carry the ARS methodology (research / writing / review protocols); Claude Code-specific machinery — slash commands, hooks, subagent orchestration — does not transfer. See docs/SETUP.md Method 5 for details.
Using Pi? Install the in-tree, community-maintained wrapper with pi install git:github.com/Imbad0202/academic-research-skills. It keeps the original ARS content authoritative and documents Pi-specific orchestration and hook limitations. See pi/README.md.
Using Codex CLI? Install the sibling distribution instead: Imbad0202/academic-research-skills-codex — same workflow content, Codex-native packaging as a single $academic-research-suite skill with ars-* aliases.
Third-party platforms and integrations that wrap or host ARS are listed in THIRD_PARTY.md — community-submitted and not reviewed or endorsed by the maintainer.
Governance: who decides, what cross-model review does and does not provide, and the project's end-of-life posture are stated in GOVERNANCE.md; security reporting and triage in SECURITY.md.
👉 docs/PERFORMANCE.md — per-mode token budgets, full-pipeline estimate (~$4–6 for a 15k-word paper), and recommended Claude Code settings (Auto mode; Agent Team optional).
Guides & articles
Features at a glance
- Deep Research — 13-agent research team with Socratic guided mode, PRISMA systematic review, intent detection, dialogue health monitoring, optional cross-model DA, Semantic Scholar API verification.
- Academic Paper — 12-agent paper writing with Style Calibration, Writing Quality Check, LaTeX hardening, visualization, revision coaching, citation conversion, anti-leakage protocol, and VLM figure verification.
- Academic Paper Reviewer — 7-agent multi-perspective peer review with criterion-bound, evidence-anchored narrative judgements (Journal-Fit Reviewer + 3 dynamic reviewers + Devil's Advocate), concession threshold protocol, attack intensity preservation, optional cross-model DA critique / calibration, R&R traceability matrix, read-only constraint. Current live reviews remain
NOT_CALIBRATED; full calibration produces a bounded candidate profile, while live-profile application is not yet wired.
- Academic Pipeline — 10-stage pipeline orchestrator with adaptive checkpoints, claim verification, Material Passport, optional
repro_lock, optional cross-model integrity verification, mid-conversation reinforcement, and narrative criterion-by-criterion regression checks (the typed trajectory carrier is deferred).
- Data Access Level Metadata (v3.3.2+) — every skill declares
data_access_level (raw / redacted / verified_only); enforced by scripts/check_data_access_level.py. Pattern adapted from Anthropic's automated-w2s-researcher (2026). See shared/ground_truth_isolation_pattern.md.
- Task Type Annotation (v3.3.2+) — every skill declares
task_type (open-ended or outcome-gradable). All current ARS skills are open-ended.
- Benchmark Report Schema (v3.3.5+) — JSON Schema + lint for honest benchmark comparisons. See
shared/benchmark_report_pattern.md.
- Artifact Reproducibility Lockfile (v3.3.5+) — optional
repro_lock sub-block on Material Passport. Configuration documentation, not replay guarantee — LLM outputs are not byte-reproducible. See shared/artifact_reproducibility_pattern.md.
- Model Tiering (#517, v3.16+) — optional
ARS_MODEL_TIERING switch with two directions: economy (execution-type agents dispatch one tier below the session model, floor Opus-class) and quality-boost (judgment-type agents at integrity gates and final review step up to the frontier tier). Default unset = byte-equivalent to pre-#517 behavior. See shared/model_tiering.md.
- Canonical Cross-Model Handoff Envelope (#527, v3.17+) — the owner→dispatcher→owner blind-checkpoint transport path (#523) now has a machine-stable
[CROSS-MODEL-HANDOFF v1] envelope with a normative Python grammar (scripts/cross_model_handoff.py) instead of prose-only enforcement, pinning agreement/divergence/malformed-result routing across all three checkpoint owners. See shared/cross_model_verification.md §"Cross-model handoff envelope".
- Experiment Provenance Intake (#260) — optional
experiment_provenance[] on the Material Passport records experiments the scholar ran externally (ARS never runs experiments), and manuscript claims join to them via claim_intent_manifest.planned_experiment_ids[]. The integrity gate (Stage 2.5/4.5) audits each experiment-backed claim against declared provenance — ALIGNED / OVERSTATED / NOT_SUPPORTED_BY_PROVENANCE / PROVENANCE_INSUFFICIENT — without judging whether the experiment itself was correct. A fail-closed experiment_intake_declaration makes "did you run experiments?" an explicit Stage 1 decision (even literature-only runs declare no_experiments_declared). See shared/handoff_schemas.md §"Experiment Provenance Intake (#260)".
Integrity and verification boundary: ARS checks the manuscript and the reported process—including citation existence, claim–source alignment, reported methodology, declared experiment–result alignment, figure/table fidelity, and reporting/process/package conformance. Some checks are sampled or LLM-mediated. ARS does not establish that procedures were actually performed, raw data are authentic, or results reproduce; a consistently reported fabrication can pass these checks. See POSITIONING.md § Integrity checks and the empirical-work boundary.
Showcase: real pipeline output
See the complete artifacts from a real 10-stage pipeline run — peer review reports, integrity verification reports, and the final paper:
Browse all pipeline artifacts →
Companion: Experiment Agent
If your research involves running experiments (code or human studies) before writing, the Experiment Agent skill fills the gap between ARS Stage 1 (RESEARCH) and Stage 2 (WRITE).
ARS Stage 1 RESEARCH → RQ Brief + Methodology Blueprint
↓
experiment-agent → run/manage experiments → validate results
↓
ARS Stage 2 WRITE → write paper with verified experiment results
What it does: executes code experiments (Python, R, etc.) with real-time monitoring, manages human study protocols with IRB ethics checklist, interprets statistics with 11-type fallacy detection, and verifies reproducibility.
How to use together: pause the ARS pipeline after Stage 1, run experiments in a separate experiment-agent session, then bring the results (with Material Passport) back to ARS Stage 2. ARS requires zero modification. See the experiment-agent README for setup instructions.
Stage 1 intake declaration (#260)
Комплексный набор навыков Claude Code, который охватывает весь цикл научной работы: обзор литературы, написание, рецензирование и доработку. Он создан как помощник, а не автопилот для научных статей.