/deep-research

by Edward Cheng-I Wuimbad0202/academic-research-skills50k stars

3,856

Universal deep research agent team. 13-agent pipeline for rigorous academic research on any topic. 8 modes: full research, quick brief, paper review, lit-review, fact-check, three-way literature scan, Socratic guided research dialogue, and systematic review with optional meta-analysis. Covers research question formulation, Socratic mentoring, methodology design, systematic literature search, source verification, cross-source synthesis, risk of bias assessment, meta-analysis, APA 7.0 report compilation, editorial review, devil's advocate challenges, ethics review, and post-research literature monitoring. Triggers on: research, deep research, literature review, systematic review, meta-analysis, PRISMA, evidence synthesis, fact-check, WHY HOW WHAT papers, 3W literature scan, guide my research, help me think through, 研究, 深度研究, 文獻回顧, 文獻探討, 系統性回顧, 後設分析, 事實查核, 三段式文獻掃描, 引導我的研究, 幫我釐清, 幫我想想, 我不確定要研究什麼, 研究方向, 研究主題, 심층 연구, 문헌 조사, 체계적 문헌고찰, 메타분석, 사실 확인, 연구 방향을 잡아줘, 연구 주제 정하는 것을 도와줘, revisión de literatura, metaanálisis

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referenceschangelog.md

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[2.9.1] - 2026-04-22

Added

Opt-in reading-check probe in Socratic Mentor. Gated by ARS_SOCRATIC_READING_PROBE=1. See agents/socratic_mentor_agent.md §"Optional Reading Probe Layer" and SKILL.md §"Opt-in Reading Probe (v3.5.1)".

Version

2.9.0 → 2.9.1 (patch; opt-in, default OFF).

Version History

Version	Date	Changes
2.4	2026-03-27	Report compiler now consumes optional Style Profile (from academic-paper intake) and runs Writing Quality Check checklist before finalizing reports. Style Profile applied as soft guide for Executive Summary and Synthesis sections; discipline conventions take priority. Writing Quality Check catches overused AI-typical terms, em dash overuse, throat-clearing openers, and monotonous sentence rhythm. See `academic-paper/references/writing_quality_check.md` and `shared/style_calibration_protocol.md`
2.3	2026-03-08	Added systematic-review mode (7th mode): PRISMA 2020 compliant pipeline with risk_of_bias_agent (RoB 2 + ROBINS-I), meta_analysis_agent (effect sizes, heterogeneity, GRADE, narrative synthesis), 2 new templates (PRISMA protocol + report), systematic_review_toolkit reference. Added monitoring_agent (post-pipeline literature monitoring with digests, retraction alerts, author tracking) + literature_monitoring_strategies reference. Enhanced socratic_mentor_agent with 4 convergence signals, 4-type question taxonomy, and auto-end triggers. Added Quick Mode Selection Guide to SKILL.md
2.2	2026-03-05	Added synthesis anti-patterns, Socratic quantified thresholds & auto-end conditions, reference existence verification (DOI + WebSearch), enhanced ethics reference integrity check (50% + Retraction Watch), mode transition matrix, cross-agent quality alignment definitions
2.1	2026-03	Added IRB decision tree, EQUATOR reporting guidelines, preregistration guide + template; enhanced ethics_review_agent with human subjects dimension; enhanced research_architect_agent with ethics/EQUATOR/preregistration integration; enhanced methodology_patterns with EQUATOR cross-references
2.0	2026-02	Added socratic mode (10th agent), failure paths, mode selection guide, handoff protocol, 2 new examples, 3 new references
1.0	2026-02	Initial release: 9 agents, 5 modes, 6-phase pipeline

Source: SKILL.md on GitHub

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The deep-research skill is a highly sophisticated research orchestration system that includes robust internal security instructions to prevent prompt injection from untrusted data. It leverages well-known scholarly APIs for data verification and uses local scripts for deterministic validation of research artifacts.
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Signed by skilld at 0d17790. This ties the file your Agent reads to that commit on GitHub. It does not review the instructions.

Last checked against GitHub 2 days ago.

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metadata: { "version": "2.12.1", "last_updated": "2026-08-15", "status": "active", "data_access_level": "raw", "task_type": "open-ended", "related_skills": [ "academic-paper", "academic-pipeline" ] }