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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

Use this Skill: https://skilld.dev/gh/imbad0202/academic-research-skills/deep-research

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referencesargumentation_reasoning_framework.md

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Argumentation & Reasoning Framework

A cognitive framework for evaluating the strength and validity of research arguments. Use this to think about argument quality, not just check boxes.

Toulmin Model of Argumentation

Every research argument has 6 components. When evaluating, identify each:

Component Question Red Flag if Missing
Claim What is being asserted? Vague or shifting thesis
Data/Evidence What evidence supports it? Claims without empirical backing
Warrant Why does the evidence support the claim? Logical gap between data and conclusion
Backing What supports the warrant itself? Assumed methodology validity
Qualifier How certain is the claim? Absolute language ("proves", "always")
Rebuttal What would undermine the claim? No acknowledged limitations

Judgment heuristic: If you can't identify the Warrant, the argument is likely weak regardless of how much Data is presented. Data without Warrant is just information.

Causal Reasoning (Bradford Hill Criteria, adapted)

When a paper claims X causes Y, evaluate against these 9 criteria:

  1. Strength of association — How large is the effect?
  2. Consistency — Replicated across studies/contexts?
  3. Specificity — Does X specifically lead to Y (not everything)?
  4. Temporality — Does X precede Y? (Only mandatory criterion)
  5. Biological/theoretical gradient — More X → more Y?
  6. Plausibility — Is there a reasonable mechanism?
  7. Coherence — Consistent with existing knowledge?
  8. Experiment — Is there experimental evidence?
  9. Analogy — Do similar causes produce similar effects?

Judgment heuristic: Most social science papers satisfy 3-5 criteria. Fewer than 3 = causal claim is unsupported. Only #4 (temporality) is strictly required; the rest are cumulative evidence.

Inference to Best Explanation (IBE)

When multiple explanations exist for the same finding:

  1. List ALL plausible explanations (not just the author's preferred one)
  2. Evaluate each on: explanatory scope (how much it explains), simplicity (fewer ad-hoc assumptions), fit (consistency with known facts), predictive power (does it predict new observations?)
  3. The best explanation is the one that scores highest across all four — not the one that fits the author's hypothesis

Judgment heuristic: If the paper only considers one explanation, that's confirmation bias regardless of how well-argued it is. At minimum, the Discussion section should address the two strongest alternative explanations.

Epistemic Status of Claims

Not all claims carry equal weight. Classify each major claim:

Status Meaning Appropriate Language
Established Replicated, peer-reviewed, high consensus "X is..."
Supported Evidence exists but not yet replicated "Evidence suggests X..."
Preliminary Single study or small sample "Preliminary findings indicate..."
Speculative Based on reasoning, not direct evidence "We hypothesize that..."
Contested Conflicting evidence exists "While some studies find X, others..."

Judgment heuristic: If a paper uses "Established" language for "Preliminary" findings, that's overclaiming — one of the most common quality issues in academic writing.

Application by Agent

Agent Primary Use
synthesis_agent Toulmin analysis of synthesized arguments; IBE for competing explanations
devils_advocate_agent Causal reasoning audit; identify missing Rebuttals and Qualifiers
source_verification_agent Epistemic status classification of source claims
socratic_mentor_agent Guide users through Toulmin decomposition of their own arguments
research_architect_agent Ensure methodology design supports causal claims at appropriate level

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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Other metadata
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"
  ]
}

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