| name | lead-researcher |
| description | Use this skill when conducting a complete, end-to-end research project — from initial idea through hypothesis generation, literature review, experiment design, execution, optional replication or paper review, and final research writing. Orchestrates all available research sub-skills (hypothesis-generation, literature-synthesis, experiment-design, code-replication, research-paper-review, research-writing, ieee-paper-generator) into a single, coherent pipeline. Activate when the user wants to pursue a new research idea, replicate or extend a paper's results, or produce a publication-ready manuscript. |
| license | Apache-2.0 |
| metadata | {"author":"aviskaar","version":"1.0","tags":"research, orchestration, pipeline, end-to-end, hypothesis, literature, experiment, writing, lead","sub-skills":["hypothesis-generation","literature-synthesis","experiment-design","code-replication","research-paper-review","research-writing","ieee-paper-generator","ollama-multi-model-writer"]} |
Lead Researcher
Orchestrate a complete research project from initial idea to publication-ready output, invoking the right sub-skills at each stage.
Overview
The Lead Researcher skill is the top-level conductor of the research pipeline. It does not replace the sub-skills — it routes to them at the appropriate moment, manages context across stages, and ensures continuity and coherence throughout the full research lifecycle.
Pipeline stages:
1. Intake & Scoping
↓
2. Hypothesis Generation [→ hypothesis-generation]
↓
3. Literature Synthesis [→ literature-synthesis]
↓
4. (Optional) Paper Review [→ research-paper-review]
↓
5. Experiment Design [→ experiment-design]
↓
6. (Optional) Code Replication [→ code-replication]
↓
7. Research Writing [→ research-writing / ieee-paper-generator]
↓
8. Final Review & Handoff
Stages 4 and 6 are conditional: invoke them when the user has a specific paper to critique or wants to replicate baseline results before proposing improvements.
Stage 1 — Intake & Scoping
Before activating any sub-skill, collect the following information. If any item is missing, ask the user explicitly before proceeding.
Required inputs
| # | Question | Why it matters |
|---|
| 1 | What is the research topic or problem? | Scopes every subsequent stage |
| 2 | Do you have a starting hypothesis, or should one be generated? | Determines whether to begin at Stage 2 |
| 3 | Do you have a set of papers to review / synthesize, or should the agent identify them? | Scopes Stage 3 and 4 |
| 4 | Is there a specific paper whose results you want to replicate or extend? | Gates Stage 6 |
| 5 | What is the target output format? (internal report / conference paper / journal article / IEEE format) | Determines which writing sub-skill to activate in Stage 7 |
| 6 | What are the compute and time constraints? | Informs experiment design in Stage 5 |
Output of Stage 1
Produce a Research Brief (markdown, ~1 page) summarizing:
- Research question (one sentence)
- Intended contribution (2–3 bullets)
- Planned pipeline path (which stages apply)
- Key constraints (compute, time, data access)
Get explicit user confirmation of the Research Brief before proceeding to Stage 2.
Stage 2 — Hypothesis Generation
Sub-skill: hypothesis-generation
Trigger: Always (unless the user supplies a finalized hypothesis).
Input from Stage 1: Research question, known literature, surprising observation or gap.
Actions:
- Frame the problem using the sub-skill's Problem Framing step.
- Generate 3–5 candidate hypotheses with mechanisms, falsifiability checks, and minimal experiment descriptions.
- Stress-test each candidate for confounds, scope, and prior coverage.
- Produce a ranked table and recommend the top hypothesis.
- Refine the top hypothesis into a paper-ready claim.
Carry forward: The refined hypothesis statement and the ranked hypothesis table.
Stage 3 — Literature Synthesis
Sub-skill: literature-synthesis
Trigger: Always.
Input from Stage 2: Refined hypothesis, key concepts and keywords, any papers the user provided.
Actions:
- Identify the scope: map the hypothesis to 2–4 relevant research threads.
- Organize papers by methodology, chronology, and findings.
- Write the structured synthesis: Background, Key Themes, Points of Consensus, Open Debates, Open Problems, Synthesis Conclusion.
- Flag papers that directly test or contradict the hypothesis from Stage 2.
- Identify the gap the hypothesis fills and confirm it is not already addressed.
Carry forward: Literature synthesis document, gap statement, and a curated reference list.
Stage 4 — Paper Review (Conditional)
Sub-skill: research-paper-review
Trigger: When the user provides a specific paper to critique, or when a closely related paper poses a risk of scooping the hypothesis.
Input from Stage 3: Candidate paper, gap statement from literature synthesis.
Actions:
- Apply the full structured review: Summary, Contributions, Methodology, Experiments, Limitations, Related Work, Verdict.
- Specifically assess: Does this paper already address the hypothesis? If yes, escalate to the user immediately.
- Identify weaknesses, open problems, and extension opportunities that the hypothesis from Stage 2 could address.
Decision gate: After the review, confirm with the user whether to:
- Proceed with the original hypothesis (it is sufficiently differentiated)
- Refine the hypothesis to differentiate further (loop back to Stage 2)
- Pivot to extending/replicating the reviewed paper (activate Stage 6)
Carry forward: Review report, identified differentiation points, updated hypothesis if revised.
Stage 5 — Experiment Design
Sub-skill: experiment-design
Trigger: Always (after hypothesis is confirmed).
Input from Stages 2–4: Finalized hypothesis, literature-derived baselines, compute constraints.
Actions:
- State the hypothesis as a falsifiable claim in the format required by the sub-skill.
- Define independent and dependent variables; list controlled variables.
- Select baselines at three levels (naive / standard / strong) using the literature synthesis to justify choices.
- Specify datasets and splits; flag any data leakage or bias risks.
- Choose metrics; specify statistical significance protocol (seeds, confidence intervals).
- State compute budget and hardware assumptions.
- Design a minimal ablation set that isolates each component's contribution.
- Identify at least two failure modes and mitigations.
Carry forward: Structured experiment plan (markdown), baseline list with citations, ablation schedule.
Stage 6 — Code Replication (Conditional)
Sub-skill: code-replication
Trigger: When the user wants to:
- Validate that a baseline from Stage 5 performs as reported before comparing against it, OR
- Extend a prior paper's method (requires reproducing it first), OR
- Demonstrate reproducibility as a research contribution in itself.
Input from Stages 3–5: Target paper, experiment plan, compute constraints.
Actions:
- Paper Audit: extract all hyperparameters, identify ambiguities, locate official code.
- Environment Setup: record exact package versions, fix random seeds.
- Minimal Reproduction: run smallest experiment to confirm pipeline integrity.
- Full Replication: run main experiment with reported settings; record all results.
- Gap Analysis: compare reproduced results to paper's reported numbers; categorize gaps.
- Produce
REPLICATION.md with full documentation.
Decision gate: After gap analysis:
- Reproduced / Close: proceed to Stage 7 with confidence.
- Discrepancy / Failed: surface the finding to the user; decide whether to investigate further, use the discrepancy as a research finding, or adjust the experiment plan.
Carry forward: Replication report, gap analysis table, confirmed baseline numbers.
Stage 7 — Research Writing
Sub-skill: research-writing (for drafts, sections, and iterative editing) or ieee-paper-generator (for a complete, publication-ready IEEE paper).
Trigger: Always (after experiment results are available or summarized by the user).
Input from all prior stages: Research Brief, hypothesis, literature synthesis, experiment plan, replication report (if applicable), experiment results.
7a — Section-by-Section Drafting (research-writing)
Use when producing an internal report, a preprint, or individual sections (abstract, introduction, related work, etc.):
- Abstract: Follow the five-part structure (Motivation, Problem, Approach, Results, Significance). Keep to 150–250 words.
- Introduction: Hook → Problem → Gap → Contributions (bulleted, verifiable) → Paper outline.
- Related Work: Organized thematically using the literature synthesis from Stage 3.
- Methodology: Draw from the experiment plan and replication notes.
- Results: Present data from experiments; narrate tables — do not just report "our method is best."
- Conclusion: Summary, takeaways, future work. No new claims.
- Editing pass: Apply all style rules (active voice, precise quantifiers, acronym expansion, sentence length).
7b — Full IEEE Paper (ieee-paper-generator)
Use when the target output is a submission to an IEEE conference or journal:
- Collect any missing inputs (authors, affiliations, target venue, page count).
- Generate all sections in IEEE Roman-numeral order with correct heading style.
- Apply the IEEE Quality Checklist before presenting the draft.
- Flag any data gaps that require user input (results tables, figures, missing citations).
- Provide word count per section and recommended next steps.
Carry forward: Draft manuscript and list of outstanding gaps.
7c — Local Ollama Multi-Model Draft (ollama-multi-model-writer)
Use when the user wants to run paper writing locally on GPU using Ollama models (no cloud APIs):
- Verify prerequisites: Confirm Ollama is running and the required models are available —
deepseek-r1:7b, phi4-reasoning, glm4:9b-chat-q4_K_M. If any are missing, surface the pull commands to the user before proceeding.
- Pass full context: Forward the Research Brief, finalized hypothesis, literature synthesis, experiment plan, and results summary to
ollama-multi-model-writer.
- Model routing (handled by sub-skill):
- DeepSeek-R1 → Methods, Results, Experimental Setup
- Phi-4-reasoning → Abstract, Introduction, Conclusions
- GLM-4.7-Flash → Full-paper synthesis and consistency pass
- Review the output: Inspect the produced
paper-{topic}-draft.md for [PLACEHOLDER] and [RESULT NEEDED] tags and surface them to the user as a numbered list of outstanding items.
- Optional handoff: If the user wants IEEE formatting, pass the draft to
ieee-paper-generator after the Ollama draft is complete.
Carry forward: Draft manuscript at paper-{topic}-draft.md, outstanding items list, model attribution table.
Stage 8 — Final Review & Handoff
Trigger: After Stage 7 produces a complete draft.
Actions:
- Internal consistency check: Ensure the hypothesis from Stage 2, the experimental setup from Stage 5, and the claims in the manuscript all align. Flag any contradiction.
- Literature coverage check: Confirm all baselines, datasets, and key related work identified in Stage 3 are cited in the manuscript.
- Reproducibility audit: Verify that enough detail is present (datasets, splits, hyperparameters, seeds, hardware) for an independent replication.
- Open items list: Produce a prioritized list of what remains — missing experiments, figures to create, citations to verify, reviewer-anticipated objections.
- Handoff summary: One-page markdown document covering:
- Research question and final hypothesis
- Key results (top-line numbers)
- Status of each pipeline stage
- Outstanding items before submission
Cross-Stage Principles
Context Continuity
Maintain a running Research Log across all stages. After completing each stage, append a brief summary entry:
## Stage N — [Name] — [Date]
Status: complete / in-progress / blocked
Key output: [1–2 sentence summary]
Decisions made: [list]
Open questions: [list]
Decision Gates
At the end of Stages 1, 4, and 6, pause and surface a clear decision to the user before proceeding. Do not auto-advance through a gate if the outcome is ambiguous.
Escalation Protocol
Escalate immediately (do not silently continue) when:
- The hypothesis is found to already exist in the literature (Stage 3 or 4).
- Replication fails with a large gap that is not explainable (Stage 6).
- Experiment results contradict the hypothesis in a way that invalidates the paper's contribution (Stage 7).
No Fabrication
At no stage generate fake data, invented citations, fabricated results, or placeholder author names intended to be left in a final document. All numbers in the manuscript must come from actual experiments or cited sources.
Quick-Start Paths
Use these shortcuts when the user's intent is clear:
| User intent | Entry point | Skipped stages |
|---|
| "I have an idea, help me turn it into a paper" | Stage 1 → full pipeline | None |
| "Review this paper and help me extend it" | Stage 4 → 2 → 3 → 5 → 7 | Stage 6 unless user wants replication |
| "Replicate this paper and beat it" | Stage 4 → 6 → 2 → 5 → 7 | — |
| "I have results, write the paper" | Stage 7 directly | Stages 2–6 (reference prior work if available) |
| "Write it locally on my GPU with Ollama" | Stage 7c (ollama-multi-model-writer) | Stages 2–6 (pass context if available) |
| "Design experiments for this hypothesis" | Stage 3 → 5 | Stages 2 (hypothesis given), 4, 6, 7 |
Output Summary
| Stage | Artifact |
|---|
| 1 | Research Brief (markdown, confirmed by user) |
| 2 | Hypothesis document with ranked table and refined claim |
| 3 | Literature synthesis with gap statement and reference list |
| 4 | Paper review report with differentiation analysis (if activated) |
| 5 | Experiment plan (markdown) |
| 6 | REPLICATION.md with gap analysis table (if activated) |
| 7 | Draft manuscript (section-by-section, full IEEE format, or local Ollama multi-model draft) |
| 8 | Handoff summary and open items list |
| All | Research Log with stage-by-stage entries |
