| name | paper-research |
| description | Research biomedical and ML papers across the internet, focusing on top venues and publishers. Use when: (1) Searching for state-of-the-art methods in a biomedical domain, (2) Finding papers from top venues (Nature Medicine, Lancet, MICCAI, NeurIPS, ICML, CVPR, TMI, MedIA), (3) Reviewing related work for a research topic, (4) Finding benchmark datasets or baselines for a task, (5) Comparing methods across papers, (6) Summarizing recent advances in a biomedical subfield.
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Paper Research
Workflow
Researching biomedical papers involves these steps:
- Define scope -- narrow the research question with the user
- Search -- query PubMed, Semantic Scholar, and arXiv
- Filter -- by venue quality, citations, recency, and code availability
- Analyze -- extract methods, datasets, metrics, and results
- Synthesize -- compare approaches, identify gaps, create comparison tables
Decision Tree
What is the search goal?
- Find SOTA methods → Search by citation count + recent years, filter by top venues. See search-strategy.md
- Comprehensive literature review → Systematic search across all sources, document inclusion/exclusion criteria. See paper-analysis.md
- Find datasets/benchmarks → Search Papers With Code, check datasets sections of top papers
- Find implementations → Search Papers With Code + GitHub. See paper-analysis.md
Which search source?
- Clinical / medical journals → PubMed (Entrez API)
- ML / AI conferences → Semantic Scholar or arXiv
- Preprints / cutting-edge → arXiv (cs.CV, cs.LG, cs.CL, eess.IV)
- Broadest coverage → Google Scholar (via WebSearch)
What quality threshold?
- Strict (established methods) → Top venues only, >50 citations
- Inclusive (emerging work) → Include workshops, preprints, low citations
ASK the user before starting:
- What is the specific research question or topic?
- What subfield (medical imaging, clinical NLP, drug discovery, genomics)?
- What time range (last 1 year, last 3 years, all time)?
- Are they looking for methods, datasets, benchmarks, or all?
- Want a broad survey or deep dive on fewer papers?
References
| File | Read When |
|---|
| references/search-strategy.md | Using PubMed, Semantic Scholar, and arXiv APIs; filtering by quality; query syntax; organizing results |
| references/top-venues.md | Identifying top venues by subfield: medical imaging, ML/AI, bioinformatics, clinical informatics, pathology |
| references/paper-analysis.md | Structured paper reading template, literature comparison tables, systematic search reporting, finding code on Papers With Code |
