paper-research

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.

Paper Research

Workflow

Researching biomedical papers involves these steps:

1. Define scope -- narrow the research question with the user
2. Search -- query PubMed, Semantic Scholar, and arXiv
3. Filter -- by venue quality, citations, recency, and code availability
4. Analyze -- extract methods, datasets, metrics, and results
5. 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