Paper-to-Agent Guide
A skill for transforming published research papers into interactive AI agents that can answer questions, explain methodology, and help replicate findings. Based on Paper2Agent (2K stars), this skill guides the agent through extracting structured knowledge from academic papers and creating conversational interfaces for deep exploration.
Overview
Traditional paper reading is linear and passive. Paper-to-Agent converts this into an active, queryable experience. By parsing a paper's structure, extracting key claims, methodology details, and results, the agent becomes an expert on that specific paper, ready to answer follow-up questions, explain complex sections, and connect findings to the broader literature.
This approach is especially valuable for interdisciplinary researchers who need to quickly understand papers outside their primary expertise, for journal clubs seeking deeper discussion, and for students learning to critically evaluate published research.
Paper Parsing Workflow
The agent should follow this structured workflow when converting a paper to an interactive agent:
Step 1: Structure Extraction
- Identify the paper's sections (abstract, introduction, methods, results, discussion, references)
- Extract the title, authors, affiliations, and publication venue
- Identify figure and table captions along with their referenced locations
- Note supplementary materials and their availability
- Detect the paper type (empirical, theoretical, review, meta-analysis)
Step 2: Claim Extraction
- Identify the primary research question or hypothesis
- Extract all major claims made in the paper
- Map each claim to its supporting evidence (data, citations, arguments)
- Note the strength of evidence for each claim (strong, moderate, suggestive)
- Identify limitations acknowledged by the authors
Step 3: Methodology Mapping
- Document the complete experimental or analytical pipeline
- Extract parameter values, dataset descriptions, and evaluation metrics
- Identify software tools and libraries used
- Note any preprocessing or data cleaning steps
- Map the methodology to established frameworks in the field
Interactive Exploration Capabilities
Once a paper has been parsed, the agent can support these interaction patterns:
Question-Answering
- Answer specific questions about the paper's content with source references
- Explain technical terms in context of how the paper uses them
- Compare the paper's approach to common alternatives
- Identify what the paper does and does not address
- Generate summaries at different levels of detail (tweet-length, abstract, detailed)
Critical Analysis
- Evaluate the validity of statistical analyses
- Identify potential confounds not addressed by the authors
- Assess whether conclusions follow from the presented evidence
- Compare results to related work in the field
- Suggest follow-up experiments that would strengthen the findings
Replication Assistance
- Generate step-by-step replication guides from the methods section
- Identify missing details needed for exact replication
- Suggest parameter ranges for robustness checks
- Create data collection templates based on the paper's design
- List required resources (compute, data, equipment) for replication
Knowledge Graph Construction
The skill supports building knowledge graphs from processed papers:
- Extract entities (methods, datasets, metrics, tools, concepts)
- Map relationships between entities (uses, extends, contradicts, supports)
- Link to external knowledge bases (OpenAlex, CrossRef, DOI)
- Track citation chains for key claims
- Identify research lineages and methodological evolution
Multi-Paper Analysis
When multiple papers have been processed, the agent can:
- Compare methodologies across papers addressing similar questions
- Identify consensus findings and areas of disagreement
- Trace the evolution of a research direction over time
- Build synthesis summaries combining evidence from multiple sources
- Detect gaps in the literature that no existing paper addresses
Integration with Research-Claw
This skill connects with other Research-Claw capabilities:
- Use literature search skills to find papers for processing
- Feed extracted knowledge into writing skills for literature reviews
- Connect methodology details to analysis skills for replication
- Store parsed papers in the local knowledge base for future reference
- Generate citation entries compatible with reference management tools
Practical Tips
- Start with the abstract and conclusion to determine if full parsing is worthwhile
- Focus deep extraction on methods and results sections for empirical papers
- For theoretical papers, prioritize definitions, theorems, and proof sketches
- Always verify extracted claims against the original text before presenting them
- Flag areas where the paper's writing is ambiguous or inconsistent
- Use the parsed representation to generate discussion questions for journal clubs
1---2name: paper-to-agent-guide3description: Transform research papers into interactive AI agents for exploration4---56# Paper-to-Agent Guide78A skill for transforming published research papers into interactive AI agents that can answer questions, explain methodology, and help replicate findings. Based on Paper2Agent (2K stars), this skill guides the agent through extracting structured knowledge from academic papers and creating conversational interfaces for deep exploration.910## Overview1112Traditional paper reading is linear and passive. Paper-to-Agent converts this into an active, queryable experience. By parsing a paper's structure, extracting key claims, methodology details, and results, the agent becomes an expert on that specific paper, ready to answer follow-up questions, explain complex sections, and connect findings to the broader literature.1314This approach is especially valuable for interdisciplinary researchers who need to quickly understand papers outside their primary expertise, for journal clubs seeking deeper discussion, and for students learning to critically evaluate published research.1516## Paper Parsing Workflow1718The agent should follow this structured workflow when converting a paper to an interactive agent:1920**Step 1: Structure Extraction**21- Identify the paper's sections (abstract, introduction, methods, results, discussion, references)22- Extract the title, authors, affiliations, and publication venue23- Identify figure and table captions along with their referenced locations24- Note supplementary materials and their availability25- Detect the paper type (empirical, theoretical, review, meta-analysis)2627**Step 2: Claim Extraction**28- Identify the primary research question or hypothesis29- Extract all major claims made in the paper30- Map each claim to its supporting evidence (data, citations, arguments)31- Note the strength of evidence for each claim (strong, moderate, suggestive)32- Identify limitations acknowledged by the authors3334**Step 3: Methodology Mapping**35- Document the complete experimental or analytical pipeline36- Extract parameter values, dataset descriptions, and evaluation metrics37- Identify software tools and libraries used38- Note any preprocessing or data cleaning steps39- Map the methodology to established frameworks in the field4041## Interactive Exploration Capabilities4243Once a paper has been parsed, the agent can support these interaction patterns:4445**Question-Answering**46- Answer specific questions about the paper's content with source references47- Explain technical terms in context of how the paper uses them48- Compare the paper's approach to common alternatives49- Identify what the paper does and does not address50- Generate summaries at different levels of detail (tweet-length, abstract, detailed)5152**Critical Analysis**53- Evaluate the validity of statistical analyses54- Identify potential confounds not addressed by the authors55- Assess whether conclusions follow from the presented evidence56- Compare results to related work in the field57- Suggest follow-up experiments that would strengthen the findings5859**Replication Assistance**60- Generate step-by-step replication guides from the methods section61- Identify missing details needed for exact replication62- Suggest parameter ranges for robustness checks63- Create data collection templates based on the paper's design64- List required resources (compute, data, equipment) for replication6566## Knowledge Graph Construction6768The skill supports building knowledge graphs from processed papers:6970- Extract entities (methods, datasets, metrics, tools, concepts)71- Map relationships between entities (uses, extends, contradicts, supports)72- Link to external knowledge bases (OpenAlex, CrossRef, DOI)73- Track citation chains for key claims74- Identify research lineages and methodological evolution7576## Multi-Paper Analysis7778When multiple papers have been processed, the agent can:7980- Compare methodologies across papers addressing similar questions81- Identify consensus findings and areas of disagreement82- Trace the evolution of a research direction over time83- Build synthesis summaries combining evidence from multiple sources84- Detect gaps in the literature that no existing paper addresses8586## Integration with Research-Claw8788This skill connects with other Research-Claw capabilities:8990- Use literature search skills to find papers for processing91- Feed extracted knowledge into writing skills for literature reviews92- Connect methodology details to analysis skills for replication93- Store parsed papers in the local knowledge base for future reference94- Generate citation entries compatible with reference management tools9596## Practical Tips9798- Start with the abstract and conclusion to determine if full parsing is worthwhile99- Focus deep extraction on methods and results sections for empirical papers100- For theoretical papers, prioritize definitions, theorems, and proof sketches101- Always verify extracted claims against the original text before presenting them102- Flag areas where the paper's writing is ambiguous or inconsistent103- Use the parsed representation to generate discussion questions for journal clubs
brycewang-stanford