@wentorai/research-plugins 1.1.0 → 1.2.1

package/skills/research/paper-review/latte-review-guide/SKILL.md

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+---
+name: latte-review-guide
+description: "Automate systematic literature reviews with LatteReview AI agents"
+metadata:
+  openclaw:
+    emoji: "☕"
+    category: "research"
+    subcategory: "paper-review"
+    keywords: ["LatteReview", "systematic review", "literature screening", "AI review", "title screening", "PRISMA"]
+    source: "https://github.com/PouriaRouzrokh/LatteReview"
+---
+
+# LatteReview Guide
+
+## Overview
+
+LatteReview is a low-code Python package that uses AI agents to automate systematic literature reviews. It handles title/abstract screening, full-text assessment, data extraction, and PRISMA-compliant reporting — tasks that typically consume hundreds of researcher-hours. Supports multiple LLM backends (Anthropic, OpenAI, local models).
+
+## Installation
+
+```bash
+pip install lattereview
+```
+
+## Core Workflow
+
+### Step 1: Initialize Review
+
+```python
+from lattereview import ReviewProject
+
+# Create a new review project
+project = ReviewProject(
+    name="ML in Medical Imaging Review",
+    research_question="What deep learning architectures are used for "
+                      "medical image segmentation?",
+    inclusion_criteria=[
+        "Uses deep learning for medical image segmentation",
+        "Published in peer-reviewed venue",
+        "Reports quantitative evaluation metrics",
+    ],
+    exclusion_criteria=[
+        "Review/survey articles",
+        "Non-English publications",
+        "Conference abstracts only",
+    ],
+)
+```
+
+### Step 2: Import Papers
+
+```python
+# Import from various sources
+project.import_papers("scopus_export.csv", source="scopus")
+project.import_papers("pubmed_export.csv", source="pubmed")
+
+# Or from a DataFrame
+import pandas as pd
+df = pd.read_csv("papers.csv")
+project.import_from_dataframe(df,
+    title_col="title",
+    abstract_col="abstract",
+    year_col="year",
+)
+
+print(f"Imported {project.total_papers} papers")
+```
+
+### Step 3: AI Screening
+
+```python
+from lattereview.agents import ScreeningAgent
+
+# Configure screening agent
+screener = ScreeningAgent(
+    llm_provider="anthropic",
+    model="claude-sonnet-4-20250514",
+    criteria=project.inclusion_criteria,
+    exclusion=project.exclusion_criteria,
+)
+
+# Title/abstract screening
+results = screener.screen(
+    project.papers,
+    mode="title_abstract",
+    confidence_threshold=0.7,
+)
+
+# Results include: decision, confidence, reasoning
+for paper in results[:3]:
+    print(f"{paper.title}")
+    print(f"  Decision: {paper.decision} "
+          f"(confidence: {paper.confidence:.2f})")
+    print(f"  Reason: {paper.reasoning}")
+```
+
+### Step 4: Data Extraction
+
+```python
+from lattereview.agents import ExtractionAgent
+
+extractor = ExtractionAgent(
+    llm_provider="anthropic",
+    fields={
+        "architecture": "Deep learning architecture used",
+        "dataset": "Medical imaging dataset",
+        "modality": "Imaging modality (CT, MRI, X-ray, etc.)",
+        "dice_score": "Best Dice similarity coefficient reported",
+        "sample_size": "Number of images/patients",
+    },
+)
+
+extracted = extractor.extract(project.included_papers)
+
+# Export structured data
+extracted.to_csv("extracted_data.csv")
+```
+
+### Step 5: Generate Report
+
+```python
+# PRISMA flow diagram
+project.generate_prisma_diagram("prisma.png")
+
+# Summary statistics
+summary = project.summarize()
+print(f"Screened: {summary['screened']}")
+print(f"Included: {summary['included']}")
+print(f"Excluded: {summary['excluded']}")
+```
+
+## Configuration
+
+```python
+# Use different LLM providers
+screener = ScreeningAgent(
+    llm_provider="openai",
+    model="gpt-4o",
+)
+
+# Local models via Ollama
+screener = ScreeningAgent(
+    llm_provider="ollama",
+    model="llama3",
+    base_url="http://localhost:11434",
+)
+```
+
+## Dual-Reviewer Mode
+
+```python
+# Simulate dual-reviewer screening for reliability
+results = screener.dual_screen(
+    project.papers,
+    models=["claude-sonnet-4-20250514", "gpt-4o"],
+    agreement_threshold=0.8,
+)
+
+# Papers with disagreement flagged for human review
+conflicts = [p for p in results if p.agreement < 0.8]
+print(f"{len(conflicts)} papers need human adjudication")
+```
+
+## Use Cases
+
+1. **Systematic reviews**: PRISMA-compliant literature reviews
+2. **Scoping reviews**: Rapid evidence mapping
+3. **Meta-analysis preparation**: Structured data extraction
+4. **Grant applications**: Quick literature landscape assessment
+
+## References
+
+- [LatteReview GitHub](https://github.com/PouriaRouzrokh/LatteReview)
+- [LatteReview Documentation](https://lattereview.readthedocs.io/)
+- Rouzrokh, P. et al. (2024). "LatteReview: AI-Assisted Systematic Literature Reviews."

package/skills/research/paper-review/paper-critique-framework/SKILL.md

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+---
+name: paper-critique-framework
+description: "Structured framework for writing peer review reports and paper critiques"
+metadata:
+  openclaw:
+    emoji: "📋"
+    category: "research"
+    subcategory: "paper-review"
+    keywords: ["peer review", "paper critique", "referee report", "academic review", "manuscript evaluation", "constructive feedback"]
+    source: "https://clawhub.ai/peer-reviewer"
+---
+
+# Paper Critique and Peer Review Framework
+
+## Overview
+
+Writing constructive peer reviews is a core academic skill. This framework provides a systematic approach to evaluating manuscripts — from initial read-through to the final referee report. It covers what reviewers should assess, how to structure feedback, and how to calibrate between different review outcomes (accept, revise, reject). Applicable to conference papers, journal articles, and internal lab reviews.
+
+## The Three-Pass Review Method
+
+### Pass 1: Orientation (15-20 minutes)
+
+Read only these elements:
+- Title, abstract, and keywords
+- Introduction (first and last paragraphs)
+- Section headings and figure captions
+- Conclusion
+
+After Pass 1, answer:
+```
+□ What is the main claim?
+□ What type of contribution? (empirical, theoretical, system, survey)
+□ Is it within the venue's scope?
+□ Does the abstract accurately represent the content?
+□ Initial impression: novel or incremental?
+```
+
+### Pass 2: Detailed Read (60-90 minutes)
+
+Read the full paper. Annotate as you go:
+
+```markdown
+Annotation symbols:
+  ? = I don't understand this
+  ! = This is interesting / strong point
+  X = I disagree / see a problem
+  → = This needs more evidence or justification
+  ≈ = This is similar to [existing work] — check novelty
+```
+
+Focus on:
+- **Claims vs. evidence**: Is every major claim supported by data?
+- **Methodology**: Are the methods appropriate for the research question?
+- **Experimental design**: Are baselines fair? Are ablations sufficient?
+- **Figures and tables**: Do they support the narrative? Are they readable?
+- **Writing quality**: Is it clear, concise, and well-organized?
+
+### Pass 3: Verification (30-60 minutes)
+
+For papers you're seriously evaluating:
+- Check key references — do they say what the authors claim?
+- Verify mathematical derivations (spot-check, not exhaustive)
+- Examine statistical claims (p-values, confidence intervals, effect sizes)
+- Check for cherry-picking in results (only best runs? selected metrics?)
+- Look for missing baselines that should have been compared
+
+## Review Report Structure
+
+```markdown
+## Summary (3-5 sentences)
+[Describe what the paper does, the approach, and the main finding.
+ Demonstrate that you understood the paper.]
+
+## Strengths (bulleted list)
+- S1: [Specific strength with evidence from the paper]
+- S2: [Another strength]
+- S3: [Another strength]
+
+## Weaknesses (bulleted list, ordered by severity)
+- W1 (Major): [Specific weakness + why it matters + suggestion to fix]
+- W2 (Major): [Another major weakness]
+- W3 (Minor): [A less critical issue]
+- W4 (Minor): [Another minor issue]
+
+## Questions for Authors
+- Q1: [Something you'd like clarified]
+- Q2: [A concern that the authors might be able to address]
+
+## Detailed Comments
+[Page/line-specific comments, typos, suggestions]
+
+## Overall Assessment
+Recommendation: [Strong Accept / Accept / Weak Accept / Borderline /
+                  Weak Reject / Reject / Strong Reject]
+Confidence: [High / Medium / Low]
+```
+
+## Assessment Criteria by Dimension
+
+| Dimension | Questions to Ask | Weight |
+|-----------|-----------------|--------|
+| **Novelty** | Is the idea new? Is the contribution beyond incremental? | High |
+| **Significance** | Would this matter to the community? Does it advance the field? | High |
+| **Soundness** | Are the methods correct? Are conclusions supported? | High |
+| **Clarity** | Is it well-written? Can it be understood and reproduced? | Medium |
+| **Completeness** | Are related works covered? Are experiments thorough? | Medium |
+| **Reproducibility** | Could someone replicate this? Code/data available? | Medium |
+
+### Calibration Guide
+
+```
+Strong Accept: Significant contribution, technically sound, well-written.
+  Would be a highlight of the venue.
+
+Accept: Solid contribution with minor issues. Advances the field.
+  Worth publishing as-is or with minor revisions.
+
+Weak Accept: Has merit but notable weaknesses. Contribution is real but modest.
+  Borderline for this venue; would be accepted at a less selective venue.
+
+Borderline: Equal arguments for and against. Significant weaknesses offset
+  by some novelty. Depends on other reviews.
+
+Weak Reject: Interesting direction but fundamental issues not addressed.
+  Major revisions needed that likely require a new submission cycle.
+
+Reject: Significant problems in novelty, soundness, or relevance.
+  Not suitable for this venue even with revisions.
+
+Strong Reject: Fundamental flaws. Clearly below threshold.
+```
+
+## Common Review Pitfalls to Avoid
+
+| Pitfall | Better Approach |
+|---------|----------------|
+| "The writing needs improvement" (vague) | Give 2-3 specific examples with suggested fixes |
+| Rejecting for not solving YOUR problem | Evaluate the paper on its own stated goals |
+| Demanding impossible experiments | Suggest feasible improvements within scope |
+| Ignoring supplementary material | Check appendix — authors may have addressed your concern |
+| Being harsh without being constructive | Every weakness should include a suggestion for improvement |
+| Reviewing too quickly | Block dedicated time; a rushed review harms both authors and science |
+| Citing only your own work as "missing" | Only cite if genuinely relevant, not self-promotion |
+
+## Reviewing Different Paper Types
+
+### Empirical Papers
+- Are datasets described completely? (Size, source, splits, preprocessing)
+- Are baselines appropriate and fairly tuned?
+- Statistical significance: error bars, multiple runs, significance tests
+- Ablation studies: which components contribute to the gain?
+
+### Systems Papers
+- Is the system actually built and evaluated (not just designed)?
+- Performance at scale: latency, throughput, resource usage
+- Comparison with existing systems (not just algorithms)
+- Deployment experience or case studies
+
+### Survey/Position Papers
+- Coverage: are major relevant works included?
+- Taxonomy: is the organizational framework useful and complete?
+- Analysis: does the survey add value beyond listing papers?
+- Recency: are the most recent advances covered?
+
+## Ethics Considerations
+
+```markdown
+During review, check:
+□ Are human subjects involved? Was IRB/ethics approval obtained?
+□ Are there potential harms from the technology described?
+□ Is the data collection ethical? (Consent, privacy, bias)
+□ Are dual-use concerns addressed? (Misuse potential)
+□ Are limitations and societal implications discussed?
+```
+
+## References
+
+- Smith, R. (2006). "Peer review: a flawed process at the heart of science and journals." *Journal of the Royal Society of Medicine*, 99(4), 178-182.
+- [NeurIPS Reviewer Guidelines](https://neurips.cc/Conferences/2025/ReviewerGuidelines)
+- [ACL Reviewer Tutorial](https://aclrollingreview.org/reviewertutorial)
+- Cormode, G. (2009). "How NOT to review a paper." *ACM SIGMOD Record*, 37(4), 100-104.

package/skills/tools/code-exec/contextplus-mcp-guide/SKILL.md

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+---
+name: contextplus-mcp-guide
+description: "Semantic code search MCP with Tree-sitter AST and RAG"
+metadata:
+  openclaw:
+    emoji: "🌳"
+    category: "tools"
+    subcategory: "code-exec"
+    keywords: ["semantic search", "code search", "Tree-sitter", "AST", "MCP", "RAG"]
+    source: "https://github.com/ForLoopCodes/contextplus"
+---
+
+# ContextPlus MCP Guide
+
+## Overview
+
+ContextPlus is an MCP server that provides semantic code search using Tree-sitter AST parsing and RAG. It indexes codebases by extracting functions, classes, and modules as semantic units, embeds them for vector search, and serves results to any MCP-compatible LLM client. Helps AI agents understand large codebases by retrieving the most relevant code context.
+
+## Installation
+
+```bash
+npm install -g @contextplus/mcp-server
+
+# Or run directly
+npx @contextplus/mcp-server --workspace ./your-project
+```
+
+## MCP Configuration
+
+```json
+{
+  "mcpServers": {
+    "contextplus": {
+      "command": "npx",
+      "args": ["@contextplus/mcp-server",
+               "--workspace", "./project"],
+      "env": {
+        "EMBEDDING_MODEL": "all-MiniLM-L6-v2",
+        "MAX_RESULTS": "10"
+      }
+    }
+  }
+}
+```
+
+## Features
+
+```markdown
+### Semantic Understanding
+- **Tree-sitter parsing**: Extract functions, classes, types
+- **AST-aware chunking**: Split code at logical boundaries
+- **Cross-reference**: Track imports, calls, dependencies
+- **Multi-language**: Python, TypeScript, Go, Rust, Java, C++
+
+### Search Capabilities
+- Natural language code search ("find auth middleware")
+- Symbol search (function/class by name)
+- Dependency graph ("what calls this function")
+- Semantic similarity (find similar implementations)
+
+### MCP Tools Provided
+- `search_code(query)` — Semantic code search
+- `get_symbol(name)` — Get symbol definition + usages
+- `get_dependencies(file)` — File dependency graph
+- `get_context(file, line)` — Surrounding context for a location
+```
+
+## Usage Examples
+
+```markdown
+### In Claude Code / LLM Chat
+
+"Find all authentication-related functions"
+→ Returns: auth middleware, login handler, token validation
+
+"What functions call the database connection pool?"
+→ Returns: dependency graph with callers
+
+"Find code similar to this error handling pattern"
+→ Returns: semantically similar try/catch blocks
+```
+
+## Indexing Configuration
+
+```json
+{
+  "indexing": {
+    "include": ["src/**/*.ts", "lib/**/*.py"],
+    "exclude": ["node_modules", "__pycache__", ".git"],
+    "languages": ["typescript", "python"],
+    "chunk_strategy": "ast",
+    "max_chunk_tokens": 500,
+    "rebuild_on_change": true
+  }
+}
+```
+
+## Use Cases
+
+1. **Code understanding**: Navigate unfamiliar codebases
+2. **Agent context**: Provide relevant code to LLM agents
+3. **Code review**: Find related patterns and similar code
+4. **Refactoring**: Discover all usages before changing code
+5. **Documentation**: Generate docs from code structure
+
+## References
+
+- [ContextPlus GitHub](https://github.com/ForLoopCodes/contextplus)
+- [Tree-sitter](https://tree-sitter.github.io/tree-sitter/)
+- [MCP Specification](https://modelcontextprotocol.io/)

package/skills/tools/diagram/clawphd-guide/SKILL.md

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+---
+name: clawphd-guide
+description: "Agent for converting papers to diagrams, posters, and videos"
+metadata:
+  openclaw:
+    emoji: "🎬"
+    category: "tools"
+    subcategory: "diagram"
+    keywords: ["paper visualization", "poster generation", "research video", "diagram agent", "visual abstract", "presentation"]
+    source: "https://github.com/ZhihaoAIRobotic/ClawPhD"
+---
+
+# ClawPhD Guide
+
+## Overview
+
+ClawPhD is an AI agent that converts research papers into visual formats — architecture diagrams, research posters, visual abstracts, and video presentations. It reads paper PDFs, extracts key concepts and results, and generates publication-ready visual materials. Useful for conference presentations, social media dissemination, and research communication.
+
+## Features
+
+```
+Paper PDF / LaTeX
+      ↓
+  Content Extraction Agent
+  ├── Key contributions
+  ├── Architecture / method
+  ├── Results tables and figures
+  └── Abstract and conclusions
+      ↓
+  Visual Generation Agent
+  ├── Architecture diagram (SVG/PNG)
+  ├── Research poster (A0 PDF)
+  ├── Visual abstract (social media)
+  ├── Slide deck (Beamer/PPTX)
+  └── Video narration (MP4)
+```
+
+## Usage
+
+```python
+from clawphd import ClawPhD
+
+agent = ClawPhD(llm_provider="anthropic")
+
+# Generate architecture diagram
+diagram = agent.generate_diagram(
+    paper="paper.pdf",
+    style="clean",       # clean, detailed, minimal
+    format="svg",
+    focus="method",      # method, pipeline, architecture
+)
+diagram.save("architecture.svg")
+
+# Generate research poster
+poster = agent.generate_poster(
+    paper="paper.pdf",
+    template="academic",   # academic, conference, minimal
+    size="A0",
+    color_scheme="blue",
+)
+poster.save("poster.pdf")
+
+# Generate visual abstract
+abstract = agent.generate_visual_abstract(
+    paper="paper.pdf",
+    format="png",
+    dimensions=(1200, 630),  # Twitter/LinkedIn optimal
+)
+abstract.save("visual_abstract.png")
+```
+
+## Diagram Styles
+
+```python
+# Architecture diagram
+diagram = agent.generate_diagram(
+    paper="paper.pdf",
+    style="clean",
+    components={
+        "show_data_flow": True,
+        "show_dimensions": True,
+        "show_loss_functions": False,
+        "annotation_level": "medium",
+    },
+)
+
+# Pipeline diagram
+pipeline = agent.generate_diagram(
+    paper="paper.pdf",
+    focus="pipeline",
+    layout="horizontal",  # horizontal, vertical, circular
+)
+
+# Comparison diagram
+comparison = agent.generate_comparison(
+    papers=["paper_a.pdf", "paper_b.pdf"],
+    aspects=["architecture", "performance", "complexity"],
+)
+```
+
+## Poster Generation
+
+```python
+# Conference poster with full customization
+poster = agent.generate_poster(
+    paper="paper.pdf",
+    template="neurips",
+    sections=[
+        "title_block",
+        "motivation",
+        "method",
+        "key_results",
+        "conclusions",
+        "qr_code",
+    ],
+    style={
+        "font_family": "Helvetica",
+        "heading_color": "#2563EB",
+        "background": "#FFFFFF",
+        "columns": 3,
+    },
+)
+```
+
+## Slide Generation
+
+```python
+# Generate presentation slides
+slides = agent.generate_slides(
+    paper="paper.pdf",
+    format="beamer",     # beamer, pptx, reveal_js
+    num_slides=15,
+    include_speaker_notes=True,
+    style="metropolis",  # Beamer theme
+)
+slides.save("presentation.tex")
+```
+
+## Use Cases
+
+1. **Conference posters**: Generate posters from papers
+2. **Social media**: Visual abstracts for paper promotion
+3. **Presentations**: Quick slide decks from papers
+4. **Architecture diagrams**: Clean method visualizations
+5. **Teaching**: Visual explanations of research papers
+
+## References
+
+- [ClawPhD GitHub](https://github.com/ZhihaoAIRobotic/ClawPhD)