@synsci/cli-darwin-x64 1.1.70 → 1.1.72

package/bin/skills/venue-templates/references/venue_writing_styles.md

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+# Venue Writing Styles: Master Guide
+
+This guide provides an overview of how writing style varies across publication venues. Understanding these differences is essential for crafting papers that read like authentic publications at each venue.
+
+**Last Updated**: 2024
+
+---
+
+## The Style Spectrum
+
+Scientific writing style exists on a spectrum from **broadly accessible** to **deeply technical**:
+
+```
+Accessible ◄─────────────────────────────────────────────► Technical
+
+Nature/Science    PNAS    Cell    IEEE Trans    NeurIPS    Specialized
+   │                │       │         │            │         Journals
+   │                │       │         │            │            │
+   ▼                ▼       ▼         ▼            ▼            ▼
+General           Mixed   Deep     Field      Dense ML      Expert
+audience         depth  biology   experts    researchers    only
+```
+
+## Quick Style Reference
+
+| Venue Type | Audience | Tone | Voice | Abstract Style |
+|------------|----------|------|-------|----------------|
+| **Nature/Science** | Educated non-specialists | Accessible, engaging | Active, first-person OK | Flowing paragraphs, no jargon |
+| **Cell Press** | Biologists | Mechanistic, precise | Mixed | Summary + eTOC blurb + Highlights |
+| **Medical (NEJM/Lancet)** | Clinicians | Evidence-focused | Formal | Structured (Background/Methods/Results/Conclusions) |
+| **PLOS/BMC** | Researchers | Standard academic | Neutral | IMRaD structured or flowing |
+| **IEEE/ACM** | Engineers/CS | Technical | Passive common | Concise, technical |
+| **ML Conferences** | ML researchers | Dense technical | Mixed | Numbers upfront, key results |
+| **NLP Conferences** | NLP researchers | Technical | Varied | Task-focused, benchmarks |
+
+---
+
+## High-Impact Journals (Nature, Science, Cell)
+
+### Core Philosophy
+
+High-impact multidisciplinary journals prioritize **broad significance** over technical depth. The question is not "Is this technically sound?" but "Why should a scientist outside this field care?"
+
+### Key Writing Principles
+
+1. **Start with the big picture**: Open with why this matters to science/society
+2. **Minimize jargon**: Define specialized terms; prefer common words
+3. **Tell a story**: Results should flow as a narrative, not a data dump
+4. **Emphasize implications**: What does this change about our understanding?
+5. **Accessible figures**: Schematics and models over raw data plots
+
+### Structural Differences
+
+**Nature/Science** vs. **Specialized Journals**:
+
+| Element | Nature/Science | Specialized Journal |
+|---------|---------------|---------------------|
+| Introduction | 3-4 paragraphs, broad → specific | Extensive literature review |
+| Methods | Often in supplement or brief | Full detail in main text |
+| Results | Organized by finding/story | Organized by experiment |
+| Discussion | Implications first, then caveats | Detailed comparison to literature |
+| Figures | Conceptual schematics valued | Raw data emphasized |
+
+### Example: Same Finding, Different Styles
+
+**Nature style**:
+> "We discovered that protein X acts as a molecular switch controlling cell fate decisions during development, resolving a longstanding question about how stem cells choose their destiny."
+
+**Specialized journal style**:
+> "Using CRISPR-Cas9 knockout in murine embryonic stem cells (mESCs), we demonstrate that protein X (encoded by gene ABC1) regulates the expression of pluripotency factors Oct4, Sox2, and Nanog through direct promoter binding, as confirmed by ChIP-seq analysis (n=3 biological replicates, FDR < 0.05)."
+
+---
+
+## Medical Journals (NEJM, Lancet, JAMA, BMJ)
+
+### Core Philosophy
+
+Medical journals prioritize **clinical relevance** and **patient outcomes**. Every finding must connect to practice.
+
+### Key Writing Principles
+
+1. **Patient-centered language**: "Patients receiving treatment X" not "Treatment X subjects"
+2. **Evidence strength**: Careful hedging based on study design
+3. **Clinical actionability**: "So what?" for practicing physicians
+4. **Absolute numbers**: Report absolute risk reduction, not just relative
+5. **Structured abstracts**: Required with labeled sections
+
+### Structured Abstract Format (Medical)
+
+```
+Background: [1-2 sentences on problem and rationale]
+
+Methods: [Study design, setting, participants, intervention, outcomes, analysis]
+
+Results: [Primary outcome with confidence intervals, secondary outcomes, adverse events]
+
+Conclusions: [Clinical implications, limitations acknowledged]
+```
+
+### Evidence Language Conventions
+
+| Study Design | Appropriate Language |
+|-------------|---------------------|
+| RCT | "Treatment X reduced mortality by..." |
+| Observational | "Treatment X was associated with reduced mortality..." |
+| Case series | "These findings suggest that treatment X may..." |
+| Case report | "This case illustrates that treatment X can..." |
+
+---
+
+## ML/AI Conferences (NeurIPS, ICML, ICLR, CVPR)
+
+### Core Philosophy
+
+ML conferences value **novelty**, **rigorous experiments**, and **reproducibility**. The focus is on advancing the state of the art with empirical evidence.
+
+### Key Writing Principles
+
+1. **Contribution bullets**: Numbered list in introduction stating exactly what's new
+2. **Baselines are critical**: Compare against strong, recent baselines
+3. **Ablations expected**: Show what parts of your method matter
+4. **Reproducibility**: Seeds, hyperparameters, compute requirements
+5. **Limitations section**: Honest acknowledgment (increasingly required)
+
+### Introduction Structure (ML Conferences)
+
+```
+[Paragraph 1: Problem motivation - why this matters]
+
+[Paragraph 2: Limitations of existing approaches]
+
+[Paragraph 3: Our approach at high level]
+
+Our contributions are as follows:
+• We propose [method name], a novel approach to [problem] that [key innovation].
+• We provide theoretical analysis showing [guarantees/properties].
+• We demonstrate state-of-the-art results on [benchmarks], improving over [baseline] by [X%].
+• We release code and models at [anonymous URL for review].
+```
+
+### Abstract Style (ML Conferences)
+
+ML abstracts are **dense and numbers-focused**:
+
+> "We present TransformerX, a novel architecture for long-range sequence modeling that achieves O(n log n) complexity while maintaining expressivity. On the Long Range Arena benchmark, TransformerX achieves 86.2% average accuracy, outperforming Transformer (65.4%) and Performer (78.1%). On language modeling, TransformerX matches GPT-2 perplexity (18.4) using 40% fewer parameters. We provide theoretical analysis showing TransformerX can approximate any continuous sequence-to-sequence function."
+
+### Experiment Section Expectations
+
+1. **Datasets**: Standard benchmarks, dataset statistics
+2. **Baselines**: Recent strong methods, fair comparisons
+3. **Main results table**: Clear, comprehensive
+4. **Ablation studies**: Remove/modify components systematically
+5. **Analysis**: Error analysis, qualitative examples, failure cases
+6. **Computational cost**: Training time, inference speed, memory
+
+---
+
+## CS Conferences (ACL, EMNLP, CHI, SIGKDD)
+
+### ACL/EMNLP (NLP)
+
+- **Task-focused**: Clear problem definition
+- **Benchmark-heavy**: Standard datasets (GLUE, SQuAD, etc.)
+- **Error analysis valued**: Where does it fail?
+- **Human evaluation**: Often expected alongside automatic metrics
+- **Ethical considerations**: Bias, fairness, environmental cost
+
+### CHI (Human-Computer Interaction)
+
+- **User-centered**: Focus on humans, not just technology
+- **Study design details**: Participant recruitment, IRB approval
+- **Qualitative accepted**: Interview studies, ethnography valid
+- **Design implications**: Concrete takeaways for practitioners
+- **Accessibility**: Consider diverse user populations
+
+### SIGKDD (Data Mining)
+
+- **Scalability emphasis**: Handle large data
+- **Real-world applications**: Industry datasets valued
+- **Efficiency metrics**: Time and space complexity
+- **Novelty in methods or applications**: Both paths valid
+
+---
+
+## Adapting Between Venue Types
+
+### Journal → ML Conference
+
+When converting a journal paper to conference format:
+
+1. **Condense introduction**: Remove extensive background
+2. **Add contribution list**: Explicitly enumerate contributions
+3. **Restructure results**: Organize as experiments, add ablations
+4. **Remove separate discussion**: Integrate interpretation briefly
+5. **Add reproducibility section**: Seeds, hyperparameters, code
+
+### ML Conference → Journal
+
+When expanding a conference paper to journal:
+
+1. **Expand related work**: Comprehensive literature review
+2. **Detailed methods**: Full algorithmic description
+3. **More experiments**: Additional datasets, analyses
+4. **Extended discussion**: Implications, limitations, future work
+5. **Appendix → main text**: Move important details up
+
+### Specialized → High-Impact Journal
+
+When targeting Nature/Science/Cell from a specialized venue:
+
+1. **Lead with significance**: Why does this matter broadly?
+2. **Reduce jargon by 80%**: Replace technical terms
+3. **Add conceptual figures**: Schematics, models, not just data
+4. **Story-driven results**: Narrative flow, not experiment-by-experiment
+5. **Broaden discussion**: Implications beyond the subfield
+
+---
+
+## Voice and Tone Guidelines
+
+### Active vs. Passive Voice
+
+| Venue | Preference | Example |
+|-------|-----------|---------|
+| Nature/Science | Active encouraged | "We discovered that..." |
+| Cell | Mixed | "Our results demonstrate..." |
+| Medical | Passive common | "Patients were randomized to..." |
+| IEEE | Passive traditional | "The algorithm was implemented..." |
+| ML Conferences | Active preferred | "We propose a method that..." |
+
+### First Person Usage
+
+| Venue | First Person | Example |
+|-------|-------------|---------|
+| Nature/Science | Yes (we) | "We show that..." |
+| Cell | Yes (we) | "We found that..." |
+| Medical | Sometimes | "We conducted a trial..." |
+| IEEE | Less common | Prefer "This paper presents..." |
+| ML Conferences | Yes (we) | "We introduce..." |
+
+### Hedging and Certainty
+
+| Claim Strength | Language |
+|---------------|----------|
+| Strong | "X causes Y" (only with causal evidence) |
+| Moderate | "X is associated with Y" / "X leads to Y" |
+| Tentative | "X may contribute to Y" / "X suggests that..." |
+| Speculative | "It is possible that X..." / "One interpretation is..." |
+
+---
+
+## Common Style Errors by Venue
+
+### Nature/Science Submissions
+
+❌ Too technical: "We used CRISPR-Cas9 with sgRNAs targeting exon 3..."
+✅ Accessible: "Using gene-editing technology, we disabled the gene..."
+
+❌ Dry opening: "Protein X is involved in cellular signaling..."
+✅ Engaging opening: "How do cells decide their fate? We discovered that..."
+
+### ML Conference Submissions
+
+❌ Vague contributions: "We present a new method for X"
+✅ Specific contributions: "We propose Method Y that achieves Z% improvement on benchmark W"
+
+❌ Missing ablations: Only showing full method results
+✅ Complete: Table showing contribution of each component
+
+### Medical Journal Submissions
+
+❌ Missing absolute numbers: "50% reduction in risk"
+✅ Complete: "50% relative reduction (ARR 2.5%, NNT 40)"
+
+❌ Causal language for observational data: "Treatment caused improvement"
+✅ Appropriate: "Treatment was associated with improvement"
+
+---
+
+## Quick Checklist Before Submission
+
+### All Venues
+- [ ] Abstract matches venue style (flowing vs. structured)
+- [ ] Voice/tone appropriate for audience
+- [ ] Jargon level appropriate
+- [ ] Figures match venue expectations
+- [ ] Citation style correct
+
+### High-Impact Journals (Nature/Science/Cell)
+- [ ] Broad significance clear in first paragraph
+- [ ] Non-specialist can understand abstract
+- [ ] Story-driven results narrative
+- [ ] Conceptual figures included
+- [ ] Implications emphasized
+
+### ML Conferences
+- [ ] Contribution list in introduction
+- [ ] Strong baselines included
+- [ ] Ablation studies present
+- [ ] Reproducibility information complete
+- [ ] Limitations acknowledged
+
+### Medical Journals
+- [ ] Structured abstract (if required)
+- [ ] Patient-centered language
+- [ ] Evidence strength appropriate
+- [ ] Absolute numbers reported
+- [ ] CONSORT/STROBE compliance
+
+---
+
+## See Also
+
+- `nature_science_style.md` - Detailed Nature/Science writing guide
+- `cell_press_style.md` - Cell family journal conventions
+- `medical_journal_styles.md` - NEJM, Lancet, JAMA, BMJ guide
+- `ml_conference_style.md` - NeurIPS, ICML, ICLR, CVPR conventions
+- `cs_conference_style.md` - ACL, CHI, SIGKDD guide
+- `reviewer_expectations.md` - What reviewers look for by venue
+
+

package/bin/skills/venue-templates/scripts/customize_template.py

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+#!/usr/bin/env python3
+"""
+Customize Template Script
+Customize LaTeX templates with author information and project details.
+
+Usage:
+    python customize_template.py --template nature_article.tex --output my_paper.tex
+    python customize_template.py --template nature_article.tex --title "My Research" --output my_paper.tex
+    python customize_template.py --interactive
+"""
+
+import argparse
+import re
+from pathlib import Path
+
+
+def get_skill_path():
+    """Get the path to the venue-templates skill directory."""
+    script_dir = Path(__file__).parent
+    skill_dir = script_dir.parent
+    return skill_dir
+
+
+def find_template(template_name):
+    """Find template file in assets directory."""
+    skill_path = get_skill_path()
+    assets_path = skill_path / "assets"
+
+    # Search in all subdirectories
+    for subdir in ["journals", "posters", "grants"]:
+        template_path = assets_path / subdir / template_name
+        if template_path.exists():
+            return template_path
+
+    return None
+
+
+def customize_template(template_path, output_path, **kwargs):
+    """Customize a template with provided information."""
+
+    # Read template
+    with open(template_path, 'r') as f:
+        content = f.read()
+
+    # Replace placeholders
+    replacements = {
+        'title': ([r'Insert Your Title Here[^}]*', r'Your [^}]*Title[^}]*Here[^}]*'], kwargs.get('title', '')),
+        'authors': (
+            [r'First Author\\textsuperscript\{1\}, Second Author[^}]*', r'First Author.*Second Author.*Third Author'],
+            kwargs.get('authors', ''),
+        ),
+        'affiliations': (
+            [r'Department Name, Institution Name, City, State[^\\]*', r'Department of [^,]*, University Name[^\\]*'],
+            kwargs.get('affiliations', ''),
+        ),
+        'email': ([r'first\.author@university\.edu', r'\[email protected\]'], kwargs.get('email', '')),
+    }
+
+    # Apply replacements
+    modified = False
+    for key, (patterns, replacement) in replacements.items():
+        if replacement:
+            for pattern in patterns:
+                if re.search(pattern, content):
+                    content = re.sub(pattern, replacement, content, count=1)
+                    modified = True
+                    print(f"✓ Replaced {key}")
+
+    # Write output
+    with open(output_path, 'w') as f:
+        f.write(content)
+
+    if modified:
+        print(f"\n✓ Customized template saved to: {output_path}")
+    else:
+        print(f"\n⚠️  Template copied to: {output_path}")
+        print("   No customizations applied (no matching placeholders found or no values provided)")
+
+    print("\nNext steps:")
+    print(f"1. Open {output_path} in your LaTeX editor")
+    print("2. Replace remaining placeholders")
+    print("3. Add your content")
+    print("4. Compile with pdflatex or your preferred LaTeX compiler")
+
+
+def interactive_mode():
+    """Run in interactive mode."""
+    print("\n=== Template Customization (Interactive Mode) ===\n")
+
+    # List available templates
+    skill_path = get_skill_path()
+    assets_path = skill_path / "assets"
+
+    print("Available templates:\n")
+    templates = []
+    for i, subdir in enumerate(["journals", "posters", "grants"], 1):
+        subdir_path = assets_path / subdir
+        if subdir_path.exists():
+            print(f"{subdir.upper()}:")
+            for j, template_file in enumerate(sorted(subdir_path.glob("*.tex")), 1):
+                templates.append(template_file)
+                print(f"  {len(templates)}. {template_file.name}")
+
+    print()
+
+    # Select template
+    while True:
+        try:
+            choice = int(input(f"Select template (1-{len(templates)}): "))
+            if 1 <= choice <= len(templates):
+                template_path = templates[choice - 1]
+                break
+            else:
+                print(f"Please enter a number between 1 and {len(templates)}")
+        except ValueError:
+            print("Please enter a valid number")
+
+    print(f"\nSelected: {template_path.name}\n")
+
+    # Get customization info
+    title = input("Paper title (press Enter to skip): ").strip()
+    authors = input("Authors (e.g., 'John Doe, Jane Smith') (press Enter to skip): ").strip()
+    affiliations = input("Affiliations (press Enter to skip): ").strip()
+    email = input("Corresponding email (press Enter to skip): ").strip()
+
+    # Output file
+    default_output = f"my_{template_path.stem}.tex"
+    output = input(f"Output filename [{default_output}]: ").strip()
+    if not output:
+        output = default_output
+
+    output_path = Path(output)
+
+    # Customize
+    print()
+    customize_template(template_path, output_path, title=title, authors=authors, affiliations=affiliations, email=email)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Customize LaTeX templates with author and project information",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  %(prog)s --interactive
+  %(prog)s --template nature_article.tex --output my_paper.tex
+  %(prog)s --template neurips_article.tex --title "My ML Research" --output my_neurips.tex
+        """,
+    )
+
+    parser.add_argument('--template', type=str, help='Template filename')
+    parser.add_argument('--output', type=str, help='Output filename')
+    parser.add_argument('--title', type=str, help='Paper title')
+    parser.add_argument('--authors', type=str, help='Author names')
+    parser.add_argument('--affiliations', type=str, help='Institutions/affiliations')
+    parser.add_argument('--email', type=str, help='Corresponding author email')
+    parser.add_argument('--interactive', action='store_true', help='Run in interactive mode')
+
+    args = parser.parse_args()
+
+    # Interactive mode
+    if args.interactive:
+        interactive_mode()
+        return
+
+    # Command-line mode
+    if not args.template or not args.output:
+        print("Error: --template and --output are required (or use --interactive)")
+        parser.print_help()
+        return
+
+    # Find template
+    template_path = find_template(args.template)
+    if not template_path:
+        print(f"Error: Template '{args.template}' not found")
+        print("\nSearched in:")
+        skill_path = get_skill_path()
+        for subdir in ["journals", "posters", "grants"]:
+            print(f"  - {skill_path}/assets/{subdir}/")
+        return
+
+    # Customize
+    output_path = Path(args.output)
+    customize_template(
+        template_path,
+        output_path,
+        title=args.title,
+        authors=args.authors,
+        affiliations=args.affiliations,
+        email=args.email,
+    )
+
+
+if __name__ == "__main__":
+    main()