From 02dae0f30c4196e53b7f46b5a4e979ecd566d953 Mon Sep 17 00:00:00 2001 From: Vinayak Agarwal Date: Tue, 21 Oct 2025 00:04:29 -0700 Subject: [PATCH] Enhance scientific writing resources with detailed guidelines on field-specific terminology, citation styles, figure and table requirements, and reporting standards. Include venue-specific structure expectations and writing style comparisons to aid authors in adapting their manuscripts for various journals and conferences. --- .../scientific-writing/SKILL.md | 95 +++++++++- .../references/citation_styles.md | 165 ++++++++++++++++++ .../references/figures_tables.md | 129 ++++++++++++++ .../references/imrad_structure.md | 135 ++++++++++++++ .../references/reporting_guidelines.md | 89 ++++++++++ .../references/writing_principles.md | 96 +++++++++- 6 files changed, 706 insertions(+), 3 deletions(-) diff --git a/scientific-thinking/scientific-writing/SKILL.md b/scientific-thinking/scientific-writing/SKILL.md index 25692fc..956f9e1 100644 --- a/scientific-thinking/scientific-writing/SKILL.md +++ b/scientific-thinking/scientific-writing/SKILL.md @@ -1,6 +1,6 @@ --- name: scientific-writing -description: Comprehensive toolkit for writing, structuring, and formatting scientific research papers, manuscripts, and academic documents. This skill should be used when drafting or revising scientific manuscripts, structuring research papers using IMRAD format, formatting citations and references, creating effective figures and tables, applying reporting guidelines (CONSORT, STROBE, PRISMA), writing abstracts or specific paper sections, adhering to journal submission requirements, or improving scientific writing clarity and precision. Supports multiple citation styles (APA, AMA, Vancouver, Chicago), provides field-specific reporting standards, and ensures compliance with academic writing conventions across biomedical, life sciences, engineering, and physical sciences disciplines. +description: Comprehensive toolkit for writing, structuring, and formatting scientific research papers, manuscripts, and academic documents. This skill should be used when drafting or revising scientific manuscripts, structuring research papers using IMRAD format, formatting citations and references, creating effective figures and tables, applying reporting guidelines (CONSORT, STROBE, PRISMA), writing abstracts or specific paper sections, adhering to journal submission requirements, ensuring proper use of field-specific terminology and nomenclature, or improving scientific writing clarity and precision. Supports multiple citation styles (APA, AMA, Vancouver, Chicago), provides field-specific reporting standards and linguistic conventions, and ensures compliance with academic writing conventions across biomedical, life sciences, engineering, physical sciences, neuroscience, ecology, and social sciences disciplines. --- # Scientific Writing @@ -20,6 +20,7 @@ Invoke this skill when: - Drafting abstracts that meet journal requirements (structured or unstructured) - Preparing manuscripts for submission to specific journals - Improving writing clarity, conciseness, and precision +- Ensuring proper use of field-specific terminology and nomenclature - Addressing reviewer comments and revising manuscripts ## Core Capabilities @@ -169,7 +170,97 @@ Adapt manuscripts to journal requirements: - Adhere to word limits for each section - Format according to template requirements when provided -### 8. Common Pitfalls to Avoid +### 8. Field-Specific Language and Terminology + +Adapt language, terminology, and conventions to match the specific scientific discipline. Each field has established vocabulary, preferred phrasings, and domain-specific conventions that signal expertise and ensure clarity for the target audience. + +**Identify Your Field's Linguistic Conventions:** +- Review terminology used in recent high-impact papers in your target journal +- Note field-specific abbreviations, units, and notation systems +- Identify preferred terms (e.g., "participants" vs. "subjects," "compound" vs. "drug," "specimens" vs. "samples") +- Observe how methods, organisms, or techniques are typically described + +**Biomedical and Clinical Sciences:** +- Use precise anatomical and clinical terminology (e.g., "myocardial infarction" not "heart attack" in formal writing) +- Follow standardized disease nomenclature (ICD, DSM, SNOMED-CT) +- Specify drug names using generic names first, brand names in parentheses if needed +- Use "patients" for clinical studies, "participants" for community-based research +- Follow Human Genome Variation Society (HGVS) nomenclature for genetic variants +- Report lab values with standard units (SI units in most international journals) + +**Molecular Biology and Genetics:** +- Use italics for gene symbols (e.g., *TP53*), regular font for proteins (e.g., p53) +- Follow species-specific gene nomenclature (uppercase for human: *BRCA1*; sentence case for mouse: *Brca1*) +- Specify organism names in full at first mention, then use accepted abbreviations (e.g., *Escherichia coli*, then *E. coli*) +- Use standard genetic notation (e.g., +/+, +/-, -/- for genotypes) +- Employ established terminology for molecular techniques (e.g., "quantitative PCR" or "qPCR," not "real-time PCR") + +**Chemistry and Pharmaceutical Sciences:** +- Follow IUPAC nomenclature for chemical compounds +- Use systematic names for novel compounds, common names for well-known substances +- Specify chemical structures using standard notation (e.g., SMILES, InChI for databases) +- Report concentrations with appropriate units (mM, μM, nM, or % w/v, v/v) +- Describe synthesis routes using accepted reaction nomenclature +- Use terms like "bioavailability," "pharmacokinetics," "IC50" consistently with field definitions + +**Ecology and Environmental Sciences:** +- Use binomial nomenclature for species (italicized: *Homo sapiens*) +- Specify taxonomic authorities at first species mention when relevant +- Employ standardized habitat and ecosystem classifications +- Use consistent terminology for ecological metrics (e.g., "species richness," "Shannon diversity index") +- Describe sampling methods with field-standard terms (e.g., "transect," "quadrat," "mark-recapture") + +**Physics and Engineering:** +- Follow SI units consistently unless field conventions dictate otherwise +- Use standard notation for physical quantities (scalars vs. vectors, tensors) +- Employ established terminology for phenomena (e.g., "quantum entanglement," "laminar flow") +- Specify equipment with model numbers and manufacturers when relevant +- Use mathematical notation consistent with field standards (e.g., ℏ for reduced Planck constant) + +**Neuroscience:** +- Use standardized brain region nomenclature (e.g., refer to atlases like Allen Brain Atlas) +- Specify coordinates for brain regions using established stereotaxic systems +- Follow conventions for neural terminology (e.g., "action potential" not "spike" in formal writing) +- Use "neural activity," "neuronal firing," "brain activation" appropriately based on measurement method +- Describe recording techniques with proper specificity (e.g., "whole-cell patch clamp," "extracellular recording") + +**Social and Behavioral Sciences:** +- Use person-first language when appropriate (e.g., "people with schizophrenia" not "schizophrenics") +- Employ standardized psychological constructs and validated assessment names +- Follow APA guidelines for reducing bias in language +- Specify theoretical frameworks using established terminology +- Use "participants" rather than "subjects" for human research + +**General Principles:** + +**Match Audience Expertise:** +- For specialized journals: Use field-specific terminology freely, define only highly specialized or novel terms +- For broad-impact journals (e.g., *Nature*, *Science*): Define more technical terms, provide context for specialized concepts +- For interdisciplinary audiences: Balance precision with accessibility, define terms at first use + +**Define Technical Terms Strategically:** +- Define abbreviations at first use: "messenger RNA (mRNA)" +- Provide brief explanations for specialized techniques when writing for broader audiences +- Avoid over-defining terms well-known to your target audience (signals unfamiliarity with field) +- Create a glossary if numerous specialized terms are unavoidable + +**Maintain Consistency:** +- Use the same term for the same concept throughout (don't alternate between "medication," "drug," and "pharmaceutical") +- Follow a consistent system for abbreviations (decide on "PCR" or "polymerase chain reaction" after first definition) +- Apply the same nomenclature system throughout (especially for genes, species, chemicals) + +**Avoid Field Mixing Errors:** +- Don't use clinical terminology for basic science (e.g., don't call mice "patients") +- Avoid colloquialisms or overly general terms in place of precise field terminology +- Don't import terminology from adjacent fields without ensuring proper usage + +**Verify Terminology Usage:** +- Consult field-specific style guides and nomenclature resources +- Check how terms are used in recent papers from your target journal +- Use domain-specific databases and ontologies (e.g., Gene Ontology, MeSH terms) +- When uncertain, cite a key reference that establishes terminology + +### 9. Common Pitfalls to Avoid **Top Rejection Reasons:** 1. Inappropriate, incomplete, or insufficiently described statistics diff --git a/scientific-thinking/scientific-writing/references/citation_styles.md b/scientific-thinking/scientific-writing/references/citation_styles.md index 7bd1cf5..e27d1bb 100644 --- a/scientific-thinking/scientific-writing/references/citation_styles.md +++ b/scientific-thinking/scientific-writing/references/citation_styles.md @@ -535,6 +535,160 @@ When converting between citation styles: 3. **Manually verify** after automatic conversion 4. **Check journal guidelines** for specific requirements +## Journal-Specific Citation Styles and Requirements + +### How to Identify a Journal's Citation Style + +**Step 1: Check Author Guidelines** +- Every journal provides author instructions (usually "Instructions for Authors" or "Author Guidelines") +- Citation style is typically specified in "References" or "Citations" section +- Look for example references formatted in the journal's style + +**Step 2: Review Recent Publications** +- Examine 3-5 recent articles from your target journal +- Note the in-text citation format (numbered vs. author-date) +- Compare reference list formatting +- Check for journal-specific variations + +**Step 3: Verify Journal-Specific Variations** +Some journals use modified versions of standard styles: +- Abbreviated vs. full journal names +- DOI inclusion requirements +- Article titles in title case vs. sentence case +- Maximum number of authors before "et al." + +### Common Journals and Their Citation Styles + +| Journal | Citation Style | Key Features | +|---------|---------------|--------------| +| **JAMA, JAMA Network journals** | AMA | Superscript numbers, abbreviated journal names, no issue numbers | +| **New England Journal of Medicine** | Modified Vancouver | Numbered brackets, abbreviated journals, limited authors (3 then et al) | +| **The Lancet** | Vancouver | Numbered brackets, PubMed abbreviations | +| **BMJ** | Vancouver | Numbered in-text, DOIs required when available | +| **Nature, Nature journals** | Nature style (numbered) | Numbered superscripts, abbreviated journals, no article titles in some journals | +| **Science** | Science style (numbered) | Numbered in-text, abbreviated format | +| **Cell, Cell Press journals** | Cell style (author-year) | Author-date, specific formatting for multiple citations | +| **PLOS journals** | Vancouver | Numbered brackets, full journal names in some PLOS journals | +| **Journal of Biological Chemistry** | JBC style (numbered) | Numbered in-text, specific abbreviation rules | +| **Psychological journals** | APA | Author-date, DOIs required | +| **IEEE journals** | IEEE | Numbered brackets, specific format for conference papers | +| **ACS journals** | ACS | Superscript or numbered, semicolons between authors | + +### Journal Family Consistency + +**Journals from the same publisher often share citation styles:** + +**Elsevier journals:** +- Vary widely; check specific journal +- Many use numbered Vancouver-style +- Some allow author-date + +**Springer Nature journals:** +- Nature journals: Nature style (numbered, abbreviated) +- Springer journals: Often numbered or author-date depending on field +- BMC journals: Vancouver with full journal names + +**Wiley journals:** +- Varies by field +- Many biomedical journals use Vancouver +- Psychology/social science journals often use APA + +**American Chemical Society (ACS):** +- All ACS journals use ACS style +- Consistent across Journal of American Chemical Society, Analytical Chemistry, etc. + +### High-Impact Journal and Conference Preferences + +| Venue | Field | Citation Preference | Key Features | +|-------|-------|-------------------|--------------| +| **Nature/Science** | Multidisciplinary | Numbered, abbreviated | Space-saving, broad readability | +| **Cell family** | Life sciences | Author-date or numbered | Attribution visibility | +| **NEJM/Lancet/JAMA** | Medicine | Vancouver/AMA numbered | Medical standard | +| **NeurIPS/ICML/ICLR** | Machine Learning | Numbered [1] or (Author, Year) | Varies by conference, check template | +| **CVPR/ICCV/ECCV** | Computer Vision | Numbered [1], IEEE-like | Compact format | +| **ACL/EMNLP** | NLP | Author-year (ACL style) | Attribution-focused | + +### Adapting Citations for Different Target Journals + +**When switching journals after desk rejection or withdrawal:** + +**Use reference management software:** +1. Import references into Zotero, Mendeley, or EndNote +2. Select target journal's citation style from software library +3. Regenerate citations and reference list automatically +4. Manually verify formatting matches journal examples + +**Key elements to check when converting:** +- In-text format (switch numbered ↔ author-date) +- Journal name abbreviation style +- Article title capitalization +- Author name format (initials vs. full names) +- DOI format and inclusion +- Issue number inclusion/exclusion +- Page number format + +**Manual verification essential for:** +- Preprints and non-standard sources +- Software/datasets citations +- Conference proceedings +- Dissertations and theses + +### Venue-Specific Evaluation Criteria + +**Content expectations:** +- **High-impact journals**: >50% citations from last 5 years; primary sources preferred +- **Medical journals**: Recent clinical evidence; systematic reviews valued +- **ML conferences**: Recent papers (last 2-3 years); preprints (arXiv) acceptable +- **Self-citation**: Keep <20% across all venues + +**Format compliance (often automated):** +- Match venue citation style exactly +- All in-text citations have corresponding references +- Include DOIs when required (journals) or arXiv IDs (ML conferences) +- Use correct abbreviations (PubMed for medical, standard for ML) + +**ML conference specifics:** +- **NeurIPS/ICML/ICLR**: ArXiv preprints widely cited; recent work heavily valued +- **Page limits strict**: Citation formatting affects space +- **Supplementary material**: Can include extended bibliography +- **Double-blind review**: Avoid obvious self-citation patterns during review + +### Citation Density by Venue Type + +| Venue Type | Expected Citations | Key Notes | +|-----------|-------------------|-----------| +| **Nature/Science research** | 30-50 | Selective, high-impact citations | +| **Medical journals (RCT)** | 25-40 | Recent clinical evidence | +| **Field-specific journals** | 30-60 | Comprehensive field coverage | +| **ML conferences (8-page)** | 20-40 | Space-limited, recent work | +| **Review articles** | 100-300+ | Comprehensive coverage | + +**ML conference citation practices:** +- **NeurIPS/ICML**: 25-40 references typical for 8-page papers +- **Workshop papers**: 15-25 references +- **ArXiv preprints**: Widely accepted and cited +- **Related work**: Concise but comprehensive; often moved to appendix +- **Recency critical**: Cite work from last 1-2 years when relevant + +### Pre-Submission Citation Checklist + +**Content:** +- [ ] ≥50% citations from last 5-10 years (or 2-3 years for ML conferences) +- [ ] <20% self-citations; balanced perspectives +- [ ] Primary sources cited (not citation chains) +- [ ] All claims supported by appropriate citations + +**Format:** +- [ ] Style matches venue exactly (check template) +- [ ] All in-text citations in reference list and vice versa +- [ ] DOIs/arXiv IDs included as required +- [ ] Abbreviations match venue style + +**ML conferences additional:** +- [ ] ArXiv preprints properly formatted +- [ ] Self-citations anonymized if double-blind review +- [ ] References fit within page limits + ## Resources for Citation Styles ### Official Manuals @@ -544,6 +698,12 @@ When converting between citation styles: - Chicago: https://www.chicagomanualofstyle.org/ - IEEE: https://ieeeauthorcenter.ieee.org/ +### Journal-Specific Style Guides +- Nature: https://www.nature.com/nature/for-authors/formatting-guide +- Science: https://www.science.org/content/page/instructions-authors +- Cell: https://www.cell.com/cell/authors +- JAMA: https://jamanetwork.com/journals/jama/pages/instructions-for-authors + ### Quick Reference Guides - Purdue OWL: https://owl.purdue.edu/ - Citation Machine: https://www.citationmachine.net/ @@ -553,3 +713,8 @@ When converting between citation styles: - Zotero: https://www.zotero.org/ - Mendeley: https://www.mendeley.com/ - EndNote: https://endnote.com/ + +### Journal Citation Style Databases +- Journal Citation Reports (Clarivate): Lists journal citation styles +- EndNote style repository: >7000 journal-specific styles +- Zotero Style Repository: https://www.zotero.org/styles diff --git a/scientific-thinking/scientific-writing/references/figures_tables.md b/scientific-thinking/scientific-writing/references/figures_tables.md index 4a3f7c6..4f61242 100644 --- a/scientific-thinking/scientific-writing/references/figures_tables.md +++ b/scientific-thinking/scientific-writing/references/figures_tables.md @@ -643,6 +643,125 @@ better cognitive function. - Script your figure generation for reproducibility - Save original data files separately from figure files +## Journal-Specific Figure and Table Requirements + +### Understanding Journal Expectations + +**Different journals have vastly different requirements for figures and tables.** Before creating display items, always consult your target journal's author guidelines for specific requirements. + +### Common Journal-Specific Variations + +| Aspect | Variation by Journal | Example Journals | +|--------|---------------------|------------------| +| **Number allowed** | 4-10 display items for research articles | Nature (4-6), PLOS ONE (unlimited), Science (4-5) | +| **File format** | TIFF, EPS, PDF, AI, or specific formats | Nature (EPS/PDF for line art), Cell (TIFF preferred) | +| **Resolution** | 300-1000 dpi depending on type | JAMA (300-600 dpi), Nature (300+ dpi) | +| **Color** | RGB vs. CMYK | Print journals: CMYK; Online: RGB | +| **Dimensions** | Single vs. double column widths | Nature (89mm or 183mm), Science (specific templates) | +| **Figure legends** | Length limits, specific format | Some journals: 150 word max per legend | +| **Table format** | Editable vs. image | Most prefer editable tables, not images | + +### Venue-Specific Requirements Summary + +| Venue Type | Display Limit | Format | Resolution | Key Features | +|-----------|--------------|--------|------------|--------------| +| **Nature/Science** | 4-6 main | EPS/PDF/TIFF | 300+ dpi | Extended data allowed; multi-panel figures | +| **Medical journals** | 3-5 | TIFF/EPS | 300-600 dpi | CONSORT diagrams; conservative design | +| **PLOS ONE** | Unlimited | TIFF/EPS/PDF | 300+ dpi | Must work in grayscale | +| **ML conferences** | 4-6 in 8-page limit | PDF (vector preferred) | Print quality | Compact design; info-dense figures | + +**ML Conference Figure Requirements:** + +**NeurIPS/ICML/ICLR:** +- Figures count toward page limit (typically 8 pages including references) +- Vector graphics (PDF) preferred for plots +- High information density expected +- Supplementary material for additional figures +- LaTeX template provided (use neurips_2024.sty or equivalent) +- Figures must be legible when printed in grayscale + +**Computer Vision (CVPR/ICCV/ECCV):** +- Qualitative results figures critical +- Side-by-side comparisons standard +- Must show failure cases +- Supplementary material for videos/additional examples +- Often 6-8 main figures in 8-page papers + +**Key ML conference figure practices:** +- **Ablation studies**: Compact tables/plots showing component contributions +- **Architecture diagrams**: Clear, professional block diagrams +- **Performance plots**: Include error bars/confidence intervals +- **Qualitative examples**: Show diverse, representative samples +- **Comparison tables**: Concise, bold best results + +### Evaluation Criteria Across Venues + +**What reviewers check:** +- **Necessity**: Each figure/table supports conclusions +- **Quality**: Professional appearance, sufficient resolution +- **Clarity**: Self-explanatory with captions; proper labeling +- **Statistics**: Error bars, sample sizes, significance indicators +- **Consistency**: Formatting uniform across display items + +**Common rejection reasons:** +- Poor resolution or image quality +- Missing error bars or sample sizes +- Unclear or missing labels +- Too many figures (exceeds venue limits) +- Figures duplicate text information + +**ML conference specific evaluation:** +- **Ablation studies**: Must demonstrate component contributions +- **Baselines**: Comparison with relevant prior work required +- **Error bars**: Confidence intervals/std dev expected +- **Architecture diagrams**: Must be clear and informative +- **Space efficiency**: Information density valued (page limits strict) + +### Caption/Legend Styles by Venue + +| Venue Type | Style | Example Features | +|-----------|-------|------------------| +| **Nature/Science** | Concise | Brief; *P<0.05; minimal methods | +| **Medical** | Formal | Title case; 95% CIs; statistical tests spelled out | +| **PLOS/BMC** | Detailed | Complete sentences; all abbreviations defined | +| **ML conferences** | Technical | Architecture details; hyperparameters; dataset info | + +**ML conference caption example:** +``` +Figure 1. Architecture of proposed model. (a) Encoder with 12 transformer layers. +(b) Attention visualization. (c) Performance vs. baseline on ImageNet (error bars: +95% CI over 3 runs). +``` +- Technical precision +- Hyperparameters when relevant +- Dataset/experimental setup details +- Compact to save space + +### Quick Adaptation Guide + +**When changing venues:** +- **Journal → ML conference**: Compress figures; increase information density; add hyperparameters to captions +- **ML conference → journal**: Expand captions; separate dense figures; add more methodological detail +- **Specialist → broad journal**: Simplify; add explanatory panels; define terms in captions +- **Broad → specialist journal**: Add technical detail; use field-standard plot types + +### Pre-Submission Figure/Table Checklist + +**Technical (all venues):** +- [ ] Meets format requirements (PDF/EPS/TIFF) +- [ ] Sufficient resolution (300+ dpi) +- [ ] Fits venue dimensions/page limits +- [ ] Self-explanatory captions +- [ ] All symbols/abbreviations defined +- [ ] Error bars defined; sample sizes noted + +**ML conferences additional:** +- [ ] Figures fit in page limit (8-9 pages typical) +- [ ] Comparison with baselines shown +- [ ] Ablation studies included +- [ ] Architecture diagram clear +- [ ] Legible in grayscale + ## Checklist for Final Review ### Before Submission @@ -650,7 +769,10 @@ better cognitive function. **For every figure:** - [ ] High enough resolution (300+ dpi)? - [ ] Correct file format per journal requirements? +- [ ] Correct dimensions for journal (single/double column)? +- [ ] Meets journal's RGB/CMYK requirements? - [ ] Self-explanatory caption with all abbreviations defined? +- [ ] Caption length within journal limits? - [ ] All symbols/colors explained in caption or legend? - [ ] Error bars included and defined? - [ ] Sample sizes noted? @@ -659,19 +781,26 @@ better cognitive function. - [ ] Readable text at final print size? - [ ] Works in grayscale or color-blind friendly? - [ ] Referenced in text in correct order? +- [ ] Style matches target journal's published figures? **For every table:** - [ ] Clear, descriptive title? +- [ ] Title capitalization matches journal style? - [ ] Column headers include units? - [ ] Appropriate numerical precision? - [ ] Abbreviations defined in footnotes? - [ ] Statistical methods explained? - [ ] Sample sizes included? - [ ] Consistent formatting with other tables? +- [ ] Editable format (not image)? - [ ] Referenced in text in correct order? +- [ ] Formatting matches target journal's tables? **Overall:** +- [ ] Number of display items within journal limits? - [ ] Appropriate number of display items (~1 per 1000 words)? - [ ] No duplication between text, figures, and tables? - [ ] Consistent formatting across all display items? - [ ] All display items necessary (each tells important part of story)? +- [ ] Visual style matches target journal? +- [ ] Quality comparable to published examples in journal? diff --git a/scientific-thinking/scientific-writing/references/imrad_structure.md b/scientific-thinking/scientific-writing/references/imrad_structure.md index c979b60..800e571 100644 --- a/scientific-thinking/scientific-writing/references/imrad_structure.md +++ b/scientific-thinking/scientific-writing/references/imrad_structure.md @@ -521,3 +521,138 @@ crisis in higher education. - Follow STROBE guidelines - Careful attention to potential confounders in Methods - Discussion addresses causality limitations + +## Venue-Specific Structure Expectations + +### Journal vs. Conference Formats + +| Venue Type | Length | Structure | Methods Placement | Key Focus | +|-----------|--------|-----------|-------------------|-----------| +| **Nature/Science** | 2,000-4,500 words | Modified IMRAD | Supplement | Broad significance | +| **Medical** | 2,700-3,500 words | Strict IMRAD | Main text | Clinical outcomes | +| **Field journals** | 3,000-6,000 words | Standard IMRAD | Main text | Technical depth | +| **ML conferences** | 8-9 pages (~6,000 words) | Intro-Method-Experiments-Conclusion | Main text (concise) | Novel contribution | + +### ML Conference Structure (NeurIPS/ICML/ICLR) + +**Typical 8-page structure:** +1. **Abstract** (150-200 words): Problem, method, key results +2. **Introduction** (1 page): Motivation, contribution summary, related work overview +3. **Method** (2-3 pages): Technical approach, architecture, algorithms +4. **Experiments** (2-3 pages): Setup, datasets, baselines, results, ablations +5. **Related Work** (0.5-1 page, often in appendix): Detailed literature comparison +6. **Conclusion** (0.25-0.5 pages): Summary, limitations, future work +7. **References** (within page limit or separate depending on conference) +8. **Appendix/Supplement** (unlimited): Additional experiments, proofs, details + +**Key differences from journals:** +- **Contribution bullets**: Often numbered list in intro (e.g., "Our contributions are: (1)... (2)... (3)...") +- **No separate Results/Discussion**: Integrated in Experiments section +- **Ablation studies**: Critical component showing what matters +- **Computational requirements**: Often required (training time, GPUs, memory) +- **Code availability**: Increasingly expected + +### Section Length Proportions + +| Venue | Intro | Methods | Results/Experiments | Discussion/Conclusion | +|-------|-------|---------|---------------------|----------------------| +| **Nature/Science** | 10% | 15%* | 40% | 35% | +| **Medical (NEJM/JAMA)** | 10% | 25% | 30% | 35% | +| **Field journals** | 20% | 25% | 30% | 25% | +| **ML conferences** | 12-15% | 30-35% | 40-45% | 5-8% | + +*Methods often in supplement for Nature/Science + +**Key medical journal features:** +- NEJM/Lancet/JAMA: Strict IMRAD; clinical focus; structured Discussion; CONSORT/STROBE compliance +- Clear primary/secondary outcomes; statistical pre-specification + +**Key ML conference features:** +- Numbered contribution list in intro +- Method details with pseudocode/equations +- Extensive experiments: main results, ablations, analysis +- Brief conclusion (limitations noted) +- Related work often in appendix + +### Writing Style by Venue + +| Venue | Audience | Intro Focus | Methods Detail | Results/Experiments | Discussion/Conclusion | +|-------|----------|-------------|----------------|---------------------|----------------------| +| **Nature/Science** | Non-specialists | Broad significance | Brief, supplement | Story-driven | Broad implications | +| **Medical** | Clinicians | Clinical problem | Comprehensive | Primary outcome first | Clinical relevance | +| **Specialized** | Experts | Field context | Full technical | By experiment | Mechanistic depth | +| **ML conferences** | ML researchers | Novel contribution | Reproducible | Baselines, ablations | Brief, limitations | + +**ML conference emphasis:** +- **Introduction**: Clear problem statement; numbered contributions; positioning vs. prior work +- **Method**: Mathematical notation; pseudocode; architecture diagrams; complexity analysis +- **Experiments**: Datasets described; multiple baselines; ablation studies; error analysis +- **Conclusion**: Summary; acknowledged limitations; broader impact (if required) + +### Evaluation Across Venues + +**What gets checked:** +- **Fit**: Appropriate for venue scope and audience +- **Length**: Within limits (strict for conferences) +- **Clarity**: Writing quality sufficient; claims supported +- **Reproducibility**: Methods enable replication +- **Completeness**: All outcomes reported; limitations acknowledged + +**Common rejection reasons:** +- Insufficient significance for venue +- Methods lack detail for reproduction +- Results don't support claims +- Discussion overstates findings +- Page/word limits exceeded (conferences strict) + +**ML conference specific evaluation:** +- Clear problem formulation and motivation +- Novelty and contribution well-articulated +- Baselines comprehensive and fair +- Ablation studies demonstrate what works +- Code/data availability (increasingly required) +- Reproducibility information (seeds, hyperparameters) + +### Quick Adaptation Guide + +**Journal → ML conference:** +- Condense intro; add numbered contributions +- Methods: keep concise, add pseudocode +- Combine Results+Discussion → Experiments section +- Add extensive ablations and baseline comparisons +- Brief conclusion with limitations + +**ML conference → Journal:** +- Expand introduction with more background +- Separate Methods section with full details +- Split Experiments into Results and Discussion +- Remove contribution numbering +- Expand limitations discussion + +**Specialist → Broad journal:** +- Simplify intro; emphasize broad significance +- Move technical methods to supplement +- Story-driven results organization +- Lead discussion with implications + +**Broad → Specialist:** +- Add detailed literature review +- Full methods in main text +- Organize results by experiment +- Add mechanistic discussion depth + +### Pre-Submission Structure Checklist + +**All venues:** +- [ ] Word/page count within limits +- [ ] Section proportions appropriate +- [ ] Writing style matches venue +- [ ] Methods enable reproducibility +- [ ] Limitations acknowledged + +**ML conferences add:** +- [ ] Contributions clearly listed +- [ ] Ablation studies included +- [ ] Baselines comprehensive +- [ ] Hyperparameters/seeds reported +- [ ] Code availability statement diff --git a/scientific-thinking/scientific-writing/references/reporting_guidelines.md b/scientific-thinking/scientific-writing/references/reporting_guidelines.md index f29ebb6..e986470 100644 --- a/scientific-thinking/scientific-writing/references/reporting_guidelines.md +++ b/scientific-thinking/scientific-writing/references/reporting_guidelines.md @@ -657,3 +657,92 @@ checklist is provided as Supplementary File 1." - [ ] Prepared checklist as supplementary file if required - [ ] Checked journal-specific requirements - [ ] Mentioned guideline adherence in cover letter + +## Venue-Specific Reporting Requirements + +### Reporting Standards by Venue Type + +| Venue Type | Guideline Use | Transparency Requirements | +|-----------|--------------|---------------------------| +| **Medical journals** | Mandatory (CONSORT, STROBE, etc.) | Checklist required at submission | +| **PLOS/BMC** | Mandatory for study types | Checklist uploaded as supplement | +| **Nature/Science** | Recommended | Methods completeness emphasized | +| **ML conferences** | No formal guidelines | Reproducibility details required | + +### ML Conference Reporting Standards + +**NeurIPS/ICML/ICLR reproducibility requirements:** +- **Datasets**: Names, versions, access methods, preprocessing +- **Code**: Availability statement; GitHub common +- **Hyperparameters**: All settings reported (learning rate, batch size, etc.) +- **Seeds**: Random seeds for reproducibility +- **Computational resources**: GPUs used, training time +- **Statistical significance**: Error bars, confidence intervals, multiple runs +- **Broader Impact** statement (NeurIPS): Societal implications + +**What to include (typically in appendix):** +- Complete hyperparameter settings +- Training details and convergence criteria +- Hardware specifications +- Software versions (PyTorch 2.0, etc.) +- Dataset splits and any preprocessing +- Evaluation metrics and protocols + +### Enforcement and Evaluation + +**What gets checked:** +- **Medical journals**: Checklist uploaded; adherence statement in Methods; systematic completeness +- **PLOS/BMC**: Mandatory checklists for certain designs; reproducibility emphasized +- **High-impact**: Methods sufficiency for replication (checklist often not required) +- **ML conferences**: Reproducibility checklist (NeurIPS); code availability increasingly expected + +**Common issues leading to rejection:** +- Missing required checklists (medical journals) +- Insufficient methods detail for reproduction +- Missing key information (randomization, blinding, power calculation) +- No data/code availability statement when required + +**Methods statement examples:** + +**Journal (STROBE):** +``` +This study followed STROBE reporting guidelines. Checklist provided in Supplement 1. +``` + +**ML conference (reproducibility):** +``` +Code available at github.com/user/project. All hyperparameters in Appendix A. +Training used 4×A100 GPUs (~20 hours). Seeds: {42, 123, 456}. +``` + +### Pre-Submission Reporting Checklist + +**For clinical trials (medical journals):** +- [ ] CONSORT checklist complete with page numbers +- [ ] Trial registration number in abstract and methods +- [ ] CONSORT flow diagram included +- [ ] Statistical analysis plan described +- [ ] Adherence statement in Methods + +**For observational studies (medical/epidemiology):** +- [ ] STROBE checklist complete +- [ ] Study design clearly stated +- [ ] Statistical methods detailed +- [ ] Confounders addressed +- [ ] Adherence statement in Methods + +**For systematic reviews:** +- [ ] PRISMA checklist complete +- [ ] PRISMA flow diagram included +- [ ] Protocol registered (PROSPERO) +- [ ] Search strategy documented +- [ ] Risk of bias assessment included + +**For ML conference papers:** +- [ ] All datasets named with versions +- [ ] Code availability stated (GitHub link if available) +- [ ] Hyperparameters listed (appendix acceptable) +- [ ] Random seeds reported +- [ ] Computational resources specified +- [ ] Error bars/confidence intervals shown +- [ ] Broader Impact statement (if required) diff --git a/scientific-thinking/scientific-writing/references/writing_principles.md b/scientific-thinking/scientific-writing/references/writing_principles.md index 2f712e3..83cb577 100644 --- a/scientific-thinking/scientific-writing/references/writing_principles.md +++ b/scientific-thinking/scientific-writing/references/writing_principles.md @@ -716,6 +716,99 @@ Most research universities offer: - Online resources and handouts - Support for non-native English speakers +## Venue-Specific Writing Styles + +### Four Major Writing Style Categories + +1. **Broad-audience accessible** (Nature, Science, PNAS) +2. **Clinical-professional** (NEJM, Lancet, JAMA) +3. **Technical-specialist** (field-specific journals) +4. **ML conference** (NeurIPS, ICML, ICLR, CVPR) + +### Writing Style Comparison + +| Aspect | Nature/Science | Medical | Specialized | ML Conference | +|--------|---------------|---------|-------------|---------------| +| **Sentence length** | 15-20 words | 12-18 words | 18-25 words | 12-20 words | +| **Vocabulary** | Minimal jargon | Clinical terms | Field-specific | Technical + math | +| **Tone** | Engaging, significant | Conservative | Formal | Direct, contribution-focused | +| **Key phrases** | "Here we show" | "We conducted" | "To elucidate" | "We propose", "Our contributions" | + +**ML Conference Style:** + +**Characteristics:** +- Direct, technical language with mathematical notation +- Contribution-focused (numbered lists common) +- Assumes ML expertise (CNNs, transformers, SGD, etc.) +- Emphasizes novelty and performance gains +- Pseudocode and equations expected + +**Example opening (NeurIPS style):** +``` +Vision transformers have achieved state-of-the-art performance on image classification, +but their quadratic complexity limits applicability to high-resolution images. We propose +Efficient-ViT, which reduces complexity to O(n log n) while maintaining accuracy. Our +contributions are: (1) a novel sparse attention mechanism, (2) theoretical analysis +showing preserved expressive power, and (3) empirical validation on ImageNet showing +15% speedup with comparable accuracy. +``` +- Problem stated with technical context +- Solution previewed +- Numbered contributions +- Quantitative claims + +### Key Writing Differences + +| Aspect | Nature/Science | Medical | Specialized | ML Conference | +|--------|---------------|---------|-------------|---------------| +| **Paragraph length** | 3-5 sentences | 5-7 sentences | 6-10 sentences | 4-6 sentences | +| **Math/equations** | Minimize | Rare | Moderate | Essential | +| **Active voice** | Preferred | Mixed | Passive OK | Preferred | +| **Hedging** | Moderate | Conservative | Detailed | Minimal (claim gains) | +| **Figure integration** | Tight | Systematic | Detailed | Dense, in-page | + +### Evaluation Focus by Venue + +| Venue | Key Evaluation Criteria | +|-------|------------------------| +| **Nature/Science** | Accessible to non-specialists? Broad significance clear? Compelling story? | +| **Medical** | Clinical relevance apparent? Professional tone? Methods adequate? | +| **Specialized** | Technical precision? Field expertise shown? Methods detailed? | +| **ML conferences** | Clear contributions? Claims supported by experiments? Reproducible? | + +**Common rejection reasons:** +- Poor writing quality/unclear prose +- Inappropriate style for venue +- Overstated claims +- Methods insufficient for reproduction +- Missing key details (baselines, ablations for ML; statistics for journals) + +### Quick Style Adaptation Guide + +| From → To | Key Changes | +|-----------|-------------| +| **Journal → ML conference** | Add numbered contributions; include equations/pseudocode; emphasize quantitative gains; condense prose | +| **ML conference → Journal** | Remove contribution numbering; expand motivation; separate Results/Discussion; reduce equations in main text | +| **Specialist → Broad** | Simplify language; emphasize broad implications; explain technical concepts; add context for non-experts | +| **Broad → Specialist** | Add technical detail; use field terminology freely; expand mechanistic discussion; cite field literature | +| **Basic science → Clinical** | Add patient/clinical context; use clinical language; emphasize outcomes/implications; cite clinical evidence | + +### Pre-Submission Style Checklist + +**All venues:** +- [ ] Writing style matches 3-5 recent papers from venue +- [ ] Sentence length appropriate +- [ ] Technical vocabulary level correct +- [ ] Tone consistent with venue +- [ ] No overstated claims + +**ML conferences add:** +- [ ] Contributions clearly numbered in intro +- [ ] Mathematical notation correct and consistent +- [ ] Pseudocode/algorithms included where appropriate +- [ ] Claims quantified (e.g., "15% faster", "2.3% accuracy gain") +- [ ] Limitations acknowledged + ## Final Thoughts Effective scientific writing is a skill developed through practice. Key principles: @@ -726,5 +819,6 @@ Effective scientific writing is a skill developed through practice. Key principl 4. **Objectivity** maintains scientific integrity 5. **Consistency** aids comprehension 6. **Logical organization** guides readers +7. **Journal-specific adaptation** maximizes publication success -**Remember:** The goal is not to impress readers with vocabulary or complexity, but to communicate your science clearly and precisely so readers can understand, evaluate, and build upon your work. +**Remember:** The goal is not to impress readers with vocabulary or complexity, but to communicate your science clearly and precisely so readers can understand, evaluate, and build upon your work. Adapt your writing style to match your target journal's expectations and audience.