Scientific Writing

Scientific Writing

Overview

This is the core skill for the deep research and writing tool—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.

Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Apply this skill for research papers and journal submissions.

Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript. Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.

When to Use This Skill

This skill should be used when:

• Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
• Structuring a research paper using IMRAD or other standard formats
• Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
• Creating, formatting, or improving figures, tables, and data visualizations
• Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)
• 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

Visual Enhancement with Scientific Schematics

⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.

This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document: 1. ALWAYS generate a graphical abstract as the first visual element 2. Generate at minimum ONE additional schematic or diagram using scientific-schematics 3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)

Graphical Abstract (REQUIRED)

Every scientific writeup MUST include a graphical abstract. This is a visual summary of your paper that:

• Appears before or immediately after the text abstract
• Captures the entire paper's key message in one image
• Is suitable for journal table of contents display
• Uses landscape orientation (typically 1200x600px)

Generate the graphical abstract FIRST:

python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png

Graphical Abstract Requirements:

• Content: Visual summary showing workflow, key methods, main findings, and conclusions
• Style: Clean, professional, suitable for journal TOC
• Elements: Include 3-5 key steps/concepts with connecting arrows or flow
• Text: Minimal labels, large readable fonts
• Log: [HH:MM:SS] GENERATED: Graphical abstract for paper summary

Additional Figures (GENERATE EXTENSIVELY)

⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.

Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.

MINIMUM Figure Requirements:

Use scientific-schematics EXTENSIVELY for technical diagrams:

python scripts/generate_schematic.py "your diagram description" -o figures/output.png

• Study design and methodology flowcharts (CONSORT, PRISMA, STROBE)
• Conceptual framework diagrams
• Experimental workflow illustrations
• Data analysis pipeline diagrams
• Biological pathway or mechanism diagrams
• System architecture visualizations
• Neural network architectures
• Decision trees, algorithm flowcharts
• Comparison matrices, timeline diagrams
• Any technical concept that benefits from schematic visualization

Use generate-image EXTENSIVELY for visual content:

python scripts/generate_image.py "your image description" -o figures/output.png

• Photorealistic illustrations of concepts
• Medical/anatomical illustrations
• Environmental/ecological scenes
• Equipment and lab setup visualizations
• Artistic visualizations, infographics
• Cover images, header graphics
• Product mockups, prototype visualizations
• Any visual that enhances understanding or engagement

The AI will automatically:

• Create publication-quality images with proper formatting
• Review and refine through multiple iterations
• Ensure accessibility (colorblind-friendly, high contrast)
• Save outputs in the figures/ directory

When in Doubt, Generate a Figure:

• Complex concept → generate a schematic
• Data discussion → generate a visualization
• Process description → generate a flowchart
• Comparison → generate a comparison diagram
• Reader benefit → generate a visual

For detailed guidance, refer to the scientific-schematics and generate-image skill documentation.

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Core Capabilities

1. Manuscript Structure and Organization

IMRAD Format: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:

• Introduction: Establish research context, identify gaps, state objectives
• Methods: Detail study design, populations, procedures, and analysis approaches
• Results: Present findings objectively without interpretation
• Discussion: Interpret results, acknowledge limitations, propose future directions

For detailed guidance on IMRAD structure, refer to references/imrad_structure.md.

Alternative Structures: Support discipline-specific formats including:

• Review articles (narrative, systematic, scoping)
• Case reports and case series
• Meta-analyses and pooled analyses
• Theoretical/modeling papers
• Methods papers and protocols

2. Section-Specific Writing Guidance

Abstract Composition: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.

Introduction Development: Build compelling introductions that:

• Establish the research problem's importance
• Review relevant literature systematically
• Identify knowledge gaps or controversies
• State clear research questions or hypotheses
• Explain the study's novelty and significance

Methods Documentation: Ensure reproducibility through:

• Detailed participant/sample descriptions
• Clear procedural documentation
• Statistical methods with justification
• Equipment and materials specifications
• Ethical approval and consent statements

Results Presentation: Present findings with:

• Logical flow from primary to secondary outcomes
• Integration with figures and tables
• Statistical significance with effect sizes
• Objective reporting without interpretation

Discussion Construction: Synthesize findings by:

• Relating results to research questions
• Comparing with existing literature
• Acknowledging limitations honestly
• Proposing mechanistic explanations
• Suggesting practical implications and future research

3. Citation and Reference Management

Apply citation styles correctly across disciplines. For comprehensive style guides, refer to references/citation_styles.md.

Major Citation Styles:

• AMA (American Medical Association): Numbered superscript citations, common in medicine
• Vancouver: Numbered citations in square brackets, biomedical standard
• APA (American Psychological Association): Author-date in-text citations, common in social sciences
• Chicago: Notes-bibliography or author-date, humanities and sciences
• IEEE: Numbered square brackets, engineering and computer science

Best Practices:

• Cite primary sources when possible
• Include recent literature (last 5-10 years for active fields)
• Balance citation distribution across introduction and discussion
• Verify all citations against original sources
• Use reference management software (Zotero, Mendeley, EndNote)

4. Figures and Tables

Create effective data visualizations that enhance comprehension. For detailed best practices, refer to references/figures_tables.md.

When to Use Tables vs. Figures:

• Tables: Precise numerical data, complex datasets, multiple variables requiring exact values
• Figures: Trends, patterns, relationships, comparisons best understood visually

Design Principles:

• Make each table/figure self-explanatory with complete captions
• Use consistent formatting and terminology across all display items
• Label all axes, columns, and rows with units
• Include sample sizes (n) and statistical annotations
• Follow the "one table/figure per 1000 words" guideline
• Avoid duplicating information between text, tables, and figures

Common Figure Types:

• Bar graphs: Comparing discrete categories
• Line graphs: Showing trends over time
• Scatterplots: Displaying correlations
• Box plots: Showing distributions and outliers
• Heatmaps: Visualizing matrices and patterns

5. Reporting Guidelines by Study Type

Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to references/reporting_guidelines.md.

Key Guidelines:

• CONSORT: Randomized controlled trials
• STROBE: Observational studies (cohort, case-control, cross-sectional)
• PRISMA: Systematic reviews and meta-analyses
• STARD: Diagnostic accuracy studies
• TRIPOD: Prediction model studies
• ARRIVE: Animal research
• CARE: Case reports
• SQUIRE: Quality improvement studies
• SPIRIT: Study protocols for clinical trials
• CHEERS: Economic evaluations

Each guideline provides checklists ensuring all critical methodological elements are reported.

6. Writing Principles and Style

Apply fundamental scientific writing principles. For detailed guidance, refer to references/writing_principles.md.

Clarity:

• Use precise, unambiguous language
• Define technical terms and abbreviations at first use
• Maintain logical flow within and between paragraphs
• Use active voice when appropriate for clarity

Conciseness:

• Eliminate redundant words and phrases
• Favor shorter sentences (15-20 words average)
• Remove unnecessary qualifiers
• Respect word limits strictly

Accuracy:

• Report exact values with appropriate precision
• Use consistent terminology throughout
• Distinguish between observations and interpretations
• Acknowledge uncertainty appropriately

Objectivity:

• Present results without bias
• Avoid overstating findings or implications
• Acknowledge conflicting evidence
• Maintain professional, neutral tone

7. Writing Process: From Outline to Full Paragraphs

CRITICAL: Always write in full paragraphs, never submit bullet points in scientific papers.

Scientific papers must be written in complete, flowing prose. Use this two-stage approach for effective writing:

Stage 1: Create Section Outlines with Key Points

When starting a new section: 1. Use the research-lookup skill to gather relevant literature and data 2. Create a structured outline with bullet points marking:

• Main arguments or findings to present
• Key studies to cite
• Data points and statistics to include
• Logical flow and organization

3. These bullet points serve as scaffolding—they are NOT the final manuscript

Example outline (Introduction section):

- Background: AI in drug discovery gaining traction
  * Cite recent reviews (Smith 2023, Jones 2024)
  * Traditional methods are slow and expensive
- Gap: Limited application to rare diseases
  * Only 2 prior studies (Lee 2022, Chen 2023)
  * Small datasets remain a challenge
- Our approach: Transfer learning from common diseases
  * Novel architecture combining X and Y
- Study objectives: Validate on 3 rare disease datasets

Stage 2: Convert Key Points to Full Paragraphs

Once the outline is complete, expand each bullet point into proper prose:

1. Transform bullet points into complete sentences with subjects, verbs, and objects 2. Add transitions between sentences and ideas (however, moreover, in contrast, subsequently) 3. Integrate citations naturally within sentences, not as lists 4. Expand with context and explanation that bullet points omit 5. Ensure logical flow from one sentence to the next within each paragraph 6. Vary sentence structure to maintain reader engagement

Example conversion to prose:

Artificial intelligence approaches have gained significant traction in drug discovery 
pipelines over the past decade (Smith, 2023; Jones, 2024). While these computational 
methods show promise for accelerating the identification of therapeutic candidates, 
traditional experimental approaches remain slow and resource-intensive, often requiring 
years of laboratory work and substantial financial investment. However, the application 
of AI to rare diseases has been limited, with only two prior studies demonstrating 
proof-of-concept results (Lee, 2022; Chen, 2023). The primary obstacle has been the 
scarcity of training data for conditions affecting small patient populations. 

To address this challenge, we developed a transfer learning approach that leverages 
knowledge from well-characterized common diseases to predict therapeutic targets for 
rare conditions. Our novel neural architecture combines convolutional layers for 
molecular feature extraction with attention mechanisms for protein-ligand interaction 
modeling. The objective of this study was to validate our approach across three 
independent rare disease datasets, assessing both predictive accuracy and biological 
interpretability of the results.

Key Differences Between Outlines and Final Text:

Common Mistakes to Avoid:

• ❌ Never leave bullet points in the final manuscript
• ❌ Never submit lists where paragraphs should be
• ❌ Don't use numbered or bulleted lists in Results or Discussion sections (except for specific cases like study hypotheses or inclusion criteria)
• ❌ Don't write sentence fragments or incomplete thoughts
• ✅ Do use occasional lists only in Methods (e.g., inclusion/exclusion criteria, materials lists)
• ✅ Do ensure every section flows as connected prose
• ✅ Do read paragraphs aloud to check for natural flow

When Lists ARE Acceptable (Limited Cases):

Lists may appear in scientific papers only in specific contexts:

• Methods: Inclusion/exclusion criteria, materials and reagents, participant characteristics
• Supplementary Materials: Extended protocols, equipment lists, detailed parameters
• Never in: Abstract, Introduction, Results, Discussion, Conclusions

Abstract Format Rule:

• ❌ NEVER use labeled sections (Background:, Methods:, Results:, Conclusions:)
• ✅ ALWAYS write as flowing paragraph(s) with natural transitions
• Exception: Only use structured format if journal explicitly requires it in author guidelines

Integration with Research Lookup:

The research-lookup skill is essential for Stage 1 (creating outlines): 1. Search for relevant papers using research-lookup 2. Extract key findings, methods, and data 3. Organize findings as bullet points in your outline 4. Then convert the outline to full paragraphs in Stage 2

This two-stage process ensures you:

• Gather and organize information systematically
• Create logical structure before writing
• Produce polished, publication-ready prose
• Maintain focus on the narrative flow

8. Professional Report Formatting (Non-Journal Documents)

For research reports, technical reports, white papers, and other professional documents that are NOT journal manuscripts, use the scientific_report.sty LaTeX style package for a polished, professional appearance.

When to Use Professional Report Formatting:

• Research reports and technical reports
• White papers and policy briefs
• Grant reports and progress reports
• Industry reports and technical documentation
• Internal research summaries
• Feasibility studies and project deliverables

When NOT to Use (Use Venue-Specific Formatting Instead):

• Journal manuscripts → Use venue-templates skill
• Conference papers → Use venue-templates skill
• Academic theses → Use institutional templates

The `scientific_report.sty` Style Package Provides:

Box Environments for Content Organization:

% Key findings (blue) - for major discoveries
\begin{keyfindings}[Title]
Content with key findings and statistics.
\end{keyfindings}

% Methodology (green) - for methods highlights
\begin{methodology}[Study Design]
Description of methods and procedures.
\end{methodology}

% Recommendations (purple) - for action items
\begin{recommendations}[Clinical Implications]
\begin{enumerate}
    \item Specific recommendation 1
    \item Specific recommendation 2
\end{enumerate}
\end{recommendations}

% Limitations (orange) - for caveats and cautions
\begin{limitations}[Study Limitations]
Description of limitations and their implications.
\end{limitations}

Professional Table Formatting:

\begin{table}[htbp]
\centering
\caption{Results Summary}
\begin{tabular}{@{}lccc@{}}
\toprule
\textbf{Variable} & \textbf{Treatment} & \textbf{Control} & \textbf{p} \\
\midrule
Outcome 1 & \meansd{42.5}{8.3} & \meansd{35.2}{7.9} & <.001\sigthree \\
\rowcolor{tablealt} Outcome 2 & \meansd{3.8}{1.2} & \meansd{3.1}{1.1} & .012\sigone \\
Outcome 3 & \meansd{18.2}{4.5} & \meansd{17.8}{4.2} & .58\signs \\
\bottomrule
\end{tabular}

{\small \siglegend}
\end{table}

Scientific Notation Commands:

Getting Started:

\documentclass[11pt,letterpaper]{report}
\usepackage{scientific_report}

\begin{document}
\makereporttitle
    {Report Title}
    {Subtitle}
    {Author Name}
    {Institution}
    {Date}

% Your content with professional formatting
\end{document}

Compilation: Use XeLaTeX or LuaLaTeX for proper Helvetica font rendering:

xelatex report.tex

For complete documentation, refer to:

• assets/scientific_report.sty: The style package
• assets/scientific_report_template.tex: Complete template example
• assets/REPORT_FORMATTING_GUIDE.md: Quick reference guide
• references/professional_report_formatting.md: Comprehensive formatting guide

9. Journal-Specific Formatting

Adapt manuscripts to journal requirements:

• Follow author guidelines for structure, length, and format
• Apply journal-specific citation styles
• Meet figure/table specifications (resolution, file formats, dimensions)
• Include required statements (funding, conflicts of interest, data availability, ethical approval)
• Adhere to word limits for each section
• Format according to template requirements when provided

10. 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 Field-Specific Linguistic Conventions:

• Review terminology used in recent high-impact papers in the 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 the 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 the target journal
• Use domain-specific databases and ontologies (e.g., Gene Ontology, MeSH terms)
• When uncertain, cite a key reference that establishes terminology

11. Common Pitfalls to Avoid

Top Rejection Reasons: 1. Inappropriate, incomplete, or insufficiently described statistics 2. Over-interpretation of results or unsupported conclusions 3. Poorly described methods affecting reproducibility 4. Small, biased, or inappropriate samples 5. Poor writing quality or difficult-to-follow text 6. Inadequate literature review or context 7. Figures and tables that are unclear or poorly designed 8. Failure to follow reporting guidelines

Writing Quality Issues:

• Mixing tenses inappropriately (use past tense for methods/results, present for established facts)
• Excessive jargon or undefined acronyms
• Paragraph breaks that disrupt logical flow
• Missing transitions between sections
• Inconsistent notation or terminology

Workflow for Manuscript Development

Stage 1: Planning 1. Identify target journal and review author guidelines 2. Determine applicable reporting guideline (CONSORT, STROBE, etc.) 3. Outline manuscript structure (usually IMRAD) 4. Plan figures and tables as the backbone of the paper

Stage 2: Drafting (Use two-stage writing process for each section) 1. Start with figures and tables (the core data story) 2. For each section below, follow the two-stage process:

• First: Create outline with bullet points using research-lookup
• Second: Convert bullet points to full paragraphs with flowing prose

3. Write Methods (often easiest to draft first) 4. Draft Results (describing figures/tables objectively) 5. Compose Discussion (interpreting findings) 6. Write Introduction (setting up the research question) 7. Craft Abstract (synthesizing the complete story) 8. Create Title (concise and descriptive)

Remember: Bullet points are for planning only—the final manuscript must be in complete paragraphs.

Stage 3: Revision 1. Check logical flow and "red thread" throughout 2. Verify consistency in terminology and notation 3. Ensure figures/tables are self-explanatory 4. Confirm adherence to reporting guidelines 5. Verify all citations are accurate and properly formatted 6. Check word counts for each section 7. Proofread for grammar, spelling, and clarity

Stage 4: Final Preparation 1. Format according to journal requirements 2. Prepare supplementary materials 3. Write cover letter highlighting significance 4. Complete submission checklists 5. Gather all required statements and forms

Integration with Other Scientific Skills

This skill works effectively with:

• Data analysis skills: For generating results to report
• Statistical analysis: For determining appropriate statistical presentations
• Literature review skills: For contextualizing research
• Figure creation tools: For developing publication-quality visualizations
• Venue-templates skill: For venue-specific writing styles and formatting (journal manuscripts)
• scientific_report.sty: For professional reports, white papers, and technical documents

Professional Reports vs. Journal Manuscripts

Choose the right formatting approach:

Venue-Specific Writing Styles

Before writing for a specific venue, consult the venue-templates skill for writing style guides:

Different venues have dramatically different writing expectations:

• Nature/Science: Accessible, story-driven, broad significance
• Cell Press: Mechanistic depth, graphical abstracts, Highlights
• Medical journals (NEJM, Lancet): Structured abstracts, evidence language
• ML conferences (NeurIPS, ICML): Contribution bullets, ablation studies
• CS conferences (CHI, ACL): Field-specific conventions

The venue-templates skill provides:

• venue_writing_styles.md: Master style comparison
• Venue-specific guides: nature_science_style.md, cell_press_style.md, medical_journal_styles.md, ml_conference_style.md, cs_conference_style.md
• reviewer_expectations.md: What reviewers look for at each venue

Workflow: First use this skill for general scientific writing principles (IMRAD, clarity, citations), then consult venue-templates for venue-specific style adaptation.

References

This skill includes comprehensive reference files covering specific aspects of scientific writing:

• references/imrad_structure.md: Detailed guide to IMRAD format and section-specific content
• references/citation_styles.md: Complete citation style guides (APA, AMA, Vancouver, Chicago, IEEE)
• references/figures_tables.md: Best practices for creating effective data visualizations
• references/reporting_guidelines.md: Study-specific reporting standards and checklists
• references/writing_principles.md: Core principles of effective scientific communication
• references/professional_report_formatting.md: Guide to professional report styling with scientific_report.sty

Assets

This skill includes LaTeX style packages and templates for professional report formatting:

• assets/scientific_report.sty: Professional LaTeX style package with Helvetica fonts, colored boxes, and attractive tables
• assets/scientific_report_template.tex: Complete report template demonstrating all style features
• assets/REPORT_FORMATTING_GUIDE.md: Quick reference guide for the style package

Key Features of `scientific_report.sty`:

• Helvetica font family for modern, professional appearance
• Professional color scheme (blues, greens, oranges, purples)
• Box environments: keyfindings, methodology, resultsbox, recommendations, limitations, criticalnotice, definition, executivesummary, hypothesis
• Tables with alternating row colors and professional headers
• Scientific notation commands for p-values, effect sizes, confidence intervals
• Professional headers and footers

For venue-specific writing styles (tone, voice, abstract format, reviewer expectations), see the venue-templates skill which provides comprehensive style guides for Nature/Science, Cell Press, medical journals, ML conferences, and CS conferences.

Load these references as needed when working on specific aspects of scientific writing.

Scientific Report Formatting Guide

Quick reference for using the scientific_report.sty style package.

Overview

The scientific_report.sty package provides professional formatting for scientific reports, technical documents, and white papers. It features:

• Helvetica font family for a clean, modern appearance
• Professional color scheme with blues, greens, and accent colors
• Colored box environments for organizing different types of content
• Attractive tables with alternating row colors and professional headers
• Scientific notation commands for p-values, effect sizes, and statistics
• Professional headers and footers with automatic section titles

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Color Palette

Primary Colors (Blues)

Scientific Colors (Greens)

Warning Colors (Orange/Red)

Recommendation Colors

Neutral Colors

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Box Environments

Key Findings Box (Blue)

For major findings, discoveries, and important results.

\begin{keyfindings}[Custom Title]
This study found that treatment A significantly outperformed
treatment B (\pvalue{0.001}, \effectsize{d}{0.75}).
\end{keyfindings}

Methodology Box (Green)

For methods, procedures, and study design highlights.

\begin{methodology}[Study Design]
This randomized controlled trial employed a 2×2 factorial design
with pre-post measurements and 6-month follow-up.
\end{methodology}

Results Box (Blue-Green)

For highlighting specific results and statistical findings.

\begin{resultsbox}[Primary Outcome]
Analysis revealed a significant main effect, F(2, 147) = 12.45,
\psig{< 0.001}, $\eta^2$ = 0.145.
\end{resultsbox}

Recommendations Box (Purple)

For recommendations, implications, and action items.

\begin{recommendations}[Clinical Implications]
\begin{enumerate}
    \item Implement screening protocol for high-risk patients
    \item Adjust treatment dosage based on biomarker levels
    \item Monitor patients at 3-month intervals
\end{enumerate}
\end{recommendations}

Limitations Box (Orange)

For limitations, cautions, and caveats.

\begin{limitations}[Study Limitations]
\begin{itemize}
    \item Sample limited to urban populations
    \item Cross-sectional design precludes causal inference
    \item Self-report measures may introduce bias
\end{itemize}
\end{limitations}

Critical Notice Box (Red)

For critical warnings, important notices, or safety information.

\begin{criticalnotice}[Safety Warning]
Patients with contraindication X should not receive this treatment.
Consult specialist before proceeding.
\end{criticalnotice}

Definition Box (Gray)

For definitions, notes, and supplementary information.

\begin{definition}[Key Term]
\textbf{Effect size} refers to a quantitative measure of the
magnitude of a phenomenon, independent of sample size.
\end{definition}

Executive Summary Box (Special)

For executive summaries with enhanced styling and shadow effect.

\begin{executivesummary}[Report Overview]
This report presents findings from a comprehensive analysis
of [topic]. Key findings indicate that...
\end{executivesummary}

Hypothesis Box (Light Blue)

For stating research hypotheses.

\begin{hypothesis}[Primary Hypothesis]
We hypothesize that intervention X will significantly improve
outcome Y compared to control conditions.
\end{hypothesis}

---

Pull Quotes

For highlighting important quotes or statements.

\begin{pullquote}
"These findings represent a paradigm shift in our understanding
of the underlying mechanisms."
\end{pullquote}

---

Statistic Boxes

For highlighting key statistics (use in rows of 3).

\begin{center}
\statbox{n = 500}{Participants}
\statbox{p < 0.001}{Significance}
\statbox{d = 0.75}{Effect Size}
\end{center}

---

Scientific Notation Commands

P-Values

\pvalue{0.023}          % Outputs: p = 0.023
\psig{< 0.001}          % Outputs: p = < 0.001 (bold for significant)

Confidence Intervals

\CI{0.45}{0.72}         % Outputs: 95% CI [0.45, 0.72]

Effect Sizes

\effectsize{d}{0.75}    % Outputs: d = 0.75
\effectsize{r}{0.42}    % Outputs: r = 0.42
\effectsize{F(2, 97)}{12.45}  % Outputs: F(2, 97) = 12.45

Sample Size

\samplesize{250}        % Outputs: n = 250

Mean with Standard Deviation

\meansd{42.5}{8.3}      % Outputs: 42.5 ± 8.3

Significance Indicators (for tables)

Result\sigone           % * for p < 0.05
Result\sigtwo           % ** for p < 0.01
Result\sigthree         % *** for p < 0.001
Result\signs            % ns for not significant

% Legend for table footnotes:
\siglegend              % Outputs: *p < 0.05; **p < 0.01; ***p < 0.001; ns not significant

Quality/Evidence Indicators

\qualityhigh            % HIGH (green)
\qualitymedium          % MEDIUM (orange)
\qualitylow             % LOW (red)

\evidencestrong         % Strong (green)
\evidencemoderate       % Moderate (orange)
\evidenceweak           % Weak (red)

Trend Indicators

\trendup                % Green up triangle ▲
\trenddown              % Red down triangle ▼
\trendflat              % Gray right arrow →

Text Highlighting

\highlight{important text}  % Blue bold text

---

Table Formatting

Standard Table with Alternating Rows

\begin{table}[htbp]
\centering
\caption{Descriptive Statistics by Group}
\label{tab:descriptives}
\begin{tabular}{@{}lccc@{}}
\toprule
\textbf{Variable} & \textbf{Group A} & \textbf{Group B} & \textbf{p} \\
\midrule
Age (years) & \meansd{42.5}{8.3} & \meansd{43.1}{7.9} & .58 \\
\rowcolor{tablealt} Score 1 & \meansd{15.2}{3.4} & \meansd{18.7}{4.1} & <.001\sigthree \\
Score 2 & \meansd{22.8}{5.1} & \meansd{23.4}{4.8} & .42 \\
\rowcolor{tablealt} Score 3 & \meansd{8.9}{2.2} & \meansd{7.2}{2.5} & .003\sigtwo \\
\bottomrule
\end{tabular}

\vspace{0.5em}
{\small \siglegend}
\end{table}

Table with Quality Indicators

\begin{tabular}{@{}llcc@{}}
\toprule
\textbf{Study} & \textbf{Design} & \textbf{Quality} & \textbf{Evidence} \\
\midrule
Smith et al. (2023) & RCT & \qualityhigh & \evidencestrong \\
\rowcolor{tablealt} Jones et al. (2022) & Cohort & \qualitymedium & \evidencemoderate \\
Lee et al. (2021) & Cross-sectional & \qualitylow & \evidenceweak \\
\bottomrule
\end{tabular}

Table with Trend Indicators

\begin{tabular}{@{}lrrl@{}}
\toprule
\textbf{Metric} & \textbf{Baseline} & \textbf{Follow-up} & \textbf{Change} \\
\midrule
Score A & 42.5 & 58.3 & \trendup +37\% \\
\rowcolor{tablealt} Score B & 18.2 & 15.1 & \trenddown -17\% \\
Score C & 7.8 & 7.9 & \trendflat +1\% \\
\bottomrule
\end{tabular}

---

Figure Formatting

Standard Figure

\begin{figure}[htbp]
\centering
\includegraphics[width=0.9\textwidth]{../figures/results_chart.png}
\caption{Comparison of Outcome Scores Across Treatment Conditions}
\label{fig:results}
\end{figure}

Figure with Source Attribution

\begin{figure}[htbp]
\centering
\includegraphics[width=0.85\textwidth]{../figures/data_visualization.png}
\caption{Distribution of Participant Responses by Category}
\figuresource{Study data, collected January-March 2024}
\label{fig:distribution}
\end{figure}

Figure with Note

\begin{figure}[htbp]
\centering
\includegraphics[width=0.8\textwidth]{../figures/model_diagram.png}
\caption{Conceptual Model of Proposed Relationships}
\figurenote{Solid arrows indicate direct effects; dashed arrows indicate moderated effects.}
\label{fig:model}
\end{figure}

---

Title Page

Standard Title Page

\makereporttitle
    {Research Report Title}              % Title
    {A Comprehensive Analysis}           % Subtitle
    {Author Name, PhD}                   % Author(s)
    {Research Institution}               % Institution
    {January 2025}                        % Date

Title Page with Cover Image

\makereporttitlewithimage
    {Research Report Title}              % Title
    {A Comprehensive Analysis}           % Subtitle
    {../figures/cover_image.png}         % Image path
    {Author Name, PhD}                   % Author(s)
    {Research Institution}               % Institution
    {January 2025}                        % Date

---

List Formatting

Lists automatically use blue bullets/numbers.

Bullet Lists

\begin{itemize}
    \item First item with automatic blue bullet
    \item Second item
    \item Third item
\end{itemize}

Numbered Lists

\begin{enumerate}
    \item First item with blue number
    \item Second item
    \item Third item
\end{enumerate}

---

Appendix Sections

\appendix

\chapter{Supplementary Materials}

\appendixsection{Additional Tables}
% Content appears in table of contents

\appendixsection{Instruments}
% Additional appendix content

---

Compilation

Compile with XeLaTeX or LuaLaTeX for best font rendering:

# Using XeLaTeX
xelatex report.tex
bibtex report        # If using BibTeX
xelatex report.tex
xelatex report.tex

# Using latexmk (recommended)
latexmk -xelatex report.tex

# Using LuaLaTeX
lualatex report.tex

---

Common Patterns

Results Section Example

\section{Primary Outcomes}

\begin{resultsbox}[Main Finding]
The intervention group showed significantly higher scores than
the control group, \effectsize{t(98)}{3.45}, \psig{< 0.001},
\effectsize{d}{0.69}, \CI{0.42}{0.96}.
\end{resultsbox}

Table~\ref{tab:outcomes} presents the complete results for all
outcome measures.

\begin{table}[htbp]
\centering
\caption{Outcome Measures by Treatment Condition}
\label{tab:outcomes}
\begin{tabular}{@{}lcccc@{}}
\toprule
\textbf{Measure} & \textbf{Control} & \textbf{Treatment} & \textbf{d} & \textbf{p} \\
\midrule
Primary & \meansd{42.1}{8.2} & \meansd{51.3}{9.1} & 0.69\sigthree & <.001 \\
\rowcolor{tablealt} Secondary & \meansd{3.2}{1.1} & \meansd{4.1}{1.3} & 0.52\sigtwo & .004 \\
Tertiary & \meansd{18.5}{4.2} & \meansd{19.2}{4.5} & 0.16\signs & .328 \\
\bottomrule
\end{tabular}
\end{table}

Discussion Section Example

\section{Interpretation of Findings}

\begin{keyfindings}[Summary]
\begin{enumerate}
    \item Primary hypothesis \highlight{supported} with large effect
    \item Secondary hypothesis partially supported
    \item Evidence quality: \evidencestrong
\end{enumerate}
\end{keyfindings}

\begin{limitations}
This study has several limitations that should be considered...
\end{limitations}

\begin{recommendations}[Future Research]
Future studies should address the following:
\begin{enumerate}
    \item Replicate findings in diverse populations
    \item Extend follow-up period to assess long-term effects
    \item Investigate moderating variables
\end{enumerate}
\end{recommendations}

---

Troubleshooting

Box Overflow

If box content overflows the page:

\newpage
\begin{keyfindings}[Continued...]

Figure Placement

Use [htbp] for flexible placement, or [H] (requires float package) for exact:

\usepackage{float}
\begin{figure}[H]

Table Too Wide

Use \resizebox or reduce font size:

\resizebox{\textwidth}{!}{
\begin{tabular}{...}
...
\end{tabular}
}

Font Issues

If Helvetica isn't rendering, ensure you're using XeLaTeX or LuaLaTeX:

xelatex report.tex   # NOT pdflatex

---

Quick Reference Card

Citation Styles Guide

Overview

Citation styles provide standardized formats for acknowledging sources in scientific writing. Different disciplines prefer different styles, and journals typically specify which style to use. The five most common citation styles in science are AMA, Vancouver, APA, Chicago, and IEEE.

Choosing the Right Style

Default recommendation: When in doubt, check the journal's author guidelines. Most biomedical journals use Vancouver or AMA style.

AMA Style (American Medical Association)

Overview

• Used primarily in medical research
• Based on the AMA Manual of Style (11th edition, 2020)
• Numbered citations appearing as superscripts
• References listed numerically in order of appearance

In-Text Citations

Basic format: Superscript numerals outside periods and commas, inside semicolons and colons.

Examples:

Several studies have demonstrated this effect.¹

The results were inconclusive,² although Smith et al³ reported otherwise.

These findings³⁻⁵ suggest a correlation.

One meta-analysis⁶ found significant heterogeneity; however, the pooled effect was significant.⁷

Multiple citations: Use commas or hyphens for ranges

Multiple studies¹,³,⁵⁻⁷ have confirmed this.

Same source cited multiple times: Use the same number throughout

Reference List Format

Journal Articles:

1. Author AA, Author BB, Author CC. Title of article. Journal Name. Year;Volume(Issue):Page range. doi:xx.xxxx

Example:

1. Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023;80(5):456-464. doi:10.1001/jamapsychiatry.2023.0123

Books:

2. Author AA. Book Title. Edition. Publisher; Year.

Book Chapters:

3. Chapter Author AA. Chapter title. In: Editor AA, Editor BB, eds. Book Title. Edition. Publisher; Year:Page range.

Online Resources:

4. Organization Name. Page title. Website name. Published date. Updated date. Accessed date. URL

Special Cases

More than 6 authors: List first 3, then "et al"

Smith JD, Jones AB, Williams CD, et al.

No author: Begin with title

Advance online publication:

Published online Month Day, Year. doi:xx.xxxx

Vancouver Style

Overview

• Developed by the International Committee of Medical Journal Editors (ICMJE)
• Described in Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals
• Also called "author-number style"
• Numbered citations in square brackets
• References listed numerically

In-Text Citations

Basic format: Numbers in square brackets after the relevant text, before periods and commas.

Examples:

Several studies have shown this effect [1].

The results were inconclusive [2], although Smith et al [3] reported otherwise.

These findings [3-5] suggest a correlation.

Multiple studies [1,3,5-7] have confirmed this.

Reference List Format

Journal Articles:

1. Author AA, Author BB, Author CC. Title of article. Journal Name. Year;Volume(Issue):Page range.

Example:

1. Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023;80(5):456-464.

Books:

2. Author AA, Author BB. Book title. Edition. Place of publication: Publisher; Year.

Book Chapters:

3. Chapter Author AA, Chapter Author BB. Chapter title. In: Editor AA, Editor BB, editors. Book title. Edition. Place: Publisher; Year. p. Page range.

Electronic Sources:

4. Author AA. Title of page [Internet]. Place: Publisher; Date of publication [cited Date of citation]. Available from: URL

Special Cases

More than 6 authors: List first 6, then "et al."

Journal title abbreviations: Use PubMed/Index Medicus abbreviations

• The Journal of the American Medical Association → JAMA
• Nature Medicine → Nat Med

No volume or issue: Use year and page numbers only

Article in press: Use "[Epub ahead of print]" notation

APA Style (American Psychological Association)

Overview

• Widely used in psychology, education, and social sciences
• Based on the Publication Manual of the APA (7th edition, 2020)
• Author-date format for in-text citations
• References listed alphabetically by author surname

In-Text Citations

Basic format: (Author, Year)

Examples:

One study found significant effects (Smith, 2023).

Smith (2023) found significant effects.

Multiple studies (Jones, 2020; Smith, 2023; Williams, 2024) support this conclusion.

Two authors: Use "&" in parentheses, "and" in narrative

(Smith & Jones, 2023)
Smith and Jones (2023) demonstrated...

Three or more authors: Use "et al." after first author

(Smith et al., 2023)
Smith et al. (2023) reported...

Multiple works by same author(s) in same year: Add letters

(Smith, 2023a, 2023b)

Direct quotations: Include page numbers

(Smith, 2023, p. 45)
"Quote text" (Smith, 2023, p. 45).
Smith (2023) stated, "Quote text" (p. 45).

Reference List Format

Journal Articles:

Author, A. A., Author, B. B., & Author, C. C. (Year). Title of article. Journal Name, Volume(Issue), page range. https://doi.org/xx.xxxx

Example:

Smith, J. D., Johnson, A. B., & Williams, C. D. (2023). Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry, 80(5), 456-464. https://doi.org/10.1001/jamapsychiatry.2023.0123

Books:

Author, A. A. (Year). Book title: Subtitle (Edition). Publisher. https://doi.org/xx.xxxx

Book Chapters:

Chapter Author, A. A., & Chapter Author, B. B. (Year). Chapter title. In E. E. Editor & F. F. Editor (Eds.), Book title (pp. page range). Publisher.

Websites:

Author, A. A. (Year, Month Day). Page title. Website Name. URL

Capitalization Rules

• Sentence case for article and book titles (capitalize only first word and proper nouns)
• Title case for journal names (capitalize all major words)

Example:

Smith, J. D. (2023). Effects of stress on cognitive performance: A meta-analysis. Journal of Experimental Psychology: General, 152(3), 456-478.

Special Cases

No author: Move title to author position

Title of work. (Year). Journal Name...

No date: Use (n.d.)

Smith, J. D. (n.d.). Title...

Up to 20 authors: List all authors with "&" before last 21 or more authors: List first 19, then "...", then final author

Chicago Style

Overview

• Based on The Chicago Manual of Style (17th edition, 2017)
• Two systems: Notes-Bibliography and Author-Date
• Notes-Bibliography common in humanities
• Author-Date common in sciences

Notes-Bibliography System

In-Text: Superscript numbers for footnotes or endnotes

One study demonstrated this effect.¹

Note format:

1. John D. Smith, Alice B. Johnson, and Carol D. Williams, "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders," JAMA Psychiatry 80, no. 5 (2023): 456-64.

Bibliography format:

Smith, John D., Alice B. Johnson, and Carol D. Williams. "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders." JAMA Psychiatry 80, no. 5 (2023): 456-64.

Author-Date System

In-Text: Similar to APA

(Smith, Johnson, and Williams 2023)
Smith, Johnson, and Williams (2023) found...

Reference list: Similar to APA but with different punctuation

Smith, John D., Alice B. Johnson, and Carol D. Williams. 2023. "Effectiveness of Cognitive Behavioral Therapy for Anxiety Disorders." JAMA Psychiatry 80 (5): 456-64.

Special Features

• Full names in bibliography (not just initials)
• Uses "and" not "&"
• Different punctuation from APA

IEEE Style

Overview

• Used in engineering, computer science, and technology
• Published by the Institute of Electrical and Electronics Engineers
• Numbered citations in square brackets
• References listed numerically

In-Text Citations

Format: Numbers in square brackets

Examples:

Several studies have demonstrated this effect [1].

The algorithm was described by Smith [2] and later improved [3], [4].

Multiple implementations [1]-[4] have been proposed.

Reference List Format

Journal Articles:

[1] A. A. Author, B. B. Author, and C. C. Author, "Title of article," Journal Name, vol. X, no. X, pp. XX-XX, Month Year.

Example:

[1] J. D. Smith, A. B. Johnson, and C. D. Williams, "Effectiveness of cognitive behavioral therapy for anxiety disorders," JAMA Psychiatry, vol. 80, no. 5, pp. 456-464, May 2023.

Books:

[2] A. A. Author, Book Title, Edition. City, State: Publisher, Year.

Conference Papers:

[3] A. A. Author, "Paper title," in Proc. Conference Name, City, State, Year, pp. XX-XX.

Online Sources:

[4] A. A. Author. "Title." Website. URL (accessed Mon. Day, Year).

Special Features

• Abbreviated first and middle names
• Uses "and" before last author (not comma)
• Month abbreviations (Jan., Feb., etc.)
• "vol." and "no." before volume and issue
• "pp." before page range

Additional Styles

ACS Style (American Chemical Society)

In-Text: Superscript numbers or numbers in parentheses

This reaction has been well studied.¹
This reaction has been well studied (1).

Reference format:

(1) Smith, J. D.; Johnson, A. B.; Williams, C. D. Title of Article. J. Am. Chem. Soc. 2023, 145, 1234-1245.

Features:

• Semicolons between authors
• Abbreviated journal names
• Year in bold
• No issue numbers

NLM Style (National Library of Medicine)

Very similar to Vancouver, used by PubMed/MEDLINE

Key differences:

• Uses PubMed journal abbreviations
• Specific format for electronic publications
• PMID or PMCID can be included

Example:

Smith JD, Johnson AB, Williams CD. Effectiveness of cognitive behavioral therapy for anxiety disorders. JAMA Psychiatry. 2023 May;80(5):456-64. doi: 10.1001/jamapsychiatry.2023.0123. PMID: 12345678.

General Citation Best Practices

Across All Styles

When to cite:

• Direct quotations
• Paraphrased ideas from others
• Statistics, data, or figures from other sources
• Theories, models, or frameworks developed by others
• Information that is not common knowledge

Citation density:

• Introduction: Cite liberally to establish context
• Methods: Cite when referencing established protocols or instruments
• Results: Rarely cite (focus on your own findings)
• Discussion: Cite frequently when comparing to prior work

Source quality:

• Prefer peer-reviewed journal articles
• Cite original sources when possible (not secondary citations)
• Use recent sources (within 5-10 years for active fields)
• Ensure sources are reputable and relevant

Common mistakes to avoid:

• Inconsistent formatting
• Missing required elements (DOI, page numbers, etc.)
• Citing sources not actually read (citation chaining)
• Over-reliance on review articles instead of primary sources
• Including uncited references or missing cited references
• Incorrect author names or initials
• Wrong year of publication
• Truncated titles

Managing Citations

Reference Management Software:

• Zotero: Free, open-source, browser integration
• Mendeley: Free, PDF annotation, social features
• EndNote: Commercial, powerful, institutional support
• RefWorks: Web-based, institutional subscriptions

Software benefits:

• Automatic formatting in multiple styles
• In-text citation insertion
• Reference list generation
• PDF organization
• Sharing capabilities

Verifying Citations

Before submission, check: 1. Every in-text citation has a corresponding reference 2. Every reference is cited in text 3. Formatting is consistent throughout 4. Author names and initials are correct 5. Titles are accurate 6. Journal names match required abbreviations 7. Volume, issue, and page numbers are correct 8. DOIs are included (when required) 9. URLs are functional (for web sources) 10. Citations appear in correct order (numerical styles)

DOI (Digital Object Identifier)

What is a DOI?

A unique alphanumeric string identifying digital content permanently.

Format:

doi:10.1001/jamapsychiatry.2023.0123
or
https://doi.org/10.1001/jamapsychiatry.2023.0123

When to include:

• Required by most journals for recent publications
• Preferred over URLs because DOIs don't change
• Look up DOIs at https://www.crossref.org/ if not provided

Style-specific formatting:

• AMA: doi:10.xxxx/xxxxx
• APA: https://doi.org/10.xxxx/xxxxx
• Vancouver: Often omitted or added at journal's discretion
• Chicago: https://doi.org/10.xxxx/xxxxx

Quick Reference: Journal Article Format

Common Abbreviations

Journal Abbreviations

Follow the journal's specified system (usually Index Medicus or ISO):

• The Journal of Biological Chemistry → J Biol Chem
• Proceedings of the National Academy of Sciences → Proc Natl Acad Sci USA
• Nature Medicine → Nat Med

Month Abbreviations

• Jan., Feb., Mar., Apr., May, June, July, Aug., Sept., Oct., Nov., Dec.
• Some styles use three-letter abbreviations without periods

Edition Abbreviations

• 1st ed., 2nd ed., 3rd ed., etc.
• Or: 1st edition, 2nd edition

Special Publication Types

Preprints

APA: Author, A. A. (Year). Title [Preprint]. Repository Name. https://doi.org/xx.xxxx

Theses and Dissertations

APA: Author, A. A. (Year). Title [Doctoral dissertation, University Name]. Repository Name. URL

Conference Proceedings

IEEE: A. A. Author, "Title," in Proc. Conf. Name, City, Year, pp. XX-XX.

Software/Code

APA: Author, A. A. (Year). Title (Version X.X) [Computer software]. Publisher. URL

Datasets

APA: Author, A. A. (Year). Title of dataset (Version X) [Data set]. Repository. https://doi.org/xx.xxxx

Transitioning Between Styles

When converting between citation styles:

1. Use reference management software for automatic conversion 2. Check these elements that vary by style:

• In-text citation format (numbered vs. author-date)
• Author name format (initials vs. full names)
• Title capitalization (sentence case vs. title case)
• Journal name formatting (abbreviated vs. full)
• Punctuation (periods, commas, semicolons)
• Use of italics and bold
• Order of elements

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 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

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

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

• AMA: https://www.amamanualofstyle.com/
• Vancouver/ICMJE: http://www.icmje.org/
• APA: https://apastyle.apa.org/
• 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/
• EasyBib: https://www.easybib.com/

Reference Management

• 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

IMRAD Structure Guide

Overview

IMRAD (Introduction, Methods, Results, And Discussion) is the predominant organizational structure for scientific journal articles of original research. Adopted as the majority format since the 1970s, it is now the standard in medical, health, biological, chemical, engineering, and computer sciences.

Why IMRAD?

The IMRAD structure mirrors the scientific method:

• Introduction: What question did you ask?
• Methods: How did you study it?
• Results: What did you find?
• Discussion: What does it mean?

This logical flow makes scientific papers easier to write, read, and evaluate.

Complete Manuscript Components

A full scientific manuscript typically includes these sections in order:

1. Title 2. Abstract 3. Introduction 4. Methods (also called Materials and Methods, Methodology) 5. Results 6. Discussion (sometimes combined with Results) 7. Conclusion (sometimes part of Discussion) 8. Acknowledgments 9. References 10. Supplementary Materials (if applicable)

Title

Purpose

Attract readers and accurately represent the paper's content.

Guidelines

• Be concise yet descriptive (typically 10-15 words)
• Include key variables and the relationship studied
• Avoid abbreviations, jargon, and question formats (unless the journal allows)
• Make it specific enough to distinguish from other studies
• Include key search terms for discoverability

Examples

• Good: "Effects of High-Intensity Interval Training on Cardiovascular Function in Older Adults"
• Too vague: "Exercise and Health"
• Too detailed: "A Randomized Controlled Trial Examining the Effects of High-Intensity Interval Training Compared to Moderate Continuous Training on Cardiovascular Function Measured by VO2 Max in Adults Aged 60-75 Years"

Abstract

Purpose

Provide a complete, standalone summary enabling readers to decide if the full paper is relevant to them.

Format: Flowing Paragraphs (Default)

⚠️ CRITICAL: Write abstracts as flowing paragraphs, NOT with labeled sections.

Most scientific papers use unstructured abstracts written as one or two cohesive paragraphs. This is the standard format for the majority of journals including Nature, Science, Cell, PNAS, and most field-specific journals.

❌ WRONG - Structured abstract with labels:

Background: Hospital-acquired infections remain a major cause of morbidity.
Methods: We conducted a 12-month before-after study...
Results: Post-intervention, surface contamination decreased by 47%...
Conclusions: UV-C disinfection significantly reduced infection rates.

✅ CORRECT - Flowing paragraph style:

Hospital-acquired infections remain a major cause of morbidity, yet optimal 
disinfection strategies remain unclear. We conducted a 12-month before-after 
study in a 500-bed teaching hospital to evaluate UV-C disinfection added to 
standard cleaning protocols. Environmental surfaces were cultured monthly and 
infection rates tracked via surveillance data. Post-intervention, surface 
contamination decreased by 47% (95% CI: 38-56%, p<0.001), and catheter-associated 
urinary tract infections declined from 3.2 to 1.8 per 1000 catheter-days (RR=0.56, 
95% CI: 0.38-0.83, p=0.004). No adverse effects were observed. These findings 
demonstrate that UV-C disinfection significantly reduces environmental contamination 
and infection rates, suggesting it may be a valuable addition to hospital infection 
control programs.

Abstract Structure (as unified paragraph)

While written as flowing prose, the abstract should cover these elements in order:

1. Context and problem (1-2 sentences): Why the research matters, what gap exists 2. Study description (1-2 sentences): What was done and how (study design, methods) 3. Key findings (2-4 sentences): Main results with specific quantitative data 4. Significance (1-2 sentences): Interpretation, implications, and conclusions

Length

• Typically 150-300 words (check journal requirements)
• Some journals allow up to 350 words

Key Rules

• Write the abstract last (after completing all other sections)
• Write as flowing paragraph(s) - no labeled sections
• Make it fully understandable without reading the paper
• Do not cite references in the abstract
• Avoid abbreviations or define them at first use
• Use past tense for methods and results, present tense for conclusions
• Include key quantitative results with statistical measures
• Use transitions to connect sentences naturally

When to Use Structured Abstracts (Exception)

Only use labeled sections (Background/Objective, Methods, Results, Conclusions) when:

• The journal explicitly requires structured abstracts in their author guidelines
• Common in some medical journals (JAMA, BMJ, Annals of Internal Medicine)
• Always check journal requirements before formatting

Even for structured abstracts, write each section as complete sentences, not fragments.

Example: Flowing Paragraph Abstract

Transcriptomic aging clocks offer unique advantages for assessing biological age by 
capturing dynamic cellular states and acute responses to perturbations. Using the 
ARCHS4 database containing uniformly processed RNA-seq data from over 1.2 million 
human samples, we developed deep neural network models to predict chronological age 
from gene expression profiles. Our best-performing model achieved a mean absolute 
error of 4.2 years (R² = 0.89) on held-out test data, substantially outperforming 
traditional machine learning approaches including elastic net regression (MAE = 6.8 
years) and random forests (MAE = 5.9 years). Feature importance analysis identified 
genes enriched in senescence, inflammation, and mitochondrial function pathways as 
the strongest predictors. Cross-tissue validation revealed that lung and blood 
samples yielded the most accurate predictions, while liver showed the highest 
variance. These findings establish deep learning as a powerful approach for 
transcriptomic age prediction and identify candidate biomarkers for biological 
aging assessment.

Introduction

Purpose

Convince readers that the research addresses an important question using an appropriate approach.

Structure and Content

Paragraph 1: The Big Picture

• Establish the broad research area
• Explain why this topic matters
• Use present tense for established facts
• Keep it accessible to non-specialists

Paragraphs 2-3: Narrowing Down

• Review relevant prior research
• Show what is already known
• Identify controversies or limitations in existing work
• Create a logical progression toward the gap

Paragraph 4: The Gap

• Explicitly identify what remains unknown
• Explain why this knowledge gap is problematic
• Connect the gap to the big picture importance

Final Paragraph: This Study

• State the specific research question or hypothesis
• Describe the overall approach briefly
• Explain how this study addresses the gap
• Optional: Preview key findings (some journals discourage this)

Length

• Typically 1.5-2 pages (depending on journal)
• Usually 4-5 paragraphs
• Shorter for letters/brief communications

Verb Tense

• Present tense: Established facts ("Exercise improves cardiovascular health")
• Past tense: Previous studies and their findings ("Smith et al. found that...")
• Present/past tense: Your study aims ("This study investigates..." or "This study investigated...")

Common Mistakes to Avoid

• Starting too broad (e.g., "Since the beginning of time...")
• Exhaustive literature review (save for review articles)
• Citing irrelevant or outdated references
• Failing to identify a clear gap
• Weak justification for the study
• Not stating a clear research question or hypothesis
• Including methods or results (these belong in later sections)

Key Questions to Answer

1. What do we know about this topic? 2. What don't we know? (the gap) 3. Why does this gap matter? 4. What did this study aim to find out?

Methods

Purpose

Provide sufficient detail for others to replicate the study and evaluate its validity.

Key Principle

Another expert in the field should be able to repeat your experiment exactly as you performed it.

Standard Subsections

Study Design

• State the overall design (e.g., randomized controlled trial, cohort study, cross-sectional survey)
• Justify the design choice if not obvious
• Mention blinding, randomization, or controls if applicable

Participants/Subjects/Sample

• Define the population of interest
• Describe inclusion and exclusion criteria precisely
• Report sample size and how it was determined (power analysis)
• Explain recruitment methods and setting
• For animals: specify species, strain, age, sex, housing conditions

Materials and Equipment

• List all materials, reagents, and equipment used
• Include manufacturer names and locations (in parentheses)
• Specify catalog numbers for specialized items
• Report software names and versions

Procedures

• Describe what was done in chronological order
• Include sufficient detail for replication
• Use subheadings to organize complex procedures
• Specify timing (e.g., "incubated for 2 hours at 37°C")
• For surveys/interviews: describe instruments, validation, administration

Measurements and Outcomes

• Define all variables measured
• Specify primary and secondary outcomes
• Describe measurement instruments and their validity
• Include units of measurement

Statistical Analysis

• Name all statistical tests used
• Justify test selection
• State significance level (typically α = 0.05)
• Report power analysis for sample size
• Name statistical software with version
• Describe handling of missing data
• Mention adjustments for multiple comparisons if applicable

Ethical Considerations

• State IRB/ethics committee approval (with approval number)
• Mention informed consent procedures
• For human studies: state adherence to Helsinki Declaration
• For animal studies: state adherence to relevant guidelines (e.g., ARRIVE)

Length

• Typically 2-4 pages
• Proportional to study complexity

Verb Tense

• Past tense for actions you performed ("We measured...", "Participants completed...")
• Present tense for established procedures ("PCR amplifies...", "The questionnaire contains...")

Common Mistakes

• Insufficient detail for replication
• Methods appearing for the first time in Results
• Including results or discussion
• Missing statistical tests
• Undefined abbreviations
• Lack of ethical approval statement

Results

Purpose

Present the findings objectively without interpretation.

Key Principle

Show, don't interpret. Save interpretation for the Discussion.

Structure and Content

Opening Paragraph

• Describe the participants/sample characteristics
• Report recruitment flow (e.g., screened, enrolled, completed)
• Consider including a CONSORT-style flow diagram

Subsequent Paragraphs

• Present results in logical order (usually primary outcome first)
• Follow the order of objectives stated in Introduction
• Organize by theme or by chronology, depending on what's clearest
• Reference figures and tables by number

Each Finding Should Include:

• The observed result
• The direction of the effect
• The magnitude of the effect
• The statistical significance
• The confidence interval

Example: "Mean systolic blood pressure decreased by 12 mmHg in the intervention group compared to 3 mmHg in controls (difference: 9 mmHg, 95% CI: 4-14 mmHg, p=0.002)."

Integration with Figures and Tables

When to Use:

• Figures: Trends, patterns, distributions, comparisons, relationships
• Tables: Precise values, demographic data, multiple variables

How to Reference:

• "Figure 1 shows the distribution of..." (not "Figure 1 below")
• "Table 2 presents baseline characteristics..."
• Don't repeat all table data in text; highlight key findings
• Each figure/table should be referenced in text

Figures and Tables Guidelines

• Number consecutively in order of mention
• Include complete, standalone captions
• Define all abbreviations in caption or footnote
• Report sample sizes (n)
• Indicate statistical significance (*, p-values)
• Use consistent formatting

Statistical Reporting

Required Elements:

• Test statistic (t, F, χ², etc.)
• Degrees of freedom
• p-value (exact if p > 0.001, otherwise report as "p < 0.001")
• Effect size and confidence interval
• Sample sizes

Example: "Groups differed significantly on test performance (t(48) = 3.21, p = 0.002, Cohen's d = 0.87, 95% CI: 0.34-1.40)."

Length

• Typically 2-4 pages
• Roughly equivalent to Methods length

Verb Tense

• Past tense for your findings ("The mean was...", "Participants showed...")

Common Mistakes

• Interpreting results (save for Discussion)
• Repeating all table/figure data in text
• Presenting new methods
• Insufficient statistical detail
• Inconsistent units or notation
• Not addressing negative or unexpected findings
• Selective reporting (all tested hypotheses should be reported)

Organization Strategies

By Objective:

Effect of intervention on primary outcome
Effect of intervention on secondary outcome A
Effect of intervention on secondary outcome B

By Analysis Type:

Descriptive statistics
Univariate analyses
Multivariate analyses

Chronological:

Baseline characteristics
Short-term outcomes (1 month)
Long-term outcomes (6 months)

Discussion

Purpose

Interpret findings, relate them to existing knowledge, acknowledge limitations, and propose future directions.

Structure and Content

Paragraph 1: Summary of Main Findings

• Restate the primary objective or hypothesis
• Summarize the principal findings in 2-4 sentences
• Avoid repeating details from Results
• State clearly whether the hypothesis was supported

Paragraphs 2-4: Interpretation in Context

• Compare your findings with previous research
• Explain agreements and disagreements with prior work
• Propose mechanisms or explanations for findings
• Discuss unexpected results
• Consider alternative explanations
• Address whether findings support or refute existing theories

Paragraph 5: Strengths and Limitations

• Acknowledge study limitations honestly
• Explain how limitations might affect interpretation
• Mention study strengths (design, sample, methods)
• Avoid generic limitations ("larger sample needed")—be specific

Paragraph 6: Implications

• Clinical implications (for medical research)
• Practical applications
• Policy implications
• Theoretical contributions

Final Paragraph: Conclusions and Future Directions

• Summarize the take-home message
• Suggest specific future research to address gaps or limitations
• End with a strong concluding statement

Length

• Typically 3-5 pages
• Usually the longest section

Verb Tense

• Past tense: Your study findings ("We found that...", "The results showed...")
• Present tense: Established facts and your interpretations ("This suggests that...", "These findings indicate...")
• Future tense: Implications and future research ("Future studies should investigate...")

Discussion Strategies

Comparing to Prior Work:

"Our finding of a 30% reduction in symptoms aligns with Smith et al. (2023), who
reported a 28% reduction using a similar intervention. However, Jones et al. (2022)
found no significant effect, possibly due to their use of a less intensive protocol."

Proposing Mechanisms:

"The observed improvement in cognitive function may result from increased cerebral
blood flow, as evidenced by the concurrent increase in functional MRI signals in the
prefrontal cortex. This interpretation is consistent with the vascular hypothesis of
cognitive enhancement."

Acknowledging Limitations:

"The cross-sectional design prevents causal inference. Additionally, the convenience
sample from a single academic medical center may limit generalizability to community
settings. Self-reported measures may introduce recall bias, though we attempted to
minimize this through structured interviews."

Common Mistakes

• Simply repeating results without interpretation
• Over-interpreting findings or claiming causation without warrant
• Ignoring inconsistent or negative findings
• Failing to compare with existing literature
• Introducing new data or methods
• Generic or superficial discussion of limitations
• Overgeneralization beyond the study population
• Missing the "so what?"—failing to explain significance

Key Questions to Answer

1. What do these findings mean? 2. How do they compare to prior research? 3. Why might differences exist? 4. What are alternative explanations? 5. What are the limitations? 6. What are the practical implications? 7. What should future research investigate?

Conclusion

Purpose

Provide a concise summary of key findings and their significance.

Placement

• May be a separate section or the final paragraph of Discussion (check journal requirements)

Content

• 1-2 paragraphs maximum
• Restate the main finding(s)
• Emphasize the significance or implications
• End with a strong, memorable statement
• Do NOT introduce new information

Example

This randomized trial demonstrates that a 12-week mindfulness intervention significantly
reduces anxiety symptoms in college students, with effects persisting at 6-month follow-up.
These findings support the integration of mindfulness-based programs into university mental
health services. Given the scalability and cost-effectiveness of group-based mindfulness
training, this approach offers a promising strategy to address the growing mental health
crisis in higher education.

Additional Sections

Acknowledgments

• Thank funding sources (with grant numbers)
• Acknowledge substantial contributions not qualifying for authorship
• Thank those who provided materials, equipment, or assistance
• Declare any conflicts of interest

References

• Format according to journal style (see citation_styles.md)
• Verify all citations are accurate
• Ensure all citations appear in text and vice versa
• Typical range: 20-50 references for original research

Supplementary Materials

• Additional figures, tables, or data sets
• Detailed protocols or questionnaires
• Video or audio files
• Large datasets or code repositories

Tense Usage Summary

IMRAD Variations

Combined Results and Discussion

• Some journals allow or require this format
• Interweaves presentation and interpretation
• Each result is presented then immediately discussed
• Useful for complex studies with multiple experiments

IMRaD without separate Conclusion

• Conclusion integrated into final Discussion paragraph
• Common in many journals

Extended IMRAD (ILMRaD)

• Adds "Literature Review" as separate section
• More common in theses and dissertations

Adapting IMRAD to Different Study Types

Clinical Trials

• Add CONSORT flow diagram in Results
• Include trial registration number in Methods
• Report adverse events in Results

Systematic Reviews/Meta-Analyses

• Methods describes search strategy and inclusion criteria
• Results includes PRISMA flow diagram and synthesis
• May have additional sections (risk of bias assessment)

Case Reports

• Introduction: background on the condition
• Case Presentation: replaces Methods and Results
• Discussion: relates case to literature

Observational Studies

• Follow STROBE guidelines
• Careful attention to potential confounders in Methods
• Discussion addresses causality limitations

Venue-Specific Structure Expectations

Journal vs. Conference Formats

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

*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

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