@synsci/cli-darwin-x64 1.1.97 → 1.1.99

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1549) hide show
  1. package/bin/synsc +0 -0
  2. package/package.json +1 -1
  3. package/bin/skills/accelerate/SKILL.md +0 -332
  4. package/bin/skills/accelerate/references/custom-plugins.md +0 -453
  5. package/bin/skills/accelerate/references/megatron-integration.md +0 -489
  6. package/bin/skills/accelerate/references/performance.md +0 -525
  7. package/bin/skills/adaptyv/SKILL.md +0 -114
  8. package/bin/skills/adaptyv/reference/api_reference.md +0 -308
  9. package/bin/skills/adaptyv/reference/examples.md +0 -913
  10. package/bin/skills/adaptyv/reference/experiments.md +0 -360
  11. package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
  12. package/bin/skills/aeon/SKILL.md +0 -374
  13. package/bin/skills/aeon/references/anomaly_detection.md +0 -154
  14. package/bin/skills/aeon/references/classification.md +0 -144
  15. package/bin/skills/aeon/references/clustering.md +0 -123
  16. package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
  17. package/bin/skills/aeon/references/distances.md +0 -256
  18. package/bin/skills/aeon/references/forecasting.md +0 -140
  19. package/bin/skills/aeon/references/networks.md +0 -289
  20. package/bin/skills/aeon/references/regression.md +0 -118
  21. package/bin/skills/aeon/references/segmentation.md +0 -163
  22. package/bin/skills/aeon/references/similarity_search.md +0 -187
  23. package/bin/skills/aeon/references/transformations.md +0 -246
  24. package/bin/skills/alphafold-database/SKILL.md +0 -513
  25. package/bin/skills/alphafold-database/references/api_reference.md +0 -423
  26. package/bin/skills/anndata/SKILL.md +0 -400
  27. package/bin/skills/anndata/references/best_practices.md +0 -525
  28. package/bin/skills/anndata/references/concatenation.md +0 -396
  29. package/bin/skills/anndata/references/data_structure.md +0 -314
  30. package/bin/skills/anndata/references/io_operations.md +0 -404
  31. package/bin/skills/anndata/references/manipulation.md +0 -516
  32. package/bin/skills/arboreto/SKILL.md +0 -243
  33. package/bin/skills/arboreto/references/algorithms.md +0 -138
  34. package/bin/skills/arboreto/references/basic_inference.md +0 -151
  35. package/bin/skills/arboreto/references/distributed_computing.md +0 -242
  36. package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
  37. package/bin/skills/astropy/SKILL.md +0 -331
  38. package/bin/skills/astropy/references/coordinates.md +0 -273
  39. package/bin/skills/astropy/references/cosmology.md +0 -307
  40. package/bin/skills/astropy/references/fits.md +0 -396
  41. package/bin/skills/astropy/references/tables.md +0 -489
  42. package/bin/skills/astropy/references/time.md +0 -404
  43. package/bin/skills/astropy/references/units.md +0 -178
  44. package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
  45. package/bin/skills/audiocraft/SKILL.md +0 -564
  46. package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
  47. package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
  48. package/bin/skills/autogpt/SKILL.md +0 -403
  49. package/bin/skills/autogpt/references/advanced-usage.md +0 -535
  50. package/bin/skills/autogpt/references/troubleshooting.md +0 -420
  51. package/bin/skills/awq/SKILL.md +0 -310
  52. package/bin/skills/awq/references/advanced-usage.md +0 -324
  53. package/bin/skills/awq/references/troubleshooting.md +0 -344
  54. package/bin/skills/axolotl/SKILL.md +0 -158
  55. package/bin/skills/axolotl/references/api.md +0 -5548
  56. package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
  57. package/bin/skills/axolotl/references/index.md +0 -15
  58. package/bin/skills/axolotl/references/other.md +0 -3563
  59. package/bin/skills/benchling-integration/SKILL.md +0 -480
  60. package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
  61. package/bin/skills/benchling-integration/references/authentication.md +0 -379
  62. package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
  63. package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
  64. package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
  65. package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
  66. package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
  67. package/bin/skills/biopython/SKILL.md +0 -443
  68. package/bin/skills/biopython/references/advanced.md +0 -577
  69. package/bin/skills/biopython/references/alignment.md +0 -362
  70. package/bin/skills/biopython/references/blast.md +0 -455
  71. package/bin/skills/biopython/references/databases.md +0 -484
  72. package/bin/skills/biopython/references/phylogenetics.md +0 -566
  73. package/bin/skills/biopython/references/sequence_io.md +0 -285
  74. package/bin/skills/biopython/references/structure.md +0 -564
  75. package/bin/skills/biorxiv-database/SKILL.md +0 -483
  76. package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
  77. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
  78. package/bin/skills/bioservices/SKILL.md +0 -361
  79. package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
  80. package/bin/skills/bioservices/references/services_reference.md +0 -636
  81. package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
  82. package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
  83. package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
  84. package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
  85. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
  86. package/bin/skills/bitsandbytes/SKILL.md +0 -411
  87. package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
  88. package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
  89. package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
  90. package/bin/skills/blip-2/SKILL.md +0 -564
  91. package/bin/skills/blip-2/references/advanced-usage.md +0 -680
  92. package/bin/skills/blip-2/references/troubleshooting.md +0 -526
  93. package/bin/skills/brenda-database/SKILL.md +0 -719
  94. package/bin/skills/brenda-database/references/api_reference.md +0 -537
  95. package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
  96. package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
  97. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
  98. package/bin/skills/cellxgene-census/SKILL.md +0 -511
  99. package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
  100. package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
  101. package/bin/skills/chembl-database/SKILL.md +0 -389
  102. package/bin/skills/chembl-database/references/api_reference.md +0 -272
  103. package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
  104. package/bin/skills/chroma/SKILL.md +0 -406
  105. package/bin/skills/chroma/references/integration.md +0 -38
  106. package/bin/skills/cirq/SKILL.md +0 -346
  107. package/bin/skills/cirq/references/building.md +0 -307
  108. package/bin/skills/cirq/references/experiments.md +0 -572
  109. package/bin/skills/cirq/references/hardware.md +0 -515
  110. package/bin/skills/cirq/references/noise.md +0 -515
  111. package/bin/skills/cirq/references/simulation.md +0 -350
  112. package/bin/skills/cirq/references/transformation.md +0 -416
  113. package/bin/skills/citation-management/SKILL.md +0 -1109
  114. package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
  115. package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
  116. package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
  117. package/bin/skills/citation-management/references/citation_validation.md +0 -794
  118. package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
  119. package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
  120. package/bin/skills/citation-management/references/pubmed_search.md +0 -839
  121. package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
  122. package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
  123. package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
  124. package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
  125. package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
  126. package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
  127. package/bin/skills/clinical-decision-support/README.md +0 -129
  128. package/bin/skills/clinical-decision-support/SKILL.md +0 -506
  129. package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
  130. package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
  131. package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
  132. package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
  133. package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
  134. package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
  135. package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
  136. package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
  137. package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
  138. package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
  139. package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
  140. package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
  141. package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
  142. package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
  143. package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
  144. package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
  145. package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
  146. package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
  147. package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
  148. package/bin/skills/clinical-reports/README.md +0 -236
  149. package/bin/skills/clinical-reports/SKILL.md +0 -1127
  150. package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
  151. package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
  152. package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
  153. package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
  154. package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
  155. package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
  156. package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
  157. package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
  158. package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
  159. package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
  160. package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
  161. package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
  162. package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
  163. package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
  164. package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
  165. package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
  166. package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
  167. package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
  168. package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
  169. package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
  170. package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
  171. package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
  172. package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
  173. package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
  174. package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
  175. package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
  176. package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
  177. package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
  178. package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
  179. package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
  180. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
  181. package/bin/skills/clinpgx-database/SKILL.md +0 -638
  182. package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
  183. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
  184. package/bin/skills/clinvar-database/SKILL.md +0 -362
  185. package/bin/skills/clinvar-database/references/api_reference.md +0 -227
  186. package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
  187. package/bin/skills/clinvar-database/references/data_formats.md +0 -358
  188. package/bin/skills/clip/SKILL.md +0 -253
  189. package/bin/skills/clip/references/applications.md +0 -207
  190. package/bin/skills/cobrapy/SKILL.md +0 -463
  191. package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
  192. package/bin/skills/cobrapy/references/workflows.md +0 -593
  193. package/bin/skills/colab-finetuning/SKILL.md +0 -153
  194. package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
  195. package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
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  197. package/bin/skills/constitutional-ai/SKILL.md +0 -290
  198. package/bin/skills/cosmic-database/SKILL.md +0 -336
  199. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
  200. package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
  201. package/bin/skills/crewai/SKILL.md +0 -498
  202. package/bin/skills/crewai/references/flows.md +0 -438
  203. package/bin/skills/crewai/references/tools.md +0 -429
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  205. package/bin/skills/dask/SKILL.md +0 -456
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  209. package/bin/skills/dask/references/dataframes.md +0 -368
  210. package/bin/skills/dask/references/futures.md +0 -541
  211. package/bin/skills/dask/references/schedulers.md +0 -504
  212. package/bin/skills/datacommons-client/SKILL.md +0 -255
  213. package/bin/skills/datacommons-client/references/getting_started.md +0 -417
  214. package/bin/skills/datacommons-client/references/node.md +0 -250
  215. package/bin/skills/datacommons-client/references/observation.md +0 -185
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  217. package/bin/skills/datamol/SKILL.md +0 -706
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  224. package/bin/skills/deepchem/SKILL.md +0 -597
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  227. package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
  228. package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
  229. package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
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- ---
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- name: ml-paper-writing
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- description: Write publication-ready ML/AI papers for NeurIPS, ICML, ICLR, ACL, AAAI, COLM. Use when drafting papers from research repos, structuring arguments, verifying citations, or preparing camera-ready submissions. Includes LaTeX templates, reviewer guidelines, and citation verification workflows.
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- version: 1.0.0
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- author: Synthetic Sciences
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- license: MIT
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- tags: [Academic Writing, NeurIPS, ICML, ICLR, ACL, AAAI, COLM, LaTeX, Paper Writing, Citations, Research]
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- dependencies: [semanticscholar, arxiv, habanero, requests]
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- ---
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-
11
- # ML Paper Writing for Top AI Conferences
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-
13
- Expert-level guidance for writing publication-ready papers targeting **NeurIPS, ICML, ICLR, ACL, AAAI, and COLM**. This skill combines writing philosophy from top researchers (Nanda, Farquhar, Karpathy, Lipton, Steinhardt) with practical tools: LaTeX templates, citation verification APIs, and conference checklists.
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-
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- ## Core Philosophy: Collaborative Writing
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-
17
- **Paper writing is collaborative, but Claude should be proactive in delivering drafts.**
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-
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- The typical workflow starts with a research repository containing code, results, and experimental artifacts. Claude's role is to:
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-
21
- 1. **Understand the project** by exploring the repo, results, and existing documentation
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- 2. **Deliver a complete first draft** when confident about the contribution
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- 3. **Search literature** using web search and APIs to find relevant citations
24
- 4. **Refine through feedback cycles** when the scientist provides input
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- 5. **Ask for clarification** only when genuinely uncertain about key decisions
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-
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- **Key Principle**: Be proactive. If the repo and results are clear, deliver a full draft. Don't block waiting for feedback on every section—scientists are busy. Produce something concrete they can react to, then iterate based on their response.
28
-
29
- ---
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-
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- ## ⚠️ CRITICAL: Never Hallucinate Citations
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-
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- **This is the most important rule in academic writing with AI assistance.**
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-
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- ### The Problem
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- AI-generated citations have a **~40% error rate**. Hallucinated references—papers that don't exist, wrong authors, incorrect years, fabricated DOIs—are a serious form of academic misconduct that can result in desk rejection or retraction.
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-
38
- ### The Rule
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- **NEVER generate BibTeX entries from memory. ALWAYS fetch programmatically.**
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-
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- | Action | ✅ Correct | ❌ Wrong |
42
- |--------|-----------|----------|
43
- | Adding a citation | Search API → verify → fetch BibTeX | Write BibTeX from memory |
44
- | Uncertain about a paper | Mark as `[CITATION NEEDED]` | Guess the reference |
45
- | Can't find exact paper | Note: "placeholder - verify" | Invent similar-sounding paper |
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-
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- ### When You Can't Verify a Citation
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-
49
- If you cannot programmatically verify a citation, you MUST:
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-
51
- ```latex
52
- % EXPLICIT PLACEHOLDER - requires human verification
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- \cite{PLACEHOLDER_author2024_verify_this} % TODO: Verify this citation exists
54
- ```
55
-
56
- **Always tell the scientist**: "I've marked [X] citations as placeholders that need verification. I could not confirm these papers exist."
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-
58
- ### Recommended: Install Exa MCP for Paper Search
59
-
60
- For the best paper search experience, install **Exa MCP** which provides real-time academic search:
61
-
62
- **Claude Code:**
63
- ```bash
64
- claude mcp add exa -- npx -y mcp-remote "https://mcp.exa.ai/mcp"
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- ```
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-
67
- **Cursor / VS Code** (add to MCP settings):
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- ```json
69
- {
70
- "mcpServers": {
71
- "exa": {
72
- "type": "http",
73
- "url": "https://mcp.exa.ai/mcp"
74
- }
75
- }
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- }
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- ```
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-
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- Exa MCP enables searches like:
80
- - "Find papers on RLHF for language models published after 2023"
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- - "Search for transformer architecture papers by Vaswani"
82
- - "Get recent work on sparse autoencoders for interpretability"
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-
84
- Then verify results with Semantic Scholar API and fetch BibTeX via DOI.
85
-
86
- ---
87
-
88
- ## Workflow 0: Starting from a Research Repository
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-
90
- When beginning paper writing, start by understanding the project:
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-
92
- ```
93
- Project Understanding:
94
- - [ ] Step 1: Explore the repository structure
95
- - [ ] Step 2: Read README, existing docs, and key results
96
- - [ ] Step 3: Identify the main contribution with the scientist
97
- - [ ] Step 4: Find papers already cited in the codebase
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- - [ ] Step 5: Search for additional relevant literature
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- - [ ] Step 6: Outline the paper structure together
100
- - [ ] Step 7: Draft sections iteratively with feedback
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- ```
102
-
103
- **Step 1: Explore the Repository**
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-
105
- ```bash
106
- # Understand project structure
107
- ls -la
108
- find . -name "*.py" | head -20
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- find . -name "*.md" -o -name "*.txt" | xargs grep -l -i "result\|conclusion\|finding"
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- ```
111
-
112
- Look for:
113
- - `README.md` - Project overview and claims
114
- - `results/`, `outputs/`, `experiments/` - Key findings
115
- - `configs/` - Experimental settings
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- - Existing `.bib` files or citation references
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- - Any draft documents or notes
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-
119
- **Step 2: Identify Existing Citations**
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-
121
- Check for papers already referenced in the codebase:
122
-
123
- ```bash
124
- # Find existing citations
125
- grep -r "arxiv\|doi\|cite" --include="*.md" --include="*.bib" --include="*.py"
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- find . -name "*.bib"
127
- ```
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-
129
- These are high-signal starting points for Related Work—the scientist has already deemed them relevant.
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-
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- **Step 3: Clarify the Contribution**
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-
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- Before writing, explicitly confirm with the scientist:
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-
135
- > "Based on my understanding of the repo, the main contribution appears to be [X].
136
- > The key results show [Y]. Is this the framing you want for the paper,
137
- > or should we emphasize different aspects?"
138
-
139
- **Never assume the narrative—always verify with the human.**
140
-
141
- **Step 4: Search for Additional Literature**
142
-
143
- Use web search to find relevant papers:
144
-
145
- ```
146
- Search queries to try:
147
- - "[main technique] + [application domain]"
148
- - "[baseline method] comparison"
149
- - "[problem name] state-of-the-art"
150
- - Author names from existing citations
151
- ```
152
-
153
- Then verify and retrieve BibTeX using the citation workflow below.
154
-
155
- **Step 5: Deliver a First Draft**
156
-
157
- **Be proactive—deliver a complete draft rather than asking permission for each section.**
158
-
159
- If the repo provides clear results and the contribution is apparent:
160
- 1. Write the full first draft end-to-end
161
- 2. Present the complete draft for feedback
162
- 3. Iterate based on scientist's response
163
-
164
- If genuinely uncertain about framing or major claims:
165
- 1. Draft what you can confidently
166
- 2. Flag specific uncertainties: "I framed X as the main contribution—let me know if you'd prefer to emphasize Y instead"
167
- 3. Continue with the draft rather than blocking
168
-
169
- **Questions to include with the draft** (not before):
170
- - "I emphasized X as the main contribution—adjust if needed"
171
- - "I highlighted results A, B, C—let me know if others are more important"
172
- - "Related work section includes [papers]—add any I missed"
173
-
174
- ---
175
-
176
- ## When to Use This Skill
177
-
178
- Use this skill when:
179
- - **Starting from a research repo** to write a paper
180
- - **Drafting or revising** specific sections
181
- - **Finding and verifying citations** for related work
182
- - **Formatting** for conference submission
183
- - **Resubmitting** to a different venue (format conversion)
184
- - **Iterating** on drafts with scientist feedback
185
-
186
- **Always remember**: First drafts are starting points for discussion, not final outputs.
187
-
188
- ---
189
-
190
- ## Balancing Proactivity and Collaboration
191
-
192
- **Default: Be proactive. Deliver drafts, then iterate.**
193
-
194
- | Confidence Level | Action |
195
- |-----------------|--------|
196
- | **High** (clear repo, obvious contribution) | Write full draft, deliver, iterate on feedback |
197
- | **Medium** (some ambiguity) | Write draft with flagged uncertainties, continue |
198
- | **Low** (major unknowns) | Ask 1-2 targeted questions, then draft |
199
-
200
- **Draft first, ask with the draft** (not before):
201
-
202
- | Section | Draft Autonomously | Flag With Draft |
203
- |---------|-------------------|-----------------|
204
- | Abstract | Yes | "Framed contribution as X—adjust if needed" |
205
- | Introduction | Yes | "Emphasized problem Y—correct if wrong" |
206
- | Methods | Yes | "Included details A, B, C—add missing pieces" |
207
- | Experiments | Yes | "Highlighted results 1, 2, 3—reorder if needed" |
208
- | Related Work | Yes | "Cited papers X, Y, Z—add any I missed" |
209
-
210
- **Only block for input when:**
211
- - Target venue is unclear (affects page limits, framing)
212
- - Multiple contradictory framings seem equally valid
213
- - Results seem incomplete or inconsistent
214
- - Explicit request to review before continuing
215
-
216
- **Don't block for:**
217
- - Word choice decisions
218
- - Section ordering
219
- - Which specific results to show (make a choice, flag it)
220
- - Citation completeness (draft with what you find, note gaps)
221
-
222
- ---
223
-
224
- ## The Narrative Principle
225
-
226
- **The single most critical insight**: Your paper is not a collection of experiments—it's a story with one clear contribution supported by evidence.
227
-
228
- Every successful ML paper centers on what Neel Nanda calls "the narrative": a short, rigorous, evidence-based technical story with a takeaway readers care about.
229
-
230
- **Three Pillars (must be crystal clear by end of introduction):**
231
-
232
- | Pillar | Description | Example |
233
- |--------|-------------|---------|
234
- | **The What** | 1-3 specific novel claims within cohesive theme | "We prove that X achieves Y under condition Z" |
235
- | **The Why** | Rigorous empirical evidence supporting claims | Strong baselines, experiments distinguishing hypotheses |
236
- | **The So What** | Why readers should care | Connection to recognized community problems |
237
-
238
- **If you cannot state your contribution in one sentence, you don't yet have a paper.**
239
-
240
- ---
241
-
242
- ## Paper Structure Workflow
243
-
244
- ### Workflow 1: Writing a Complete Paper (Iterative)
245
-
246
- Copy this checklist and track progress. **Each step involves drafting → feedback → revision:**
247
-
248
- ```
249
- Paper Writing Progress:
250
- - [ ] Step 1: Define the one-sentence contribution (with scientist)
251
- - [ ] Step 2: Draft Figure 1 → get feedback → revise
252
- - [ ] Step 3: Draft abstract → get feedback → revise
253
- - [ ] Step 4: Draft introduction → get feedback → revise
254
- - [ ] Step 5: Draft methods → get feedback → revise
255
- - [ ] Step 6: Draft experiments → get feedback → revise
256
- - [ ] Step 7: Draft related work → get feedback → revise
257
- - [ ] Step 8: Draft limitations → get feedback → revise
258
- - [ ] Step 9: Complete paper checklist (required)
259
- - [ ] Step 10: Final review cycle and submission
260
- ```
261
-
262
- **Step 1: Define the One-Sentence Contribution**
263
-
264
- **This step requires explicit confirmation from the scientist.**
265
-
266
- Before writing anything, articulate and verify:
267
- - What is the single thing your paper contributes?
268
- - What was not obvious or present before your work?
269
-
270
- > "I propose framing the contribution as: '[one sentence]'. Does this capture
271
- > what you see as the main takeaway? Should we adjust the emphasis?"
272
-
273
- **Step 2: Draft Figure 1**
274
-
275
- Figure 1 deserves special attention—many readers skip directly to it.
276
- - Convey core idea, approach, or most compelling result
277
- - Use vector graphics (PDF/EPS for plots)
278
- - Write captions that stand alone without main text
279
- - Ensure readability in black-and-white (8% of men have color vision deficiency)
280
-
281
- **Step 3: Write Abstract (5-Sentence Formula)**
282
-
283
- From Sebastian Farquhar (DeepMind):
284
-
285
- ```
286
- 1. What you achieved: "We introduce...", "We prove...", "We demonstrate..."
287
- 2. Why this is hard and important
288
- 3. How you do it (with specialist keywords for discoverability)
289
- 4. What evidence you have
290
- 5. Your most remarkable number/result
291
- ```
292
-
293
- **Delete** generic openings like "Large language models have achieved remarkable success..."
294
-
295
- **Step 4: Write Introduction (1-1.5 pages max)**
296
-
297
- Must include:
298
- - 2-4 bullet contribution list (max 1-2 lines each in two-column format)
299
- - Clear problem statement
300
- - Brief approach overview
301
- - Methods should start by page 2-3 maximum
302
-
303
- **Step 5: Methods Section**
304
-
305
- Enable reimplementation:
306
- - Conceptual outline or pseudocode
307
- - All hyperparameters listed
308
- - Architectural details sufficient for reproduction
309
- - Present final design decisions; ablations go in experiments
310
-
311
- **Step 6: Experiments Section**
312
-
313
- For each experiment, explicitly state:
314
- - What claim it supports
315
- - How it connects to main contribution
316
- - Experimental setting (details in appendix)
317
- - What to observe: "the blue line shows X, which demonstrates Y"
318
-
319
- Requirements:
320
- - Error bars with methodology (standard deviation vs standard error)
321
- - Hyperparameter search ranges
322
- - Compute infrastructure (GPU type, total hours)
323
- - Seed-setting methods
324
-
325
- **Step 7: Related Work**
326
-
327
- Organize methodologically, not paper-by-paper:
328
-
329
- **Good:** "One line of work uses Floogledoodle's assumption [refs] whereas we use Doobersnoddle's assumption because..."
330
-
331
- **Bad:** "Snap et al. introduced X while Crackle et al. introduced Y."
332
-
333
- Cite generously—reviewers likely authored relevant papers.
334
-
335
- **Step 8: Limitations Section (REQUIRED)**
336
-
337
- All major conferences require this. Counter-intuitively, honesty helps:
338
- - Reviewers are instructed not to penalize honest limitation acknowledgment
339
- - Pre-empt criticisms by identifying weaknesses first
340
- - Explain why limitations don't undermine core claims
341
-
342
- **Step 9: Paper Checklist**
343
-
344
- NeurIPS, ICML, and ICLR all require paper checklists. See [references/checklists.md](references/checklists.md).
345
-
346
- ---
347
-
348
- ## Writing Philosophy for Top ML Conferences
349
-
350
- **This section distills the most important writing principles from leading ML researchers.** These aren't optional style suggestions—they're what separates accepted papers from rejected ones.
351
-
352
- > "A paper is a short, rigorous, evidence-based technical story with a takeaway readers care about." — Neel Nanda
353
-
354
- ### The Sources Behind This Guidance
355
-
356
- This skill synthesizes writing philosophy from researchers who have published extensively at top venues:
357
-
358
- | Source | Key Contribution | Link |
359
- |--------|-----------------|------|
360
- | **Neel Nanda** (Google DeepMind) | The Narrative Principle, What/Why/So What framework | [How to Write ML Papers](https://www.alignmentforum.org/posts/eJGptPbbFPZGLpjsp/highly-opinionated-advice-on-how-to-write-ml-papers) |
361
- | **Sebastian Farquhar** (DeepMind) | 5-sentence abstract formula | [How to Write ML Papers](https://sebastianfarquhar.com/on-research/2024/11/04/how_to_write_ml_papers/) |
362
- | **Gopen & Swan** | 7 principles of reader expectations | [Science of Scientific Writing](https://cseweb.ucsd.edu/~swanson/papers/science-of-writing.pdf) |
363
- | **Zachary Lipton** | Word choice, eliminating hedging | [Heuristics for Scientific Writing](https://www.approximatelycorrect.com/2018/01/29/heuristics-technical-scientific-writing-machine-learning-perspective/) |
364
- | **Jacob Steinhardt** (UC Berkeley) | Precision, consistent terminology | [Writing Tips](https://bounded-regret.ghost.io/) |
365
- | **Ethan Perez** (Anthropic) | Micro-level clarity tips | [Easy Paper Writing Tips](https://ethanperez.net/easy-paper-writing-tips/) |
366
- | **Andrej Karpathy** | Single contribution focus | Various lectures |
367
-
368
- **For deeper dives into any of these, see:**
369
- - [references/writing-guide.md](references/writing-guide.md) - Full explanations with examples
370
- - [references/sources.md](references/sources.md) - Complete bibliography
371
-
372
- ### Time Allocation (From Neel Nanda)
373
-
374
- Spend approximately **equal time** on each of:
375
- 1. The abstract
376
- 2. The introduction
377
- 3. The figures
378
- 4. Everything else combined
379
-
380
- **Why?** Most reviewers form judgments before reaching your methods. Readers encounter your paper as: **title → abstract → introduction → figures → maybe the rest.**
381
-
382
- ### Writing Style Guidelines
383
-
384
- #### Sentence-Level Clarity (Gopen & Swan's 7 Principles)
385
-
386
- These principles are based on how readers actually process prose. Violating them forces readers to spend cognitive effort on structure rather than content.
387
-
388
- | Principle | Rule | Example |
389
- |-----------|------|---------|
390
- | **Subject-verb proximity** | Keep subject and verb close | ❌ "The model, which was trained on..., achieves" → ✅ "The model achieves... after training on..." |
391
- | **Stress position** | Place emphasis at sentence ends | ❌ "Accuracy improves by 15% when using attention" → ✅ "When using attention, accuracy improves by **15%**" |
392
- | **Topic position** | Put context first, new info after | ✅ "Given these constraints, we propose..." |
393
- | **Old before new** | Familiar info → unfamiliar info | Link backward, then introduce new |
394
- | **One unit, one function** | Each paragraph makes one point | Split multi-point paragraphs |
395
- | **Action in verb** | Use verbs, not nominalizations | ❌ "We performed an analysis" → ✅ "We analyzed" |
396
- | **Context before new** | Set stage before presenting | Explain before showing equation |
397
-
398
- **Full 7 principles with detailed examples:** See [references/writing-guide.md](references/writing-guide.md#the-7-principles-of-reader-expectations)
399
-
400
- #### Micro-Level Tips (Ethan Perez)
401
-
402
- These small changes accumulate into significantly clearer prose:
403
-
404
- - **Minimize pronouns**: ❌ "This shows..." → ✅ "This result shows..."
405
- - **Verbs early**: Position verbs near sentence start
406
- - **Unfold apostrophes**: ❌ "X's Y" → ✅ "The Y of X" (when awkward)
407
- - **Delete filler words**: "actually," "a bit," "very," "really," "basically," "quite," "essentially"
408
-
409
- **Full micro-tips with examples:** See [references/writing-guide.md](references/writing-guide.md#micro-level-writing-tips)
410
-
411
- #### Word Choice (Zachary Lipton)
412
-
413
- - **Be specific**: ❌ "performance" → ✅ "accuracy" or "latency" (say what you mean)
414
- - **Eliminate hedging**: Drop "may" and "can" unless genuinely uncertain
415
- - **Avoid incremental vocabulary**: ❌ "combine," "modify," "expand" → ✅ "develop," "propose," "introduce"
416
- - **Delete intensifiers**: ❌ "provides *very* tight approximation" → ✅ "provides tight approximation"
417
-
418
- #### Precision Over Brevity (Jacob Steinhardt)
419
-
420
- - **Consistent terminology**: Different terms for same concept creates confusion. Pick one and stick with it.
421
- - **State assumptions formally**: Before theorems, list all assumptions explicitly
422
- - **Intuition + rigor**: Provide intuitive explanations alongside formal proofs
423
-
424
- ### What Reviewers Actually Read
425
-
426
- Understanding reviewer behavior helps prioritize your effort:
427
-
428
- | Paper Section | % Reviewers Who Read | Implication |
429
- |---------------|---------------------|-------------|
430
- | Abstract | 100% | Must be perfect |
431
- | Introduction | 90%+ (skimmed) | Front-load contribution |
432
- | Figures | Examined before methods | Figure 1 is critical |
433
- | Methods | Only if interested | Don't bury the lede |
434
- | Appendix | Rarely | Put only supplementary details |
435
-
436
- **Bottom line**: If your abstract and intro don't hook reviewers, they may never read your brilliant methods section.
437
-
438
- ---
439
-
440
- ## Conference Requirements Quick Reference
441
-
442
- | Conference | Page Limit | Extra for Camera-Ready | Key Requirement |
443
- |------------|------------|------------------------|-----------------|
444
- | **NeurIPS 2025** | 9 pages | +0 | Mandatory checklist, lay summary for accepted |
445
- | **ICML 2026** | 8 pages | +1 | Broader Impact Statement required |
446
- | **ICLR 2026** | 9 pages | +1 | LLM disclosure required, reciprocal reviewing |
447
- | **ACL 2025** | 8 pages (long) | varies | Limitations section mandatory |
448
- | **AAAI 2026** | 7 pages | +1 | Strict style file adherence |
449
- | **COLM 2025** | 9 pages | +1 | Focus on language models |
450
-
451
- **Universal Requirements:**
452
- - Double-blind review (anonymize submissions)
453
- - References don't count toward page limit
454
- - Appendices unlimited but reviewers not required to read
455
- - LaTeX required for all venues
456
-
457
- **LaTeX Templates:** See [templates/](templates/) directory for all conference templates.
458
-
459
- ---
460
-
461
- ## Using LaTeX Templates Properly
462
-
463
- ### Workflow 4: Starting a New Paper from Template
464
-
465
- **Always copy the entire template directory first, then write within it.**
466
-
467
- ```
468
- Template Setup Checklist:
469
- - [ ] Step 1: Copy entire template directory to new project
470
- - [ ] Step 2: Verify template compiles as-is (before any changes)
471
- - [ ] Step 3: Read the template's example content to understand structure
472
- - [ ] Step 4: Replace example content section by section
473
- - [ ] Step 5: Keep template comments/examples as reference until done
474
- - [ ] Step 6: Clean up template artifacts only at the end
475
- ```
476
-
477
- **Step 1: Copy the Full Template**
478
-
479
- ```bash
480
- # Create your paper directory with the complete template
481
- cp -r templates/neurips2025/ ~/papers/my-new-paper/
482
- cd ~/papers/my-new-paper/
483
-
484
- # Verify structure is complete
485
- ls -la
486
- # Should see: main.tex, neurips.sty, Makefile, etc.
487
- ```
488
-
489
- **⚠️ IMPORTANT**: Copy the ENTIRE directory, not just `main.tex`. Templates include:
490
- - Style files (`.sty`) - required for compilation
491
- - Bibliography styles (`.bst`) - required for references
492
- - Example content - useful as reference
493
- - Makefiles - for easy compilation
494
-
495
- **Step 2: Verify Template Compiles First**
496
-
497
- Before making ANY changes, compile the template as-is:
498
-
499
- ```bash
500
- # Using latexmk (recommended)
501
- latexmk -pdf main.tex
502
-
503
- # Or manual compilation
504
- pdflatex main.tex
505
- bibtex main
506
- pdflatex main.tex
507
- pdflatex main.tex
508
- ```
509
-
510
- If the unmodified template doesn't compile, fix that first. Common issues:
511
- - Missing TeX packages → install via `tlmgr install <package>`
512
- - Wrong TeX distribution → use TeX Live (recommended)
513
-
514
- **Step 3: Keep Template Content as Reference**
515
-
516
- Don't immediately delete all example content. Instead:
517
-
518
- ```latex
519
- % KEEP template examples commented out as you write
520
- % This shows you the expected format
521
-
522
- % Template example (keep for reference):
523
- % \begin{figure}[t]
524
- % \centering
525
- % \includegraphics[width=0.8\linewidth]{example-image}
526
- % \caption{Template shows caption style}
527
- % \end{figure}
528
-
529
- % Your actual figure:
530
- \begin{figure}[t]
531
- \centering
532
- \includegraphics[width=0.8\linewidth]{your-figure.pdf}
533
- \caption{Your caption following the same style.}
534
- \end{figure}
535
- ```
536
-
537
- **Step 4: Replace Content Section by Section**
538
-
539
- Work through the paper systematically:
540
-
541
- ```
542
- Replacement Order:
543
- 1. Title and authors (anonymize for submission)
544
- 2. Abstract
545
- 3. Introduction
546
- 4. Methods
547
- 5. Experiments
548
- 6. Related Work
549
- 7. Conclusion
550
- 8. References (your .bib file)
551
- 9. Appendix
552
- ```
553
-
554
- For each section:
555
- 1. Read the template's example content
556
- 2. Note any special formatting or macros used
557
- 3. Replace with your content following the same patterns
558
- 4. Compile frequently to catch errors early
559
-
560
- **Step 5: Use Template Macros**
561
-
562
- Templates often define useful macros. Check the preamble for:
563
-
564
- ```latex
565
- % Common template macros to use:
566
- \newcommand{\method}{YourMethodName} % Consistent method naming
567
- \newcommand{\eg}{e.g.,\xspace} % Proper abbreviations
568
- \newcommand{\ie}{i.e.,\xspace}
569
- \newcommand{\etal}{\textit{et al.}\xspace}
570
- ```
571
-
572
- **Step 6: Clean Up Only at the End**
573
-
574
- Only remove template artifacts when paper is nearly complete:
575
-
576
- ```latex
577
- % BEFORE SUBMISSION - remove these:
578
- % - Commented-out template examples
579
- % - Unused packages
580
- % - Template's example figures/tables
581
- % - Lorem ipsum or placeholder text
582
-
583
- % KEEP these:
584
- % - All style files (.sty)
585
- % - Bibliography style (.bst)
586
- % - Required packages from template
587
- % - Any custom macros you're using
588
- ```
589
-
590
- ### Template Pitfalls to Avoid
591
-
592
- | Pitfall | Problem | Solution |
593
- |---------|---------|----------|
594
- | Copying only `main.tex` | Missing `.sty`, won't compile | Copy entire directory |
595
- | Modifying `.sty` files | Breaks conference formatting | Never edit style files |
596
- | Adding random packages | Conflicts, breaks template | Only add if necessary |
597
- | Deleting template content too early | Lose formatting reference | Keep as comments until done |
598
- | Not compiling frequently | Errors accumulate | Compile after each section |
599
-
600
- ### Quick Template Reference
601
-
602
- | Conference | Main File | Key Style File | Notes |
603
- |------------|-----------|----------------|-------|
604
- | NeurIPS 2025 | `main.tex` | `neurips.sty` | Has Makefile |
605
- | ICML 2026 | `example_paper.tex` | `icml2026.sty` | Includes algorithm packages |
606
- | ICLR 2026 | `iclr2026_conference.tex` | `iclr2026_conference.sty` | Has math_commands.tex |
607
- | ACL | `acl_latex.tex` | `acl.sty` | Strict formatting |
608
- | AAAI 2026 | `aaai2026-unified-template.tex` | `aaai2026.sty` | Very strict compliance |
609
- | COLM 2025 | `colm2025_conference.tex` | `colm2025_conference.sty` | Similar to ICLR |
610
-
611
- ---
612
-
613
- ## Conference Resubmission & Format Conversion
614
-
615
- When a paper is rejected or withdrawn from one venue and resubmitted to another, format conversion is required. This is a common workflow in ML research.
616
-
617
- ### Workflow 3: Converting Between Conference Formats
618
-
619
- ```
620
- Format Conversion Checklist:
621
- - [ ] Step 1: Identify source and target template differences
622
- - [ ] Step 2: Create new project with target template
623
- - [ ] Step 3: Copy content sections (not preamble)
624
- - [ ] Step 4: Adjust page limits and content
625
- - [ ] Step 5: Update conference-specific requirements
626
- - [ ] Step 6: Verify compilation and formatting
627
- ```
628
-
629
- **Step 1: Key Template Differences**
630
-
631
- | From → To | Page Change | Key Adjustments |
632
- |-----------|-------------|-----------------|
633
- | NeurIPS → ICML | 9 → 8 pages | Cut 1 page, add Broader Impact if missing |
634
- | ICML → ICLR | 8 → 9 pages | Can expand experiments, add LLM disclosure |
635
- | NeurIPS → ACL | 9 → 8 pages | Restructure for NLP conventions, add Limitations |
636
- | ICLR → AAAI | 9 → 7 pages | Significant cuts needed, strict style adherence |
637
- | Any → COLM | varies → 9 | Reframe for language model focus |
638
-
639
- **Step 2: Content Migration (NOT Template Merge)**
640
-
641
- **Never copy LaTeX preambles between templates.** Instead:
642
-
643
- ```bash
644
- # 1. Start fresh with target template
645
- cp -r templates/icml2026/ new_submission/
646
-
647
- # 2. Copy ONLY content sections from old paper
648
- # - Abstract text
649
- # - Section content (between \section{} commands)
650
- # - Figures and tables
651
- # - Bibliography entries
652
-
653
- # 3. Paste into target template structure
654
- ```
655
-
656
- **Step 3: Adjusting for Page Limits**
657
-
658
- When cutting pages (e.g., NeurIPS 9 → AAAI 7):
659
- - Move detailed proofs to appendix
660
- - Condense related work (cite surveys instead of individual papers)
661
- - Combine similar experiments into unified tables
662
- - Use smaller figure sizes with subfigures
663
- - Tighten writing: eliminate redundancy, use active voice
664
-
665
- When expanding (e.g., ICML 8 → ICLR 9):
666
- - Add ablation studies reviewers requested
667
- - Expand limitations discussion
668
- - Include additional baselines
669
- - Add qualitative examples
670
-
671
- **Step 4: Conference-Specific Adjustments**
672
-
673
- | Target Venue | Required Additions |
674
- |--------------|-------------------|
675
- | **ICML** | Broader Impact Statement (after conclusion) |
676
- | **ICLR** | LLM usage disclosure, reciprocal reviewing agreement |
677
- | **ACL/EMNLP** | Limitations section (mandatory), Ethics Statement |
678
- | **AAAI** | Strict adherence to style file (no modifications) |
679
- | **NeurIPS** | Paper checklist (appendix), lay summary if accepted |
680
-
681
- **Step 5: Update References**
682
-
683
- ```latex
684
- % Remove self-citations that reveal identity (for blind review)
685
- % Update any "under review" citations to published versions
686
- % Add new relevant work published since last submission
687
- ```
688
-
689
- **Step 6: Addressing Previous Reviews**
690
-
691
- When resubmitting after rejection:
692
- - **Do** address reviewer concerns in the new version
693
- - **Do** add experiments/clarifications reviewers requested
694
- - **Don't** include a "changes from previous submission" section (blind review)
695
- - **Don't** reference the previous submission or reviews
696
-
697
- **Common Conversion Pitfalls:**
698
- - ❌ Copying `\usepackage` commands (causes conflicts)
699
- - ❌ Keeping old conference header/footer commands
700
- - ❌ Forgetting to update `\bibliography{}` path
701
- - ❌ Missing conference-specific required sections
702
- - ❌ Exceeding page limit after format change
703
-
704
- ---
705
-
706
- ## Citation Workflow (Hallucination Prevention)
707
-
708
- **⚠️ CRITICAL**: AI-generated citations have ~40% error rate. **Never write BibTeX from memory.**
709
-
710
- ### The Golden Rule
711
-
712
- ```
713
- IF you cannot programmatically fetch a citation:
714
- → Mark it as [CITATION NEEDED] or [PLACEHOLDER - VERIFY]
715
- → Tell the scientist explicitly
716
- → NEVER invent a plausible-sounding reference
717
- ```
718
-
719
- ### Workflow 2: Adding Citations
720
-
721
- ```
722
- Citation Verification (MANDATORY for every citation):
723
- - [ ] Step 1: Search using Exa MCP or Semantic Scholar API
724
- - [ ] Step 2: Verify paper exists in 2+ sources (Semantic Scholar + arXiv/CrossRef)
725
- - [ ] Step 3: Retrieve BibTeX via DOI (programmatically, not from memory)
726
- - [ ] Step 4: Verify the claim you're citing actually appears in the paper
727
- - [ ] Step 5: Add verified BibTeX to bibliography
728
- - [ ] Step 6: If ANY step fails → mark as placeholder, inform scientist
729
- ```
730
-
731
- **Step 0: Use Exa MCP for Initial Search (Recommended)**
732
-
733
- If Exa MCP is installed, use it to find relevant papers:
734
- ```
735
- Search: "RLHF language model alignment 2023"
736
- Search: "sparse autoencoders interpretability"
737
- Search: "attention mechanism transformers Vaswani"
738
- ```
739
-
740
- Then verify each result with Semantic Scholar and fetch BibTeX via DOI.
741
-
742
- **Step 1: Search Semantic Scholar**
743
-
744
- ```python
745
- from semanticscholar import SemanticScholar
746
-
747
- sch = SemanticScholar()
748
- results = sch.search_paper("attention mechanism transformers", limit=5)
749
- for paper in results:
750
- print(f"{paper.title} - {paper.paperId}")
751
- print(f" DOI: {paper.externalIds.get('DOI', 'N/A')}")
752
- ```
753
-
754
- **Step 2: Verify Existence**
755
-
756
- Confirm paper appears in at least two sources (Semantic Scholar + CrossRef/arXiv).
757
-
758
- **Step 3: Retrieve BibTeX via DOI**
759
-
760
- ```python
761
- import requests
762
-
763
- def doi_to_bibtex(doi: str) -> str:
764
- """Get verified BibTeX from DOI via CrossRef."""
765
- response = requests.get(
766
- f"https://doi.org/{doi}",
767
- headers={"Accept": "application/x-bibtex"}
768
- )
769
- response.raise_for_status()
770
- return response.text
771
-
772
- # Example
773
- bibtex = doi_to_bibtex("10.48550/arXiv.1706.03762")
774
- print(bibtex)
775
- ```
776
-
777
- **Step 4: Verify Claims**
778
-
779
- Before citing for a specific claim, access the paper and confirm the attributed claim actually appears.
780
-
781
- **Step 5: Handle Failures Explicitly**
782
-
783
- If you cannot verify a citation at ANY step:
784
-
785
- ```latex
786
- % Option 1: Explicit placeholder
787
- \cite{PLACEHOLDER_smith2023_verify} % TODO: Could not verify - scientist must confirm
788
-
789
- % Option 2: Note in text
790
- ... as shown in prior work [CITATION NEEDED - could not verify Smith et al. 2023].
791
- ```
792
-
793
- **Always inform the scientist:**
794
- > "I could not verify the following citations and have marked them as placeholders:
795
- > - Smith et al. 2023 on reward hacking - could not find in Semantic Scholar
796
- > - Jones 2022 on scaling laws - found similar paper but different authors
797
- > Please verify these before submission."
798
-
799
- ### Summary: Citation Rules
800
-
801
- | Situation | Action |
802
- |-----------|--------|
803
- | Found paper, got DOI, fetched BibTeX | ✅ Use the citation |
804
- | Found paper, no DOI | ✅ Use arXiv BibTeX or manual entry from paper |
805
- | Paper exists but can't fetch BibTeX | ⚠️ Mark placeholder, inform scientist |
806
- | Uncertain if paper exists | ❌ Mark `[CITATION NEEDED]`, inform scientist |
807
- | "I think there's a paper about X" | ❌ **NEVER cite** - search first or mark placeholder |
808
-
809
- **🚨 NEVER generate BibTeX from memory—always fetch programmatically. 🚨**
810
-
811
- See [references/citation-workflow.md](references/citation-workflow.md) for complete API documentation.
812
-
813
- ---
814
-
815
- ## Common Issues and Solutions
816
-
817
- **Issue: Abstract too generic**
818
-
819
- Delete first sentence if it could be prepended to any ML paper. Start with your specific contribution.
820
-
821
- **Issue: Introduction exceeds 1.5 pages**
822
-
823
- Split background into Related Work. Front-load contribution bullets. Methods should start by page 2-3.
824
-
825
- **Issue: Experiments lack explicit claims**
826
-
827
- Add sentence before each experiment: "This experiment tests whether [specific claim]..."
828
-
829
- **Issue: Reviewers find paper hard to follow**
830
-
831
- - Add explicit signposting: "In this section, we show X"
832
- - Use consistent terminology throughout
833
- - Include figure captions that stand alone
834
-
835
- **Issue: Missing statistical significance**
836
-
837
- Always include:
838
- - Error bars (specify: std dev or std error)
839
- - Number of runs
840
- - Statistical tests if comparing methods
841
-
842
- ---
843
-
844
- ## Reviewer Evaluation Criteria
845
-
846
- Reviewers assess papers on four dimensions:
847
-
848
- | Criterion | What Reviewers Look For |
849
- |-----------|------------------------|
850
- | **Quality** | Technical soundness, well-supported claims |
851
- | **Clarity** | Clear writing, reproducible by experts |
852
- | **Significance** | Community impact, advances understanding |
853
- | **Originality** | New insights (doesn't require new method) |
854
-
855
- **Scoring (NeurIPS 6-point scale):**
856
- - 6: Strong Accept - Groundbreaking, flawless
857
- - 5: Accept - Technically solid, high impact
858
- - 4: Borderline Accept - Solid, limited evaluation
859
- - 3: Borderline Reject - Solid but weaknesses outweigh
860
- - 2: Reject - Technical flaws
861
- - 1: Strong Reject - Known results or ethics issues
862
-
863
- See [references/reviewer-guidelines.md](references/reviewer-guidelines.md) for detailed reviewer instructions.
864
-
865
- ---
866
-
867
- ## Tables and Figures
868
-
869
- ### Tables
870
-
871
- Use `booktabs` LaTeX package for professional tables:
872
-
873
- ```latex
874
- \usepackage{booktabs}
875
- \begin{tabular}{lcc}
876
- \toprule
877
- Method & Accuracy ↑ & Latency ↓ \\
878
- \midrule
879
- Baseline & 85.2 & 45ms \\
880
- \textbf{Ours} & \textbf{92.1} & 38ms \\
881
- \bottomrule
882
- \end{tabular}
883
- ```
884
-
885
- **Rules:**
886
- - Bold best value per metric
887
- - Include direction symbols (↑ higher is better, ↓ lower is better)
888
- - Right-align numerical columns
889
- - Consistent decimal precision
890
-
891
- ### Figures
892
-
893
- - **Vector graphics** (PDF, EPS) for all plots and diagrams
894
- - **Raster** (PNG 600 DPI) only for photographs
895
- - Use **colorblind-safe palettes** (Okabe-Ito or Paul Tol)
896
- - Verify **grayscale readability** (8% of men have color vision deficiency)
897
- - **No title inside figure**—the caption serves this function
898
- - **Self-contained captions**—reader should understand without main text
899
-
900
- ---
901
-
902
- ## References & Resources
903
-
904
- ### Reference Documents (Deep Dives)
905
-
906
- | Document | Contents |
907
- |----------|----------|
908
- | [writing-guide.md](references/writing-guide.md) | Gopen & Swan 7 principles, Ethan Perez micro-tips, word choice |
909
- | [citation-workflow.md](references/citation-workflow.md) | Citation APIs, Python code, BibTeX management |
910
- | [checklists.md](references/checklists.md) | NeurIPS 16-item, ICML, ICLR, ACL requirements |
911
- | [reviewer-guidelines.md](references/reviewer-guidelines.md) | Evaluation criteria, scoring, rebuttals |
912
- | [sources.md](references/sources.md) | Complete bibliography of all sources |
913
-
914
- ### LaTeX Templates
915
-
916
- Templates in `templates/` directory: **ICML 2026**, **ICLR 2026**, **NeurIPS 2025**, **ACL/EMNLP**, **AAAI 2026**, **COLM 2025**.
917
-
918
- **Compiling to PDF:**
919
- - **VS Code/Cursor**: Install LaTeX Workshop extension + TeX Live → Save to auto-compile
920
- - **Command line**: `latexmk -pdf main.tex` or `pdflatex` + `bibtex` workflow
921
- - **Online**: Upload to [Overleaf](https://overleaf.com)
922
-
923
- See [templates/README.md](templates/README.md) for detailed setup instructions.
924
-
925
- ### Key External Sources
926
-
927
- **Writing Philosophy:**
928
- - [Neel Nanda: How to Write ML Papers](https://www.alignmentforum.org/posts/eJGptPbbFPZGLpjsp/highly-opinionated-advice-on-how-to-write-ml-papers) - Narrative, "What/Why/So What"
929
- - [Farquhar: How to Write ML Papers](https://sebastianfarquhar.com/on-research/2024/11/04/how_to_write_ml_papers/) - 5-sentence abstract
930
- - [Gopen & Swan: Science of Scientific Writing](https://cseweb.ucsd.edu/~swanson/papers/science-of-writing.pdf) - 7 reader expectation principles
931
- - [Lipton: Heuristics for Scientific Writing](https://www.approximatelycorrect.com/2018/01/29/heuristics-technical-scientific-writing-machine-learning-perspective/) - Word choice
932
- - [Perez: Easy Paper Writing Tips](https://ethanperez.net/easy-paper-writing-tips/) - Micro-level clarity
933
-
934
- **APIs:** [Semantic Scholar](https://api.semanticscholar.org/api-docs/) | [CrossRef](https://www.crossref.org/documentation/retrieve-metadata/rest-api/) | [arXiv](https://info.arxiv.org/help/api/basics.html)
935
-
936
- **Venues:** [NeurIPS](https://neurips.cc/Conferences/2025/PaperInformation/StyleFiles) | [ICML](https://icml.cc/Conferences/2025/AuthorInstructions) | [ICLR](https://iclr.cc/Conferences/2026/AuthorGuide) | [ACL](https://github.com/acl-org/acl-style-files)
937
-