@pikaa-ai/pikaa 0.3.1 → 0.3.4

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 (1870) hide show
  1. package/dist/cli.js +1169 -601
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
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  210. package/skills/database-lookup/references/clinvar.md +0 -91
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  212. package/skills/database-lookup/references/cosmic.md +0 -59
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  218. package/skills/database-lookup/references/drugbank.md +0 -54
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  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
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  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
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1
- # Nature/Science Abstract Examples
2
-
3
- Examples of well-crafted abstracts for high-impact multidisciplinary journals. These demonstrate the flowing paragraph style with broad accessibility expected at Nature, Science, and related venues.
4
-
5
- ---
6
-
7
- ## Example 1: Molecular Biology / Cell Biology
8
-
9
- **Topic**: CRISPR gene editing discovery
10
-
11
- ```
12
- The ability to precisely edit DNA sequences in living cells has transformed
13
- biological research and holds promise for treating genetic diseases. However,
14
- current genome editing tools can introduce unwanted mutations at off-target
15
- sites, limiting their clinical potential. Here we describe prime editing, a
16
- versatile and precise genome editing method that directly writes new genetic
17
- information into a specified DNA site using a reverse transcriptase fused to a
18
- CRISPR nickase. Prime editing can make all 12 types of point mutations, as
19
- well as small insertions and deletions, with minimal off-target editing and
20
- without requiring double-strand breaks or donor DNA templates. In human cells,
21
- we used prime editing to correct the primary genetic causes of sickle cell
22
- disease and Tay-Sachs disease, and to install protective mutations that
23
- reduce risk of prion disease. Prime editing expands the scope and capabilities
24
- of genome editing and may address approximately 89% of known human genetic
25
- disease variants.
26
- ```
27
-
28
- **Why this works**:
29
- - Opens with broad significance (genetic disease treatment)
30
- - States the problem clearly (off-target mutations)
31
- - Describes the approach accessibly ("writes new genetic information")
32
- - Includes specific results (all 12 point mutations, specific diseases)
33
- - Ends with quantified impact (89% of variants)
34
-
35
- ---
36
-
37
- ## Example 2: Neuroscience
38
-
39
- **Topic**: Memory consolidation mechanism
40
-
41
- ```
42
- Sleep is essential for memory consolidation, yet how the sleeping brain
43
- transforms labile memories into stable long-term representations remains
44
- poorly understood. We used multi-site electrophysiology in freely behaving
45
- mice to record the activity of thousands of neurons across hippocampus and
46
- cortex during learning and subsequent sleep. We discovered that specific
47
- neurons that encode a newly learned memory reactivate in precisely timed
48
- sequences during slow-wave sleep, with hippocampal reactivation preceding
49
- cortical reactivation by 10-15 milliseconds. Optogenetic disruption of this
50
- temporal coordination impaired memory retention by 78%, whereas artificial
51
- enhancement of the temporal relationship strengthened memories beyond normal
52
- levels. These results reveal that the temporal ordering of hippocampal-cortical
53
- replay is not merely correlative but causally necessary for memory
54
- consolidation. Our findings suggest new therapeutic approaches for memory
55
- disorders based on optimizing the temporal dynamics of sleep.
56
- ```
57
-
58
- **Why this works**:
59
- - Connects to well-known phenomenon (sleep and memory)
60
- - States what was unknown
61
- - Describes approach (multi-site recordings)
62
- - Key finding with specific number (10-15 ms)
63
- - Causal evidence (disruption and enhancement experiments)
64
- - Broader implications (therapeutic approaches)
65
-
66
- ---
67
-
68
- ## Example 3: Climate Science
69
-
70
- **Topic**: Carbon cycle feedback
71
-
72
- ```
73
- Arctic permafrost contains approximately 1,500 billion tonnes of organic
74
- carbon—twice the amount currently in the atmosphere. As the Arctic warms,
75
- this carbon may be released to the atmosphere, accelerating global warming
76
- through a positive feedback loop. However, the magnitude and timing of this
77
- feedback remain highly uncertain because microbial decomposition rates in
78
- thawing permafrost are poorly constrained. Here we present a 15-year
79
- field experiment across 25 sites spanning the Arctic, tracking carbon
80
- fluxes in warming permafrost under natural conditions. We find that
81
- microbial respiration increases exponentially with temperature until soils
82
- reach 3°C, then plateaus due to substrate limitation—a threshold effect
83
- not captured by current Earth system models. Our results suggest that
84
- permafrost carbon feedback will be 30-50% lower than current projections
85
- during this century, providing more time to limit warming, but will
86
- accelerate dramatically if deep permafrost begins to thaw.
87
- ```
88
-
89
- **Why this works**:
90
- - Opens with striking number (1,500 billion tonnes)
91
- - Clear problem statement (feedback uncertainty)
92
- - Specific methodology (15 years, 25 sites)
93
- - Novel finding (threshold at 3°C)
94
- - Implications both reassuring and cautionary
95
-
96
- ---
97
-
98
- ## Example 4: Physics / Materials Science
99
-
100
- **Topic**: Room-temperature superconductivity
101
-
102
- ```
103
- Superconductivity—the flow of electricity without resistance—has been
104
- confined to extremely low temperatures since its discovery over a century
105
- ago, limiting practical applications. The recent demonstration of
106
- superconductivity in hydrogen-rich materials at high pressure has raised
107
- hopes for higher transition temperatures, but achieving room-temperature
108
- superconductivity at ambient pressure has remained elusive. Here we report
109
- superconductivity at 21°C (294 K) in a nitrogen-doped lutetium hydride
110
- (Lu-N-H) compound at pressures of approximately 1 GPa—nearly ambient
111
- conditions. Electrical resistance drops to zero below the transition
112
- temperature with a sharp transition width of 2 K, and we observe the Meissner
113
- effect confirming bulk superconductivity. Density functional theory
114
- calculations suggest that nitrogen incorporation stabilizes the high-symmetry
115
- structure that enables strong electron-phonon coupling. These results
116
- establish a pathway toward practical room-temperature superconductors.
117
- ```
118
-
119
- **Why this works**:
120
- - Opens with accessible explanation of significance
121
- - Historical context (century-old limitation)
122
- - Precise results (21°C, 1 GPa, 2 K transition width)
123
- - Multiple lines of evidence (resistance + Meissner effect)
124
- - Theoretical explanation briefly included
125
- - Forward-looking conclusion
126
-
127
- ---
128
-
129
- ## Example 5: Evolution / Ecology
130
-
131
- **Topic**: Rapid evolution in response to climate
132
-
133
- ```
134
- Climate change is driving rapid shifts in the geographic distributions of
135
- species, but whether organisms can adapt quickly enough to keep pace with
136
- warming remains a critical question for biodiversity conservation. Here we
137
- document real-time evolution in wild populations of a widespread forest tree,
138
- Scots pine, along a 1,000 km latitudinal gradient in Scandinavia. By combining
139
- whole-genome sequencing with phenotypic measurements across 25 common gardens,
140
- we detect signatures of selection at 47 loci associated with cold tolerance,
141
- phenology, and drought resistance over just 50 years—approximately
142
- five tree generations. Alleles conferring warmer-adapted phenotypes have
143
- increased in frequency by 4-12% across northern populations, matching
144
- predictions from models of climate-driven selection. However, migration of
145
- warm-adapted genotypes from the south appears limited by geographic barriers.
146
- These results demonstrate that trees can evolve rapidly in response to
147
- climate change but suggest that assisted gene flow may be necessary to
148
- prevent local maladaptation.
149
- ```
150
-
151
- **Why this works**:
152
- - Opens with pressing question (climate adaptation)
153
- - Specific system (Scots pine) and scale (1,000 km)
154
- - Methods described briefly (genomics + common gardens)
155
- - Quantitative results (47 loci, 4-12% frequency shift, 5 generations)
156
- - Mechanism identified (limited migration)
157
- - Conservation implications stated
158
-
159
- ---
160
-
161
- ## Common Elements Across Examples
162
-
163
- ### Structure (Implicit)
164
- 1. **Hook**: Why this matters broadly (1-2 sentences)
165
- 2. **Gap**: What was unknown or problematic (1 sentence)
166
- 3. **Approach**: What was done (1 sentence)
167
- 4. **Findings**: Key results with numbers (2-3 sentences)
168
- 5. **Significance**: Why this matters going forward (1 sentence)
169
-
170
- ### Style Features
171
- - **Active voice**: "We discovered," "We find," "We report"
172
- - **Specific numbers**: Exact values, not vague quantities
173
- - **Accessible language**: Minimal jargon, explained when needed
174
- - **Compelling opening**: Broad hook before technical details
175
- - **Strong close**: Implications or future directions
176
-
177
- ### Word Count
178
- - Nature: 150-200 words (examples above: 185-210 words)
179
- - Science: ≤125 words (would need tightening)
180
-
181
- ---
182
-
183
- ## What to Avoid
184
-
185
- ❌ **Too technical opening**:
186
- > "The CRISPR-Cas9 system with guide RNA targeting PAM sequences..."
187
-
188
- ✅ **Better opening**:
189
- > "The ability to precisely edit DNA in living cells..."
190
-
191
- ---
192
-
193
- ❌ **Vague results**:
194
- > "Our method significantly outperformed existing approaches..."
195
-
196
- ✅ **Better results**:
197
- > "Our method reduced off-target editing by 78% compared to standard Cas9..."
198
-
199
- ---
200
-
201
- ❌ **Weak significance statement**:
202
- > "These findings may have implications for the field..."
203
-
204
- ✅ **Better significance**:
205
- > "These findings suggest new therapeutic approaches for memory disorders..."
206
-
207
- ---
208
-
209
- ## See Also
210
-
211
- - `nature_science_style.md` - Comprehensive Nature/Science writing guide
212
- - `venue_writing_styles.md` - Style comparison across venues
213
-
@@ -1,245 +0,0 @@
1
- # NeurIPS/ICML Introduction Example
2
-
3
- This example demonstrates the distinctive ML conference introduction structure with numbered contributions and technical precision.
4
-
5
- ---
6
-
7
- ## Full Introduction Example
8
-
9
- **Paper Topic**: Efficient Long-Context Transformers
10
-
11
- ---
12
-
13
- ### Paragraph 1: Problem Motivation
14
-
15
- ```
16
- Large language models (LLMs) have demonstrated remarkable capabilities in
17
- natural language understanding, code generation, and reasoning tasks [1, 2, 3].
18
- These capabilities scale with both model size and context length—longer
19
- contexts enable processing of entire documents, multi-turn conversations,
20
- and complex reasoning chains that span many steps [4, 5]. However, the
21
- standard Transformer attention mechanism [6] has O(N²) time and memory
22
- complexity with respect to sequence length N, creating a fundamental
23
- bottleneck for processing long sequences. For a context window of 100K
24
- tokens, computing full attention requires 10 billion scalar operations
25
- and 40 GB of memory for the attention matrix alone, making training and
26
- inference prohibitively expensive on current hardware.
27
- ```
28
-
29
- **Key features**:
30
- - States why this matters (LLM capabilities)
31
- - Connects to scaling (longer contexts = better performance)
32
- - Specific numbers (O(N²), 100K tokens, 10 billion ops, 40 GB)
33
- - Citations to establish credibility
34
-
35
- ---
36
-
37
- ### Paragraph 2: Limitations of Existing Approaches
38
-
39
- ```
40
- Prior work has addressed attention efficiency through three main approaches.
41
- Sparse attention patterns [7, 8, 9] reduce complexity to O(N√N) or O(N log N)
42
- by restricting attention to local windows, fixed stride patterns, or learned
43
- sparse masks. Linear attention approximations [10, 11, 12] reformulate
44
- attention using kernel feature maps that enable O(N) computation, but
45
- sacrifice the ability to model arbitrary pairwise interactions. Low-rank
46
- factorizations [13, 14] approximate the attention matrix as a product of
47
- smaller matrices, achieving efficiency at the cost of expressivity. While
48
- these methods reduce theoretical complexity, they introduce approximation
49
- errors that compound in deep networks, often resulting in 2-5% accuracy
50
- degradation on long-range modeling benchmarks [15]. Perhaps more importantly,
51
- they fundamentally change the attention mechanism, making it difficult to
52
- apply advances in standard attention (e.g., rotary positional embeddings,
53
- grouped-query attention) to efficient variants.
54
- ```
55
-
56
- **Key features**:
57
- - Organized categorization of prior work
58
- - Complexity stated for each approach
59
- - Limitations clearly identified
60
- - Quantified shortcomings (2-5% degradation)
61
- - Deeper issue identified (incompatibility with advances)
62
-
63
- ---
64
-
65
- ### Paragraph 3: Your Approach (High-Level)
66
-
67
- ```
68
- We take a different approach: rather than approximating attention, we
69
- accelerate exact attention by optimizing memory access patterns. Our key
70
- observation is that on modern GPUs, attention is bottlenecked by memory
71
- bandwidth, not compute. Reading and writing the N × N attention matrix to
72
- and from GPU high-bandwidth memory (HBM) dominates runtime, while the GPU's
73
- tensor cores remain underutilized. We propose LongFlash, an IO-aware exact
74
- attention algorithm that computes attention block-by-block in fast on-chip
75
- SRAM, never materializing the full attention matrix in HBM. By carefully
76
- orchestrating the tiling pattern and fusing the softmax computation with
77
- matrix multiplications, LongFlash reduces HBM accesses from O(N²) to
78
- O(N²d/M) where d is the head dimension and M is the SRAM size, achieving
79
- asymptotically optimal IO complexity.
80
- ```
81
-
82
- **Key features**:
83
- - Clear differentiation from prior work ("different approach")
84
- - Key insight stated explicitly
85
- - Technical mechanism explained
86
- - Complexity improvement quantified
87
- - Method name introduced
88
-
89
- ---
90
-
91
- ### Paragraph 4: Contributions (CRITICAL)
92
-
93
- ```
94
- Our contributions are as follows:
95
-
96
- • We propose LongFlash, an IO-aware exact attention algorithm that achieves
97
- 2-4× speedup over FlashAttention [16] and up to 9× over standard PyTorch
98
- attention on sequences from 1K to 128K tokens (Section 3).
99
-
100
- • We provide theoretical analysis proving that LongFlash achieves optimal
101
- IO complexity of O(N²d/M) among all algorithms that compute exact
102
- attention, and analyze the regime where our algorithm provides maximum
103
- benefit (Section 3.3).
104
-
105
- • We introduce sequence parallelism techniques that enable LongFlash to
106
- scale to sequences of 1M+ tokens across multiple GPUs with near-linear
107
- weak scaling efficiency (Section 4).
108
-
109
- • We demonstrate that LongFlash enables training with 8× longer contexts
110
- on the same hardware: we train a 7B parameter model on 128K token
111
- contexts using the same memory that previously limited us to 16K tokens
112
- (Section 5).
113
-
114
- • We release optimized CUDA kernels achieving 80% of theoretical peak
115
- FLOPS on A100 and H100 GPUs, along with PyTorch and JAX bindings, at
116
- [anonymous URL] (Section 6).
117
- ```
118
-
119
- **Key features**:
120
- - Numbered/bulleted format
121
- - Each contribution is specific and quantified
122
- - Section references for each claim
123
- - Both methodological and empirical contributions
124
- - Code release mentioned
125
- - Self-contained bullets (each makes sense alone)
126
-
127
- ---
128
-
129
- ## Alternative Opening Paragraphs
130
-
131
- ### For a Methods Paper
132
-
133
- ```
134
- Scalable optimization algorithms are fundamental to modern machine learning.
135
- Stochastic gradient descent (SGD) and its variants [1, 2, 3] have enabled
136
- training of models with billions of parameters on massive datasets. However,
137
- these first-order methods exhibit slow convergence on ill-conditioned
138
- problems, often requiring thousands of iterations to converge on tasks
139
- where second-order methods would converge in tens of iterations [4, 5].
140
- ```
141
-
142
- ### For an Applications Paper
143
-
144
- ```
145
- Drug discovery is a costly and time-consuming process, with the average new
146
- drug requiring 10-15 years and $2.6 billion to develop [1]. Machine learning
147
- offers the potential to accelerate this process by predicting molecular
148
- properties, identifying promising candidates, and optimizing lead compounds
149
- computationally [2, 3]. Recent successes in protein structure prediction [4]
150
- and molecular generation [5] have demonstrated that deep learning can
151
- capture complex chemical patterns, raising hopes for ML-driven drug discovery.
152
- ```
153
-
154
- ### For a Theory Paper
155
-
156
- ```
157
- Understanding why deep neural networks generalize well despite having more
158
- parameters than training examples remains one of the central puzzles of
159
- modern machine learning [1, 2]. Classical statistical learning theory
160
- predicts that such overparameterized models should overfit dramatically,
161
- yet in practice, large networks trained with SGD achieve excellent test
162
- accuracy [3]. This gap between theory and practice has motivated a rich
163
- literature on implicit regularization [4], neural tangent kernels [5],
164
- and feature learning [6], but a complete theoretical picture remains elusive.
165
- ```
166
-
167
- ---
168
-
169
- ## Contribution Bullet Templates
170
-
171
- ### For a New Method
172
-
173
- ```
174
- • We propose [Method Name], a novel [type of method] that [key innovation]
175
- achieving [performance improvement] over [baseline] on [benchmark].
176
- ```
177
-
178
- ### For Theoretical Analysis
179
-
180
- ```
181
- • We prove that [statement], providing the first [type of result] for
182
- [problem setting]. This resolves an open question from [prior work].
183
- ```
184
-
185
- ### For Empirical Study
186
-
187
- ```
188
- • We conduct a comprehensive evaluation of [N] methods across [M] datasets,
189
- revealing that [key finding] and identifying [failure mode/best practice].
190
- ```
191
-
192
- ### For Code/Data Release
193
-
194
- ```
195
- • We release [resource name], a [description] containing [scale/scope],
196
- available at [URL]. This enables [future work/reproducibility].
197
- ```
198
-
199
- ---
200
-
201
- ## Common Mistakes to Avoid
202
-
203
- ### Vague Contributions
204
-
205
- ❌ **Bad**:
206
- ```
207
- • We propose a novel method for attention
208
- • We show our method is better than baselines
209
- • We provide theoretical analysis
210
- ```
211
-
212
- ✅ **Good**:
213
- ```
214
- • We propose LongFlash, achieving 2-4× speedup over FlashAttention
215
- • We prove LongFlash achieves optimal O(N²d/M) IO complexity
216
- • We enable 8× longer context training on fixed hardware budget
217
- ```
218
-
219
- ### Missing Quantification
220
-
221
- ❌ **Bad**: "Our method significantly outperforms prior work"
222
- ✅ **Good**: "Our method improves accuracy by 3.2% on GLUE and 4.1% on SuperGLUE"
223
-
224
- ### Overlapping Bullets
225
-
226
- ❌ **Bad**:
227
- ```
228
- • We propose a new attention mechanism
229
- • We introduce LongFlash attention
230
- • Our novel attention approach...
231
- ```
232
- (These say the same thing three times)
233
-
234
- ### Buried Contributions
235
-
236
- ❌ **Bad**: Contribution bullets at the end of page 2
237
- ✅ **Good**: Contribution bullets clearly visible by end of page 1
238
-
239
- ---
240
-
241
- ## See Also
242
-
243
- - `ml_conference_style.md` - Comprehensive ML conference guide
244
- - `venue_writing_styles.md` - Style comparison across venues
245
-
@@ -1,237 +0,0 @@
1
- % NIH Specific Aims Page Template
2
- % Writing scaffold; not an NIH-issued format page
3
- % Reviewed: 2026-07-20
4
- % Specific Aims is generally limited to one page.
5
- % Recheck the NOFO and current application guide before use:
6
- % https://grants.nih.gov/grants-process/write-application/how-to-apply-application-guide
7
-
8
- \documentclass[11pt,letterpaper]{article}
9
-
10
- % Formatting
11
- \usepackage[margin=0.5in]{geometry} % 0.5 inch minimum margins
12
- \usepackage{helvet} % Arial-like font
13
- \renewcommand{\familydefault}{\sfdefault}
14
-
15
- \usepackage{setspace}
16
- \usepackage{color}
17
- \usepackage{soul} % For highlighting (remove in final version)
18
-
19
- % Remove page numbers (optional)
20
- \pagestyle{empty}
21
-
22
- \begin{document}
23
-
24
- % Optional: Highlight template text to remind yourself to replace
25
- % Remove \hl{} and color in final version
26
- \definecolor{highlight}{RGB}{255,255,200}
27
- \sethlcolor{highlight}
28
-
29
- % ====================
30
- % SPECIFIC AIMS PAGE
31
- % ====================
32
-
33
- \begin{center}
34
- \textbf{\large Your Project Title Here: Concise and Descriptive}
35
- \end{center}
36
-
37
- \vspace{0.3cm}
38
-
39
- % OPENING PARAGRAPH: The Hook and Gap
40
- % 2-3 sentences establishing significance and the knowledge gap
41
-
42
- \textbf{[Disease/condition]} affects \textbf{[number]} people worldwide and results in \textbf{[burden: mortality, morbidity, cost]}. \textbf{[Current treatment/understanding]} has improved outcomes, but \textbf{[limitation/gap]} remains a critical barrier to \textbf{[desired outcome]}. Understanding \textbf{[specific mechanism/relationship]} is essential for \textbf{[future advance: therapy, prevention, diagnosis]}.
43
-
44
- \vspace{0.2cm}
45
-
46
- % LONG-TERM GOAL
47
- % 1 sentence on your overarching research vision
48
-
49
- Our \textbf{long-term goal} is to \textbf{[overarching vision: develop cure, understand mechanism, improve treatment]} for \textbf{[disease/population]}.
50
-
51
- \vspace{0.2cm}
52
-
53
- % OBJECTIVE AND CENTRAL HYPOTHESIS
54
- % 1-2 sentences on what THIS proposal will accomplish
55
-
56
- The \textbf{objective} of this proposal is to \textbf{[specific objective for this project]}. Our \textbf{central hypothesis} is that \textbf{[clearly stated, testable hypothesis]}.
57
-
58
- \vspace{0.2cm}
59
-
60
- % RATIONALE
61
- % 2-3 sentences explaining WHY you expect success (preliminary data!)
62
-
63
- This hypothesis is based on our \textbf{preliminary data} showing that \textbf{[key preliminary finding 1]} and \textbf{[key preliminary finding 2]}. These findings suggest that \textbf{[mechanistic explanation or expected outcome]}.
64
-
65
- \vspace{0.2cm}
66
-
67
- % TRANSITION TO AIMS
68
- % 1 sentence introducing the specific aims
69
-
70
- To test this hypothesis and achieve our objective, we will pursue the following \textbf{Specific Aims}:
71
-
72
- \vspace{0.3cm}
73
-
74
- % ====================
75
- % SPECIFIC AIM 1
76
- % ====================
77
-
78
- \noindent\textbf{Specific Aim 1: [Concise, active verb title describing what you'll do].}
79
-
80
- \textit{Working Hypothesis:} \hl{State testable hypothesis for this aim.}
81
-
82
- We will \textbf{[approach/method]} to determine \textbf{[what you'll learn]}. We will use \textbf{[model system/approach]} to test whether \textbf{[specific prediction]}.
83
-
84
- \textbf{Expected Outcome:} We expect to find that \textbf{[predicted result]}. This outcome will demonstrate that \textbf{[significance of finding]} and will be \textbf{[positive/negative/innovative/transformative]} because \textbf{[why it matters]}.
85
-
86
- \vspace{0.3cm}
87
-
88
- % ====================
89
- % SPECIFIC AIM 2
90
- % ====================
91
-
92
- \noindent\textbf{Specific Aim 2: [Title of second aim].}
93
-
94
- \textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 2.}
95
-
96
- Building on Aim 1, we will \textbf{[approach]} to \textbf{[objective]}. We will employ \textbf{[method/technique]} in \textbf{[model/population]} to test the hypothesis that \textbf{[specific prediction]}.
97
-
98
- \textbf{Expected Outcome:} These studies will reveal \textbf{[predicted finding]}. This is significant because \textbf{[impact on field/understanding]}.
99
-
100
- \vspace{0.3cm}
101
-
102
- % ====================
103
- % SPECIFIC AIM 3 (OPTIONAL)
104
- % ====================
105
-
106
- \noindent\textbf{Specific Aim 3: [Title of third aim].}
107
-
108
- \textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 3.}
109
-
110
- To translate findings from Aims 1-2, we will \textbf{[approach]} to determine \textbf{[translational objective]}. We will \textbf{[method]} using \textbf{[clinically relevant model/patient samples]} to test whether \textbf{[translational prediction]}.
111
-
112
- \textbf{Expected Outcome:} We anticipate that \textbf{[result]}, which will provide \textbf{[proof-of-concept/validation/mechanism]} for \textbf{[therapeutic/diagnostic/preventive strategy]}.
113
-
114
- \vspace{0.3cm}
115
-
116
- % ====================
117
- % PAYOFF PARAGRAPH
118
- % ====================
119
-
120
- % 2-3 sentences on IMPACT, INNOVATION, and FUTURE DIRECTIONS
121
-
122
- \textbf{Impact and Innovation:} This project is \textbf{innovative} because it \textbf{[novel aspect: new concept, method, approach, application]}. The proposed research is \textbf{significant} because it will \textbf{[advance the field by...]} and will ultimately lead to \textbf{[long-term impact: improved treatment, new therapeutic target, diagnostic tool]}. Upon completion of these studies, we will be positioned to \textbf{[next steps: clinical trial, mechanistic studies, therapeutic development]}.
123
-
124
- \vspace{0.5cm}
125
-
126
- % ====================
127
- % ALTERNATIVE STRUCTURE (if preferred)
128
- % ====================
129
-
130
- % Some successful Specific Aims pages use this alternative structure:
131
- % - Open with hook (same as above)
132
- % - State long-term goal and objective (same)
133
- % - Present central hypothesis with 2-3 supporting pieces of preliminary data
134
- % - Then state: "We will test this hypothesis through three Specific Aims:"
135
- % - List aims more concisely (1-2 sentences each, plus expected outcome)
136
- % - Conclude with payoff paragraph emphasizing innovation, significance, impact
137
-
138
- \end{document}
139
-
140
- % ====================
141
- % TIPS FOR WRITING SPECIFIC AIMS
142
- % ====================
143
-
144
- % 1. START WITH A HOOK
145
- % - Open with the big picture: disease burden, societal cost, mortality
146
- % - Use compelling statistics
147
- % - Make it clear why anyone should care
148
-
149
- % 2. IDENTIFY THE GAP
150
- % - What's currently known?
151
- % - What's the critical barrier or unknown?
152
- % - Why does it matter?
153
-
154
- % 3. STATE YOUR HYPOTHESIS EXPLICITLY
155
- % - Clear, testable hypothesis
156
- % - Not "We hypothesize that we will study..." (that's not a hypothesis!)
157
- % - "We hypothesize that [mechanism] causes [outcome]"
158
-
159
- % 4. SHOW PRELIMINARY DATA
160
- % - Demonstrate feasibility
161
- % - Prove you're not starting from scratch
162
- % - Build confidence in your approach
163
-
164
- % 5. THREE AIMS (TYPICALLY)
165
- % - Can be 2 or 4, but 3 is most common
166
- % - Aims should be related but somewhat independent
167
- % - Failure of one aim shouldn't sink the whole project
168
- % - Aims can build on each other (Aim 1 → Aim 2 → Aim 3)
169
-
170
- % 6. EACH AIM SHOULD HAVE:
171
- % - Clear title (active verb)
172
- % - Working hypothesis
173
- % - Approach/method
174
- % - Expected outcome
175
- % - Significance/impact
176
-
177
- % 7. END WITH PAYOFF
178
- % - Innovation: What's new/different?
179
- % - Significance: Why does it matter?
180
- % - Impact: What will change?
181
- % - Future: Where does this lead?
182
-
183
- % 8. COMMON MISTAKES TO AVOID
184
- % - Too much background (this is not a mini-review)
185
- % - Vague hypotheses or objectives
186
- % - Missing expected outcomes
187
- % - No preliminary data mentioned
188
- % - Too ambitious (can't do it all in 5 years)
189
- % - Not addressing innovation and significance
190
- % - Poor logical flow between aims
191
- % - Exceeding 1 page (auto-reject!)
192
-
193
- % 9. FORMATTING RULES (STRICTLY ENFORCED)
194
- % - 1 page maximum (including all text, no figures typically)
195
- % - Arial 11pt minimum (or equivalent)
196
- % - 0.5 inch margins minimum
197
- % - Any spacing (single, 1.5, double acceptable)
198
- % - No smaller fonts allowed (even for superscripts/subscripts)
199
-
200
- % 10. REVISION STRATEGY
201
- % - Write, get feedback, revise 10+ times
202
- % - Every word must earn its place
203
- % - Test on non-specialist colleagues
204
- % - Read aloud to check flow
205
- % - Have it reviewed by successful R01 holders
206
- % - Mock study section review
207
-
208
- % ====================
209
- % EXAMPLES OF STRONG OPENING SENTENCES
210
- % ====================
211
-
212
- % DISEASE BURDEN APPROACH:
213
- % "[Condition] affects [current, cited population estimate] and causes
214
- % [current, cited burden], yet [specific unmet need remains]."
215
-
216
- % MECHANISTIC GAP APPROACH:
217
- % "Despite decades of research, the molecular mechanisms driving metastasis remain poorly understood,
218
- % limiting our ability to develop effective therapies for the 90% of cancer deaths caused by metastatic disease."
219
-
220
- % TRANSLATIONAL APPROACH:
221
- % "Current immunotherapies fail in 70% of patients with melanoma, largely because we cannot predict
222
- % who will respond, highlighting an urgent need for biomarkers of treatment response."
223
-
224
- % ====================
225
- % REMEMBER
226
- % ====================
227
-
228
- % The Specific Aims page is often the ONLY page reviewers read carefully before
229
- % forming their initial opinion. A weak Specific Aims page can doom an otherwise
230
- % excellent proposal. Invest the time to make it compelling, clear, and concise.
231
-
232
- % Get feedback from:
233
- % - Successful R01 awardees in your field
234
- % - Grant writing office at your institution
235
- % - Colleagues who've served on NIH study sections
236
- % - Non-specialists (if they can't understand it, reviewers may struggle too)
237
-