flonat-research 0.1.0

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  1. package/.claude/agents/domain-reviewer.md +336 -0
  2. package/.claude/agents/fixer.md +226 -0
  3. package/.claude/agents/paper-critic.md +370 -0
  4. package/.claude/agents/peer-reviewer.md +289 -0
  5. package/.claude/agents/proposal-reviewer.md +215 -0
  6. package/.claude/agents/referee2-reviewer.md +367 -0
  7. package/.claude/agents/references/journal-referee-profiles.md +354 -0
  8. package/.claude/agents/references/paper-critic/council-personas.md +77 -0
  9. package/.claude/agents/references/paper-critic/council-prompts.md +198 -0
  10. package/.claude/agents/references/peer-reviewer/report-template.md +199 -0
  11. package/.claude/agents/references/peer-reviewer/sa-prompts.md +260 -0
  12. package/.claude/agents/references/peer-reviewer/security-scan.md +188 -0
  13. package/.claude/agents/references/proposal-reviewer/report-template.md +144 -0
  14. package/.claude/agents/references/proposal-reviewer/sa-prompts.md +149 -0
  15. package/.claude/agents/references/referee-config.md +114 -0
  16. package/.claude/agents/references/referee2-reviewer/audit-checklists.md +287 -0
  17. package/.claude/agents/references/referee2-reviewer/report-template.md +334 -0
  18. package/.claude/rules/design-before-results.md +52 -0
  19. package/.claude/rules/ignore-agents-md.md +17 -0
  20. package/.claude/rules/ignore-gemini-md.md +17 -0
  21. package/.claude/rules/lean-claude-md.md +45 -0
  22. package/.claude/rules/learn-tags.md +99 -0
  23. package/.claude/rules/overleaf-separation.md +67 -0
  24. package/.claude/rules/plan-first.md +175 -0
  25. package/.claude/rules/read-docs-first.md +50 -0
  26. package/.claude/rules/scope-discipline.md +28 -0
  27. package/.claude/settings.json +125 -0
  28. package/.context/current-focus.md +33 -0
  29. package/.context/preferences/priorities.md +36 -0
  30. package/.context/preferences/task-naming.md +28 -0
  31. package/.context/profile.md +29 -0
  32. package/.context/projects/_index.md +41 -0
  33. package/.context/projects/papers/nudge-exp.md +22 -0
  34. package/.context/projects/papers/uncertainty.md +31 -0
  35. package/.context/resources/claude-scientific-writer-review.md +48 -0
  36. package/.context/resources/cunningham-multi-analyst-agents.md +104 -0
  37. package/.context/resources/cunningham-multilang-code-audit.md +62 -0
  38. package/.context/resources/google-ai-co-scientist-review.md +72 -0
  39. package/.context/resources/karpathy-llm-council-review.md +58 -0
  40. package/.context/resources/multi-coder-reliability-protocol.md +175 -0
  41. package/.context/resources/pedro-santanna-takeaways.md +96 -0
  42. package/.context/resources/venue-rankings/abs_ajg_2024.csv +1823 -0
  43. package/.context/resources/venue-rankings/abs_ajg_2024_econ.csv +356 -0
  44. package/.context/resources/venue-rankings/cabs_4_4star_theory.csv +40 -0
  45. package/.context/resources/venue-rankings/core_2026.csv +801 -0
  46. package/.context/resources/venue-rankings.md +147 -0
  47. package/.context/workflows/README.md +69 -0
  48. package/.context/workflows/daily-review.md +91 -0
  49. package/.context/workflows/meeting-actions.md +108 -0
  50. package/.context/workflows/replication-protocol.md +155 -0
  51. package/.context/workflows/weekly-review.md +113 -0
  52. package/.mcp-server-biblio/formatters.py +158 -0
  53. package/.mcp-server-biblio/pyproject.toml +11 -0
  54. package/.mcp-server-biblio/server.py +678 -0
  55. package/.mcp-server-biblio/sources/__init__.py +14 -0
  56. package/.mcp-server-biblio/sources/base.py +73 -0
  57. package/.mcp-server-biblio/sources/formatters.py +83 -0
  58. package/.mcp-server-biblio/sources/models.py +22 -0
  59. package/.mcp-server-biblio/sources/multi_source.py +243 -0
  60. package/.mcp-server-biblio/sources/openalex_source.py +183 -0
  61. package/.mcp-server-biblio/sources/scopus_source.py +309 -0
  62. package/.mcp-server-biblio/sources/wos_source.py +508 -0
  63. package/.mcp-server-biblio/uv.lock +896 -0
  64. package/.scripts/README.md +161 -0
  65. package/.scripts/ai_pattern_density.py +446 -0
  66. package/.scripts/conf +445 -0
  67. package/.scripts/config.py +122 -0
  68. package/.scripts/count_inventory.py +275 -0
  69. package/.scripts/daily_digest.py +288 -0
  70. package/.scripts/done +177 -0
  71. package/.scripts/extract_meeting_actions.py +223 -0
  72. package/.scripts/focus +176 -0
  73. package/.scripts/generate-codex-agents-md.py +217 -0
  74. package/.scripts/inbox +194 -0
  75. package/.scripts/notion_helpers.py +325 -0
  76. package/.scripts/openalex/query_helpers.py +306 -0
  77. package/.scripts/papers +227 -0
  78. package/.scripts/query +223 -0
  79. package/.scripts/session-history.py +201 -0
  80. package/.scripts/skill-health.py +516 -0
  81. package/.scripts/skill-log-miner.py +273 -0
  82. package/.scripts/sync-to-codex.sh +252 -0
  83. package/.scripts/task +213 -0
  84. package/.scripts/tasks +190 -0
  85. package/.scripts/week +206 -0
  86. package/CLAUDE.md +197 -0
  87. package/LICENSE +21 -0
  88. package/MEMORY.md +38 -0
  89. package/README.md +269 -0
  90. package/docs/agents.md +44 -0
  91. package/docs/bibliography-setup.md +55 -0
  92. package/docs/council-mode.md +36 -0
  93. package/docs/getting-started.md +245 -0
  94. package/docs/hooks.md +38 -0
  95. package/docs/mcp-servers.md +82 -0
  96. package/docs/notion-setup.md +109 -0
  97. package/docs/rules.md +33 -0
  98. package/docs/scripts.md +303 -0
  99. package/docs/setup-overview/setup-overview.pdf +0 -0
  100. package/docs/skills.md +70 -0
  101. package/docs/system.md +159 -0
  102. package/hooks/block-destructive-git.sh +66 -0
  103. package/hooks/context-monitor.py +114 -0
  104. package/hooks/postcompact-restore.py +157 -0
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  108. package/hooks/resume-context-loader.sh +53 -0
  109. package/hooks/startup-context-loader.sh +102 -0
  110. package/package.json +51 -0
  111. package/packages/cli-council/.github/workflows/claude-code-review.yml +44 -0
  112. package/packages/cli-council/.github/workflows/claude.yml +50 -0
  113. package/packages/cli-council/README.md +100 -0
  114. package/packages/cli-council/pyproject.toml +43 -0
  115. package/packages/cli-council/src/cli_council/__init__.py +19 -0
  116. package/packages/cli-council/src/cli_council/__main__.py +185 -0
  117. package/packages/cli-council/src/cli_council/backends/__init__.py +8 -0
  118. package/packages/cli-council/src/cli_council/backends/base.py +81 -0
  119. package/packages/cli-council/src/cli_council/backends/claude.py +25 -0
  120. package/packages/cli-council/src/cli_council/backends/codex.py +27 -0
  121. package/packages/cli-council/src/cli_council/backends/gemini.py +26 -0
  122. package/packages/cli-council/src/cli_council/checkpoint.py +212 -0
  123. package/packages/cli-council/src/cli_council/config.py +51 -0
  124. package/packages/cli-council/src/cli_council/council.py +391 -0
  125. package/packages/cli-council/src/cli_council/models.py +46 -0
  126. package/packages/llm-council/.github/workflows/claude-code-review.yml +44 -0
  127. package/packages/llm-council/.github/workflows/claude.yml +50 -0
  128. package/packages/llm-council/README.md +453 -0
  129. package/packages/llm-council/pyproject.toml +42 -0
  130. package/packages/llm-council/src/llm_council/__init__.py +23 -0
  131. package/packages/llm-council/src/llm_council/__main__.py +259 -0
  132. package/packages/llm-council/src/llm_council/checkpoint.py +193 -0
  133. package/packages/llm-council/src/llm_council/client.py +253 -0
  134. package/packages/llm-council/src/llm_council/config.py +232 -0
  135. package/packages/llm-council/src/llm_council/council.py +482 -0
  136. package/packages/llm-council/src/llm_council/models.py +46 -0
  137. package/packages/mcp-bibliography/MEMORY.md +31 -0
  138. package/packages/mcp-bibliography/_app.py +226 -0
  139. package/packages/mcp-bibliography/formatters.py +158 -0
  140. package/packages/mcp-bibliography/log/2026-03-13-2100.md +35 -0
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  152. package/packages/mcp-bibliography/tools/openreview.py +179 -0
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+ # NeurIPS/ICML Introduction Example
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+
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+ This example demonstrates the distinctive ML conference introduction structure with numbered contributions and technical precision.
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+
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+ ---
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+
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+ ## Full Introduction Example
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+
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+ **Paper Topic**: Efficient Long-Context Transformers
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+
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+ ---
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+
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+ ### Paragraph 1: Problem Motivation
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+
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+ ```
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+ Large language models (LLMs) have demonstrated remarkable capabilities in
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+ natural language understanding, code generation, and reasoning tasks [1, 2, 3].
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+ These capabilities scale with both model size and context length—longer
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+ contexts enable processing of entire documents, multi-turn conversations,
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+ and complex reasoning chains that span many steps [4, 5]. However, the
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+ standard Transformer attention mechanism [6] has O(N²) time and memory
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+ complexity with respect to sequence length N, creating a fundamental
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+ bottleneck for processing long sequences. For a context window of 100K
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+ tokens, computing full attention requires 10 billion scalar operations
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+ and 40 GB of memory for the attention matrix alone, making training and
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+ inference prohibitively expensive on current hardware.
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+ ```
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+
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+ **Key features**:
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+ - States why this matters (LLM capabilities)
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+ - Connects to scaling (longer contexts = better performance)
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+ - Specific numbers (O(N²), 100K tokens, 10 billion ops, 40 GB)
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+ - Citations to establish credibility
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+
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+ ---
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+
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+ ### Paragraph 2: Limitations of Existing Approaches
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+
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+ ```
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+ Prior work has addressed attention efficiency through three main approaches.
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+ Sparse attention patterns [7, 8, 9] reduce complexity to O(N√N) or O(N log N)
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+ by restricting attention to local windows, fixed stride patterns, or learned
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+ sparse masks. Linear attention approximations [10, 11, 12] reformulate
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+ attention using kernel feature maps that enable O(N) computation, but
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+ sacrifice the ability to model arbitrary pairwise interactions. Low-rank
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+ factorizations [13, 14] approximate the attention matrix as a product of
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+ smaller matrices, achieving efficiency at the cost of expressivity. While
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+ these methods reduce theoretical complexity, they introduce approximation
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+ errors that compound in deep networks, often resulting in 2-5% accuracy
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+ degradation on long-range modeling benchmarks [15]. Perhaps more importantly,
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+ they fundamentally change the attention mechanism, making it difficult to
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+ apply advances in standard attention (e.g., rotary positional embeddings,
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+ grouped-query attention) to efficient variants.
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+ ```
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+
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+ **Key features**:
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+ - Organized categorization of prior work
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+ - Complexity stated for each approach
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+ - Limitations clearly identified
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+ - Quantified shortcomings (2-5% degradation)
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+ - Deeper issue identified (incompatibility with advances)
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+
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+ ---
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+
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+ ### Paragraph 3: Your Approach (High-Level)
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+
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+ ```
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+ We take a different approach: rather than approximating attention, we
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+ accelerate exact attention by optimizing memory access patterns. Our key
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+ observation is that on modern GPUs, attention is bottlenecked by memory
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+ bandwidth, not compute. Reading and writing the N × N attention matrix to
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+ and from GPU high-bandwidth memory (HBM) dominates runtime, while the GPU's
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+ tensor cores remain underutilized. We propose LongFlash, an IO-aware exact
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+ attention algorithm that computes attention block-by-block in fast on-chip
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+ SRAM, never materializing the full attention matrix in HBM. By carefully
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+ orchestrating the tiling pattern and fusing the softmax computation with
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+ matrix multiplications, LongFlash reduces HBM accesses from O(N²) to
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+ O(N²d/M) where d is the head dimension and M is the SRAM size, achieving
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+ asymptotically optimal IO complexity.
80
+ ```
81
+
82
+ **Key features**:
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+ - 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)
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+
93
+ ```
94
+ Our contributions are as follows:
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+
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).
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+
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).
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+
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).
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+
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
+ ```
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+
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+ **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
+