@saibolla/ada 0.1.2

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Files changed (1432) hide show
  1. package/.ada/SYSTEM.md +81 -0
  2. package/.ada/agents/researcher.md +69 -0
  3. package/.ada/agents/reviewer.md +92 -0
  4. package/.ada/agents/verifier.md +45 -0
  5. package/.ada/agents/writer.md +54 -0
  6. package/.ada/settings.json +32 -0
  7. package/.ada/themes/ada.json +85 -0
  8. package/.env.example +31 -0
  9. package/AGENTS.md +79 -0
  10. package/LICENSE +191 -0
  11. package/README.md +188 -0
  12. package/bin/ada.js +26 -0
  13. package/dist/bootstrap/sync.js +143 -0
  14. package/dist/cli.js +404 -0
  15. package/dist/config/paths.js +32 -0
  16. package/dist/index.js +10 -0
  17. package/dist/model/catalog.js +255 -0
  18. package/dist/model/commands.js +180 -0
  19. package/dist/pi/launch.js +33 -0
  20. package/dist/pi/package-presets.js +55 -0
  21. package/dist/pi/runtime.js +81 -0
  22. package/dist/pi/settings.js +108 -0
  23. package/dist/pi/web-access.js +74 -0
  24. package/dist/search/commands.js +12 -0
  25. package/dist/setup/doctor.js +126 -0
  26. package/dist/setup/preview.js +117 -0
  27. package/dist/setup/prompts.js +34 -0
  28. package/dist/setup/setup.js +98 -0
  29. package/dist/setup/update.js +133 -0
  30. package/dist/system/executables.js +38 -0
  31. package/dist/system/node-version.js +31 -0
  32. package/dist/system/open-url.js +35 -0
  33. package/dist/system/promise-polyfill.js +12 -0
  34. package/dist/ui/terminal.js +64 -0
  35. package/dist/web/launch.js +48 -0
  36. package/dist/web-search.js +1 -0
  37. package/extensions/docparser/constants.ts +62 -0
  38. package/extensions/docparser/deps.ts +584 -0
  39. package/extensions/docparser/doctor.ts +353 -0
  40. package/extensions/docparser/index.ts +9 -0
  41. package/extensions/docparser/input.ts +230 -0
  42. package/extensions/docparser/request.ts +67 -0
  43. package/extensions/docparser/schema.ts +82 -0
  44. package/extensions/docparser/tool.ts +305 -0
  45. package/extensions/docparser/types.ts +99 -0
  46. package/extensions/research-tools/alpha.ts +107 -0
  47. package/extensions/research-tools/header.ts +284 -0
  48. package/extensions/research-tools/help.ts +93 -0
  49. package/extensions/research-tools/project-scaffold.ts +64 -0
  50. package/extensions/research-tools/project.ts +123 -0
  51. package/extensions/research-tools/shared.ts +16 -0
  52. package/extensions/research-tools.ts +42 -0
  53. package/logo.d.mts +3 -0
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  55. package/metadata/commands.d.mts +46 -0
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  63. package/prompts/jobs.md +16 -0
  64. package/prompts/litreview.md +18 -0
  65. package/prompts/log.md +14 -0
  66. package/prompts/replicate.md +24 -0
  67. package/prompts/review.md +18 -0
  68. package/prompts/watch.md +16 -0
  69. package/scripts/build-native-bundle.mjs +349 -0
  70. package/scripts/check-node-version.mjs +35 -0
  71. package/scripts/patch-embedded-pi.mjs +588 -0
  72. package/scripts/prepare-runtime-workspace.mjs +162 -0
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+ # Reviewer Expectations by Venue
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+
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+ Understanding what reviewers look for at different venues is essential for crafting successful submissions. This guide covers evaluation criteria, common rejection reasons, and how to address reviewer concerns.
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+
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+ **Last Updated**: 2024
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+
7
+ ---
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+
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+ ## Overview
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+
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+ Reviewers at different venues prioritize different aspects. Understanding these priorities helps you:
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+ 1. Frame your contribution appropriately
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+ 2. Anticipate likely criticisms
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+ 3. Prepare effective rebuttals
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+ 4. Decide where to submit
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+
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+ ---
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+
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+ ## High-Impact Journals (Nature, Science, Cell)
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+
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+ ### What Reviewers Look For
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+
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+ | Priority | Weight | Description |
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+ |----------|--------|-------------|
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+ | **Broad significance** | Critical | Impact beyond the specific subfield |
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+ | **Novelty** | Critical | First to show this or major advance |
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+ | **Technical rigor** | High | Sound methodology, appropriate controls |
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+ | **Clarity** | High | Accessible to non-specialists |
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+ | **Completeness** | Moderate | Thorough but not exhaustive |
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+
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+ ### Review Process
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+
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+ 1. **Editorial triage**: Most papers rejected without review (Nature: ~92%)
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+ 2. **Expert review**: 2-4 reviewers if sent out
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+ 3. **Cross-discipline reviewer**: Often includes non-specialist
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+ 4. **Quick turnaround**: First decision typically 2-4 weeks
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+
38
+ ### What Gets a Paper Rejected
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+
40
+ **At Editorial Stage**:
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+ - Findings not significant enough for broad audience
42
+ - Incremental advance over prior work
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+ - Too specialized for the journal
44
+ - Topic doesn't fit current editorial interests
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+
46
+ **At Review Stage**:
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+ - Claims not supported by data
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+ - Missing critical controls
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+ - Alternative interpretations not addressed
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+ - Statistical concerns
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+ - Prior work not adequately acknowledged
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+ - Writing inaccessible to non-specialists
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+
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+ ### How to Address Nature/Science Reviewers
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+
56
+ **In the paper**:
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+ - Lead with significance in the first paragraph
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+ - Explain why findings matter broadly
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+ - Include controls for all major claims
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+ - Use clear, accessible language
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+ - Include conceptual figures
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+
63
+ **In rebuttal**:
64
+ - Address every point (even minor ones)
65
+ - Provide new data when requested
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+ - Acknowledge valid criticisms gracefully
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+ - Explain significance if questioned
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+
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+ ### Sample Reviewer Concerns and Responses
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+
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+ **Reviewer**: "The significance of this work is unclear to a general audience."
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+
73
+ **Response**: "We have revised the introduction to clarify the broader significance. As now stated in paragraph 1, our findings have implications for [X] because [Y]. We have also added a discussion of how these results inform understanding of [Z] (p. 8, lines 15-28)."
74
+
75
+ ---
76
+
77
+ ## Medical Journals (NEJM, Lancet, JAMA)
78
+
79
+ ### What Reviewers Look For
80
+
81
+ | Priority | Weight | Description |
82
+ |----------|--------|-------------|
83
+ | **Clinical relevance** | Critical | Will this change practice? |
84
+ | **Methodological rigor** | Critical | CONSORT/STROBE compliance |
85
+ | **Patient outcomes** | Critical | Focus on what matters to patients |
86
+ | **Statistical validity** | High | Appropriate analysis, power |
87
+ | **Generalizability** | High | Applicability to broader populations |
88
+
89
+ ### Review Process
90
+
91
+ 1. **Statistical review**: Dedicated statistical reviewer common
92
+ 2. **Clinical expertise**: Subspecialty experts
93
+ 3. **Methodological review**: Focus on study design
94
+ 4. **Multiple rounds**: Revisions often requested
95
+
96
+ ### What Gets a Paper Rejected
97
+
98
+ **Major Issues**:
99
+ - Underpowered study
100
+ - Inappropriate control/comparator
101
+ - Confounding not addressed
102
+ - Selective outcome reporting
103
+ - Missing safety data
104
+ - Claims exceed evidence
105
+
106
+ **Moderate Issues**:
107
+ - Unclear generalizability
108
+ - Missing subgroup analyses
109
+ - Incomplete CONSORT/STROBE reporting
110
+ - Statistical methods not described adequately
111
+
112
+ ### Sample Reviewer Concerns and Responses
113
+
114
+ **Reviewer**: "The study appears underpowered for the primary outcome. With 200 participants and an event rate of 5%, there is insufficient power to detect a clinically meaningful difference."
115
+
116
+ **Response**: "We appreciate this concern. Our power calculation (Methods, p. 5) was based on a 5% event rate in the control arm and a 50% relative reduction (to 2.5%). While the observed event rate (4.8%) was close to projected, we acknowledge the confidence interval is wide (HR 0.65, 95% CI 0.38-1.12). We have added this as a limitation (Discussion, p. 12). Importantly, the direction and magnitude of effect are consistent with the larger XYZ trial (n=5000), suggesting our findings merit confirmation in a larger study."
117
+
118
+ ---
119
+
120
+ ## Cell Press Journals
121
+
122
+ ### What Reviewers Look For
123
+
124
+ | Priority | Weight | Description |
125
+ |----------|--------|-------------|
126
+ | **Mechanistic insight** | Critical | How does this work? |
127
+ | **Depth of investigation** | Critical | Multiple approaches, comprehensive |
128
+ | **Biological significance** | High | Importance for the field |
129
+ | **Technical rigor** | High | Quantification, statistics, replication |
130
+ | **Novelty** | Moderate-High | New findings, not just confirmation |
131
+
132
+ ### Review Process
133
+
134
+ 1. **Extended review**: 3+ reviewers typical
135
+ 2. **Revision cycles**: Multiple rounds common
136
+ 3. **Comprehensive revision**: Major new experiments often requested
137
+ 4. **Detailed assessment**: Figure-by-figure evaluation
138
+
139
+ ### What Reviewers Expect
140
+
141
+ - **Multiple complementary approaches**: Same finding shown different ways
142
+ - **In vivo validation**: For cell biology claims
143
+ - **Rescue experiments**: For knockdown/knockout studies
144
+ - **Quantification**: Not just representative images
145
+ - **Complete figure panels**: All conditions, all controls
146
+
147
+ ### Sample Reviewer Concerns and Responses
148
+
149
+ **Reviewer**: "The authors show that protein X is required for process Y using siRNA knockdown. However, a single RNAi reagent is used, and off-target effects cannot be excluded. Additional evidence is needed."
150
+
151
+ **Response**: "We agree that additional validation is important. In the revised manuscript, we now show: (1) two independent siRNAs against protein X produce identical phenotypes (new Fig. S3A-B); (2) CRISPR-Cas9 knockout cells recapitulate the phenotype (new Fig. 2D-E); and (3) expression of siRNA-resistant protein X rescues the phenotype (new Fig. 2F-G). These complementary approaches strongly support the conclusion that protein X is required for process Y."
152
+
153
+ ---
154
+
155
+ ## ML Conferences (NeurIPS, ICML, ICLR)
156
+
157
+ ### What Reviewers Look For
158
+
159
+ | Priority | Weight | Description |
160
+ |----------|--------|-------------|
161
+ | **Novelty** | Critical | New method, insight, or perspective |
162
+ | **Technical soundness** | Critical | Correct implementation, fair comparisons |
163
+ | **Significance** | High | Advances the field |
164
+ | **Experimental rigor** | High | Strong baselines, proper ablations |
165
+ | **Reproducibility** | Moderate-High | Can others replicate? |
166
+ | **Clarity** | Moderate | Well-written and organized |
167
+
168
+ ### Review Process
169
+
170
+ 1. **Area Chair assignment**: Grouped by topic
171
+ 2. **3-4 reviewers**: With expertise in the area
172
+ 3. **Author rebuttal**: Opportunity to respond
173
+ 4. **Reviewer discussion**: After rebuttal
174
+ 5. **AC recommendation**: Meta-review
175
+
176
+ ### Scoring Dimensions
177
+
178
+ Typical NeurIPS/ICML scoring:
179
+
180
+ | Dimension | Score Range | What's Evaluated |
181
+ |-----------|-------------|------------------|
182
+ | **Soundness** | 1-4 | Technical correctness |
183
+ | **Contribution** | 1-4 | Significance of results |
184
+ | **Presentation** | 1-4 | Clarity and organization |
185
+ | **Overall** | 1-10 | Holistic assessment |
186
+ | **Confidence** | 1-5 | Reviewer expertise |
187
+
188
+ ### What Gets a Paper Rejected
189
+
190
+ **Critical Issues**:
191
+ - Weak baselines or unfair comparisons
192
+ - Missing ablation studies
193
+ - Results not significantly better than SOTA
194
+ - Technical errors in method or analysis
195
+ - Overclaiming without evidence
196
+
197
+ **Moderate Issues**:
198
+ - Limited novelty over prior work
199
+ - Narrow evaluation (few datasets/tasks)
200
+ - Missing reproducibility details
201
+ - Poor presentation
202
+ - Limited analysis or insights
203
+
204
+ ### Red Flags for ML Reviewers
205
+
206
+ ❌ "We compare against methods from 2018" (outdated baselines)
207
+ ❌ "Our method achieves 0.5% improvement" (marginal gain)
208
+ ❌ "We evaluate on one dataset" (limited generalization)
209
+ ❌ "Implementation details are in the supplementary" (core info missing)
210
+ ❌ "We leave ablations for future work" (incomplete evaluation)
211
+
212
+ ### Sample Reviewer Concerns and Responses
213
+
214
+ **Reviewer**: "The proposed method is only compared against Transformer and Performer. Recent works like FlashAttention and Longformer should be included."
215
+
216
+ **Response**: "Thank you for this suggestion. We have added comparisons to FlashAttention (Dao et al., 2022), Longformer (Beltagy et al., 2020), and BigBird (Zaheer et al., 2020). As shown in new Table 2, our method outperforms all baselines: FlashAttention (3.2% worse), Longformer (5.1% worse), and BigBird (4.8% worse). We also include a new analysis (Section 4.3) explaining why our approach is particularly effective for sequences > 16K tokens."
217
+
218
+ ---
219
+
220
+ ## HCI Conferences (CHI, CSCW)
221
+
222
+ ### What Reviewers Look For
223
+
224
+ | Priority | Weight | Description |
225
+ |----------|--------|-------------|
226
+ | **Contribution to HCI** | Critical | New design, insight, or method |
227
+ | **User-centered approach** | High | Focus on human needs |
228
+ | **Appropriate evaluation** | High | Matches claims and contribution |
229
+ | **Design rationale** | Moderate-High | Justified design decisions |
230
+ | **Implications** | Moderate | Guidance for future work |
231
+
232
+ ### Contribution Types
233
+
234
+ CHI explicitly categorizes contributions:
235
+
236
+ | Type | What Reviewers Expect |
237
+ |------|----------------------|
238
+ | **Empirical** | Rigorous user study, clear findings |
239
+ | **Artifact** | Novel system/tool, evaluation of use |
240
+ | **Methodological** | New research method, validation |
241
+ | **Theoretical** | Conceptual framework, intellectual contribution |
242
+ | **Survey** | Comprehensive, well-organized coverage |
243
+
244
+ ### What Gets a Paper Rejected
245
+
246
+ **Critical Issues**:
247
+ - Mismatch between claims and evaluation
248
+ - Insufficient participants for conclusions
249
+ - Missing ethical considerations (no IRB)
250
+ - Technology-focused without user insight
251
+ - Limited contribution to HCI community
252
+
253
+ **Moderate Issues**:
254
+ - Weak design rationale
255
+ - Limited generalizability
256
+ - Missing related work in HCI
257
+ - Unclear implications for practitioners
258
+
259
+ ### Sample Reviewer Concerns and Responses
260
+
261
+ **Reviewer**: "The evaluation consists of a short-term lab study with 12 participants. It's unclear how this system would perform in real-world use over time."
262
+
263
+ **Response**: "We acknowledge this limitation, which we now discuss explicitly (Section 7.2). We have added a 2-week deployment study with 8 participants from our original cohort (new Section 6.3). This longitudinal data shows sustained engagement (mean usage: 4.2 times/day) and reveals additional insights about how use patterns evolve over time. However, we agree that larger and longer deployments would strengthen ecological validity."
264
+
265
+ ---
266
+
267
+ ## NLP Conferences (ACL, EMNLP)
268
+
269
+ ### What Reviewers Look For
270
+
271
+ | Priority | Weight | Description |
272
+ |----------|--------|-------------|
273
+ | **Task performance** | High | SOTA or competitive results |
274
+ | **Analysis quality** | High | Error analysis, insights |
275
+ | **Methodology** | High | Sound approach, fair comparisons |
276
+ | **Reproducibility** | High | Full details provided |
277
+ | **Novelty** | Moderate-High | New approach or insight |
278
+
279
+ ### ACL Rolling Review (ARR)
280
+
281
+ Since 2022, ACL venues use a shared review system:
282
+ - Reviews transfer between venues
283
+ - Action editors manage papers
284
+ - Commitment to specific venue after review
285
+
286
+ ### Responsible NLP Checklist
287
+
288
+ Reviewers check for:
289
+ - Limitations section (required)
290
+ - Risks and ethical considerations
291
+ - Compute/carbon footprint
292
+ - Bias analysis (when applicable)
293
+ - Data documentation
294
+
295
+ ### Sample Reviewer Concerns and Responses
296
+
297
+ **Reviewer**: "The paper lacks analysis of failure cases. When and why does the proposed method fail?"
298
+
299
+ **Response**: "We have added Section 5.4 on error analysis. We manually examined 100 errors and categorized them into three types: (1) complex coreference chains (42%), (2) implicit references (31%), and (3) domain-specific knowledge requirements (27%). Figure 4 shows representative examples of each. This analysis reveals that our method particularly struggles with implicit references, which we discuss as a direction for future work."
300
+
301
+ ---
302
+
303
+ ## Data Mining (KDD, WWW)
304
+
305
+ ### What Reviewers Look For
306
+
307
+ | Priority | Weight | Description |
308
+ |----------|--------|-------------|
309
+ | **Scalability** | High | Handles large datasets |
310
+ | **Practical impact** | High | Real-world applicability |
311
+ | **Experimental rigor** | High | Comprehensive evaluation |
312
+ | **Technical novelty** | Moderate-High | New method or application |
313
+ | **Reproducibility** | Moderate | Code/data availability |
314
+
315
+ ### What Impresses KDD Reviewers
316
+
317
+ - Large-scale experiments (millions of samples)
318
+ - Industry deployment or A/B tests
319
+ - Efficiency comparisons (runtime, memory)
320
+ - Real datasets alongside benchmarks
321
+ - Complexity analysis (time and space)
322
+
323
+ ### Sample Reviewer Concerns and Responses
324
+
325
+ **Reviewer**: "The experiments are limited to small datasets (< 100K samples). How does the method scale to industry-scale data?"
326
+
327
+ **Response**: "We have added experiments on two large-scale datasets: (1) ogbn-papers100M (111M nodes, 1.6B edges) and (2) a proprietary e-commerce graph (500M nodes, 4B edges) provided by [company]. Table 4 (new) shows our method scales near-linearly with data size, completing in 42 minutes on ogbn-papers where baselines run out of memory. Section 5.5 (new) provides detailed scalability analysis."
328
+
329
+ ---
330
+
331
+ ## General Rebuttal Strategies
332
+
333
+ ### Do's
334
+
335
+ ✅ **Address every point**: Even minor issues
336
+ ✅ **Provide evidence**: New experiments, data, or citations
337
+ ✅ **Be specific**: Reference exact sections, lines, figures
338
+ ✅ **Acknowledge valid criticisms**: Show you understand the concern
339
+ ✅ **Be concise**: Reviewers read many rebuttals
340
+ ✅ **Stay professional**: Even for unfair reviews
341
+ ✅ **Prioritize critical issues**: Address major concerns first
342
+
343
+ ### Don'ts
344
+
345
+ ❌ **Be defensive**: Accept valid criticisms
346
+ ❌ **Argue without evidence**: Back up claims
347
+ ❌ **Ignore points**: Even ones you disagree with
348
+ ❌ **Be vague**: Be specific about changes
349
+ ❌ **Attack reviewers**: Maintain professionalism
350
+ ❌ **Promise future work**: Do the work now if possible
351
+
352
+ ### Rebuttal Template
353
+
354
+ ```
355
+ We thank the reviewers for their constructive feedback. We address
356
+ the main concerns below:
357
+
358
+ **R1/R2 Concern: [Shared concern from multiple reviewers]**
359
+
360
+ [Your response with specific actions taken and references to where
361
+ changes are made in the revised manuscript]
362
+
363
+ **R1-1: [Specific point]**
364
+
365
+ [Response with evidence]
366
+
367
+ **R2-3: [Specific point]**
368
+
369
+ [Response with evidence]
370
+
371
+ We have also made the following additional improvements:
372
+ • [Improvement 1]
373
+ • [Improvement 2]
374
+ ```
375
+
376
+ ---
377
+
378
+ ## Pre-Submission Self-Review
379
+
380
+ Before submitting, review your paper as a reviewer would:
381
+
382
+ ### All Venues
383
+ - [ ] Are claims supported by evidence?
384
+ - [ ] Are baselines appropriate and recent?
385
+ - [ ] Is the contribution clearly stated?
386
+ - [ ] Are limitations acknowledged?
387
+ - [ ] Is reproducibility information complete?
388
+
389
+ ### High-Impact Journals
390
+ - [ ] Is significance clear to a non-specialist?
391
+ - [ ] Are figures accessible and clear?
392
+ - [ ] Are controls adequate for claims?
393
+
394
+ ### Medical Journals
395
+ - [ ] Is CONSORT/STROBE compliance complete?
396
+ - [ ] Are absolute numbers reported?
397
+ - [ ] Is clinical relevance clear?
398
+
399
+ ### ML Conferences
400
+ - [ ] Are ablations comprehensive?
401
+ - [ ] Are comparisons fair?
402
+ - [ ] Is reproducibility information complete?
403
+
404
+ ### HCI Conferences
405
+ - [ ] Is the user-centered perspective clear?
406
+ - [ ] Is the evaluation appropriate for claims?
407
+ - [ ] Are design implications actionable?
408
+
409
+ ---
410
+
411
+ ## See Also
412
+
413
+ - `venue_writing_styles.md` - Writing style by venue
414
+ - `nature_science_style.md` - Nature/Science detailed guide
415
+ - `ml_conference_style.md` - ML conference detailed guide
416
+ - `medical_journal_styles.md` - Medical journal detailed guide
417
+