@researai/deepscientist 1.5.16 → 1.6.0

package/src/skills/nature-polishing/SKILL.md

@@ -0,0 +1,385 @@
+---
+name: nature-polishing
+description: Polish, restructure, or translate academic prose into Nature-leaning English using the paper-architecture and writing-strategy principles from Scientific English Writing & Communication, with phrase-level support from Academic Phrasebank. Use whenever the user asks to polish a manuscript paragraph, abstract, introduction, results, discussion, conclusion, title, methods section, or Chinese academic draft for publication-quality English.
+version: 5.0.0
+author: Yuan1z skill rebuilt from course notes plus Academic Phrasebank
+skill_role: companion
+---
+
+# Nature-Style Academic Polishing
+
+This companion skill is adapted from `Yuan1z0825/nature-skills/tree/main/nature-polishing`.
+See `UPSTREAM_LICENSE.txt` for the upstream MIT license.
+
+## DeepScientist integration
+
+- Follow the shared interaction contract injected by the system prompt.
+- Use this inside `write`, `review`, or `rebuttal` when the user asks for Nature-leaning English, Chinese-to-English manuscript polishing, section restructuring, or publication-quality academic prose.
+- Apply it after the evidence and claim boundary are clear. Do not use style polishing to hide missing support, overstate novelty, or make unsupported claims sound stronger.
+- Keep DeepScientist manuscript hygiene rules authoritative: no user/operator/agent provenance, route-control wording, prompt state, or local implementation shorthand in paper-facing prose.
+
+Use this skill to improve scientific writing at two levels:
+
+- `main strategy`: paper architecture, section logic, reader workflow, evidence thresholds, and ethics
+- `reference support`: reusable phrase families, move patterns, transitions, and style checks
+
+The main strategy should come from the course notes in `Chapter1-Week1-7`. The reference wording layer should come from `Academic Phrasebank`.
+
+## Default stance
+
+- Language serves argument. Do not polish sentences while leaving the reasoning broken.
+- Write with empathy for the reader: relevance first, then novelty, then trust, then reuse, then meaning.
+- There should be no mystery for the writer, but there may be one for the reader.
+- Do not invent data, references, mechanisms, or novelty claims.
+- Do not let AI draft the paper's core scientific argument from scratch.
+- If the draft is Chinese or structurally rough, reconstruct the logic first and the prose second.
+
+## When to open extra files
+
+These files are reference support. Use them after the section's rhetorical job is clear.
+
+| File | Open when |
+|---|---|
+| [references/section-moves.md](references/section-moves.md) | You need section-specific move orders or phrase patterns derived from Academic Phrasebank |
+| [references/phrasebank-playbook.md](references/phrasebank-playbook.md) | You need hedging, transition, evidence, limitation, or future-work phrase families |
+| [references/style-guardrails.md](references/style-guardrails.md) | You need academic-style checks, paragraph/sentence checks, article use, register, or mechanics |
+
+## Core architecture
+
+### 1. Identify the paper type first
+
+Before editing, determine what kind of paper or section this is.
+
+- `Research paper`: the reader asks why the phenomenon matters, what was done, what was found, and what it means.
+- `Methods paper`: the reader asks whether the method works, whether it is reproducible, and whether it is better under a fair comparison.
+- `Hypothesis-based work`: the argument tries to establish or rule out a causal explanation.
+- `Algorithmic or device work`: the argument proposes a procedure, tool, or system and must show that it performs reliably and advantageously.
+
+Do not use one narrative logic for all paper types.
+
+### 2. Write for the reader, not for the draft chronology
+
+Most readers follow a stable sequence:
+
+1. Is this relevant to me?
+2. What is new here?
+3. Do I trust it?
+4. Can I reuse it?
+5. What does it mean, and where are the boundaries?
+
+Polishing should help the paper answer these questions in this order.
+
+### 3. Use the hourglass structure
+
+Strong papers often mirror an hourglass:
+
+- `Introduction`: open broadly, then narrow to the specific gap, question, hypothesis, methods, and study
+- `Discussion/Conclusion`: widen again, connecting the findings back to the literature and explaining how the knowledge gap was filled
+
+If a paragraph or section violates this architecture, rebuild it before polishing wording.
+
+### 4. Use the correct writing order
+
+For a research article, a productive writing order is:
+
+1. Results
+2. Introduction and Conclusion
+3. Title
+4. Discussion
+5. Materials and Methods
+6. Authors
+7. Abstract
+
+For a methods paper, a productive writing order often begins with:
+
+1. Methods
+2. Results
+3. Introduction
+4. Conclusion
+5. Discussion
+6. Abstract
+
+The skill should follow the logic of evidence and argument, not the raw order in which the user drafted sentences.
+
+### 5. Protect the core argument
+
+The paper's core argument includes:
+
+- the scientific question the paper actually answers
+- why that question matters
+- how the work differs from existing research
+- what the results imply
+- how the main line of reasoning unfolds
+
+AI may help polish, structure, or compare phrasings. AI should not invent or author the core argument. If the argument is weak or unclear, expose that weakness rather than hiding it under polished language.
+
+### 6. Diagnose the failure mode before editing
+
+Before rewriting, identify the main problem:
+
+- wrong paper type logic
+- missing gap or poor positioning
+- claim without evidence
+- evidence without a clear claim
+- missing boundary or limitation
+- Results and Discussion mixed together
+- weak title or abstract signal
+- sentence-level clutter only
+
+Prioritize in this order:
+
+`paper type -> section job -> paragraph logic -> claim/evidence/boundary -> sentence polish`
+
+## Section responsibilities
+
+### Introduction
+
+The Introduction should:
+
+- tell the reader why the work matters
+- explain what gap it fills
+- explain why that gap matters
+- state what is already known
+- state what remains unresolved
+- state what question the paper asks
+- indicate how the study addresses it
+
+Do not summarize the Results section here. Do not summarize the Conclusion here.
+
+### Results
+
+Results are a summary of the data collected to address the problem stated in the Introduction.
+
+Results writing should:
+
+- stay mainly in past tense
+- report what was observed, under what conditions, and with what quantitative support
+- use statistics correctly and sparingly
+- use supplementary data sparingly
+
+Results should answer `what happened`, not `what it ultimately means`.
+
+### Discussion
+
+Discussion should answer:
+
+- how the work fits within the broader field
+- what has been added to understanding
+- who should be credited for earlier work
+- whether the findings support, complicate, or revise earlier results
+- how the findings are interpreted
+- when that interpretation may fail
+
+Short rule:
+
+- `Results = what we observed`
+- `Discussion = how we understand it, and when it may fail`
+
+### Conclusion
+
+Use the three-part close:
+
+1. restate the central contribution
+2. summarize the key evidence or outcome
+3. state the implication with a boundary
+
+Do not introduce new data in the conclusion. Always run an overclaim check here.
+
+### Title
+
+A strong title should:
+
+- tell the reader what to expect
+- avoid unnecessary technical language
+- be easy to search
+- be substantiated by data
+- create curiosity without sacrificing credibility
+
+Use `curiosity with credibility`, not empty cleverness. A hook is only acceptable if the claim remains fully defensible.
+
+### Materials and Methods
+
+Methods should be specific, complete, transparent, and reproducible.
+
+Another group should be able to determine:
+
+- whether the work conforms to ethical norms
+- what materials and conditions were used
+- which key parameters, controls, and replicates were used
+- how data were processed and analysed
+- which statistical tests and software versions were used
+
+It is acceptable to abbreviate by citing an earlier report only when that report truly contains the necessary detail.
+
+Never leave vague phrases such as:
+
+- `under standard conditions`
+- `using routine methods`
+- `data were analyzed statistically`
+- `differences were significant`
+- `samples were randomly assigned`
+- `the method was validated`
+
+Replace them with the actual reproducible information.
+
+### Methods-paper variant
+
+In a methods paper, the Results section must show the advantages of the method over existing methods. Typical questions are:
+
+- Is it more reliable?
+- Is it faster?
+- Does it require fewer resources?
+- Is the comparison fair and reproducible?
+
+The Methods section in a methods paper may need additional detail such as:
+
+- axioms, conditions, and assumptions
+- hardware and software environment
+- mathematical derivations
+- evaluation protocol
+- datasets, baselines, metrics, splits, and hyperparameters
+
+### Abstract
+
+The abstract is a mini-paper:
+
+`context/problem -> gap/objective -> approach -> key results -> implication`
+
+It should answer:
+
+1. What question was addressed?
+2. How was it addressed?
+3. What was found?
+4. Why should anyone care?
+
+Some journals require a strict abstract format. Follow the journal if it conflicts with the generic pattern.
+
+## Sentence and paragraph control
+
+### Sentence rules
+
+- Keep every sentence at `<= 30` words.
+- If any sentence exceeds `20` words, check whether it contains more than one main proposition.
+- Split overloaded sentences rather than polishing them cosmetically.
+- The last sentence of a paragraph often becomes the longest and weakest. Check it explicitly.
+- Prefer one core subject-verb proposition per sentence.
+
+### Paragraph rules
+
+- Each paragraph should have one controlling idea followed by support.
+- Supporting material may include data, comparison, explanation, consequence, literature, or limitation.
+- If a new idea appears, start a new paragraph instead of stacking it onto the old one.
+- Use thematic linking, not repetitive `This suggests ...` openings.
+
+### Results vs Discussion sentence types
+
+Results sentences usually report:
+
+- `was detected`
+- `increased`
+- `showed`
+- `enabled`
+- `achieved`
+
+Discussion sentences usually interpret:
+
+- `may reflect`
+- `suggests that`
+- `could indicate`
+- `is likely due to`
+- `may facilitate`
+
+Do not let a Results paragraph drift into Discussion syntax unless the transition is intentional.
+
+### Chinese-to-English mode
+
+When the source is Chinese or strongly Chinese-influenced English:
+
+- extract the core propositions first
+- do not translate clause-by-clause mechanically
+- reconstruct explicit logical links: contrast, cause, implication, limitation
+- verify terminology, causality, hedging, and disciplinary nuance
+- keep key technical terms stable
+
+## Citation, ethics, and AI boundaries
+
+### Intellectual debt
+
+Originality is usually an amendment, combination, or extension of prior knowledge. A careful writer acknowledges that debt openly.
+
+Do not minimize others' contributions just to make the present work seem more original.
+
+### Position attribution clearly
+
+Make it obvious:
+
+- how the paper builds on prior work
+- who was responsible for the earlier idea, method, data, or interpretation
+- where the reader can locate the source
+
+### Cite the source you actually read and verified
+
+- Cite paper `A` for `A`'s own data, methods, claims, or conclusions.
+- Cite paper `B` for `B`'s interpretation, comparison, critique, or commentary on `A`.
+- Avoid leaning on secondary sources when the source article can be cited directly.
+
+### What needs citation
+
+- someone else's ideas
+- data
+- methods
+- wording
+- structure
+- images
+- distinctive interpretation
+
+Do not assume internet material is public domain just because it is online.
+
+### Proofreading checks
+
+Always verify:
+
+- grammatical errors
+- typographical errors
+- figure numbering
+- missing citations
+- whether the paper is a pleasure or an ordeal to read
+
+### AI traffic-light boundary
+
+`Green`: generally acceptable with author verification
+
+- improve grammar, clarity, concision, or tone
+- generate outline options or paragraph structures
+- produce alternative titles or abstract phrasings
+- summarize literature for categorization, not as a substitute for reading
+- translate with terminology and hedging checks
+
+`Yellow`: allowed only with strong human control
+
+- explain methods or results for wording support
+- draft reviewer-response frameworks that are then checked line by line
+- help with code or statistics explanations only if outputs are reproduced and validated
+
+`Red`: generally inappropriate
+
+- ask AI to draft the paper's core argument from scratch
+- insert AI-generated references, data, or claims without checking them
+- upload unpublished manuscripts, sensitive data, or peer-review material to public models
+- use AI to fabricate, manipulate, or conceal substantive image creation
+
+The main danger is not that AI cannot write. The main danger is that it can write incorrectly with great confidence.
+
+## Output format
+
+Default output:
+
+1. The polished text as plain prose, not in a code block.
+2. `Revision notes:` with `3-5` short bullets on the major structural and stylistic changes.
+3. If the rewrite changed section logic, say so explicitly.
+
+If the user asks for side-by-side revision, provide:
+
+- `Original`
+- `Polished`
+- `Why changed`

package/src/skills/nature-polishing/UPSTREAM_LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Yuan Yizhe
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/src/skills/nature-polishing/agents/openai.yaml

@@ -0,0 +1,4 @@
+interface:
+  display_name: "Nature Polishing"
+  short_description: "Polish academic prose into Nature-leaning English"
+  default_prompt: "Use $nature-polishing to polish this manuscript section into Nature-leaning academic English without overstating the evidence."

package/src/skills/nature-polishing/references/phrasebank-playbook.md

@@ -0,0 +1,162 @@
+# Phrasebank Playbook
+
+Use this file after the main argument and section role are already clear. It is a phrasebank layer derived from `Academic Phrasebank`, not a substitute for deciding what the paragraph is trying to do.
+
+## Evidence strength
+
+Choose verbs that match the evidence.
+
+### Strong
+
+- `show`
+- `demonstrate`
+- `establish`
+- `reveal`
+- `identify`
+
+Use only when the design and data justify a strong claim.
+
+### Moderate
+
+- `suggest`
+- `indicate`
+- `support the view that`
+- `are consistent with`
+- `point to`
+
+Use when the interpretation is plausible but not definitive.
+
+### Speculative
+
+- `may reflect`
+- `could arise from`
+- `appears to`
+- `seems likely`
+- `might be explained by`
+
+Use when moving beyond direct observation.
+
+## Evidence collocations
+
+Adjectives for evidence:
+
+- weak: `limited`, `scant`, `insufficient`
+- developing: `growing`, `emerging`, `accumulating`
+- strong: `robust`, `reliable`, `convincing`, `considerable`
+
+Useful patterns:
+
+- `The evidence presented here suggests that ...`
+- `The available evidence supports the view that ...`
+- `Current evidence raises important questions about ...`
+- `The data point to a need for ...`
+
+## Transition families
+
+### Contrast
+
+- `however`
+- `by contrast`
+- `nevertheless`
+- `despite this`
+- `whereas`
+
+### Addition
+
+- `furthermore`
+- `in addition`
+- `moreover`
+- `also`
+
+### Consequence
+
+- `therefore`
+- `thus`
+- `consequently`
+- `as a result`
+- `thereby`
+
+### Qualification
+
+- `notably`
+- `importantly`
+- `approximately`
+- `in part`
+- `at least in this cohort`
+
+Prefer the smallest connective that does the job. Do not decorate every sentence with a transition word.
+
+## Paragraph linking without sounding repetitive
+
+Prefer these patterns over repeated `This suggests`:
+
+- restate the noun: `Such heterogeneity ...`
+- definite noun phrase: `The resulting gradient ...`
+- participial summary: `Taken together, ...`
+- zero-connective progression when the logic is already obvious
+
+Limit demonstrative-led openings. One per paragraph is usually enough.
+
+## Gap language
+
+Use gap statements that are precise rather than dramatic:
+
+- `remains poorly understood`
+- `has not been examined in ...`
+- `has received limited attention`
+- `few studies have addressed ...`
+- `evidence remains sparse for ...`
+
+Avoid:
+
+- `no one has ever studied`
+- `completely unknown`
+- `ignored by all previous work`
+
+## Comparison with prior work
+
+To align with earlier work:
+
+- `These results are consistent with ...`
+- `This finding accords with ...`
+- `Our observations broadly support ...`
+
+To mark divergence fairly:
+
+- `In contrast to earlier reports, ...`
+- `This finding differs from ...`
+- `One possible reason for this discrepancy is ...`
+
+## Limitation language
+
+Useful patterns:
+
+- `These findings should be interpreted with caution because ...`
+- `A limitation of this study is that ...`
+- `The generalisability of these results is limited by ...`
+- `We cannot exclude the possibility that ...`
+- `Another source of uncertainty is ...`
+
+Pair limitation language with the actual source of uncertainty, not with vague modesty.
+
+## Implication language
+
+Useful patterns:
+
+- `An implication of this is that ...`
+- `These findings may help to explain ...`
+- `These data support further investigation of ...`
+- `This work has implications for ...`
+
+Implications should stay within the evidence boundary.
+
+## Future-work language
+
+Useful patterns:
+
+- `Further work is needed to determine whether ...`
+- `Future studies should examine ...`
+- `A useful next step would be to ...`
+- `Larger studies are required to validate ...`
+
+Future work should emerge from an actual limitation, uncertainty, or opportunity.