psyclaw 0.28.1 → 0.28.3
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.
- package/README.md +5 -5
- package/agents/recommended/catalog.json +1 -1
- package/dist/src/adapters/pi/extension.js +79 -25
- package/dist/src/adapters/pi/extension.js.map +1 -1
- package/dist/src/ars/keybindings.d.ts +13 -0
- package/dist/src/ars/keybindings.js +50 -0
- package/dist/src/ars/keybindings.js.map +1 -0
- package/dist/src/ars/mode-editor.d.ts +25 -0
- package/dist/src/ars/mode-editor.js +78 -0
- package/dist/src/ars/mode-editor.js.map +1 -0
- package/dist/src/ars/profile.d.ts +4 -1
- package/dist/src/ars/profile.js +23 -6
- package/dist/src/ars/profile.js.map +1 -1
- package/dist/src/chat.js +3 -0
- package/dist/src/chat.js.map +1 -1
- package/dist/src/panel/server.js +1 -1
- package/dist/src/panel/server.js.map +1 -1
- package/package.json +10 -3
- package/vendor/academic-paper-skills/LICENSE +21 -0
- package/vendor/academic-paper-skills/NOTICE.md +7 -0
- package/vendor/academic-paper-skills/PSYCLAW_SOURCE.json +14 -0
- package/vendor/academic-paper-skills/academic-paper-composer/SKILL.md +840 -0
- package/vendor/academic-paper-skills/academic-paper-composer/references/section_guides.md +675 -0
- package/vendor/academic-paper-skills/academic-paper-composer/references/writing_standards.md +629 -0
- package/vendor/academic-paper-skills/academic-paper-composer/scripts/chapter_quality_check.py +470 -0
- package/vendor/academic-paper-skills/academic-paper-composer/scripts/final_evaluation.py +550 -0
- package/vendor/academic-paper-skills/academic-paper-strategist/SKILL.md +670 -0
- package/vendor/academic-paper-skills/academic-paper-strategist/references/quality_standards.md +336 -0
- package/vendor/academic-paper-skills/academic-paper-strategist/references/search_strategy.md +459 -0
- package/vendor/academic-paper-skills/academic-paper-strategist/scripts/evaluate_samples.py +300 -0
- package/vendor/academic-paper-skills/academic-paper-strategist/scripts/gap_analysis.py +399 -0
- package/vendor/ars/pi/wrapper.js +9 -0
- package/vendor/nature-skills/LICENSE +201 -0
- package/vendor/nature-skills/NOTICE.md +7 -0
- package/vendor/nature-skills/PSYCLAW_SOURCE.json +19 -0
- package/vendor/nature-skills/skills/nature-figure/README.md +107 -0
- package/vendor/nature-skills/skills/nature-figure/README_EN.md +107 -0
- package/vendor/nature-skills/skills/nature-figure/SKILL.md +154 -0
- package/vendor/nature-skills/skills/nature-figure/agents/openai.yaml +4 -0
- package/vendor/nature-skills/skills/nature-figure/evals/evals.json +325 -0
- package/vendor/nature-skills/skills/nature-figure/manifest.yaml +103 -0
- package/vendor/nature-skills/skills/nature-figure/references/ai-graphical-abstract-workflow.md +129 -0
- package/vendor/nature-skills/skills/nature-figure/references/api.md +576 -0
- package/vendor/nature-skills/skills/nature-figure/references/asset-adaptation.md +72 -0
- package/vendor/nature-skills/skills/nature-figure/references/backend-selection.md +118 -0
- package/vendor/nature-skills/skills/nature-figure/references/chart-types.md +348 -0
- package/vendor/nature-skills/skills/nature-figure/references/common-patterns.md +371 -0
- package/vendor/nature-skills/skills/nature-figure/references/demos.md +58 -0
- package/vendor/nature-skills/skills/nature-figure/references/design-theory.md +467 -0
- package/vendor/nature-skills/skills/nature-figure/references/figure-contract.md +122 -0
- package/vendor/nature-skills/skills/nature-figure/references/figure-legend-conventions.md +90 -0
- package/vendor/nature-skills/skills/nature-figure/references/multipanel-evidence-architecture.md +268 -0
- package/vendor/nature-skills/skills/nature-figure/references/nature-2026-observations.md +124 -0
- package/vendor/nature-skills/skills/nature-figure/references/nature-article-requirements.md +149 -0
- package/vendor/nature-skills/skills/nature-figure/references/openrouter-image-generation.md +141 -0
- package/vendor/nature-skills/skills/nature-figure/references/qa-contract.md +344 -0
- package/vendor/nature-skills/skills/nature-figure/references/r-template-index.md +66 -0
- package/vendor/nature-skills/skills/nature-figure/references/r-workflow.md +234 -0
- package/vendor/nature-skills/skills/nature-figure/references/template-catalog.md +33 -0
- package/vendor/nature-skills/skills/nature-figure/references/tutorials.md +260 -0
- package/vendor/nature-skills/skills/nature-figure/requirements.txt +1 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/audit_figure_collisions.py +742 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/audit_panel_alignment.py +933 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/audit_pdf_text.py +152 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/figure_safety.py +50 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/generate_openrouter_schematic.py +260 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/nature_figure_backend.py +93 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/panel_alignment.R +188 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/plot_templates.py +604 -0
- package/vendor/nature-skills/skills/nature-figure/scripts/validate_figure.py +835 -0
- package/vendor/nature-skills/skills/nature-figure/static/core/contract.md +55 -0
- package/vendor/nature-skills/skills/nature-figure/static/core/stance.md +41 -0
- package/vendor/nature-skills/skills/nature-figure/static/fragments/backend/python.md +56 -0
- package/vendor/nature-skills/skills/nature-figure/static/fragments/backend/r.md +63 -0
- package/vendor/nature-skills/skills/nature-figure/tests/test_figure_safety.py +209 -0
- package/vendor/nature-skills/skills/nature-polishing/README.md +58 -0
- package/vendor/nature-skills/skills/nature-polishing/README_EN.md +58 -0
- package/vendor/nature-skills/skills/nature-polishing/SKILL.md +111 -0
- package/vendor/nature-skills/skills/nature-polishing/agents/openai.yaml +4 -0
- package/vendor/nature-skills/skills/nature-polishing/manifest.yaml +101 -0
- package/vendor/nature-skills/skills/nature-polishing/references/latex-layout.md +211 -0
- package/vendor/nature-skills/skills/nature-polishing/references/nat-comms-2025-diction.md +73 -0
- package/vendor/nature-skills/skills/nature-polishing/references/phrasebank-playbook.md +175 -0
- package/vendor/nature-skills/skills/nature-polishing/references/published-article-patterns.md +126 -0
- package/vendor/nature-skills/skills/nature-polishing/references/section-moves.md +252 -0
- package/vendor/nature-skills/skills/nature-polishing/references/style-guardrails.md +94 -0
- package/vendor/nature-skills/skills/nature-polishing/references/writing-strategy.md +160 -0
- package/vendor/nature-skills/skills/nature-polishing/static/core/failure-modes.md +29 -0
- package/vendor/nature-skills/skills/nature-polishing/static/core/output-format.md +21 -0
- package/vendor/nature-skills/skills/nature-polishing/static/core/stance.md +26 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/generic.md +17 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-comms.md +38 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-mach-intell.md +102 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nature.md +19 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/en.md +19 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/zh-to-en.md +19 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/algorithmic.md +18 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/hypothesis.md +17 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/methods.md +35 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/research.md +29 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/review.md +17 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/abstract.md +26 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/conclusion.md +15 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/discussion.md +48 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/intro.md +33 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/methods.md +26 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/results.md +61 -0
- package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/title.md +17 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/README.md +44 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/README_EN.md +44 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/SKILL.md +196 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/agents/openai.yaml +4 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/manifest.yaml +19 -0
- package/vendor/nature-skills/skills/nature-ref-verifier/references/common-patterns.md +96 -0
- package/vendor/nature-skills/skills/nature-shared/README.md +43 -0
- package/vendor/nature-skills/skills/nature-shared/README_EN.md +43 -0
- package/vendor/nature-skills/skills/nature-shared/SKILL.md +33 -0
- package/vendor/nature-skills/skills/nature-shared/agents/openai.yaml +6 -0
- package/vendor/nature-skills/skills/nature-shared/core/consistency-sweep.md +122 -0
- package/vendor/nature-skills/skills/nature-shared/core/discussion-argument-language.md +192 -0
- package/vendor/nature-skills/skills/nature-shared/core/ethics.md +88 -0
- package/vendor/nature-skills/skills/nature-shared/core/main-text-discipline.md +179 -0
- package/vendor/nature-skills/skills/nature-shared/core/nature-abstract.md +171 -0
- package/vendor/nature-skills/skills/nature-shared/core/nature-introduction.md +164 -0
- package/vendor/nature-skills/skills/nature-shared/core/nature-results-discussion.md +215 -0
- package/vendor/nature-skills/skills/nature-shared/core/paper-type-taxonomy.md +41 -0
- package/vendor/nature-skills/skills/nature-shared/core/reader-workflow.md +21 -0
- package/vendor/nature-skills/skills/nature-shared/core/research-compliance.md +192 -0
- package/vendor/nature-skills/skills/nature-shared/core/terminology-ledger.md +58 -0
- package/vendor/nature-skills/skills/nature-shared/journal-formats/nat-comms.md +139 -0
- package/vendor/nature-skills/skills/nature-shared/journal-formats/nature-machine-intelligence.md +431 -0
- package/vendor/nature-skills/skills/nature-shared/journal-formats/nature.md +313 -0
- package/vendor/nature-skills/skills/nature-shared/manifest.yaml +52 -0
- package/vendor/nature-skills/skills/nature-shared/scripts/check_consistency.py +273 -0
- package/vendor/nature-skills/skills/nature-shared/tests/test_check_consistency.py +63 -0
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# Nature Abstract Corpus Guidance
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Use this reference when drafting, restructuring, or polishing an abstract for
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flagship **Nature**, **Nature Communications**, **Nature Machine Intelligence**,
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or another **Nature Portfolio** title. The patterns were initially distilled
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from an author-supplied reading set of published NMI papers and are generalized
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here as Nature-style defaults. They are **corpus-derived writing guidance, not
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official journal requirements**. Current target-journal instructions,
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article-type rules, reporting standards, and the paper's actual evidence always
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take precedence.
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## Contents
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- [Treat the abstract as the shortest evidence chain](#treat-the-abstract-as-the-shortest-evidence-chain)
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- [Use a discovery-centred architecture](#use-a-discovery-centred-architecture)
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- [Make the gap sharp and brief](#make-the-gap-sharp-and-brief)
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- [Keep only answer-enabling method logic](#keep-only-answer-enabling-method-logic)
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- [Select one main claim](#select-one-main-claim)
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- [Use numbers by necessity](#use-numbers-by-necessity)
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- [End with the conceptual payoff](#end-with-the-conceptual-payoff)
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- [Align the abstract with the manuscript](#align-the-abstract-with-the-manuscript)
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- [Run the Nature abstract audit](#run-the-nature-abstract-audit)
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## Treat the abstract as the shortest evidence chain
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Do not write the abstract as a compressed Introduction or a catalogue of
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sections. Compress the entire paper into the shortest chain that makes the
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central discovery understandable, credible, and consequential:
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`precise problem or gap -> what the study does to resolve it -> main discovery -> decisive support or boundary -> what the discovery establishes -> why it matters`
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Draft the abstract after the Introduction question, Results evidence chain,
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and Discussion synthesis are stable. The abstract should reveal the paper's
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argument, not the chronology of the research process.
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## Use a discovery-centred architecture
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Use this default move order for a Nature Portfolio research article:
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1. known phenomenon or important problem
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2. precise unresolved question
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3. study design or conceptual move used to answer it
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4. main discovery
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5. one or two critical supporting findings or boundaries
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6. conceptual, technical, or field-level implication
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Move rapidly into the present study. Spend only enough background to make the
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gap intelligible. The centre of gravity must be `we found X`, not `we evaluated
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many models and datasets` or `we propose a framework`.
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This move order is rhetorical guidance, not a requirement for six sentences.
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Combine moves when needed to satisfy the current target-journal abstract limit.
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## Make the gap sharp and brief
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Use one sentence, or at most the minimum needed, to join the known phenomenon
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to the exact unknown. Prefer:
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`X is increasingly used or observed, but whether, why, or under what conditions Y remains unclear.`
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Do not spend abstract space proving that the whole field is important,
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summarizing several generations of prior work, or rehearsing the Introduction
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funnel. Avoid generic gaps such as `existing methods still face challenges`
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when the paper addresses a precise source, condition, mechanism, or boundary.
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## Keep only answer-enabling method logic
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Describe the method at the minimum level needed to understand why the design
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can answer the stated question. Include, when central:
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- the controlled factor or contrast that identifies the claim
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- the perturbation, intervention, or decomposition that tests the proposed
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source or mechanism
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- the scope needed to judge generalization
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- the theoretical property needed to understand the contribution
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Omit learning rates, hardware, routine data splits, implementation modules,
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and dataset-by-dataset detail unless one of them defines the discovery or its
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boundary. The abstract is not a Methods summary.
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## Select one main claim
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Choose one central claim and at most one or two supporting claims. Compress the
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remaining Results into evidence categories or omit them.
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Use this hierarchy:
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| Role | Abstract decision |
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| Main claim | State explicitly and give it the most space |
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| Decisive support | Keep when needed to make the main claim credible |
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| Boundary | Keep when it materially changes how the claim must be read |
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| Scope credential | Mention briefly only when breadth itself supports the inference |
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| Secondary analysis | Omit or reserve for the main text/SI |
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credibility cue, not the protagonist: use `across ... settings` only when that
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scope is necessary to understand generality or confidence.
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empirical.
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Include a number only when it performs one of these functions:
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- defines the strength or threshold of the main discovery
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- is itself the paper's principal law, prediction, or selection result
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- makes a decisive comparison interpretable
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- establishes a boundary that qualitative wording would obscure
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Omit numbers when the conceptual or mechanistic claim is the contribution and
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the number would displace the evidence logic. Comparative wording may be
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adequate when the exact effect size is not the headline claim.
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If several numbers compete for space, keep the one that most changes the
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reader's understanding of the central claim. Do not report sample counts,
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benchmarks, models, metrics, and multiple effect sizes simply because they are
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available.
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make predictable. Prefer a bounded field-level payoff over self-evaluation:
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- a mechanism or principle becomes identifiable
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- a design or architecture choice becomes predictable
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- a method becomes applicable to a previously inaccessible regime
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- two areas become conceptually connected
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- a practical decision gains a quantitative or mechanistic basis
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Do not end with `the proposed method achieves superior performance` or a broad
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promise unsupported by the tested scope.
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## Align the abstract with the manuscript
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- **Abstract:** the manuscript's shortest claim–evidence–implication chain
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- **Introduction:** why the exact question must be asked
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- **Results:** the full escalating evidence chain that answers it
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- **Discussion:** what the answers mean together
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Every abstract claim must map to visible Results evidence. The final implication
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must match the Discussion synthesis without exceeding its boundaries. Do not
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introduce a claim, mechanism, or application in the abstract that the main text
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does not establish.
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## Run the Nature abstract audit
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Build this compact map before sentence polishing:
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| Abstract move | Content | Manuscript support | Keep test |
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| Gap | Exact unresolved question | Introduction | Can it be stated in one sharp sentence? |
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| Design | Answer-enabling logic | Methods/Results | Does it explain why the question is answerable? |
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| Main discovery | One central claim | Results | Is this the paper's real advance? |
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| Support/boundary | One or two decisive findings | Results | Does each materially strengthen or bound the claim? |
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# Nature Introduction Corpus Guidance
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Use this reference when drafting, restructuring, or polishing an Introduction
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for flagship **Nature**, **Nature Communications**, **Nature Machine
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Intelligence**, or another **Nature Portfolio** title. The patterns were
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initially distilled from an author-supplied reading set of published NMI papers
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and are generalized here as Nature-style defaults. They are **corpus-derived
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writing guidance, not official journal requirements**. Current target-journal
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instructions, article-type rules, reporting standards, and the paper's actual
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evidence always take precedence.
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## Contents
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- [State an exact knowledge gap](#state-an-exact-knowledge-gap)
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- [Use literature to construct the gap](#use-literature-to-construct-the-gap)
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- [Frame a scientific question](#frame-a-scientific-question)
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- [Let the answer emerge late](#let-the-answer-emerge-late)
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- [End with a compact research route](#end-with-a-compact-research-route)
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- [Align Introduction, Results, and Discussion](#align-introduction-results-and-discussion)
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- [Run the Nature Introduction audit](#run-the-nature-introduction-audit)
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## Make the Introduction converge
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Build a narrowing argument rather than an extended topic overview:
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`important problem -> specific phenomenon or difficulty -> what existing approaches establish -> unresolved limitation or tension -> exact unknown -> research question or hypothesis -> what this study does`
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Move quickly. Assume the target journal's readers understand the broad field's
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importance; use only enough context to make the specific unresolved problem
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intelligible. By the end of the opening paragraph, expose the concrete
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phenomenon, contradiction, failure condition, or bottleneck whenever the
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material permits it.
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Delete or compress background that neither narrows the problem nor makes the
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eventual question necessary. A history of the field is not a substitute for a
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problem funnel.
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## State an exact knowledge gap
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Express the gap as something genuinely unknown, disputed, or untested. Prefer:
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- what causes an observed advantage or failure
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- under what conditions a claimed benefit appears or disappears
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- which mechanism, information source, or design choice is necessary
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- why two credible bodies of evidence disagree
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- whether a proposed representation or signal adds information beyond the
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current baseline
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Avoid `existing methods have limitations` unless the next clause names the
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specific limitation and why resolving it matters. The reader should be able to
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complete the sentence:
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> It remains unclear whether, why, or under what conditions ______.
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Do not define the gap as the absence of the author's method. `No one has used
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our architecture for this task` is not yet a scientific unknown.
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## Use literature to construct the gap
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Organize citations by argumentative function, not as an author-by-author
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catalogue:
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1. establish the known capability, phenomenon, or prevailing explanation
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2. show what prior work has already resolved
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3. expose the unresolved condition, boundary, or contradiction
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4. make the present research question unavoidable
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When the literature contains tension, state both sides fairly and use the
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tension to motivate a discriminating question. Avoid generic transitions such
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as `substantial progress has been made, but challenges remain` when the cited
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work supports a more exact conflict or boundary.
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Every literature paragraph must earn its place by narrowing the question. Move
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material that only demonstrates breadth to Related Work, Methods context, or a
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shorter citation cluster.
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## Frame a scientific question
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Prefer a question about a phenomenon, condition, mechanism, or boundary over a
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method-demand claim:
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- weak: `Existing methods are limited; therefore, a new method is needed.`
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- stronger: `Performance improves in some settings but deteriorates in others;
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which condition determines whether the proposed mechanism is beneficial?`
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Let novelty arise from the unanswered question and the study design capable of
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answering it. Remove unsupported novelty adjectives such as `novel`,
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`groundbreaking`, `unprecedented`, or `innovative` when the question,
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controlled comparison, or diagnostic perturbation already demonstrates the
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advance.
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## Let the answer emerge late
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Do not force the paper's preferred concept, mechanism, or framework into the
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opening before the problem logic has motivated it. First establish the
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phenomenon, limitation, and exact unknown; then introduce the study's conceptual
|
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move as the natural way to resolve that unknown.
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Use transitions such as `To address this question`, `To test this possibility`,
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or `To this end` only after the question is explicit. Do not use the transition
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to conceal a missing gap.
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## End with a compact research route
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Prefer one connected closing paragraph over a ceremonial contribution list for
|
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a Nature Portfolio research article, unless the target journal, article type,
|
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editor, or user requires another structure. The paragraph should state:
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`research question -> study design or conceptual move -> decisive evaluation route -> principal scope of inference`
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Preview the logic of the Results without replaying all findings, metrics, or
|
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figure-level detail. A restrained result-level statement is acceptable when it
|
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clarifies the paper's answer, but do not turn the final paragraph into an
|
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abstract or Discussion.
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The route should tell the reader why the chosen comparisons, perturbations,
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decompositions, or boundary tests can answer the stated question. Method names
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alone do not provide that logic.
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## Align Introduction, Results, and Discussion
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Treat the three sections as one story at different levels:
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- **Introduction:** establish why each central question must be asked.
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- **Results:** answer the questions through an escalating evidence chain.
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- **Discussion:** synthesize what those answers mean together.
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Draft backward from the paper's actual Results claims. For every central
|
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Results subsection, identify the question that the Introduction must motivate.
|
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For every question or hypothesis introduced, identify the Results subsection
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that answers it. Do not create parallel stories.
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A useful alignment pattern is:
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`Introduction: phenomenon -> unresolved source -> necessary-condition question -> decomposition question`
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`Results: establish phenomenon -> identify source -> perturb or test necessity -> decompose contributions -> establish boundaries`
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`Discussion: synthesize the answers -> relate to theory and prior work -> state implications and limits`
|
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|
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## Run the Nature Introduction audit
|
|
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+
|
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First state the paper's exact unknown in one sentence. If that sentence is
|
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vague, repair the gap before polishing prose.
|
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+
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|
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Then build this reverse-outline table:
|
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|
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| Introduction unit | Narrowing move | Literature function | Question motivated | Results answer |
|
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|---|---|---|---|---|
|
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| Paragraph or sentence block | What becomes more specific here? | Establish, resolve, contrast, or expose gap | Which exact question follows? | Which Results subsection answers it? |
|
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+
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Flag and revise any unit that:
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- adds field background without narrowing the problem
|
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- lists studies without constructing a known–unknown transition
|
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- introduces the solution before the reader can see why it is needed
|
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+
- claims novelty mainly through adjectives
|
|
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- previews a Results claim for which no question has been motivated
|
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- motivates a question that the Results never answer
|
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+
|
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162
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Before finalizing, run a deletion test: if removing a paragraph leaves the
|
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|
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exact gap, research question, and Results roadmap intact, compress, relocate, or
|
|
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+
delete that paragraph.
|
|
@@ -0,0 +1,215 @@
|
|
|
1
|
+
# Nature Results–Discussion Corpus Guidance
|
|
2
|
+
|
|
3
|
+
Use this reference when drafting, restructuring, or polishing Results and
|
|
4
|
+
Discussion for flagship **Nature**, **Nature Communications**, **Nature Machine
|
|
5
|
+
Intelligence**, or another **Nature Portfolio** title. The patterns were
|
|
6
|
+
initially distilled from an author-supplied NMI reading set and reinforced by a
|
|
7
|
+
second author-supplied comparison set of flagship Nature papers. They are
|
|
8
|
+
generalized here as Nature-style defaults and remain **corpus-derived writing
|
|
9
|
+
guidance, not official journal requirements**. Current target-journal
|
|
10
|
+
instructions, article-type rules, reporting standards, and the paper's actual
|
|
11
|
+
evidence always take precedence.
|
|
12
|
+
|
|
13
|
+
## Contents
|
|
14
|
+
|
|
15
|
+
- [Core division of labour](#core-division-of-labour)
|
|
16
|
+
- [Build Results as claim escalation](#build-results-as-claim-escalation)
|
|
17
|
+
- [Choose an evidence-chain archetype](#choose-an-evidence-chain-archetype)
|
|
18
|
+
- [Prevent same-level repetition](#prevent-same-level-repetition)
|
|
19
|
+
- [Prefer diagnostic experiments when mechanism matters](#prefer-diagnostic-experiments-when-mechanism-matters)
|
|
20
|
+
- [End evidence units with an inference](#end-evidence-units-with-an-inference)
|
|
21
|
+
- [Apply the local-interpretation gate](#apply-the-local-interpretation-gate)
|
|
22
|
+
- [Write Discussion as synthesis, not re-demonstration](#write-discussion-as-synthesis-not-re-demonstration)
|
|
23
|
+
- [Run the Nature claim-escalation audit](#run-the-nature-claim-escalation-audit)
|
|
24
|
+
|
|
25
|
+
## Core division of labour
|
|
26
|
+
|
|
27
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- **Results:** establish and advance the paper's scientific claims through an
|
|
28
|
+
evidence chain. Results may include comparison, ablation, perturbation,
|
|
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|
+
robustness, failure analysis, directly evidence-bound interpretation, and a
|
|
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|
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local inference.
|
|
31
|
+
- **Discussion:** synthesize several established claims into a higher-order
|
|
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|
+
understanding, relate that understanding to prior work, explain its
|
|
33
|
+
importance, and bound its implications.
|
|
34
|
+
|
|
35
|
+
Do not enforce the mechanical split `Results = facts only` and
|
|
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|
+
`Discussion = all interpretation`. The operative boundary is local versus
|
|
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|
+
synthetic interpretation: keep an explanation in Results when it directly
|
|
38
|
+
resolves the experiment just reported; move broader theory, literature
|
|
39
|
+
integration, general implications, and extended speculation to Discussion.
|
|
40
|
+
|
|
41
|
+
## Build Results as claim escalation
|
|
42
|
+
|
|
43
|
+
Make each Results subsection answer one scientific question and establish one
|
|
44
|
+
new claim. Prefer a conclusion-bearing heading over a procedural experiment
|
|
45
|
+
label when the evidence supports it.
|
|
46
|
+
|
|
47
|
+
Order adjacent subsections so that each result creates the next question:
|
|
48
|
+
|
|
49
|
+
`observation -> unresolved question -> targeted experiment -> comparison or perturbation -> local interpretation -> stronger claim -> next question`
|
|
50
|
+
|
|
51
|
+
At paper level, prefer an escalating arc such as:
|
|
52
|
+
|
|
53
|
+
`phenomenon -> source -> necessary condition or mechanism -> decomposition -> boundary or robustness`
|
|
54
|
+
|
|
55
|
+
Do not substitute repeated demonstrations of the same claim for escalation.
|
|
56
|
+
Two subsections may share data, conditions, or methods; they become redundant
|
|
57
|
+
only when they collapse to the same inferential conclusion.
|
|
58
|
+
|
|
59
|
+
## Choose an evidence-chain archetype
|
|
60
|
+
|
|
61
|
+
Organize Results by inferential function, not by a routine inventory such as
|
|
62
|
+
`system description -> benchmark -> ablation`. Select or combine the archetype
|
|
63
|
+
that matches the scientific claim:
|
|
64
|
+
|
|
65
|
+
### Discovery loop
|
|
66
|
+
|
|
67
|
+
Use when evidence changes what should be tested next:
|
|
68
|
+
|
|
69
|
+
`initial hypothesis -> real or decisive test -> analyse the resulting evidence -> refine the hypothesis -> next test -> architecture or mechanism validation`
|
|
70
|
+
|
|
71
|
+
The Results should preserve the epistemic loop without becoming a chronological
|
|
72
|
+
lab notebook. Keep only iterations that change the claim or the next scientific
|
|
73
|
+
question.
|
|
74
|
+
|
|
75
|
+
### Core capability and validation envelope
|
|
76
|
+
|
|
77
|
+
Use when the paper establishes one central capability, then asks whether it is
|
|
78
|
+
reliable, safe, general, or confounded:
|
|
79
|
+
|
|
80
|
+
`establish core capability -> validate in decisive settings -> test safety or bias -> rule out central alternatives -> define limits`
|
|
81
|
+
|
|
82
|
+
Treat medication, subgroup, decision, bias, or perturbation analyses as the
|
|
83
|
+
validation envelope of the main story when they answer whether the same core
|
|
84
|
+
capability survives important conditions. Do not present each check as an
|
|
85
|
+
unrelated second discovery.
|
|
86
|
+
|
|
87
|
+
### Capability ladder
|
|
88
|
+
|
|
89
|
+
Use when a system or model supports progressively stronger claims:
|
|
90
|
+
|
|
91
|
+
`quantitative performance -> robustness to data properties -> stronger competitors or tuned ensembles -> interpretability -> broader foundation or transfer abilities`
|
|
92
|
+
|
|
93
|
+
Each rung must justify a stronger inference. More datasets or another benchmark
|
|
94
|
+
at the same inferential level do not automatically create a new rung.
|
|
95
|
+
|
|
96
|
+
Across archetypes, the most common functional chain is:
|
|
97
|
+
|
|
98
|
+
`establish the phenomenon -> stress-test it -> rule out alternatives -> broaden it -> interpret it -> bound it`
|
|
99
|
+
|
|
100
|
+
Not every paper needs every move. Preserve the shortest chain sufficient for
|
|
101
|
+
the central claim.
|
|
102
|
+
|
|
103
|
+
## Prevent same-level repetition
|
|
104
|
+
|
|
105
|
+
A later subsection may reuse an earlier baseline, control, or reference
|
|
106
|
+
contrast, but it must not present the same comparison and conclusion as a new
|
|
107
|
+
result. Treat reused conditions as **necessary comparators**, not as the centre
|
|
108
|
+
of the later subsection.
|
|
109
|
+
|
|
110
|
+
Ask what deeper discriminator the later analysis adds:
|
|
111
|
+
|
|
112
|
+
- content versus correct correspondence
|
|
113
|
+
- association versus necessity
|
|
114
|
+
- nominal performance versus robustness
|
|
115
|
+
- apparent gain versus a data, compute, or tuning confound
|
|
116
|
+
- one setting versus the boundary of generalization
|
|
117
|
+
|
|
118
|
+
Make the new perturbation, falsification, stronger comparator, or boundary test
|
|
119
|
+
the subsection's decisive evidence. If two adjacent subsections can both be
|
|
120
|
+
summarized as `X helps`, merge them, compress the repeated contrast, or move the
|
|
121
|
+
weaker demonstration to SI. A valid progression looks like:
|
|
122
|
+
|
|
123
|
+
`X is associated with the effect -> disrupting the proposed relation removes the effect -> therefore the relation, not merely the presence of X, is necessary within the tested design`
|
|
124
|
+
|
|
125
|
+
## Prefer diagnostic experiments when mechanism matters
|
|
126
|
+
|
|
127
|
+
When the claim concerns why a result occurs, do more than show performance with
|
|
128
|
+
and without a component. Where scientifically valid, perturb, shuffle, mask,
|
|
129
|
+
misalign, remove, or otherwise disrupt the proposed information or mechanism,
|
|
130
|
+
then test whether the predicted degradation occurs.
|
|
131
|
+
|
|
132
|
+
Use the logic:
|
|
133
|
+
|
|
134
|
+
`association -> targeted disruption -> predicted degradation -> bounded mechanism inference`
|
|
135
|
+
|
|
136
|
+
Do not turn this pattern into automatic causal language. Calibrate the
|
|
137
|
+
inference to the intervention, controls, design, and alternative explanations.
|
|
138
|
+
|
|
139
|
+
## End evidence units with an inference
|
|
140
|
+
|
|
141
|
+
After a coherent group of measurements, state what the evidence establishes;
|
|
142
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do not stop at a sequence of numbers. The inference must be no broader than the
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evaluated conditions.
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Report failures, reversals, anomalous scaling, weak subgroups, and performance
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trade-offs when they materially define where the claim holds, weakens, or
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fails. Do not hide a conclusion-changing boundary in Supplementary
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Information.
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Place robustness in the main text when it establishes a necessary condition,
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rules out a central alternative, reveals a failure boundary, or otherwise
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creates an independent scientific inference. Route it to SI when it only adds
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reassurance that the same conclusion survives another seed, estimator,
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threshold, or secondary specification.
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+
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## Apply the local-interpretation gate
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+
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Results may use calibrated language such as `suggests`, `indicates`, `likely
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because`, `probably owing to`, or `we speculate that` only when all of the
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following hold:
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+
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1. the interpretation answers the question raised by the immediately preceding
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result
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2. the evidence for it is visible in the current subsection
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3. uncertainty and alternative explanations remain explicit
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4. the passage closes the local evidence unit instead of opening a broad field
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discussion
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+
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169
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+
If several sentences are needed to reconcile theory, prior literature, or
|
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competing mechanisms, state the bounded local inference in Results and move the
|
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+
extended synthesis to Discussion or SI as appropriate.
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172
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+
|
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173
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+
## Write Discussion as synthesis, not re-demonstration
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174
|
+
|
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175
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+
Use the move order:
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176
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+
|
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+
`brief central finding anchor -> cross-Results synthesis -> relation to prior work or theory -> importance -> boundary conditions and limitations -> broader implications or future directions`
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+
|
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179
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+
Open by redefining the paper's central discovery in one compressed judgement.
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+
A short recap—and occasionally one indispensable anchor number—is acceptable.
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+
Then move immediately to mechanism or conceptual interpretation, significance,
|
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|
+
limitations, and future directions. Do not repeat the full comparison, effect
|
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|
+
size, statistical test, and inference already used to demonstrate the claim in
|
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|
+
Results.
|
|
185
|
+
|
|
186
|
+
Distinguish:
|
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187
|
+
|
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188
|
+
- **necessary recap / anchor:** `Results establishes X; taken together, X implies Y`
|
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189
|
+
- **redundant re-demonstration:** Results and Discussion both replay
|
|
190
|
+
`A versus B -> effect -> test -> therefore X`
|
|
191
|
+
|
|
192
|
+
Some published Nature Portfolio content types may use a Conclusion rather than
|
|
193
|
+
a standalone Discussion. Treat that as corpus variation, not permission to
|
|
194
|
+
ignore the current target-journal article-type instructions or an
|
|
195
|
+
editor-provided template.
|
|
196
|
+
|
|
197
|
+
## Run the Nature claim-escalation audit
|
|
198
|
+
|
|
199
|
+
For each Results subsection, record:
|
|
200
|
+
|
|
201
|
+
| Audit field | Question |
|
|
202
|
+
|---|---|
|
|
203
|
+
| Scientific question | What unresolved question does this subsection answer? |
|
|
204
|
+
| New claim | What proposition becomes supportable here that was not supportable before? |
|
|
205
|
+
| Evidence-chain role | Establish, stress-test, discriminate, broaden, interpret, or bound? |
|
|
206
|
+
| Decisive evidence | Which comparison, perturbation, or analysis establishes it? |
|
|
207
|
+
| Inference gain | What independent inference would disappear if the subsection were removed? |
|
|
208
|
+
| Next question | What uncertainty naturally motivates the following subsection? |
|
|
209
|
+
|
|
210
|
+
Flag adjacent subsections when their `New claim` or `Inference gain` entries are
|
|
211
|
+
substantively identical. Merge, compress, or move the weaker repetition to SI.
|
|
212
|
+
|
|
213
|
+
Before finalizing Discussion, map every repeated claim to a distinct rhetorical
|
|
214
|
+
function: `anchor`, `synthesize`, `relate`, `bound`, or `extend`. Delete any
|
|
215
|
+
repetition that only re-demonstrates the Results evidence.
|
|
@@ -0,0 +1,41 @@
|
|
|
1
|
+
# Paper-type taxonomy
|
|
2
|
+
|
|
3
|
+
Canonical 5-type vocabulary used by both `nature-polishing` and `nature-writing` (and any future skill on the `paper_type` axis).
|
|
4
|
+
|
|
5
|
+
## The five types
|
|
6
|
+
|
|
7
|
+
| Type | One-line definition | Reader's central question |
|
|
8
|
+
|---|---|---|
|
|
9
|
+
| **research** | Reports a phenomenon, mechanism, or finding from primary observation or experiment. | What was found and what does it mean? |
|
|
10
|
+
| **methods** | Proposes a new method, protocol, or measurement and demonstrates its advantage. | Does it work? Is it better? Is it reproducible? |
|
|
11
|
+
| **hypothesis** | Establishes or rules out a causal explanation through targeted evidence. | Is the proposed mechanism the right one? |
|
|
12
|
+
| **algorithmic** | Proposes a procedure, model, system, or device and shows it performs reliably and advantageously. | Does it perform under fair comparison? Where does it fail? |
|
|
13
|
+
| **review** | Synthesizes the state of a field, organizing the literature by argument, not by paper. | What is known, where is the disagreement, what is open? |
|
|
14
|
+
|
|
15
|
+
## Detection guidance
|
|
16
|
+
|
|
17
|
+
- If the user names a paper type, use it.
|
|
18
|
+
- If the manuscript reports experiments testing a stated mechanism → **hypothesis**.
|
|
19
|
+
- If the manuscript proposes a procedure/model and reports comparisons → **algorithmic**.
|
|
20
|
+
- If the manuscript proposes a measurement or protocol and reports validation → **methods**.
|
|
21
|
+
- If the manuscript synthesizes prior literature without new primary data → **review**.
|
|
22
|
+
- Otherwise → **research** (default).
|
|
23
|
+
|
|
24
|
+
## Notes on legacy vocab
|
|
25
|
+
|
|
26
|
+
Some older notes use a longer taxonomy (mechanism / method / resource / device / model / clinical / materials / computational / interdisciplinary). Map onto the five canonical types:
|
|
27
|
+
|
|
28
|
+
- mechanism, clinical, materials → **research** or **hypothesis** depending on whether a causal claim is central
|
|
29
|
+
- method → **methods**
|
|
30
|
+
- model, device, computational → **algorithmic**
|
|
31
|
+
- resource → usually **methods** (a dataset/benchmark paper) or **research**
|
|
32
|
+
- interdisciplinary → use the dominant argument structure, not the field label
|
|
33
|
+
|
|
34
|
+
## Skill-specific action layers
|
|
35
|
+
|
|
36
|
+
Each skill's `static/fragments/paper_type/<type>.md` adds the **action layer** for that skill on top of this taxonomy:
|
|
37
|
+
|
|
38
|
+
- `nature-polishing` adds diagnostic rules (what to look for, what to fix).
|
|
39
|
+
- `nature-writing` adds constructive rules (argument chain, drafting order).
|
|
40
|
+
|
|
41
|
+
The taxonomy here is the **shared vocabulary**; the action is skill-specific.
|
|
@@ -0,0 +1,21 @@
|
|
|
1
|
+
# Reader workflow
|
|
2
|
+
|
|
3
|
+
Used by both `nature-polishing` and `nature-writing`. Always-loaded shared core.
|
|
4
|
+
|
|
5
|
+
## The reader's question sequence
|
|
6
|
+
|
|
7
|
+
Most readers of a scientific paper follow a stable sequence:
|
|
8
|
+
|
|
9
|
+
1. **Relevance** — Is this for me?
|
|
10
|
+
2. **Novelty** — What is new here?
|
|
11
|
+
3. **Trust** — Do I believe it?
|
|
12
|
+
4. **Reuse** — Can I use it?
|
|
13
|
+
5. **Meaning** — What does it mean, and where are the boundaries?
|
|
14
|
+
|
|
15
|
+
Whether the task is drafting from scratch or polishing existing prose, the paper should help the reader answer these questions in this order.
|
|
16
|
+
|
|
17
|
+
## Implications
|
|
18
|
+
|
|
19
|
+
- A draft that buries novelty (question 2) behind methods detail (which serves question 3) will lose readers in the first paragraph.
|
|
20
|
+
- A polish that improves sentence-level fluency without surfacing relevance (question 1) earlier may still fail with broad-audience readers.
|
|
21
|
+
- "Where are the boundaries" (question 5) is the most commonly skipped. Both drafting and polishing should expose it, not paper over it.
|