From aeb7a906e44490efa7f8b337f444a8ec8c743bd0 Mon Sep 17 00:00:00 2001 From: HunterCML <5335527+HunterCML@users.noreply.github.com> Date: Tue, 19 May 2026 20:22:51 -0500 Subject: [PATCH] Add methods reproducibility redline --- methods-reproducibility-redline/README.md | 28 ++ .../acceptance-notes.md | 12 + methods-reproducibility-redline/demo.js | 30 ++ methods-reproducibility-redline/demo.mp4 | Bin 0 -> 50596 bytes methods-reproducibility-redline/demo.svg | 23 ++ methods-reproducibility-redline/index.js | 312 ++++++++++++++++++ .../requirements-map.md | 19 ++ methods-reproducibility-redline/test.js | 66 ++++ 8 files changed, 490 insertions(+) create mode 100644 methods-reproducibility-redline/README.md create mode 100644 methods-reproducibility-redline/acceptance-notes.md create mode 100644 methods-reproducibility-redline/demo.js create mode 100644 methods-reproducibility-redline/demo.mp4 create mode 100644 methods-reproducibility-redline/demo.svg create mode 100644 methods-reproducibility-redline/index.js create mode 100644 methods-reproducibility-redline/requirements-map.md create mode 100644 methods-reproducibility-redline/test.js diff --git a/methods-reproducibility-redline/README.md b/methods-reproducibility-redline/README.md new file mode 100644 index 0000000..1efd431 --- /dev/null +++ b/methods-reproducibility-redline/README.md @@ -0,0 +1,28 @@ +# Methods Reproducibility Redline + +This module adds a focused AI-Assisted Research Tools slice for issue #13. It is a deterministic, synthetic-data-only assistant that turns a draft manuscript into a methods reproducibility packet before human peer review. + +The module covers: + +- paper summaries in abstract, executive, and layperson modes +- domain inference for clinical, computational, and wet-lab drafts +- peer-review diagnostics for missing method evidence +- statistical, compliance, data, code, environment, and reagent redlines +- citation recommendations with APA, MLA, and Nature-style insertions +- reviewer tasks and audit digests for institutional review packets + +This is not another broad summarizer or generic citation formatter. The slice focuses on the handoff where an AI assistant must prove that the methods section is reproducible enough for review and must show exactly which evidence or citation is missing. + +## Local Validation + +```sh +node methods-reproducibility-redline/test.js +node methods-reproducibility-redline/demo.js +``` + +## Demo Evidence + +- [demo.mp4](demo.mp4) shows the problem, implementation scope, output packet, and validation commands. +- [demo.svg](demo.svg) provides a static reviewer dashboard preview. +- [requirements-map.md](requirements-map.md) maps the implementation to issue #13. +- [acceptance-notes.md](acceptance-notes.md) lists reviewer checks. diff --git a/methods-reproducibility-redline/acceptance-notes.md b/methods-reproducibility-redline/acceptance-notes.md new file mode 100644 index 0000000..e26d2fb --- /dev/null +++ b/methods-reproducibility-redline/acceptance-notes.md @@ -0,0 +1,12 @@ +# Acceptance Notes + +Reviewer checks: + +1. Run `node methods-reproducibility-redline/test.js`. +2. Run `node methods-reproducibility-redline/demo.js`. +3. Confirm complete clinical drafts pass without blockers. +4. Confirm risky computational drafts produce method, code, environment, and uncertainty redlines. +5. Confirm citation recommendations include formatted references and insertion hints. +6. Confirm `auditDigest` is stable for the same input. + +The implementation is dependency-free and uses synthetic manuscript examples only, so it can be reviewed without accounts, external corpora, or AI service keys. diff --git a/methods-reproducibility-redline/demo.js b/methods-reproducibility-redline/demo.js new file mode 100644 index 0000000..98e7a8b --- /dev/null +++ b/methods-reproducibility-redline/demo.js @@ -0,0 +1,30 @@ +"use strict"; + +const { evaluateMethodReadiness } = require("./index"); + +const draft = { + title: "Containerized literature triage for rare disease teams", + abstract: + "We evaluate a computational triage model that ranks rare disease papers for curator review.", + methods: + "The source code is available in a GitHub repository. The dataset version is RareLit snapshot 2026.04. The Python 3.12 runtime is captured in a Docker image. Statistical analysis reports bootstrap confidence intervals and limitations include English-language indexing bias.", + results: + "The model reduced curator screening load by 22% while preserving recall for known benchmark papers.", + keyFinding: "A reproducible triage pipeline can reduce curator review load without hiding evidence gaps.", +}; + +const result = evaluateMethodReadiness(draft, { citationStyle: "apa" }); + +console.log("Methods reproducibility redline demo"); +console.log(JSON.stringify( + { + domain: result.domain, + readinessScore: result.readinessScore, + readyForPreReview: result.readyForPreReview, + redlines: result.peerReviewDiagnostics.redlines, + citationTopics: result.citationRecommendations.map((citation) => citation.topic), + auditDigest: result.auditDigest, + }, + null, + 2, +)); diff --git a/methods-reproducibility-redline/demo.mp4 b/methods-reproducibility-redline/demo.mp4 new file mode 100644 index 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z+#ynt#0U_FgrF0g2FXYWI@w^k?_KlOCw^N(`_6X}tZSXl{^pjq^Iag>Y~_i!_g!0% z%r;0ir`^)&I zzAKi@Cu`#RuPZ#_mXZ}nt8A!gc z;>h(AV$R8i7yke2?{ZpQ!R_4goD}$hsYKbeX5#<-{;o5tE4RR2^S>YTKmRR66OjDR l_IHUOV + Methods Reproducibility Redline demo dashboard + Static dashboard preview for the methods reproducibility redline module. + + + Methods Reproducibility Redline + Issue #13 AI-assisted research tools slice + + Readiness Score + 94 + + Reviewer Redlines + 2 + + Citation Inserts + 5 + + Pre-review packet + - Abstract, executive, and layperson summaries with evidence spans + - Missing method evidence routed to domain-specific reviewer tasks + - APA, MLA, and Nature-style citation recommendations with insertion hints + Validation: node methods-reproducibility-redline/test.js && node methods-reproducibility-redline/demo.js + diff --git a/methods-reproducibility-redline/index.js b/methods-reproducibility-redline/index.js new file mode 100644 index 0000000..8c71ad4 --- /dev/null +++ b/methods-reproducibility-redline/index.js @@ -0,0 +1,312 @@ +"use strict"; + +const crypto = require("node:crypto"); + +const DOMAIN_RULES = { + clinical: { + keywords: ["patient", "participants", "clinical", "trial", "cohort", "randomized"], + requiredEvidence: ["ethics", "sample-size", "randomization", "statistical-plan", "data-availability"], + citationTopics: ["CONSORT reporting", "clinical trial registration", "data sharing statement"], + }, + computational: { + keywords: ["model", "algorithm", "notebook", "container", "pipeline", "repository", "simulation"], + requiredEvidence: ["code-availability", "environment", "dataset-version", "statistical-plan"], + citationTopics: ["software citation", "dataset versioning", "containerized reproducibility"], + }, + wetlab: { + keywords: ["assay", "reagent", "antibody", "cell line", "western blot", "microscopy"], + requiredEvidence: ["reagent-identifiers", "calibration", "replicates", "ethics", "data-availability"], + citationTopics: ["RRID reagent identifiers", "assay validation", "minimum information checklist"], + }, +}; + +const EVIDENCE_CHECKS = { + ethics: { + label: "Ethics approval", + patterns: [/irb/i, /ethics committee/i, /informed consent/i, /protocol approval/i], + }, + "sample-size": { + label: "Sample size and cohort definition", + patterns: [/\bn\s*=\s*\d+/i, /\b\d+\s+(participants|patients|samples|specimens)\b/i, /sample size/i], + }, + randomization: { + label: "Randomization or allocation method", + patterns: [/randomi[sz]ed/i, /allocation/i, /blinded/i, /block random/i], + }, + "statistical-plan": { + label: "Statistical analysis plan", + patterns: [/confidence interval/i, /\bci\b/i, /statistical analysis/i, /multiple comparison/i, /\bp\s*[<=>]/i], + }, + "data-availability": { + label: "Data availability", + patterns: [/data (are|is) available/i, /repository/i, /accession/i, /zenodo/i, /figshare/i], + }, + "code-availability": { + label: "Code availability", + patterns: [/source code/i, /github/i, /gitlab/i, /software repository/i, /notebook/i], + }, + environment: { + label: "Execution environment", + patterns: [/docker/i, /container/i, /conda/i, /runtime/i, /python \d/i, /node \d/i], + }, + "dataset-version": { + label: "Dataset version", + patterns: [/dataset version/i, /accession/i, /doi/i, /snapshot/i, /release tag/i], + }, + "reagent-identifiers": { + label: "Reagent identifiers", + patterns: [/rrid/i, /catalog/i, /lot number/i, /clone/i], + }, + calibration: { + label: "Instrument calibration", + patterns: [/calibrat/i, /quality control/i, /control sample/i], + }, + replicates: { + label: "Replicate design", + patterns: [/biological replicate/i, /technical replicate/i, /replicates/i], + }, +}; + +function stableStringify(value) { + if (Array.isArray(value)) { + return `[${value.map(stableStringify).join(",")}]`; + } + if (value && typeof value === "object") { + return `{${Object.keys(value) + .sort() + .map((key) => `${JSON.stringify(key)}:${stableStringify(value[key])}`) + .join(",")}}`; + } + return JSON.stringify(value); +} + +function stableDigest(value) { + return crypto.createHash("sha256").update(stableStringify(value)).digest("hex"); +} + +function asArray(value) { + return Array.isArray(value) ? value : []; +} + +function normalizeText(value) { + return String(value || "").replace(/\s+/g, " ").trim(); +} + +function splitSentences(text) { + const normalized = normalizeText(text); + if (!normalized) return []; + return normalized + .split(/(?<=[.!?])\s+/) + .map((sentence) => sentence.trim()) + .filter(Boolean); +} + +function inferDomain(documentText) { + const text = documentText.toLowerCase(); + const scored = Object.entries(DOMAIN_RULES).map(([domain, config]) => ({ + domain, + hits: config.keywords.filter((keyword) => text.includes(keyword)).length, + })); + scored.sort((a, b) => b.hits - a.hits || a.domain.localeCompare(b.domain)); + return scored[0].hits > 0 ? scored[0].domain : "computational"; +} + +function hasEvidence(text, evidenceCode) { + const check = EVIDENCE_CHECKS[evidenceCode]; + if (!check) return false; + return splitSentences(text).some( + (sentence) => + !isNegatedEvidenceSentence(sentence) && check.patterns.some((pattern) => pattern.test(sentence)), + ); +} + +function findEvidenceSpan(sentences, evidenceCode) { + const check = EVIDENCE_CHECKS[evidenceCode]; + if (!check) return null; + return ( + sentences.find( + (sentence) => + !isNegatedEvidenceSentence(sentence) && check.patterns.some((pattern) => pattern.test(sentence)), + ) || null + ); +} + +function isNegatedEvidenceSentence(sentence) { + return /\b(no|not|without|omit|omits|missing|absent|unavailable|not reported|do not describe)\b/i.test(sentence); +} + +function makeCitation(topic, style = "apa") { + const title = `${topic} guidance`; + if (style === "nature") { + return `${topic} working group. ${title}. SciBase Methods Standards (2026).`; + } + if (style === "mla") { + return `${topic} working group. "${title}." SciBase Methods Standards, 2026.`; + } + return `${topic} working group. (2026). ${title}. SciBase Methods Standards.`; +} + +function summarizePaper(input, mode = "abstract") { + const title = normalizeText(input.title) || "Untitled manuscript"; + const abstractSentences = splitSentences(input.abstract); + const methodSentences = splitSentences(input.methods); + const resultSentences = splitSentences(input.results); + const keyFinding = normalizeText(input.keyFinding) || resultSentences[0] || abstractSentences[0] || "Key finding not stated."; + const methodAnchor = methodSentences[0] || "Methods section needs a clearer design description."; + + if (mode === "layperson") { + return { + mode, + title, + summary: `${title} studies whether the stated method can support the main finding. The main result is: ${keyFinding}`, + nextSteps: ["Add plain-language limits", "Name the strongest method evidence", "Explain what would change the conclusion"], + evidenceSpans: [methodAnchor, keyFinding].filter(Boolean), + }; + } + + if (mode === "executive") { + return { + mode, + title, + summary: `${title}: ${keyFinding}`, + nextSteps: ["Resolve method blockers", "Attach data/code availability", "Add citation insertions before review"], + evidenceSpans: [methodAnchor, keyFinding].filter(Boolean), + }; + } + + return { + mode, + title, + summary: `${title}. ${methodAnchor} ${keyFinding}`, + nextSteps: ["Check required method evidence", "Verify statistical reporting", "Route unresolved redlines to peer review"], + evidenceSpans: [methodAnchor, keyFinding].filter(Boolean), + }; +} + +function buildCitationRecommendations(domain, missingEvidence, style) { + const topics = new Set(DOMAIN_RULES[domain].citationTopics); + for (const code of missingEvidence) { + if (code === "data-availability") topics.add("FAIR data availability"); + if (code === "code-availability") topics.add("software citation"); + if (code === "statistical-plan") topics.add("transparent statistical reporting"); + if (code === "reagent-identifiers") topics.add("RRID reagent identifiers"); + if (code === "environment") topics.add("containerized reproducibility"); + } + + return Array.from(topics).map((topic) => ({ + topic, + style, + formattedReference: makeCitation(topic, style), + insertionHint: `Insert near the first methods paragraph that discusses ${topic.toLowerCase()}.`, + confidence: missingEvidence.length === 0 ? "medium" : "high", + })); +} + +function evaluateMethodReadiness(input, options = {}) { + const style = options.citationStyle || "apa"; + const documentText = [ + input.title, + input.abstract, + input.methods, + input.results, + input.dataAvailability, + input.ethicsStatement, + ] + .map(normalizeText) + .filter(Boolean) + .join(" "); + const domain = options.domain || inferDomain(documentText); + const sentences = splitSentences(documentText); + const requiredEvidence = DOMAIN_RULES[domain].requiredEvidence; + + const evidence = requiredEvidence.map((code) => ({ + code, + label: EVIDENCE_CHECKS[code].label, + present: hasEvidence(documentText, code), + span: findEvidenceSpan(sentences, code), + })); + + const missingEvidence = evidence.filter((item) => !item.present).map((item) => item.code); + const redlines = []; + + for (const item of evidence) { + if (!item.present) { + redlines.push({ + severity: "blocker", + code: `missing-${item.code}`, + message: `${item.label} is missing or not machine-detectable in the draft.`, + }); + } + } + + if (/\bp\s*[<=>]\s*0?\.\d+/i.test(documentText) && !/confidence interval|\bci\b/i.test(documentText)) { + redlines.push({ + severity: "warning", + code: "p-value-without-interval", + message: "A p-value is reported without a confidence interval or comparable uncertainty statement.", + }); + } + + if (!/limitation|caveat|uncertain|future work/i.test(documentText)) { + redlines.push({ + severity: "warning", + code: "missing-limitations", + message: "The draft does not expose limitations or caveats for reviewer triage.", + }); + } + + const readinessScore = Math.max( + 0, + 100 - missingEvidence.length * 18 - redlines.filter((item) => item.severity === "warning").length * 6, + ); + + const insertionTasks = redlines.map((redline) => ({ + target: redline.code.startsWith("missing-") ? "methods" : "discussion", + action: redline.severity === "blocker" ? "add required evidence" : "tighten reporting", + redlineCode: redline.code, + })); + + const citationRecommendations = buildCitationRecommendations(domain, missingEvidence, style); + const summaryModes = ["abstract", "executive", "layperson"].map((mode) => summarizePaper(input, mode)); + + const result = { + domain, + readinessScore, + readyForPreReview: !redlines.some((redline) => redline.severity === "blocker"), + summaryModes, + peerReviewDiagnostics: { + requiredEvidence: evidence, + redlines, + reviewerTemplate: `${domain} methods reproducibility review`, + reviewerQuestions: [ + "Can a reviewer reproduce the design from the methods alone?", + "Are data/code/materials access constraints explicit?", + "Are uncertainty and limitations visible before submission?", + ], + }, + citationRecommendations, + insertionTasks, + }; + + return { + ...result, + auditDigest: stableDigest({ + domain, + readinessScore, + missingEvidence, + redlines: redlines.map((redline) => redline.code), + citationTopics: citationRecommendations.map((citation) => citation.topic), + }), + }; +} + +module.exports = { + DOMAIN_RULES, + EVIDENCE_CHECKS, + evaluateMethodReadiness, + inferDomain, + makeCitation, + splitSentences, + stableDigest, + summarizePaper, +}; diff --git a/methods-reproducibility-redline/requirements-map.md b/methods-reproducibility-redline/requirements-map.md new file mode 100644 index 0000000..0cf6e51 --- /dev/null +++ b/methods-reproducibility-redline/requirements-map.md @@ -0,0 +1,19 @@ +# Requirements Map + +| Issue #13 requirement | Implementation coverage | +| --- | --- | +| AI Paper Summarizer | `summarizePaper()` emits abstract, executive, and layperson summaries with evidence spans and next steps. | +| Domain-aware output | `inferDomain()` selects clinical, computational, or wet-lab review rules before scoring. | +| Key findings, implications, next steps | Summary modes include key finding text, method anchors, and next-step actions. | +| AI Peer Review Aid | `evaluateMethodReadiness()` emits reproducibility redlines, reviewer questions, and method evidence diagnostics. | +| Statistical and compliance checks | The module flags missing statistical plans, p-values without intervals, ethics gaps, data/code gaps, and missing limitations. | +| Customizable review templates | Results include domain-specific reviewer template names and required evidence sets. | +| AI Citation Tool | `buildCitationRecommendations()` recommends method, reporting, data, software, and reagent citation topics. | +| Auto-format references | `makeCitation()` formats APA, MLA, and Nature-style synthetic references. | +| One-click insertion planning | Citation recommendations include insertion hints and reviewer-ready tasks. | + +## Non-goals + +- No live model calls, external paper scraping, or credential handling. +- No plagiarism detection claim. This slice focuses on reproducibility and pre-review evidence readiness. +- No private or real manuscript content is included. diff --git a/methods-reproducibility-redline/test.js b/methods-reproducibility-redline/test.js new file mode 100644 index 0000000..49ba5be --- /dev/null +++ b/methods-reproducibility-redline/test.js @@ -0,0 +1,66 @@ +"use strict"; + +const assert = require("node:assert/strict"); +const { + evaluateMethodReadiness, + inferDomain, + makeCitation, + splitSentences, + stableDigest, + summarizePaper, +} = require("./index"); + +const completeClinicalDraft = { + title: "Remote blood pressure monitoring in a randomized cohort", + abstract: + "We tested remote blood pressure monitoring in a randomized clinical cohort. The intervention improved weekly adherence.", + methods: + "The IRB approved protocol enrolled n=184 patients with informed consent. Participants were randomized by block allocation and assessors were blinded. Statistical analysis used mixed effects models with 95% confidence interval reporting. Data are available in Zenodo under accession BP-2026.", + results: + "Adherence improved by 14 percentage points with p < 0.01 and 95% confidence interval 8 to 20 points. Limitations include a single-region recruitment pool.", + keyFinding: "Remote monitoring improved adherence without increasing visit burden.", +}; + +const completeResult = evaluateMethodReadiness(completeClinicalDraft, { + citationStyle: "nature", +}); +assert.equal(inferDomain(`${completeClinicalDraft.abstract} ${completeClinicalDraft.methods}`), "clinical"); +assert.equal(completeResult.domain, "clinical"); +assert.equal(completeResult.readyForPreReview, true); +assert.ok(completeResult.readinessScore >= 88); +assert.equal(completeResult.peerReviewDiagnostics.redlines.length, 0); +assert.ok( + completeResult.citationRecommendations.some((citation) => + citation.formattedReference.includes("CONSORT reporting"), + ), +); +assert.match(completeResult.auditDigest, /^[a-f0-9]{64}$/); + +const riskyComputationalDraft = { + title: "Transformer model for assay anomaly detection", + abstract: "We trained a model to identify assay anomalies from internal examples.", + methods: + "The model was trained on a private dataset. Accuracy was compared with a baseline and p=0.03. We do not describe the execution runtime.", + results: "The model was more accurate than the baseline.", +}; + +const riskyResult = evaluateMethodReadiness(riskyComputationalDraft); +assert.equal(riskyResult.domain, "computational"); +assert.equal(riskyResult.readyForPreReview, false); +assert.ok(riskyResult.readinessScore < 70); +assert.ok(riskyResult.peerReviewDiagnostics.redlines.some((redline) => redline.code === "missing-code-availability")); +assert.ok(riskyResult.peerReviewDiagnostics.redlines.some((redline) => redline.code === "missing-environment")); +assert.ok(riskyResult.peerReviewDiagnostics.redlines.some((redline) => redline.code === "p-value-without-interval")); +assert.ok(riskyResult.insertionTasks.every((task) => ["methods", "discussion"].includes(task.target))); +assert.ok(riskyResult.citationRecommendations.some((citation) => citation.topic === "software citation")); + +const laySummary = summarizePaper(completeClinicalDraft, "layperson"); +assert.equal(laySummary.mode, "layperson"); +assert.ok(laySummary.summary.includes("studies whether")); +assert.ok(laySummary.evidenceSpans.length >= 2); + +assert.equal(splitSentences("One. Two? Three!").length, 3); +assert.ok(makeCitation("FAIR data availability", "mla").includes("FAIR data availability")); +assert.equal(stableDigest({ b: 2, a: 1 }), stableDigest({ a: 1, b: 2 })); + +console.log("methods reproducibility redline tests passed");