diff --git a/external-validity-transfer-assistant/README.md b/external-validity-transfer-assistant/README.md
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--- /dev/null
+++ b/external-validity-transfer-assistant/README.md
@@ -0,0 +1,38 @@
+# External Validity Transfer Assistant
+
+This module is a focused slice for SCIBASE issue #16, AI-Powered Research Assistant Suite.
+
+It adds a deterministic research-assistant review gate for external validity and population-transfer risk before AI-generated peer-review packets are shown to authors, reviewers, funders, or lab leads.
+
+## What It Checks
+
+- Whether broad manuscript claims are backed by evidence from the asserted populations.
+- Whether claimed deployment settings are covered by linked study artifacts.
+- Whether assay or instrument contexts match the manuscript language.
+- Whether runtime environments have reproducible rerun evidence.
+- Whether strong claims are missing required subgroup coverage.
+- Whether a broad transfer claim lacks external validation.
+
+## Outputs
+
+The demo creates:
+
+- `reports/summary.json`: structured review packet.
+- `reports/reviewer-packet.md`: reviewer-facing findings, actions, and research gaps.
+- `reports/summary.svg`: visual transfer-risk summary.
+
+## Why This Is Distinct
+
+This is not another broad AI assistant, preregistration checker, retraction sentinel, prompt-safety guard, statistical review, benchmark-leakage auditor, figure/table checker, supplement-readiness module, funding/COI checker, or evidence-trace assistant.
+
+It focuses specifically on whether a manuscript's claims transfer beyond the exact population, setting, assay, and runtime contexts represented by the linked evidence.
+
+## Local Validation
+
+```bash
+npm run check
+npm test
+npm run demo
+```
+
+The module uses synthetic data only. It makes no network calls and uses no credentials, private manuscripts, protected health information, payment data, or external APIs.
diff --git a/external-validity-transfer-assistant/demo-video.js b/external-validity-transfer-assistant/demo-video.js
new file mode 100644
index 00000000..38293ac6
--- /dev/null
+++ b/external-validity-transfer-assistant/demo-video.js
@@ -0,0 +1,174 @@
+const fs = require("fs");
+const os = require("os");
+const path = require("path");
+const { execFileSync } = require("child_process");
+
+const reportDir = path.join(__dirname, "reports");
+const outputPath = path.join(reportDir, "demo.webm");
+
+const chromeCandidates = [
+ process.env.CHROME_PATH,
+ "C:\\Program Files (x86)\\Google\\Chrome\\Application\\chrome.exe",
+ "C:\\Program Files\\Google\\Chrome\\Application\\chrome.exe",
+ "C:\\Program Files (x86)\\Microsoft\\Edge\\Application\\msedge.exe",
+ "C:\\Program Files\\Microsoft\\Edge\\Application\\msedge.exe"
+].filter(Boolean);
+
+function findBrowser() {
+ const found = chromeCandidates.find((candidate) => fs.existsSync(candidate));
+ if (!found) {
+ throw new Error("Chrome or Edge was not found. Set CHROME_PATH to generate reports/demo.webm.");
+ }
+ return found;
+}
+
+function fileUrl(filePath) {
+ return `file:///${filePath.replace(/\\/g, "/")}`;
+}
+
+const html = String.raw`
+
+
+
+ External validity transfer assistant demo
+
+
+
+
+ recording
+
+
+`;
+
+fs.mkdirSync(reportDir, { recursive: true });
+
+const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), "external-validity-demo-"));
+const htmlPath = path.join(tempDir, "demo.html");
+const profileDir = path.join(tempDir, "profile");
+fs.writeFileSync(htmlPath, html, "utf8");
+
+const browserPath = findBrowser();
+const stdout = execFileSync(
+ browserPath,
+ [
+ "--headless=new",
+ "--disable-gpu",
+ "--disable-dev-shm-usage",
+ "--autoplay-policy=no-user-gesture-required",
+ "--run-all-compositor-stages-before-draw",
+ "--virtual-time-budget=7000",
+ `--user-data-dir=${profileDir}`,
+ "--dump-dom",
+ fileUrl(htmlPath)
+ ],
+ { encoding: "utf8", maxBuffer: 30 * 1024 * 1024 }
+);
+
+const match = stdout.match(/data:video\/webm;base64,([A-Za-z0-9+/=]+)/);
+if (!match) {
+ throw new Error(`Demo video generation failed. Browser output ended with: ${stdout.slice(-600)}`);
+}
+
+fs.writeFileSync(outputPath, Buffer.from(match[1], "base64"));
+console.log(`Generated ${path.relative(process.cwd(), outputPath)}`);
diff --git a/external-validity-transfer-assistant/demo.js b/external-validity-transfer-assistant/demo.js
new file mode 100644
index 00000000..b1c7c2d5
--- /dev/null
+++ b/external-validity-transfer-assistant/demo.js
@@ -0,0 +1,22 @@
+const fs = require("fs");
+const path = require("path");
+const { project } = require("./sample-data");
+const { buildReviewPacket, renderMarkdownReport, renderSvgSummary } = require("./index");
+
+const reportDir = path.join(__dirname, "reports");
+fs.mkdirSync(reportDir, { recursive: true });
+
+const packet = buildReviewPacket(project);
+
+fs.writeFileSync(
+ path.join(reportDir, "summary.json"),
+ `${JSON.stringify(packet, null, 2)}\n`,
+ "utf8"
+);
+fs.writeFileSync(path.join(reportDir, "reviewer-packet.md"), renderMarkdownReport(packet), "utf8");
+fs.writeFileSync(path.join(reportDir, "summary.svg"), renderSvgSummary(packet), "utf8");
+
+console.log(`Generated reports for ${packet.assistant}`);
+console.log(`Decision: ${packet.decision}`);
+console.log(`Average score: ${packet.averageScore}`);
+console.log(`Findings: ${packet.peerReviewSuggestions.length}`);
diff --git a/external-validity-transfer-assistant/index.js b/external-validity-transfer-assistant/index.js
new file mode 100644
index 00000000..aba2a708
--- /dev/null
+++ b/external-validity-transfer-assistant/index.js
@@ -0,0 +1,360 @@
+const DEFAULT_WEIGHTS = {
+ critical: 35,
+ high: 22,
+ medium: 12,
+ low: 6
+};
+
+function unique(values) {
+ return [...new Set((values || []).filter(Boolean))];
+}
+
+function toScopeSet(records, key) {
+ return new Set(records.map((record) => record[key]).filter(Boolean));
+}
+
+function missingFromScope(expected, observed) {
+ const observedSet = observed instanceof Set ? observed : new Set(observed);
+ return unique(expected).filter((value) => !observedSet.has(value));
+}
+
+function hasExternalValidation(records) {
+ return records.some((record) => record.externalValidation || record.type === "external-validation");
+}
+
+function hasRunnableEvidence(records) {
+ return records.some((record) => record.reproducible && record.environment);
+}
+
+function severityForMissing(count, expectedCount) {
+ if (count === 0) {
+ return null;
+ }
+ if (expectedCount >= 3 && count >= 2) {
+ return "high";
+ }
+ if (count === expectedCount) {
+ return "high";
+ }
+ return "medium";
+}
+
+function addFinding(findings, severity, rule, message, action) {
+ findings.push({ severity, rule, message, action });
+}
+
+function evaluateClaim(claim, evidence, manuscript) {
+ const linkedEvidence = evidence.filter((record) => claim.evidenceIds.includes(record.id));
+ const findings = [];
+ const scope = claim.assertedScope || {};
+
+ if (linkedEvidence.length === 0) {
+ addFinding(
+ findings,
+ "critical",
+ "missing-evidence",
+ `Claim ${claim.id} has no linked evidence artifacts.`,
+ "Link at least one dataset, runbook, protocol, or validation artifact before review."
+ );
+ }
+
+ const observedPopulations = toScopeSet(linkedEvidence, "population");
+ const observedSettings = toScopeSet(linkedEvidence, "setting");
+ const observedInstruments = toScopeSet(linkedEvidence, "instrument");
+ const observedEnvironments = toScopeSet(linkedEvidence, "environment");
+
+ const missingPopulations = missingFromScope(scope.populations, observedPopulations);
+ const missingSettings = missingFromScope(scope.settings, observedSettings);
+ const missingInstruments = missingFromScope(scope.instruments, observedInstruments);
+ const missingEnvironments = missingFromScope(scope.environments, observedEnvironments);
+
+ const populationSeverity = severityForMissing(missingPopulations.length, (scope.populations || []).length);
+ if (populationSeverity) {
+ addFinding(
+ findings,
+ populationSeverity,
+ "population-transfer-gap",
+ `Claim ${claim.id} asserts populations not represented in linked evidence: ${missingPopulations.join(", ")}.`,
+ "Narrow the claim wording or add external validation for each missing population."
+ );
+ }
+
+ const settingSeverity = severityForMissing(missingSettings.length, (scope.settings || []).length);
+ if (settingSeverity) {
+ addFinding(
+ findings,
+ settingSeverity,
+ "setting-transfer-gap",
+ `Claim ${claim.id} asserts settings not represented in linked evidence: ${missingSettings.join(", ")}.`,
+ "Add site-level validation evidence or mark the setting as a future research gap."
+ );
+ }
+
+ if (missingInstruments.length > 0) {
+ addFinding(
+ findings,
+ "medium",
+ "assay-transfer-gap",
+ `Claim ${claim.id} references unsupported assay or instrument contexts: ${missingInstruments.join(", ")}.`,
+ "Separate assay-specific claims and document conversion limits before reviewer release."
+ );
+ }
+
+ if (missingEnvironments.length > 0) {
+ addFinding(
+ findings,
+ "medium",
+ "runtime-transfer-gap",
+ `Claim ${claim.id} references runtime environments not covered by rerun evidence: ${missingEnvironments.join(", ")}.`,
+ "Run the pipeline in each deployment-like environment or downgrade deployment readiness language."
+ );
+ }
+
+ const broadScope = (scope.populations || []).length > 1 || (scope.settings || []).length > 1;
+ if (broadScope && !hasExternalValidation(linkedEvidence)) {
+ addFinding(
+ findings,
+ "high",
+ "no-external-validation",
+ `Claim ${claim.id} has broad transfer language without external validation evidence.`,
+ "Hold broad generalizability language until at least one independent validation artifact is linked."
+ );
+ }
+
+ if (!hasRunnableEvidence(linkedEvidence)) {
+ addFinding(
+ findings,
+ "high",
+ "no-runnable-transfer-evidence",
+ `Claim ${claim.id} lacks reproducible runtime evidence for the asserted context.`,
+ "Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible."
+ );
+ }
+
+ const missingRequiredSubgroups = missingFromScope(manuscript.requiredSubgroups || [], observedPopulations);
+ if (claim.confidence === "strong" && missingRequiredSubgroups.length > 0) {
+ addFinding(
+ findings,
+ "medium",
+ "strong-claim-subgroup-undercoverage",
+ `Strong claim ${claim.id} does not cover required subgroup evidence: ${missingRequiredSubgroups.join(", ")}.`,
+ "Convert the claim to qualified language or create a subgroup-specific validation plan."
+ );
+ }
+
+ const score = Math.max(
+ 0,
+ 100 - findings.reduce((total, finding) => total + DEFAULT_WEIGHTS[finding.severity], 0)
+ );
+
+ return {
+ id: claim.id,
+ text: claim.text,
+ score,
+ decision: decisionFromScore(score),
+ evidenceCount: linkedEvidence.length,
+ observedScope: {
+ populations: [...observedPopulations],
+ settings: [...observedSettings],
+ instruments: [...observedInstruments],
+ environments: [...observedEnvironments],
+ externalValidation: hasExternalValidation(linkedEvidence),
+ runnableEvidence: hasRunnableEvidence(linkedEvidence)
+ },
+ findings
+ };
+}
+
+function decisionFromScore(score) {
+ if (score >= 82) {
+ return "review-ready";
+ }
+ if (score >= 62) {
+ return "revise-before-release";
+ }
+ if (score >= 42) {
+ return "hold-for-transfer-evidence";
+ }
+ return "quarantine-from-review-packet";
+}
+
+function summarizeSeverity(claimReviews) {
+ const summary = { critical: 0, high: 0, medium: 0, low: 0 };
+ for (const review of claimReviews) {
+ for (const finding of review.findings) {
+ summary[finding.severity] += 1;
+ }
+ }
+ return summary;
+}
+
+function createResearchGaps(project, claimReviews) {
+ const missingTerms = new Set();
+ for (const review of claimReviews) {
+ for (const finding of review.findings) {
+ if (finding.rule.includes("population") || finding.rule.includes("subgroup")) {
+ for (const value of review.text.match(/pediatric|underrepresented ancestry|adult/g) || []) {
+ missingTerms.add(value);
+ }
+ }
+ if (finding.rule.includes("setting") || finding.rule.includes("runtime")) {
+ for (const value of review.text.match(/low-resource clinic|community hospital|international site|cpu-only/g) || []) {
+ missingTerms.add(value);
+ }
+ }
+ }
+ }
+
+ const generated = project.corpusSignals
+ .filter((signal) => signal.labFit.some((capability) => project.labCapabilities.includes(capability)))
+ .map((signal) => ({
+ id: signal.id,
+ topic: signal.topic,
+ reason: signal.reason,
+ priority: missingTerms.size > 0 ? "high" : "medium",
+ suggestedNextStep: `Use ${signal.topic} as a targeted validation or grant-planning workstream.`
+ }));
+
+ return generated.slice(0, 5);
+}
+
+function createReproducibilityActions(claimReviews) {
+ const actions = [];
+ for (const review of claimReviews) {
+ for (const finding of review.findings) {
+ if (finding.rule.includes("runtime") || finding.rule.includes("runnable") || finding.rule.includes("external")) {
+ actions.push({
+ claimId: review.id,
+ priority: finding.severity === "high" || finding.severity === "critical" ? "blocking" : "recommended",
+ action: finding.action
+ });
+ }
+ }
+ }
+ return actions;
+}
+
+function buildReviewPacket(project) {
+ const claimReviews = project.manuscript.claims.map((claim) =>
+ evaluateClaim(claim, project.evidence, project.manuscript)
+ );
+ const severitySummary = summarizeSeverity(claimReviews);
+ const averageScore = Math.round(
+ claimReviews.reduce((total, review) => total + review.score, 0) / claimReviews.length
+ );
+
+ return {
+ projectId: project.id,
+ title: project.title,
+ assistant: "external-validity-transfer-assistant",
+ issue: "SCIBASE-AI/SCIBASE.AI#16",
+ averageScore,
+ decision: decisionFromScore(averageScore),
+ severitySummary,
+ claimReviews,
+ peerReviewSuggestions: claimReviews.flatMap((review) =>
+ review.findings.map((finding) => ({
+ claimId: review.id,
+ severity: finding.severity,
+ suggestion: finding.message,
+ action: finding.action
+ }))
+ ),
+ reproducibilityActions: createReproducibilityActions(claimReviews),
+ researchGaps: createResearchGaps(project, claimReviews),
+ safetyNotes: [
+ "Synthetic data only.",
+ "No external APIs, credentials, private manuscripts, or live clinical data are used.",
+ "The assistant produces deterministic review packets suitable for pre-submission review."
+ ]
+ };
+}
+
+function renderMarkdownReport(packet) {
+ const lines = [
+ `# ${packet.title}`,
+ "",
+ `Assistant: ${packet.assistant}`,
+ `Overall decision: ${packet.decision}`,
+ `Average transfer score: ${packet.averageScore}`,
+ "",
+ "## Severity Summary",
+ "",
+ `- Critical: ${packet.severitySummary.critical}`,
+ `- High: ${packet.severitySummary.high}`,
+ `- Medium: ${packet.severitySummary.medium}`,
+ `- Low: ${packet.severitySummary.low}`,
+ "",
+ "## Claim Reviews",
+ ""
+ ];
+
+ for (const review of packet.claimReviews) {
+ lines.push(`### ${review.id}`);
+ lines.push("");
+ lines.push(`Decision: ${review.decision}`);
+ lines.push(`Score: ${review.score}`);
+ lines.push(`Evidence artifacts: ${review.evidenceCount}`);
+ if (review.findings.length === 0) {
+ lines.push("- No transfer-risk findings.");
+ } else {
+ for (const finding of review.findings) {
+ lines.push(`- ${finding.severity.toUpperCase()} ${finding.rule}: ${finding.message}`);
+ lines.push(` Action: ${finding.action}`);
+ }
+ }
+ lines.push("");
+ }
+
+ lines.push("## Reproducibility Actions");
+ lines.push("");
+ for (const action of packet.reproducibilityActions) {
+ lines.push(`- ${action.priority}: ${action.claimId} - ${action.action}`);
+ }
+
+ lines.push("");
+ lines.push("## Research Gap Prompts");
+ lines.push("");
+ for (const gap of packet.researchGaps) {
+ lines.push(`- ${gap.priority}: ${gap.topic} - ${gap.reason}`);
+ }
+
+ return `${lines.join("\n")}\n`;
+}
+
+function renderSvgSummary(packet) {
+ const barWidth = Math.max(10, packet.averageScore * 4);
+ const statusColor = packet.averageScore >= 62 ? "#2563eb" : "#b91c1c";
+ const rows = packet.claimReviews
+ .map((review, index) => {
+ const y = 130 + index * 52;
+ const width = Math.max(10, review.score * 4);
+ return [
+ `${review.id}`,
+ ``,
+ ``,
+ `${review.score} - ${review.decision}`
+ ].join("\n");
+ })
+ .join("\n");
+
+ return [
+ ``
+ ].join("\n");
+}
+
+module.exports = {
+ buildReviewPacket,
+ evaluateClaim,
+ renderMarkdownReport,
+ renderSvgSummary
+};
diff --git a/external-validity-transfer-assistant/package.json b/external-validity-transfer-assistant/package.json
new file mode 100644
index 00000000..13d41e83
--- /dev/null
+++ b/external-validity-transfer-assistant/package.json
@@ -0,0 +1,14 @@
+{
+ "name": "external-validity-transfer-assistant",
+ "version": "1.0.0",
+ "description": "Deterministic AI research assistant slice for external validity and population transfer review.",
+ "main": "index.js",
+ "private": true,
+ "type": "commonjs",
+ "scripts": {
+ "check": "node --check index.js && node --check sample-data.js && node --check demo.js && node --check demo-video.js && node --check test.js",
+ "test": "node test.js",
+ "demo": "node demo.js",
+ "demo:video": "node demo-video.js"
+ }
+}
diff --git a/external-validity-transfer-assistant/reports/demo.webm b/external-validity-transfer-assistant/reports/demo.webm
new file mode 100644
index 00000000..1dee4557
Binary files /dev/null and b/external-validity-transfer-assistant/reports/demo.webm differ
diff --git a/external-validity-transfer-assistant/reports/reviewer-packet.md b/external-validity-transfer-assistant/reports/reviewer-packet.md
new file mode 100644
index 00000000..595d6676
--- /dev/null
+++ b/external-validity-transfer-assistant/reports/reviewer-packet.md
@@ -0,0 +1,66 @@
+# Portable biomarker triage assistant for multi-site oncology cohorts
+
+Assistant: external-validity-transfer-assistant
+Overall decision: hold-for-transfer-evidence
+Average transfer score: 44
+
+## Severity Summary
+
+- Critical: 0
+- High: 5
+- Medium: 5
+- Low: 0
+
+## Claim Reviews
+
+### claim-generalizable-oncology
+
+Decision: quarantine-from-review-packet
+Score: 0
+Evidence artifacts: 2
+- HIGH population-transfer-gap: Claim claim-generalizable-oncology asserts populations not represented in linked evidence: pediatric, underrepresented ancestry.
+ Action: Narrow the claim wording or add external validation for each missing population.
+- HIGH setting-transfer-gap: Claim claim-generalizable-oncology asserts settings not represented in linked evidence: community hospital, international site.
+ Action: Add site-level validation evidence or mark the setting as a future research gap.
+- MEDIUM assay-transfer-gap: Claim claim-generalizable-oncology references unsupported assay or instrument contexts: single-cell-rna-seq.
+ Action: Separate assay-specific claims and document conversion limits before reviewer release.
+- MEDIUM runtime-transfer-gap: Claim claim-generalizable-oncology references runtime environments not covered by rerun evidence: cuda, cpu-only.
+ Action: Run the pipeline in each deployment-like environment or downgrade deployment readiness language.
+- HIGH no-external-validation: Claim claim-generalizable-oncology has broad transfer language without external validation evidence.
+ Action: Hold broad generalizability language until at least one independent validation artifact is linked.
+- MEDIUM strong-claim-subgroup-undercoverage: Strong claim claim-generalizable-oncology does not cover required subgroup evidence: pediatric, underrepresented ancestry.
+ Action: Convert the claim to qualified language or create a subgroup-specific validation plan.
+
+### claim-reproducible-pipeline
+
+Decision: review-ready
+Score: 100
+Evidence artifacts: 3
+- No transfer-risk findings.
+
+### claim-deployment-ready
+
+Decision: quarantine-from-review-packet
+Score: 32
+Evidence artifacts: 1
+- MEDIUM setting-transfer-gap: Claim claim-deployment-ready asserts settings not represented in linked evidence: low-resource clinic.
+ Action: Add site-level validation evidence or mark the setting as a future research gap.
+- HIGH no-external-validation: Claim claim-deployment-ready has broad transfer language without external validation evidence.
+ Action: Hold broad generalizability language until at least one independent validation artifact is linked.
+- HIGH no-runnable-transfer-evidence: Claim claim-deployment-ready lacks reproducible runtime evidence for the asserted context.
+ Action: Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible.
+- MEDIUM strong-claim-subgroup-undercoverage: Strong claim claim-deployment-ready does not cover required subgroup evidence: pediatric, underrepresented ancestry.
+ Action: Convert the claim to qualified language or create a subgroup-specific validation plan.
+
+## Reproducibility Actions
+
+- recommended: claim-generalizable-oncology - Run the pipeline in each deployment-like environment or downgrade deployment readiness language.
+- blocking: claim-generalizable-oncology - Hold broad generalizability language until at least one independent validation artifact is linked.
+- blocking: claim-deployment-ready - Hold broad generalizability language until at least one independent validation artifact is linked.
+- blocking: claim-deployment-ready - Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible.
+
+## Research Gap Prompts
+
+- high: pediatric oncology RNA-seq validation - frequently cited limitation with low replication coverage
+- high: CPU-only low-resource clinic reproducibility run - deployment claim depends on clinic-like runtime evidence
+- high: ancestry-balanced external validation - underrepresented ancestry is asserted but not evidenced
diff --git a/external-validity-transfer-assistant/reports/summary.json b/external-validity-transfer-assistant/reports/summary.json
new file mode 100644
index 00000000..ccc8f2c5
--- /dev/null
+++ b/external-validity-transfer-assistant/reports/summary.json
@@ -0,0 +1,263 @@
+{
+ "projectId": "project-transfer-001",
+ "title": "Portable biomarker triage assistant for multi-site oncology cohorts",
+ "assistant": "external-validity-transfer-assistant",
+ "issue": "SCIBASE-AI/SCIBASE.AI#16",
+ "averageScore": 44,
+ "decision": "hold-for-transfer-evidence",
+ "severitySummary": {
+ "critical": 0,
+ "high": 5,
+ "medium": 5,
+ "low": 0
+ },
+ "claimReviews": [
+ {
+ "id": "claim-generalizable-oncology",
+ "text": "The model generalizes across oncology patient populations and hospital settings.",
+ "score": 0,
+ "decision": "quarantine-from-review-packet",
+ "evidenceCount": 2,
+ "observedScope": {
+ "populations": [
+ "adult"
+ ],
+ "settings": [
+ "academic hospital"
+ ],
+ "instruments": [
+ "bulk-rna-seq"
+ ],
+ "environments": [
+ "python-3.11"
+ ],
+ "externalValidation": false,
+ "runnableEvidence": true
+ },
+ "findings": [
+ {
+ "severity": "high",
+ "rule": "population-transfer-gap",
+ "message": "Claim claim-generalizable-oncology asserts populations not represented in linked evidence: pediatric, underrepresented ancestry.",
+ "action": "Narrow the claim wording or add external validation for each missing population."
+ },
+ {
+ "severity": "high",
+ "rule": "setting-transfer-gap",
+ "message": "Claim claim-generalizable-oncology asserts settings not represented in linked evidence: community hospital, international site.",
+ "action": "Add site-level validation evidence or mark the setting as a future research gap."
+ },
+ {
+ "severity": "medium",
+ "rule": "assay-transfer-gap",
+ "message": "Claim claim-generalizable-oncology references unsupported assay or instrument contexts: single-cell-rna-seq.",
+ "action": "Separate assay-specific claims and document conversion limits before reviewer release."
+ },
+ {
+ "severity": "medium",
+ "rule": "runtime-transfer-gap",
+ "message": "Claim claim-generalizable-oncology references runtime environments not covered by rerun evidence: cuda, cpu-only.",
+ "action": "Run the pipeline in each deployment-like environment or downgrade deployment readiness language."
+ },
+ {
+ "severity": "high",
+ "rule": "no-external-validation",
+ "message": "Claim claim-generalizable-oncology has broad transfer language without external validation evidence.",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "severity": "medium",
+ "rule": "strong-claim-subgroup-undercoverage",
+ "message": "Strong claim claim-generalizable-oncology does not cover required subgroup evidence: pediatric, underrepresented ancestry.",
+ "action": "Convert the claim to qualified language or create a subgroup-specific validation plan."
+ }
+ ]
+ },
+ {
+ "id": "claim-reproducible-pipeline",
+ "text": "The manuscript includes enough artifacts for an independent lab to rerun the triage pipeline.",
+ "score": 100,
+ "decision": "review-ready",
+ "evidenceCount": 3,
+ "observedScope": {
+ "populations": [
+ "adult"
+ ],
+ "settings": [
+ "academic hospital",
+ "community hospital"
+ ],
+ "instruments": [
+ "bulk-rna-seq"
+ ],
+ "environments": [
+ "python-3.11"
+ ],
+ "externalValidation": true,
+ "runnableEvidence": true
+ },
+ "findings": []
+ },
+ {
+ "id": "claim-deployment-ready",
+ "text": "The assistant is ready for deployment guidance in low-resource clinics.",
+ "score": 32,
+ "decision": "quarantine-from-review-packet",
+ "evidenceCount": 1,
+ "observedScope": {
+ "populations": [
+ "adult"
+ ],
+ "settings": [
+ "community hospital"
+ ],
+ "instruments": [
+ "bulk-rna-seq"
+ ],
+ "environments": [
+ "cpu-only"
+ ],
+ "externalValidation": false,
+ "runnableEvidence": false
+ },
+ "findings": [
+ {
+ "severity": "medium",
+ "rule": "setting-transfer-gap",
+ "message": "Claim claim-deployment-ready asserts settings not represented in linked evidence: low-resource clinic.",
+ "action": "Add site-level validation evidence or mark the setting as a future research gap."
+ },
+ {
+ "severity": "high",
+ "rule": "no-external-validation",
+ "message": "Claim claim-deployment-ready has broad transfer language without external validation evidence.",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "severity": "high",
+ "rule": "no-runnable-transfer-evidence",
+ "message": "Claim claim-deployment-ready lacks reproducible runtime evidence for the asserted context.",
+ "action": "Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible."
+ },
+ {
+ "severity": "medium",
+ "rule": "strong-claim-subgroup-undercoverage",
+ "message": "Strong claim claim-deployment-ready does not cover required subgroup evidence: pediatric, underrepresented ancestry.",
+ "action": "Convert the claim to qualified language or create a subgroup-specific validation plan."
+ }
+ ]
+ }
+ ],
+ "peerReviewSuggestions": [
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "high",
+ "suggestion": "Claim claim-generalizable-oncology asserts populations not represented in linked evidence: pediatric, underrepresented ancestry.",
+ "action": "Narrow the claim wording or add external validation for each missing population."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "high",
+ "suggestion": "Claim claim-generalizable-oncology asserts settings not represented in linked evidence: community hospital, international site.",
+ "action": "Add site-level validation evidence or mark the setting as a future research gap."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "medium",
+ "suggestion": "Claim claim-generalizable-oncology references unsupported assay or instrument contexts: single-cell-rna-seq.",
+ "action": "Separate assay-specific claims and document conversion limits before reviewer release."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "medium",
+ "suggestion": "Claim claim-generalizable-oncology references runtime environments not covered by rerun evidence: cuda, cpu-only.",
+ "action": "Run the pipeline in each deployment-like environment or downgrade deployment readiness language."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "high",
+ "suggestion": "Claim claim-generalizable-oncology has broad transfer language without external validation evidence.",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "severity": "medium",
+ "suggestion": "Strong claim claim-generalizable-oncology does not cover required subgroup evidence: pediatric, underrepresented ancestry.",
+ "action": "Convert the claim to qualified language or create a subgroup-specific validation plan."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "severity": "medium",
+ "suggestion": "Claim claim-deployment-ready asserts settings not represented in linked evidence: low-resource clinic.",
+ "action": "Add site-level validation evidence or mark the setting as a future research gap."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "severity": "high",
+ "suggestion": "Claim claim-deployment-ready has broad transfer language without external validation evidence.",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "severity": "high",
+ "suggestion": "Claim claim-deployment-ready lacks reproducible runtime evidence for the asserted context.",
+ "action": "Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "severity": "medium",
+ "suggestion": "Strong claim claim-deployment-ready does not cover required subgroup evidence: pediatric, underrepresented ancestry.",
+ "action": "Convert the claim to qualified language or create a subgroup-specific validation plan."
+ }
+ ],
+ "reproducibilityActions": [
+ {
+ "claimId": "claim-generalizable-oncology",
+ "priority": "recommended",
+ "action": "Run the pipeline in each deployment-like environment or downgrade deployment readiness language."
+ },
+ {
+ "claimId": "claim-generalizable-oncology",
+ "priority": "blocking",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "priority": "blocking",
+ "action": "Hold broad generalizability language until at least one independent validation artifact is linked."
+ },
+ {
+ "claimId": "claim-deployment-ready",
+ "priority": "blocking",
+ "action": "Add a deterministic runbook, manifest, or notebook rerun before the assistant marks the claim reproducible."
+ }
+ ],
+ "researchGaps": [
+ {
+ "id": "gap-pediatric-oncology-rnaseq",
+ "topic": "pediatric oncology RNA-seq validation",
+ "reason": "frequently cited limitation with low replication coverage",
+ "priority": "high",
+ "suggestedNextStep": "Use pediatric oncology RNA-seq validation as a targeted validation or grant-planning workstream."
+ },
+ {
+ "id": "gap-cpu-only-clinic-run",
+ "topic": "CPU-only low-resource clinic reproducibility run",
+ "reason": "deployment claim depends on clinic-like runtime evidence",
+ "priority": "high",
+ "suggestedNextStep": "Use CPU-only low-resource clinic reproducibility run as a targeted validation or grant-planning workstream."
+ },
+ {
+ "id": "gap-ancestry-balanced-evaluation",
+ "topic": "ancestry-balanced external validation",
+ "reason": "underrepresented ancestry is asserted but not evidenced",
+ "priority": "high",
+ "suggestedNextStep": "Use ancestry-balanced external validation as a targeted validation or grant-planning workstream."
+ }
+ ],
+ "safetyNotes": [
+ "Synthetic data only.",
+ "No external APIs, credentials, private manuscripts, or live clinical data are used.",
+ "The assistant produces deterministic review packets suitable for pre-submission review."
+ ]
+}
diff --git a/external-validity-transfer-assistant/reports/summary.svg b/external-validity-transfer-assistant/reports/summary.svg
new file mode 100644
index 00000000..f07fd95f
--- /dev/null
+++ b/external-validity-transfer-assistant/reports/summary.svg
@@ -0,0 +1,21 @@
+
\ No newline at end of file
diff --git a/external-validity-transfer-assistant/requirements-map.md b/external-validity-transfer-assistant/requirements-map.md
new file mode 100644
index 00000000..8650ed6f
--- /dev/null
+++ b/external-validity-transfer-assistant/requirements-map.md
@@ -0,0 +1,29 @@
+# Requirements Map
+
+## SCIBASE #16 Capability Mapping
+
+### Auto Peer Review Reports
+
+- Produces structured claim-level peer-review findings.
+- Flags clarity and scope mismatch where claims overstate population, setting, assay, or runtime support.
+- Emits reviewer-ready actions for claim wording, validation evidence, and transfer-risk holds.
+
+### Reproducibility Checker
+
+- Checks whether linked evidence includes reproducible runtime artifacts.
+- Flags claims that depend on deployment environments without matching rerun evidence.
+- Produces blocking or recommended reproducibility actions for reviewer packets.
+
+### Research Gap Finder
+
+- Converts missing transfer contexts into research-gap prompts.
+- Ranks gaps that fit the lab's declared capabilities.
+- Highlights pediatric validation, ancestry-balanced evaluation, and CPU-only clinic rerun gaps from synthetic corpus signals.
+
+## Acceptance Notes
+
+- Dependency-free CommonJS module.
+- Deterministic synthetic sample data.
+- Local tests for broad-claim holds, missing evidence quarantine, external validation handling, report rendering, and research-gap output.
+- Generated JSON, Markdown, and SVG artifacts via `npm run demo`.
+- No external API calls, credentials, private research data, or live clinical records.
diff --git a/external-validity-transfer-assistant/sample-data.js b/external-validity-transfer-assistant/sample-data.js
new file mode 100644
index 00000000..23f571e2
--- /dev/null
+++ b/external-validity-transfer-assistant/sample-data.js
@@ -0,0 +1,149 @@
+const project = {
+ id: "project-transfer-001",
+ title: "Portable biomarker triage assistant for multi-site oncology cohorts",
+ domain: "clinical-ai",
+ labCapabilities: ["rna-seq", "clinical-metadata", "containerized-python", "external-cohort-review"],
+ manuscript: {
+ title: "A generalizable biomarker triage model for oncology screening",
+ targetUse: "pre-submission peer review",
+ claims: [
+ {
+ id: "claim-generalizable-oncology",
+ text: "The model generalizes across oncology patient populations and hospital settings.",
+ assertedScope: {
+ populations: ["adult", "pediatric", "underrepresented ancestry"],
+ settings: ["academic hospital", "community hospital", "international site"],
+ instruments: ["bulk-rna-seq", "single-cell-rna-seq"],
+ environments: ["python-3.11", "cuda", "cpu-only"]
+ },
+ evidenceIds: ["internal-adult-cohort", "academic-hospital-runbook"],
+ confidence: "strong"
+ },
+ {
+ id: "claim-reproducible-pipeline",
+ text: "The manuscript includes enough artifacts for an independent lab to rerun the triage pipeline.",
+ assertedScope: {
+ populations: ["adult"],
+ settings: ["academic hospital"],
+ instruments: ["bulk-rna-seq"],
+ environments: ["python-3.11"]
+ },
+ evidenceIds: ["container-runbook", "clean-data-manifest", "external-adult-validation"],
+ confidence: "moderate"
+ },
+ {
+ id: "claim-deployment-ready",
+ text: "The assistant is ready for deployment guidance in low-resource clinics.",
+ assertedScope: {
+ populations: ["adult"],
+ settings: ["low-resource clinic", "community hospital"],
+ instruments: ["bulk-rna-seq"],
+ environments: ["cpu-only"]
+ },
+ evidenceIds: ["community-hospital-protocol"],
+ confidence: "strong"
+ }
+ ],
+ requiredSubgroups: ["adult", "pediatric", "underrepresented ancestry"],
+ declaredLimitations: [
+ "The pilot cohort is single-country.",
+ "No pediatric external cohort is currently available."
+ ]
+ },
+ evidence: [
+ {
+ id: "internal-adult-cohort",
+ type: "internal-cohort",
+ population: "adult",
+ setting: "academic hospital",
+ instrument: "bulk-rna-seq",
+ environment: "python-3.11",
+ sampleSize: 820,
+ reproducible: true,
+ externalValidation: false,
+ limitations: ["single-country", "academic-site-only"]
+ },
+ {
+ id: "academic-hospital-runbook",
+ type: "runbook",
+ population: "adult",
+ setting: "academic hospital",
+ instrument: "bulk-rna-seq",
+ environment: "python-3.11",
+ sampleSize: 0,
+ reproducible: true,
+ externalValidation: false,
+ limitations: ["no-community-site-smoke-test"]
+ },
+ {
+ id: "container-runbook",
+ type: "runtime-evidence",
+ population: "adult",
+ setting: "academic hospital",
+ instrument: "bulk-rna-seq",
+ environment: "python-3.11",
+ sampleSize: 0,
+ reproducible: true,
+ externalValidation: false,
+ limitations: []
+ },
+ {
+ id: "clean-data-manifest",
+ type: "artifact-manifest",
+ population: "adult",
+ setting: "academic hospital",
+ instrument: "bulk-rna-seq",
+ environment: "python-3.11",
+ sampleSize: 820,
+ reproducible: true,
+ externalValidation: false,
+ limitations: []
+ },
+ {
+ id: "external-adult-validation",
+ type: "external-validation",
+ population: "adult",
+ setting: "community hospital",
+ instrument: "bulk-rna-seq",
+ environment: "python-3.11",
+ sampleSize: 290,
+ reproducible: true,
+ externalValidation: true,
+ limitations: ["adult-only"]
+ },
+ {
+ id: "community-hospital-protocol",
+ type: "protocol",
+ population: "adult",
+ setting: "community hospital",
+ instrument: "bulk-rna-seq",
+ environment: "cpu-only",
+ sampleSize: 0,
+ reproducible: false,
+ externalValidation: false,
+ limitations: ["protocol-only", "no-completed-run"]
+ }
+ ],
+ corpusSignals: [
+ {
+ id: "gap-pediatric-oncology-rnaseq",
+ topic: "pediatric oncology RNA-seq validation",
+ reason: "frequently cited limitation with low replication coverage",
+ labFit: ["rna-seq", "external-cohort-review"]
+ },
+ {
+ id: "gap-cpu-only-clinic-run",
+ topic: "CPU-only low-resource clinic reproducibility run",
+ reason: "deployment claim depends on clinic-like runtime evidence",
+ labFit: ["containerized-python"]
+ },
+ {
+ id: "gap-ancestry-balanced-evaluation",
+ topic: "ancestry-balanced external validation",
+ reason: "underrepresented ancestry is asserted but not evidenced",
+ labFit: ["clinical-metadata", "external-cohort-review"]
+ }
+ ]
+};
+
+module.exports = { project };
diff --git a/external-validity-transfer-assistant/test.js b/external-validity-transfer-assistant/test.js
new file mode 100644
index 00000000..265d7471
--- /dev/null
+++ b/external-validity-transfer-assistant/test.js
@@ -0,0 +1,57 @@
+const assert = require("assert");
+const { project } = require("./sample-data");
+const { buildReviewPacket, evaluateClaim, renderMarkdownReport, renderSvgSummary } = require("./index");
+
+const packet = buildReviewPacket(project);
+
+assert.strictEqual(packet.assistant, "external-validity-transfer-assistant");
+assert.strictEqual(packet.issue, "SCIBASE-AI/SCIBASE.AI#16");
+assert.ok(packet.peerReviewSuggestions.length >= 6, "expected transfer-risk peer review suggestions");
+assert.ok(packet.reproducibilityActions.length >= 3, "expected reproducibility actions");
+assert.ok(packet.researchGaps.length >= 3, "expected research-gap prompts");
+
+const broadClaim = packet.claimReviews.find((review) => review.id === "claim-generalizable-oncology");
+assert.ok(broadClaim, "expected broad generalizability claim review");
+assert.ok(
+ ["hold-for-transfer-evidence", "quarantine-from-review-packet"].includes(broadClaim.decision),
+ "broad claim should be held or quarantined until transfer evidence exists"
+);
+assert.ok(
+ broadClaim.findings.some((finding) => finding.rule === "population-transfer-gap"),
+ "broad claim should flag missing population transfer evidence"
+);
+assert.ok(
+ broadClaim.findings.some((finding) => finding.rule === "no-external-validation"),
+ "broad claim should require external validation"
+);
+
+const reproducibleClaim = packet.claimReviews.find((review) => review.id === "claim-reproducible-pipeline");
+assert.ok(reproducibleClaim.score > broadClaim.score, "reproducible claim should score better than broad claim");
+assert.strictEqual(reproducibleClaim.observedScope.externalValidation, true);
+assert.strictEqual(reproducibleClaim.observedScope.runnableEvidence, true);
+
+const emptyClaim = {
+ id: "claim-empty",
+ text: "The model works for every lab.",
+ assertedScope: {
+ populations: ["adult"],
+ settings: ["international site"],
+ instruments: ["bulk-rna-seq"],
+ environments: ["python-3.11"]
+ },
+ evidenceIds: [],
+ confidence: "strong"
+};
+const emptyReview = evaluateClaim(emptyClaim, project.evidence, project.manuscript);
+assert.strictEqual(emptyReview.decision, "quarantine-from-review-packet");
+assert.ok(emptyReview.findings.some((finding) => finding.rule === "missing-evidence"));
+
+const markdown = renderMarkdownReport(packet);
+assert.ok(markdown.includes("## Claim Reviews"));
+assert.ok(markdown.includes("## Research Gap Prompts"));
+
+const svg = renderSvgSummary(packet);
+assert.ok(svg.includes("