[codex] Add AI output evidence verifier

ai-output-evidence-verifier/README.md

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+# AI Output Evidence Verifier
+
+This module is a focused implementation slice for SCIBASE issue #13, "AI-Assisted Research Tools (MVP Level)." It models the reviewer gate that should run before AI-generated summaries, peer-review aids, citation suggestions, or manuscript action packets are shown as trustworthy research guidance.
+
+The verifier answers four practical questions:
+
+- Are the AI tool's claims backed by known project sources?
+- Are any cited sources retracted, under expression of concern, or too stale for the claim type?
+- Does each output mode include the disclosure and citation fields expected by a research assistant?
+- Which concrete reviewer actions should be completed before the output is released?
+
+## Files
+
+- `src/ai-output-evidence-verifier.js` contains deterministic evidence checks and audit digest generation.
+- `data/sample-assistant-output.json` provides a mixed research-assistant output packet.
+- `test/ai-output-evidence-verifier.test.js` covers blocked and releasable output paths.
+- `scripts/demo.js` prints a concise release-readiness report for the sample packet.
+- `docs/demo.svg` and `docs/demo.mp4` show the intended reviewer surface.
+
+## Run
+
+```sh
+npm test
+npm run demo
+npm run demo:video
+```
+
+The implementation is dependency-free and uses synthetic project data only.

ai-output-evidence-verifier/data/sample-assistant-output.json

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+{
+  "project": {
+    "id": "proj-neuro-imaging-42",
+    "title": "Neurovascular Calcium Imaging Protocol",
+    "domain": "neuroscience",
+    "reviewDate": "2026-05-16",
+    "requiredDisclosures": [
+      "ai-generated",
+      "human-review-required",
+      "source-coverage"
+    ]
+  },
+  "sources": [
+    {
+      "id": "paper-astrocyte-2025",
+      "title": "Astrocyte calcium signaling during sleep spindle propagation",
+      "type": "preprint",
+      "status": "active",
+      "publishedAt": "2025-11-20",
+      "reviewedAt": "2026-05-10",
+      "tags": ["calcium-imaging", "sleep-spindles", "two-photon"],
+      "url": "https://example.org/preprints/astrocyte-calcium-2025",
+      "license": "CC-BY-4.0"
+    },
+    {
+      "id": "dataset-ca-raw",
+      "title": "Raw calcium-imaging dataset and segmentation masks",
+      "type": "dataset",
+      "status": "active",
+      "publishedAt": "2026-01-12",
+      "reviewedAt": "2026-05-14",
+      "tags": ["calcium-imaging", "raw-data", "segmentation"],
+      "url": "https://example.org/datasets/ca-raw",
+      "license": "CC0-1.0"
+    },
+    {
+      "id": "paper-retired-marker",
+      "title": "Legacy glial activation marker in fixed tissue",
+      "type": "article",
+      "status": "retracted",
+      "publishedAt": "2021-03-10",
+      "reviewedAt": "2024-01-10",
+      "tags": ["fixed-tissue", "marker-panel"],
+      "url": "https://example.org/articles/retracted-marker",
+      "license": "unknown"
+    }
+  ],
+  "outputs": [
+    {
+      "id": "summary-main",
+      "mode": "summary",
+      "audience": "collaborator",
+      "generatedAt": "2026-05-16T17:30:00Z",
+      "disclosures": ["ai-generated", "human-review-required", "source-coverage"],
+      "claims": [
+        {
+          "id": "c1",
+          "text": "Sleep spindle events correlate with astrocyte calcium transients in the sample cohort.",
+          "sourceIds": ["paper-astrocyte-2025", "dataset-ca-raw"],
+          "tags": ["calcium-imaging", "sleep-spindles"],
+          "confidence": 0.84
+        },
+        {
+          "id": "c2",
+          "text": "The analysis proves a causal glial mechanism for all sleep-stage transitions.",
+          "sourceIds": [],
+          "tags": ["causality", "sleep-stages"],
+          "confidence": 0.61
+        }
+      ]
+    },
+    {
+      "id": "peer-review-aid",
+      "mode": "peer-review",
+      "audience": "author",
+      "generatedAt": "2026-05-16T17:34:00Z",
+      "disclosures": ["ai-generated", "human-review-required"],
+      "claims": [
+        {
+          "id": "c3",
+          "text": "The marker panel is validated for fixed tissue and can be cited without caveats.",
+          "sourceIds": ["paper-retired-marker"],
+          "tags": ["marker-panel"],
+          "confidence": 0.72
+        },
+        {
+          "id": "c4",
+          "text": "The manuscript should disclose segmentation mask provenance next to the methods section.",
+          "sourceIds": ["dataset-ca-raw"],
+          "tags": ["raw-data", "segmentation"],
+          "confidence": 0.9
+        }
+      ]
+    },
+    {
+      "id": "citation-suggestions",
+      "mode": "citation-recommendation",
+      "audience": "editor",
+      "generatedAt": "2026-05-16T17:36:00Z",
+      "disclosures": ["ai-generated", "human-review-required", "source-coverage"],
+      "claims": [
+        {
+          "id": "c5",
+          "text": "Prioritize the calcium-imaging preprint and raw dataset in the collaborator handoff.",
+          "sourceIds": ["paper-astrocyte-2025", "dataset-ca-raw"],
+          "tags": ["citation", "handoff"],
+          "confidence": 0.88
+        }
+      ]
+    }
+  ]
+}

ai-output-evidence-verifier/docs/requirement-map.md

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+# Requirement Map
+
+Issue #13 asks for AI-assisted research tools that help with summaries, peer-review diagnostics, citation management, and research quality without asking reviewers to trust ungrounded model output. This slice implements a deterministic evidence gate for those tool outputs.
+
+| Requirement area | Implementation evidence |
+| --- | --- |
+| AI paper summarizer | Validates summary claims, source IDs, source freshness, and required AI disclosures before release. |
+| AI peer review aid | Blocks peer-review suggestions that cite retracted sources or omit source coverage disclosure. |
+| Citation management | Verifies citation-recommendation claims cite known source records of acceptable types. |
+| Technical issue checking | Produces reviewer tasks for unsupported claims, unsafe source status, stale review evidence, and missing disclosure. |
+| MVP-level local demo | `npm run demo` prints a deterministic release-readiness report from synthetic data. |
+| Reviewer confidence | `auditDigest` provides a stable hash of the reviewed outputs, policy thresholds, findings, and source coverage. |
+| Demo video | `npm run demo:video` renders `docs/demo.mp4` without service credentials or external APIs. |
+
+This module intentionally avoids live LLM calls, scraping, external credentials, and private data. It is the trust layer around AI outputs, not another generic model wrapper.

ai-output-evidence-verifier/package.json

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+{
+  "name": "ai-output-evidence-verifier",
+  "version": "0.1.0",
+  "private": true,
+  "description": "Evidence verifier for AI-assisted research tool outputs for SCIBASE issue #13.",
+  "type": "module",
+  "scripts": {
+    "test": "node test/ai-output-evidence-verifier.test.js",
+    "demo": "node scripts/demo.js",
+    "demo:video": "clang -fobjc-arc -framework Foundation -framework AppKit -framework AVFoundation -framework CoreMedia -framework CoreVideo scripts/render-demo-video.m -o /tmp/scibase-ai-output-evidence-demo && /tmp/scibase-ai-output-evidence-demo docs/demo.mp4"
+  },
+  "engines": {
+    "node": ">=18"
+  }
+}

ai-output-evidence-verifier/scripts/demo.js

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+import { readFile } from "node:fs/promises";
+import { fileURLToPath } from "node:url";
+import { dirname, join } from "node:path";
+import { verifyAiOutputEvidence } from "../src/ai-output-evidence-verifier.js";
+
+const here = dirname(fileURLToPath(import.meta.url));
+const samplePath = join(here, "..", "data", "sample-assistant-output.json");
+const sample = JSON.parse(await readFile(samplePath, "utf8"));
+const report = verifyAiOutputEvidence(sample);
+
+console.log(`Project: ${report.project.title}`);
+console.log(`Ready: ${report.ready ? "yes" : "no"}`);
+console.log(`Recommendation: ${report.recommendation}`);
+console.log(`Outputs: ${report.counts.outputs}`);
+console.log(`Claims: ${report.counts.claims}`);
+console.log(`Sources: ${report.counts.sources}`);
+console.log(`Source coverage: ${report.sourceCoverage.knownCount}/${report.sourceCoverage.referencedCount} known`);
+console.log(`Blockers: ${report.counts.blockers}`);
+console.log(`Warnings: ${report.counts.warnings}`);
+console.log(`Reviewer tasks: ${report.counts.reviewerTasks}`);
+console.log(`Audit digest: ${report.auditDigest}`);
+
+for (const task of report.reviewerTasks.slice(0, 5)) {
+  console.log(`- [${task.severity}] ${task.target}: ${task.action}`);
+}

ai-output-evidence-verifier/scripts/render-demo-video.m

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+#import <Foundation/Foundation.h>
+#import <AppKit/AppKit.h>
+#import <AVFoundation/AVFoundation.h>
+#import <CoreVideo/CoreVideo.h>
+
+static NSColor *RGB(CGFloat r, CGFloat g, CGFloat b) {
+  return [NSColor colorWithCalibratedRed:r / 255.0 green:g / 255.0 blue:b / 255.0 alpha:1.0];
+}
+
+static void FillRounded(NSRect rect, CGFloat radius, NSColor *color) {
+  NSBezierPath *path = [NSBezierPath bezierPathWithRoundedRect:rect xRadius:radius yRadius:radius];
+  [color setFill];
+  [path fill];
+}
+
+static void StrokeRounded(NSRect rect, CGFloat radius, NSColor *color) {
+  NSBezierPath *path = [NSBezierPath bezierPathWithRoundedRect:rect xRadius:radius yRadius:radius];
+  [color setStroke];
+  [path setLineWidth:2.0];
+  [path stroke];
+}
+
+static void DrawText(NSString *text, NSRect rect, CGFloat size, NSColor *color, NSFontWeight weight) {
+  NSMutableParagraphStyle *style = [[NSMutableParagraphStyle alloc] init];
+  style.lineBreakMode = NSLineBreakByWordWrapping;
+  NSDictionary *attrs = @{
+    NSFontAttributeName: [NSFont systemFontOfSize:size weight:weight],
+    NSForegroundColorAttributeName: color,
+    NSParagraphStyleAttributeName: style
+  };
+  [text drawInRect:rect withAttributes:attrs];
+}
+
+static void DrawCard(NSString *title, NSArray<NSString *> *lines, NSRect rect, NSColor *fill, NSColor *stroke, NSColor *titleColor, NSColor *bodyColor) {
+  FillRounded(rect, 14.0, fill);
+  StrokeRounded(rect, 14.0, stroke);
+  DrawText(title, NSMakeRect(rect.origin.x + 22, rect.origin.y + rect.size.height - 56, rect.size.width - 44, 30), 22, titleColor, NSFontWeightBold);
+  for (NSUInteger i = 0; i < lines.count; i++) {
+    DrawText(lines[i], NSMakeRect(rect.origin.x + 22, rect.origin.y + rect.size.height - 96 - (CGFloat)i * 31, rect.size.width - 44, 28), 18, bodyColor, NSFontWeightRegular);
+  }
+}
+
+static void DrawFrame(CGContextRef cg, int width, int height, int frame) {
+  [NSGraphicsContext saveGraphicsState];
+  NSGraphicsContext *context = [NSGraphicsContext graphicsContextWithCGContext:cg flipped:NO];
+  [NSGraphicsContext setCurrentContext:context];
+
+  [RGB(245, 247, 249) setFill];
+  NSRectFill(NSMakeRect(0, 0, width, height));
+
+  FillRounded(NSMakeRect(64, 54, 1152, 612), 18, [NSColor whiteColor]);
+  StrokeRounded(NSMakeRect(64, 54, 1152, 612), 18, RGB(207, 216, 223));
+
+  CGFloat progress = MIN(1.0, MAX(0.0, ((CGFloat)frame - 8.0) / 72.0));
+  DrawText(@"AI Output Evidence Verifier", NSMakeRect(104, 595, 760, 48), 36, RGB(23, 33, 43), NSFontWeightBold);
+  DrawText(@"Research-assistant output trust gate for SCIBASE issue #13", NSMakeRect(104, 563, 860, 28), 18, RGB(82, 99, 113), NSFontWeightRegular);
+
+  DrawCard(@"Source Coverage", @[@"known sources", @"missing IDs", @"source types"], NSMakeRect(104, 362, 252, 152), RGB(233, 246, 240), RGB(159, 208, 186), RGB(23, 72, 49), RGB(39, 99, 74));
+  DrawCard(@"Evidence Risk", @[@"unsupported claims", @"retracted sources", @"high-risk tags"], NSMakeRect(386, 362, 252, 152), RGB(255, 240, 230), RGB(233, 180, 137), RGB(121, 59, 16), RGB(143, 78, 32));
+  DrawCard(@"Disclosure Gate", @[@"AI generated", @"human review", @"source coverage"], NSMakeRect(668, 362, 252, 152), RGB(237, 242, 251), RGB(171, 192, 231), RGB(32, 60, 105), RGB(49, 85, 143));
+  DrawCard(@"Audit Digest", @[@"policy hash", @"review packet", @"stable handoff"], NSMakeRect(950, 362, 226, 152), RGB(248, 237, 247), RGB(213, 171, 208), RGB(90, 40, 84), RGB(115, 56, 107));
+
+  FillRounded(NSMakeRect(104, 136, 1072, 174), 14, RGB(23, 33, 43));
+  DrawText(@"Neurovascular Calcium Imaging Protocol", NSMakeRect(132, 250, 740, 34), 24, [NSColor whiteColor], NSFontWeightBold);
+  DrawText(@"3 AI outputs, 5 claims, 3 sources, deterministic reviewer tasks", NSMakeRect(132, 209, 930, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+  DrawText(@"Recommendation: hold for evidence fix before collaborator release", NSMakeRect(132, 172, 930, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+  DrawText(@"Blocks unsupported, high-risk, and retracted-source claims", NSMakeRect(132, 135, 930, 28), 18, RGB(200, 211, 220), NSFontWeightRegular);
+
+  FillRounded(NSMakeRect(132, 93, 980.0 * progress, 10), 5, RGB(219, 88, 66));
+  DrawText(@"evidence gate running", NSMakeRect(132 + 980.0 * progress + 14, 84, 220, 28), 14, RGB(82, 99, 113), NSFontWeightMedium);
+
+  [NSGraphicsContext restoreGraphicsState];
+}
+
+int main(int argc, const char *argv[]) {
+  @autoreleasepool {
+    if (argc < 2) {
+      fprintf(stderr, "usage: render-demo-video output.mp4\n");
+      return 2;
+    }
+
+    NSString *outputPath = [NSString stringWithUTF8String:argv[1]];
+    NSURL *outputURL = [NSURL fileURLWithPath:outputPath];
+    [[NSFileManager defaultManager] removeItemAtURL:outputURL error:nil];
+
+    const int width = 1280;
+    const int height = 720;
+    NSError *error = nil;
+    AVAssetWriter *writer = [[AVAssetWriter alloc] initWithURL:outputURL fileType:AVFileTypeMPEG4 error:&error];
+    if (!writer) {
+      NSLog(@"writer error: %@", error);
+      return 1;
+    }
+
+    NSDictionary *videoSettings = @{
+      AVVideoCodecKey: AVVideoCodecTypeH264,
+      AVVideoWidthKey: @(width),
+      AVVideoHeightKey: @(height)
+    };
+    AVAssetWriterInput *input = [AVAssetWriterInput assetWriterInputWithMediaType:AVMediaTypeVideo outputSettings:videoSettings];
+    input.expectsMediaDataInRealTime = NO;
+
+    NSDictionary *pixelBufferAttributes = @{
+      (NSString *)kCVPixelBufferPixelFormatTypeKey: @(kCVPixelFormatType_32ARGB),
+      (NSString *)kCVPixelBufferWidthKey: @(width),
+      (NSString *)kCVPixelBufferHeightKey: @(height)
+    };
+    AVAssetWriterInputPixelBufferAdaptor *adaptor = [AVAssetWriterInputPixelBufferAdaptor assetWriterInputPixelBufferAdaptorWithAssetWriterInput:input sourcePixelBufferAttributes:pixelBufferAttributes];
+
+    if (![writer canAddInput:input]) {
+      NSLog(@"cannot add writer input");
+      return 1;
+    }
+    [writer addInput:input];
+    [writer startWriting];
+    [writer startSessionAtSourceTime:kCMTimeZero];
+
+    CGColorSpaceRef colorSpace = CGColorSpaceCreateDeviceRGB();
+    for (int frame = 0; frame < 96; frame++) {
+      while (!input.readyForMoreMediaData) {
+        [NSThread sleepForTimeInterval:0.01];
+      }
+
+      CVPixelBufferRef buffer = NULL;
+      CVPixelBufferPoolCreatePixelBuffer(NULL, adaptor.pixelBufferPool, &buffer);
+      CVPixelBufferLockBaseAddress(buffer, 0);
+      void *baseAddress = CVPixelBufferGetBaseAddress(buffer);
+      size_t bytesPerRow = CVPixelBufferGetBytesPerRow(buffer);
+      CGContextRef cg = CGBitmapContextCreate(baseAddress, width, height, 8, bytesPerRow, colorSpace, kCGImageAlphaNoneSkipFirst);
+      DrawFrame(cg, width, height, frame);
+      CGContextRelease(cg);
+      CVPixelBufferUnlockBaseAddress(buffer, 0);
+
+      CMTime presentationTime = CMTimeMake(frame, 24);
+      [adaptor appendPixelBuffer:buffer withPresentationTime:presentationTime];
+      CVPixelBufferRelease(buffer);
+    }
+
+    CGColorSpaceRelease(colorSpace);
+    [input markAsFinished];
+
+    dispatch_semaphore_t sema = dispatch_semaphore_create(0);
+    [writer finishWritingWithCompletionHandler:^{
+      dispatch_semaphore_signal(sema);
+    }];
+    dispatch_semaphore_wait(sema, DISPATCH_TIME_FOREVER);
+
+    if (writer.status != AVAssetWriterStatusCompleted) {
+      NSLog(@"writer failed: %@", writer.error);
+      return 1;
+    }
+  }
+
+  return 0;
+}