From 172c3b25902575104e1f9e1e80f0bf8a03950e9f Mon Sep 17 00:00:00 2001 From: Research Assistant Date: Sun, 28 Jun 2026 23:40:08 +0800 Subject: [PATCH] audit: vision audit of 2HEUD5P9 + 4AG67PBH (4 oracle agents) 2HEUD5P9 (10 findings): - Frontmatter P1: 17/17 correct (PASS) - Figures P4/P6/P9/P10/P15/P21: all correct (PASS) - Figure on P13: caption mislabeled as body_paragraph (BUG) - Boundary P23: clean body/ref transition (PASS) 4AG67PBH (11 findings): - Frontmatter P1: 3 footnote->affiliation mismatches (BUG) - Frontmatter P1: 2 frontmatter_noise->support mismatches (MINOR) - Figures P3: non_body_insert->figure_caption_candidate (BUG) - Figures P10: panel D over-segmented (MINOR) - Figures P25: author-bio page backmatter mislabel (BUG) - Boundary P21: Conflict of Interest heading/body wrong (BUG) - Figures P4/10/13/14/15: correctly grouped (PASS) Cross-paper patterns identified: 1. footnote_vs_affiliation (4AG67PBH) 2. figure_caption_mislabel_as_body (both papers) 3. backmatter_page_mislabel (4AG67PBH) 4. zone_leak_frontmatter_to_body (both papers) 5. reference_boundary_body_mix (both papers) 6. title_repeat_on_page_2 (2HEUD5P9) --- audit/2026-06-28-data-audit-findings.json | 186 +++++++- audit/2HEUD5P9/block_review_boundary.jsonl | 12 + audit/2HEUD5P9/block_review_figures.jsonl | 12 + audit/2HEUD5P9/block_review_frontmatter.jsonl | 17 + audit/2HEUD5P9/body_map.json | 4 + audit/2HEUD5P9/figure_map.json | 439 ++++++++++++++++++ audit/2HEUD5P9/frontmatter_map.json | 144 ++++++ audit/2HEUD5P9/reference_map.json | 6 + audit/2HEUD5P9/reference_map_23.json | 371 +++++++++++++++ audit/4AG67PBH/block_review_boundary.jsonl | 15 + audit/4AG67PBH/block_review_figures.jsonl | 46 ++ audit/4AG67PBH/block_review_frontmatter.jsonl | 20 + audit/4AG67PBH/body_map.json | 12 + audit/4AG67PBH/figure_map.json | 312 +++++++++++++ audit/4AG67PBH/frontmatter_map.json | 168 +++++++ audit/4AG67PBH/reference_map.json | 6 + audit/4AG67PBH/reference_map_21.json | 329 +++++++++++++ 17 files changed, 2087 insertions(+), 12 deletions(-) create mode 100644 audit/2HEUD5P9/block_review_boundary.jsonl create mode 100644 audit/2HEUD5P9/block_review_figures.jsonl create mode 100644 audit/2HEUD5P9/block_review_frontmatter.jsonl create mode 100644 audit/2HEUD5P9/body_map.json create mode 100644 audit/2HEUD5P9/figure_map.json create mode 100644 audit/2HEUD5P9/frontmatter_map.json create mode 100644 audit/2HEUD5P9/reference_map.json create mode 100644 audit/2HEUD5P9/reference_map_23.json create mode 100644 audit/4AG67PBH/block_review_boundary.jsonl create mode 100644 audit/4AG67PBH/block_review_figures.jsonl create mode 100644 audit/4AG67PBH/block_review_frontmatter.jsonl create mode 100644 audit/4AG67PBH/body_map.json create mode 100644 audit/4AG67PBH/figure_map.json create mode 100644 audit/4AG67PBH/frontmatter_map.json create mode 100644 audit/4AG67PBH/reference_map.json create mode 100644 audit/4AG67PBH/reference_map_21.json diff --git a/audit/2026-06-28-data-audit-findings.json b/audit/2026-06-28-data-audit-findings.json index a40fb2b6..1fda3945 100644 --- a/audit/2026-06-28-data-audit-findings.json +++ b/audit/2026-06-28-data-audit-findings.json @@ -17,7 +17,10 @@ }, { "severity": "BUG", - "pages": ["1", "23"], + "pages": [ + "1", + "23" + ], "block_role": "frontmatter_noise", "zone": "body_zone", "text": "ORCID + Received/Revised dates", @@ -27,7 +30,20 @@ }, { "severity": "MINOR", - "pages": ["2", "3", "6", "8", "10", "12", "16", "19", "22", "23", "25", "26"], + "pages": [ + "2", + "3", + "6", + "8", + "10", + "12", + "16", + "19", + "22", + "23", + "25", + "26" + ], "block_role": "unknown_structural", "zone": "body_zone", "text": "empty or whitespace", @@ -39,20 +55,63 @@ "severity": "BUG", "page": 23, "zone_mix": true, - "zones": ["body_zone(7)", "reference_zone(45)", "frontmatter_side_zone(1)"], + "zones": [ + "body_zone(7)", + "reference_zone(45)", + "frontmatter_side_zone(1)" + ], "issue": "body blocks intermixed with reference zone on page 23 — body blocks before reference boundary", "expected": "body blocks should be pre-reference and reference_zone should start cleanly", "category": "reference_boundary_body_leak" }, { "severity": "INFO", - "pages": ["1"], + "pages": [ + "1" + ], "note": "Frontmatter clean: paper_title (2 blocks), authors (1 block) in frontmatter_main_zone" }, { "severity": "INFO", - "pages": ["1"], + "pages": [ + "1" + ], "note": "Abstract: 1 abstract_body in body_zone — correct" + }, + { + "severity": "PASS", + "domain": "frontmatter", + "note": "17/17 blocks correct on page 1", + "category": "visual_audit" + }, + { + "severity": "BUG", + "domain": "figures", + "page": 13, + "block": "p13:6", + "issue": "Figure 4 caption mislabeled as body_paragraph (should be figure_caption)", + "category": "figure_caption_mislabel" + }, + { + "severity": "PASS", + "domain": "boundary", + "page": 23, + "note": "Clean body/ref transition. No body-ref mixing found.", + "category": "visual_audit" + }, + { + "severity": "PASS", + "domain": "figures", + "pages": [ + 4, + 6, + 9, + 10, + 15, + 21 + ], + "note": "All figures correctly grouped, captions correct, panels covered.", + "category": "visual_audit" } ] }, @@ -84,20 +143,93 @@ "severity": "BUG", "page": 21, "zone_mix": true, - "zones": ["body_zone(8)", "reference_zone(35)", "frontmatter_side_zone(1)"], + "zones": [ + "body_zone(8)", + "reference_zone(35)", + "frontmatter_side_zone(1)" + ], "issue": "Mixed body + reference zone on page 21 with Conflict of Interest in frontmatter_side_zone", "expected": "conflict of interest should be in tail zone or body_zone", "category": "reference_boundary_mix" }, { "severity": "INFO", - "pages": ["1"], + "pages": [ + "1" + ], "note": "Frontmatter clean: paper_title (1), authors (1) in frontmatter_main_zone" }, { "severity": "INFO", - "pages": ["1"], + "pages": [ + "1" + ], "note": "Abstract: 1 abstract_body in body_zone — correct" + }, + { + "severity": "BUG", + "domain": "frontmatter", + "page": 1, + "blocks": [ + "p1:11", + "p1:13", + "p1:15" + ], + "issue": "Affiliation blocks misclassified as footnote (3 blocks)", + "category": "footnote_vs_affiliation" + }, + { + "severity": "MINOR", + "domain": "frontmatter", + "page": 1, + "blocks": [ + "p1:12", + "p1:16" + ], + "issue": "DOI/copyright: frontmatter_noise -> frontmatter_support", + "category": "noise_vs_support" + }, + { + "severity": "BUG", + "domain": "figures", + "page": 3, + "blocks": [ + "3:4", + "3:7", + "3:10" + ], + "issue": "non_body_insert vs figure_caption_candidate mislabel", + "category": "figure_caption_mislabel" + }, + { + "severity": "MINOR", + "domain": "figures", + "page": 10, + "issue": "Panel D split across 2 asset blocks", + "category": "figure_over_segmentation" + }, + { + "severity": "BUG", + "domain": "figures", + "page": 25, + "blocks": [ + "25:4", + "25:8", + "25:10" + ], + "issue": "Author-bio page: caption/ref_item -> backmatter_body", + "category": "backmatter_mislabel" + }, + { + "severity": "BUG", + "domain": "boundary", + "page": 21, + "blocks": [ + "21:8", + "21:9" + ], + "issue": "Conflict Interest heading/body mislabeled", + "category": "backmatter_heading_mislabel" } ] } @@ -105,21 +237,51 @@ "cross_paper_patterns": { "zone_leak_frontmatter_to_body": { "count": 2, - "papers": ["2HEUD5P9", "4AG67PBH"], + "papers": [ + "2HEUD5P9", + "4AG67PBH" + ], "description": "ORCID/copyright/DOI/date metadata blocks in body_zone — likely from frontmatter normalization missing these specific text patterns", "fix": "Add ORCID, DOI, and date text patterns to frontmatter_noise normalization in _normalize_frontmatter_blocks" }, "reference_boundary_body_mix": { "count": 2, - "papers": ["2HEUD5P9", "4AG67PBH"], + "papers": [ + "2HEUD5P9", + "4AG67PBH" + ], "description": "Body paragraphs intermixed with reference zone on reference boundary pages", "fix": "P1 backmatter boundary redesign should handle this — verify ref-anchored partition" }, "title_repeat_on_page_2": { "count": 1, - "papers": ["2HEUD5P9"], + "papers": [ + "2HEUD5P9" + ], "description": "Section heading on page 2 classified as paper_title", "fix": "Tighten doc_title raw_label check for page 2: only accept if text matches page 1 title" + }, + "footnote_vs_affiliation": { + "count": 1, + "papers": [ + "4AG67PBH" + ], + "fix": "Add address-specific patterns to footnote detection." + }, + "figure_caption_mislabel_as_body": { + "count": 2, + "papers": [ + "2HEUD5P9", + "4AG67PBH" + ], + "fix": "Relax caption rules for blocks below figure assets in display zones." + }, + "backmatter_page_mislabel": { + "count": 1, + "papers": [ + "4AG67PBH" + ], + "fix": "Add backmatter page guard: pages after reference boundary should not create new figure objects." } } -} +} \ No newline at end of file diff --git a/audit/2HEUD5P9/block_review_boundary.jsonl b/audit/2HEUD5P9/block_review_boundary.jsonl new file mode 100644 index 00000000..cec05e41 --- /dev/null +++ b/audit/2HEUD5P9/block_review_boundary.jsonl @@ -0,0 +1,12 @@ +{"block_id":"p23:3","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This is regular concluding body text in the upper-left column, clearly above the reference list area."} +{"block_id":"p23:4","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This paragraph continues the article discussion in the upper-left column and remains outside the reference list."} +{"block_id":"p23:5","page":23,"review_status":"reviewed","truth_role":"sub_subsection_heading","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Acknowledgements' is an endmatter heading in the left column before the reference entries start."} +{"block_id":"p23:6","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This acknowledgement funding text belongs to the pre-reference body/endmatter zone rather than the reference list."} +{"block_id":"p23:7","page":23,"review_status":"reviewed","truth_role":"subsection_heading","truth_zone":"frontmatter_side_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Conflict of Interest' is a short endmatter heading in the left column and is separate from the reference zone."} +{"block_id":"p23:8","page":23,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"frontmatter_side_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"The single sentence declaring no conflict is ancillary article metadata/endmatter beside the body-to-reference transition, not a reference entry."} +{"block_id":"p23:9","page":23,"review_status":"reviewed","truth_role":"sub_subsection_heading","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"'Keywords' is another endmatter heading above the start of the references in the lower-left column."} +{"block_id":"p23:10","page":23,"review_status":"reviewed","truth_role":"body_paragraph","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This keyword line is non-reference article metadata and remains above the first numbered reference item."} +{"block_id":"p23:11","page":23,"review_status":"reviewed","truth_role":"frontmatter_noise","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"The received/revised/published dates are article metadata placed just above the reference list boundary, not reference content."} +{"block_id":"p23:12","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This is the first visible numbered citation in the lower-left column, marking the start of the reference zone on page 23."} +{"block_id":"p23:23","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This numbered citation at the top of the right column is a standard reference entry and confirms the right column is fully in the reference zone."} +{"block_id":"p23:55","page":23,"review_status":"reviewed","truth_role":"reference_item","truth_zone":"reference_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_023.png","method":"visual"},"short_reason":"This bottom-right numbered citation remains part of the continuous reference list, showing the reference zone extends to the page end without body-text intrusion."} diff --git a/audit/2HEUD5P9/block_review_figures.jsonl b/audit/2HEUD5P9/block_review_figures.jsonl new file mode 100644 index 00000000..25671bc0 --- /dev/null +++ b/audit/2HEUD5P9/block_review_figures.jsonl @@ -0,0 +1,12 @@ +{"block_id":"p4:25","page":4,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_004.png","method":"visual"},"short_reason":"This is the true caption for Figure 2; it sits directly below one composite multi-panel figure spanning panels A-I, and the surrounding figure-asset boxes cover the visible panels on the page."} +{"block_id":"p4:18","page":4,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_004.png","method":"visual"},"short_reason":"The tiny '(I)' text above the bottom-right image group is only a panel label for subpanel I, not a standalone figure caption or separate figure."} +{"block_id":"p6:3","page":6,"review_status":"reviewed","truth_role":"table_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_006.png","method":"visual"},"short_reason":"This page contains Table 1 only; the displayed text is a table title above tabular rows and there is no figure on the page."} +{"block_id":"p9:26","page":9,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_009.png","method":"visual"},"short_reason":"This is the correct caption for the single composite Figure 3. The page shows one grouped figure with panels A-K, and the asset boxes cover those visible sub-panels without introducing a second caption."} +{"block_id":"p10:2","page":10,"review_status":"reviewed","truth_role":"table_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_010.png","method":"visual"},"short_reason":"This is the caption for Table 2 above a large table; page 10 is not a figure page and contains no figure caption or figure assets."} +{"block_id":"p13:6","page":13,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"This block is the true caption for Figure 4. It appears immediately above the Figure 4 panels A-E and describes the images beneath it, so it is not body paragraph text."} +{"block_id":"p13:13","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The small '4 W' text is an in-panel timepoint label inside Figure 5E, not a figure caption or heading."} +{"block_id":"p13:15","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The small '8 W' text is another in-panel timepoint label inside Figure 5E, not a caption or section heading."} +{"block_id":"p13:39","page":13,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"This is the correct caption for the lower composite Figure 5. The page visually contains one grouped figure with panels A-L, and the asset boxes cover the visible panels while the true caption sits directly below them."} +{"block_id":"p13:26","page":13,"review_status":"reviewed","truth_role":"figure_label","truth_zone":"body_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_013.png","method":"visual"},"short_reason":"The tiny '(I)' marker above the lower-right image stack is just the panel label for Figure 5I, not a real figure caption."} +{"block_id":"p15:25","page":15,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_015.png","method":"visual"},"short_reason":"This is the correct caption for composite Figure 6. The caption text matches the visible panels A-G below it, and the colored asset boxes cover the sub-panels on the page rather than a heading or body block."} +{"block_id":"p21:17","page":21,"review_status":"reviewed","truth_role":"figure_caption","truth_zone":"display_zone","evidence":{"annotated_page":"audit/2HEUD5P9/annotated_pages/page_021.png","method":"visual"},"short_reason":"This is the correct caption for composite Figure 8. 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This work was financially suppor" + }, + { + "id": "7", + "role": "subsection_heading", + "zone": "frontmatter_side_zone", + "text": "Conflict of Interest" + }, + { + "id": "8", + "role": "frontmatter_noise", + "zone": "frontmatter_side_zone", + "text": "The authors declare no conflict of interest." + }, + { + "id": "9", + "role": "sub_subsection_heading", + "zone": "body_zone", + "text": "Keywords" + }, + { + "id": "10", + "role": "body_paragraph", + "zone": "body_zone", + "text": "advanced techniques, bioactive materials, bone regeneration, molecular mechanism" + }, + { + "id": "11", + "role": "frontmatter_noise", + "zone": "body_zone", + "text": "Received: September 22, 2023 \nRevised: November 4, 2023 \nPublished online: Mar" + }, + { + "id": "12", + "role": "reference_item", + "zone": "reference_zone", + "text": "[1] V. Jayachandran, S. S. Murugan, P. A. Dalavi, Y. D. 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The authors acknowledge" + }, + { + "id": "8", + "role": "subsection_heading", + "zone": "frontmatter_side_zone", + "text": "Conflict of Interest" + }, + { + "id": "9", + "role": "frontmatter_noise", + "zone": "frontmatter_side_zone", + "text": "The authors declare no conflict of interest." + }, + { + "id": "10", + "role": "sub_subsection_heading", + "zone": "body_zone", + "text": "Keywords" + }, + { + "id": "11", + "role": "backmatter_body", + "zone": "body_zone", + "text": "animal models, clinical studies, combined magnetic fields (CMF), inductive coupl" + }, + { + "id": "12", + "role": "backmatter_body", + "zone": "body_zone", + "text": "Received: November 21, 2023" + }, + { + "id": "13", + "role": "backmatter_body", + "zone": "body_zone", + "text": "Revised: February 5, 2024" + }, + { + "id": "14", + "role": "backmatter_body", + "zone": "body_zone", + "text": "Published online: February 26, 2024" + }, + { + "id": "15", + "role": "reference_item", + "zone": "reference_zone", + "text": "[1] T. 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