{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37481739", "kind": "science-record", "revision": 3, "content_hash": "sha256:11f41a731d0aeeeb5d0c6e1c488adabc1d7335140b2dcd3ca9b56123750991d7", "created_at": "2026-11-01T19:02:15Z", "updated_at": "2026-11-01T22:09:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The activity of cuproptosis pathway calculated by AUCell algorithm was employed to construct cuproptosis landscape in lung adenocarcinoma.", "doi": "10.1007/s12672-023-00755-7", "pmid": "37481739", "authors": ["Weixian Lin", "Jiaren Wang", "Jing Ge", "Rui Zhou", "Yahui Hu", "Lushan Xiao", "Quanzhou Peng", "Zemao Zheng"], "journal": "Discover oncology", "year": 2023, "abstract": "Cuproptosis is a recently described copper-dependent cell death pathway. Consequently, there are still few studies on lung adenocarcinoma (LUAD)-related cuproptosis, and we aimed to deepen in this matter. In this study, data from 503 patients with lung cancer from the TCGA-LUAD cohort data collection and 11 LUAD single-cells from GSE131907 as well as from 10 genes associated with cuproptosis were analyzed. The AUCell R package was used to determine the copper-dependent cell death pathway activity for each cell subpopulation, calculate the CellChat score, and display cell communication for each cell subpopulation. The PROGENy score was calculated to show the scores of tumor-related pathways in different cell populations. GO and KEGG analyses were used to calculate pathway activity. Univariate COX and random forest analyses were used to screen prognosis-associated genes and construct models. The ssGSEA and xCell algorithms were used to calculate the immunocyte infiltration score. Based on data from the GDSC database, the drug sensitivity score was calculated using oncoPredict. Finally, in vitro experiments were performed to determine the role of TLE1, the most important gene in the prognostic model. The 11 LUAD single-cell samples were classified into 8 different cell populations, from which epithelial cells showed the highest copper-dependent cell death pathway activity. Epithelial cell subsets were significantly positively correlated with MAKP, hypoxia, and other pathways. In addition, cell subgroup communication showed highly active collagen and APP pathways. Using the Findmark algorithm, differentially expressed genes (DEGs) between epithelial and other cell types were identified. Combined with the bulk data in the TCGA-LUAD database, DEGs were enriched in pathways such as EGFR tyrosine kinase inhibitor resistance, Hippo signaling pathway, and tight junction. Subsequently, we selected 4 genes (out of 112) with prognostic significance, ANKRD29, RHOV, TLE1, and NPAS2, and used them to construct a prognostic model. The high- and low-risk groups, distinguished by the median risk score, showed significantly different prognoses. Finally, we chose TLE1 as a biomarker based on the relative importance score in the prognostic model. In vitro experiments showed that TLE1 promotes tumor proliferation and migration and inhibits apoptosis.", "claims": [{"id": "claim-method", "statement": "Subsequently, univariate COX survival analysis was performed on DEGs using the tinyarray package (p < 0.01), and 112 genes were selected (Fig. 4D).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37481739", "locator": "sections[20] \"Construction of a prognostic model\" paragraph 4", "quote": "Subsequently, univariate COX survival analysis was performed on DEGs using the tinyarray package (p < 0.01), and 112 genes were selected (Fig. 4D)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37481739", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Univariate COX and random forest analyses were used to screen prognosis-associated genes and construct models.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37481739", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Univariate COX and random forest analyses were used to screen prognosis-associated genes and construct models."}, {"asset": "source:pmid:37481739", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In this study, data from 503 patients with lung cancer from the TCGA-LUAD cohort data collection and 11 LUAD single-cells from GSE131907 as well as from 10 genes associated with cuproptosis were analyzed."}, {"asset": "source:pmid:37481739", "locator": "sections[20] \"Construction of a prognostic model\" paragraph 4", "quote": "Then, 4 prognostic genes, ANKRD29, RHOV, TLE1, and NPAS2, were selected from the 112 genes in the TCGA-LUAD cohort according to the random forest analysis results, and a prognostic model was constructed using them (Fig. 4E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Univariate COX and random forest analyses were used to screen prognosis-associated genes and construct models.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:37481739"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE131907"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE131907"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37481739", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s12672-023-00755-7", "sha256": "sha256:a93778e5516974ea9b4d7297b7fdf1f68013f45c0bf5758bdf460154dd3dfe70", "bytes": 34160, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s12672-023-00755-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10363522", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE131907", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131907", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE131907", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3827114", "GSM3827115", "GSM3827116", "GSM3827117", "GSM3827118", "GSM3827119", "GSM3827120", "GSM3827121", "GSM3827122", "GSM3827123", "GSM3827124", "GSM3827125", "GSM3827126", "GSM3827127", "GSM3827128", "GSM3827129", "GSM3827130", "GSM3827131", "GSM3827132", "GSM3827133", "GSM3827134", "GSM3827135", "GSM3827136", "GSM3827137", "GSM3827138", "GSM3827139", "GSM3827140", "GSM3827141", "GSM3827142", "GSM3827143", "GSM3827144", "GSM3827145", "GSM3827146", "GSM3827147", "GSM3827148", "GSM3827149", "GSM3827150", "GSM3827151", "GSM3827152", "GSM3827153", "GSM3827154", "GSM3827155", "GSM3827156", "GSM3827157", "GSM3827158", "GSM3827159", "GSM3827160", "GSM3827161", "GSM3827162", "GSM3827163", "GSM3827164", "GSM3827165", "GSM3827166", "GSM3827167", "GSM3827168", "GSM3827169", "GSM3827170", "GSM3827171"], "sample_count": 58, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Single cell RNA sequencing of lung adenocarcinoma", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE131907 not downloaded", "asset:data:geo:GSE131907 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subsequently, univariate COX survival analysis was performed on DEGs using the tinyarray package (p < 0.01), and 112 genes were selected (Fig. 4D)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "KM"}}, {"id": "method-3", "family": "multi_omics_integration", "specific": "pathway_progeny", "label": "Multi-omics integration", "dsl_operations": ["multiomics_factor_analysis", "joint_pathway_score"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["aligned_multi_layer_matrices"], "evidence": {"score": 0.7, "band": "medium", "quote": "PROGENy"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor", "method.machine_learning_random_forest"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["machine_learning_random_forest"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_forest."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE131907"], "resolved_accessions": ["GSE131907"], "statements": ["The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE131907 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37481739", "data:geo:GSE131907"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "machine_learning_random_forest", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE131907"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:47:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9345, "completion_tokens": 1802, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:37481739", "type": "paper", "label": "pmid:37481739"}, {"id": "source:pmid:37481739", "type": "manuscript", "label": "PMID 37481739 full text"}, {"id": "data:geo:GSE131907", "type": "dataset", "label": "GEO GSE131907"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37481739", "type": "paper", "label": "pmid:37481739"}, {"id": "source:pmid:37481739", "type": "manuscript", "label": "PMID 37481739 full text"}, {"id": "data:geo:GSE131907", "type": "dataset", "label": "GEO GSE131907"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37481739", "type": "extraction", "used": ["source:pmid:37481739"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE131907", "type": "accession_resolution", "used": ["data:geo:GSE131907"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:37481739", "parent_hash": "sha256:bc8e6364ce6fa8c591a7cb73c720689caf34199b171ec1575fdf8c7960702f83", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE131907 licence not read", "asset:data:geo:GSE131907 not downloaded", "execution.not_run", "method.machine_learning_random_forest", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:machine_learning_random_forest"], "assays": [{"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["mor proliferation and migration and inhibits apoptosis.", "on ability of lung cancer cells and promoted apoptosis. In addition, TLE1 knockdown significantly i"], "order_basis": "paper_text_order:2453", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["re Collection (ATCC, Rockville, MD, USA) and cultured in KM and DMEM high glucose media supplemented", "lial cells HBE135-E6E7 and lung cancer cells A549, NCI-H2073 were purchased from the American", "ls and lung cancer cell lines. We found that A549 non-small cell lung cancer cells were signif", "howing expression of TLE1 in HBE135-E6E7 and A549 cells. E Western blot showing TLE1 knockdown"], "order_basis": "paper_text_order:2553", "id": "assay:2"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["osstalk of LUAD in multicellular ecosystems, scRNA-seq analysis was performed on 11 LUAD samples af"], "order_basis": "paper_text_order:3036", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ession of TLE1 associated with cell cycle. D Western blot showing expression of TLE1 in HBE135-E6E7 an", "ion of TLE1 in HBE135-E6E7 and A549 cells. E Western blot showing TLE1 knockdown efficiency in A549 ce", "iency in NCI-H2073 cell line was verified by Western blot. H Colony formation was measured in cells tr", "ciency of the TLE1 knockdown was verified by western blot analysis (Fig. 9E). TLE1 knockdown significa"], "order_basis": "paper_text_order:5650", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["NA. F Colony formation was measured in cells transfected with control or si-TLE1. Transwell assay sho", "ot. H Colony formation was measured in cells transfected with control or overexpressing TLE1. Transwe", "and A549 cells. E Western blot showing TLE1 knockdown efficiency in A549 cells by independent siRN", "l transfer in control cells compared to TLE1 knockdown cells. G TLE1 overexpression efficiency in N"], "order_basis": "paper_text_order:5750", "id": "assay:5"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Subsequently, univariate COX survival analysis was performed on DEGs using the tinyarray package (p < 0.01), and 112 genes were selected (Fig. 4D)."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:47:12+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}