{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30106117", "kind": "science-record", "revision": 8, "content_hash": "sha256:70cc9e689dcebc2621b751cac36b796b045dea74ec4f0a117c7cd901f80b6d42", "created_at": "2026-11-01T15:40:36Z", "updated_at": "2026-11-01T22:43:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment of a SVM classifier to predict recurrence of ovarian cancer.", "doi": "10.3892/mmr.2018.9362", "pmid": "30106117", "authors": ["Jinting Zhou", "Lin Li", "Liling Wang", "Xiaofang Li", "Hui Xing", "Li Cheng"], "journal": "Molecular medicine reports", "year": 2018, "abstract": "Gene expression data using retrieved ovarian cancer (OC) samples were used to identify genes of interest and a support vector machine (SVM) classifier was subsequently established to predict the recurrence of OC. Three datasets (GSE17260, GSE44104 and GSE51088) investigating OC gene expression were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) in samples from patients with non‑recurrent and recurrent OC were revealed via a homogeneity test and quality control analysis. A protein‑protein interaction (PPI) network was subsequently established for the DEGs using data from Biological General Repository for Interaction Datasets, Human Protein Reference Database and Database of Interacting Proteins. Degrees of interaction and betweenness centrality (BC) scores were calculated for each node in the PPI network. The top 100 genes ranked by BC scores were selected to identify feature genes via recursive feature elimination using the GSE17260 dataset. Following this, a SVM classifier was constructed and further validated using the GSE44104 and GSE51088 datasets and independent gene expression data obtained from the Cancer Genome Atlas (TCGA). A total of 639 DEGs were identified from the three gene expression datasets, and a PPI network including 249 nodes and 354 edges was constructed. A SVM classifier consisting of 39 feature genes (including cullin 3, mouse double minute 2 homolog, aurora kinase A, WW domain containing oxidoreducatase, large tumor suppressor kinase 2, sirtuin 6, staphylococcal nuclease and tudor domain containing 1, leucine rich repeats and immunoglobulin like domains 1 and aurora kinase 1 interacting protein 1) was subsequently constructed. The prediction accuracies of the SVM classifier for GSE17260, GSE44104 and GSE51088 datasets as well as data downloaded from TCGA were revealed to be 92.7, 93.3, 96.6 and 90.4%, respectively. Furthermore, the results of the present study revealed that patients with predicted non‑recurrent OC survived significantly longer compared with the patients with predicted recurrent OC (P=6.598x10‑6). A SVM classifier consisting of 39 feature genes was established for predicting the recurrence and prognosis of OC. Therefore, the results of the present study suggested that the 39 feature genes may serve important roles in the development of OC and may represent therapeutic biomarkers of OC.", "claims": [{"id": "claim-method", "statement": "The SVM classifier was subsequently established to predict OC recurrence based on the expression levels of the screened feature genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30106117", "locator": "sections[7] \"Construction of the SVM classifier\" paragraph 5", "quote": "The SVM classifier was subsequently established to predict OC recurrence based on the expression levels of the screened feature genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30106117", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used a 39-feature-gene SVM classifier, trained using GSE17260 and validated with GSE44104, GSE51088, and independent TCGA gene-expression data; the classifier achieved 90.4% accuracy and an AUROC of 0.981 in the TCGA validation.", "kind": "quantitative", "target": {"value": 90.4, "unit": "per cent", "tolerance": null, "source": "Prediction accuracy of independent gene expression data downloaded from TCGA was revealed to be 90.4% [357 out of 395 samples (138 samples from patients with non-recurrent OC and 219 samples from patients with recurrent OC)], with an AUROC value of 0.981 (Table VI, Fig. 6A)."}, "evidence": [{"asset": "source:pmid:30106117", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Following this, a SVM classifier was constructed and further validated using the GSE44104 and GSE51088 datasets and independent gene expression data obtained from the Cancer Genome Atlas (TCGA)."}, {"asset": "source:pmid:30106117", "locator": "sections[14] \"Results of validation\" paragraph 2", "quote": "Prediction accuracy of independent gene expression data downloaded from TCGA was revealed to be 90.4% [357 out of 395 samples (138 samples from patients with non-recurrent OC and 219 samples from patients with recurrent OC)], with an AUROC value of 0.981 (Table VI, Fig. 6A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used a 39-feature-gene SVM classifier, trained using GSE17260 and validated with GSE44104, GSE51088, and independent TCGA gene-expression data; the classifier achieved 90.4% accuracy and an AUROC of 0.981 in the TCGA validation.", "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:30106117"], "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. 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"0.525464", "0", "1.42154"], ["HNRNPK", "0.50414", "13", "0.011236", "0.026482", "1.021909", "0.599923", "0", "−0.96217"], ["RAD21", "0.490358", "12", "0.014482", "0.034133", "0.386617", "0.824228", "0", "2.596818"], ["WWOX", "0.458579", "10", "0.013516", "0.031857", "0.857721", "0.651251", "0", "−3.74564"], ["IGBP1", "0.449997", "7", "0.011454", "0.026997", "0.47506", "0.788573", "0", "0.321061"], ["IPO7", "0.442128", "5", "0.002717", "0.006405", "1.598947", "0.449566", "0", "−1.03747"], ["RAD23A", "0.441265", "8", "0.012419", "0.02927", "0.900161", "0.637577", "0", "1.194153"], ["TSTA3", "0.436658", "5", "0.010425", "0.02457", "0.358922", "0.835721", "0", "2.936405"], ["BRCA2", "0.435695", "5", "0.003583", "0.008444", "0.100529", "0.950978", "0", "1.948855"], ["FHL3", "0.433658", "6", "0.001257", "0.002963", "0.279246", "0.869686", "0", "0.987126"], ["LATS2", "0.430752", "4", "0.011053", "0.026051", "0.09771", "0.952319", "0", "0.4797"], ["NOC2L", "0.430291", "4", "0.013451", "0.031703", "0.014566", "0.992743", "0", "1.077813"], ["CD2AP", "0.42926", "4", "0.018901", "0.044548", "0.026358", "0.986908", "0", "−1.79036"], ["TPM4", "0.428095", "7", "0.013303", "0.031355", "1.621492", "0.444526", "0", "2.932572"], ["MCM5", "0.427881", "7", "0.006661", "0.0157", "0.397359", "0.819813", "0", "0.44911"], ["CTBP2", "0.427047", "5", "0.013728", "0.032356", "1.715255", "0.424167", "0", "0.877948"], ["SIRT6", "0.426042", "6", "0.009524", "0.022448", "0.145688", "0.929746", "0", "−0.81214"], ["RALBP1", "0.42506", "3", "0.008046", "0.018964", "1.608012", "0.447533", "0", "1.788163"], ["DBN1", "0.422172", "9", "0.001295", "0.003052", "1.479727", "0.477179", "0", "1.499493"], ["FAF1", "0.420131", "4", "0.014442", "0.034039", "1.184726", "0.553019", "0", "1.782133"], ["SMC4", "0.416491", "5", "0.005295", "0.01248", "0.238612", "0.887536", "0", "1.769396"], ["SND1", "0.41646", "3", "0.003913", "0.009222", "0.920509", "0.631123", "0", "1.238259"], ["TEAD4", "0.414377", "2", "0.008077", "0.019037", "1.729928", "0.421067", "0", "0.992568"], ["BANP", "0.411436", "3", "0.004271", "0.010067", "0.305887", "0.858178", "0", "0.759078"], ["SART1", "0.409053", "3", "0.01088", "0.025643", "0.068045", "0.96655", "0", "1.254434"], ["INPPL1", "0.408929", "2", "9.41E-05", "0.000222", "1.3698", "0.504141", "0", "2.084808"], ["LRIG1", "0.408929", "2", "0.018088", "0.042633", "1.901966", "0.386361", "0", "−1.42735"], ["LRRC49", "0.408929", "2", "0.011943", "0.028148", "0.263645", "0.876497", "0", "−1.66365"], ["PCSK9", "0.408929", "2", "0.000332", "0.000782", "0.045994", "0.977266", "0", "−5.13551"], ["PHPT1", "0.408929", "2", "0.009973", "0.023507", "0.52427", "0.769407", "0", "−1.60935"], ["POLR2G", "0.408929", "2", "0.010377", "0.024458", "0.509447", "0.775131", "0", "1.450648"], ["PPA2", "0.408929", "2", "0.002415", "0.005691", "0.983689", "0.611498", "0", "−0.77017"], ["USP47", "0.408929", "2", "0.016431", "0.038727", "1.485343", "0.475841", "0", "−2.70658"], ["TTK", "0.408856", "3", "0.019272", "0.045422", "0.154504", "0.925656", "0", "−0.23932"], ["ARFIP1", "0.408051", "3", "5.30E-06", "1.25E-05", "1.795171", "0.407552", "0", "−2.91913"], ["FTL", "0.407729", "2", "0.00145", "0.003417", "1.83461", "0.399595", "0", "2.012816"], ["AURKAIP1", "0.407431", "2", "0.006809", "0.016048", "0.532797", "0.766134", "0", "0.828771"]], "row_count": 40, "column_count": 9, "numeric_cells": 316, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tV-mmr-18-04-3589"}}, {"id": "asset:table:pmid:30106117:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1760c390fdc67d64341efc74906d1c1863efc5aad45f7b99115079d03c7ebcae", "bytes": 682, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#tVI-mmr-18-04-3589", "version": null, "note": "Prediction results of the support vector machine classifier using sample data from GSE17260, GSE44104 and GSE51088.", "structure": {"pmcid": "PMC6131358", "section_index": 13, "section_title": "SVM classifier", "row_count": 5, "column_count": 9}, "table": {"label": "Table VI.", "caption": "Prediction results of the support vector machine classifier using sample data from GSE17260, GSE44104 and GSE51088.", "rows": [["Datasets", "Number of samples", "Correct samples", "Correct rate", "Sensitivity", "Specificity", "PPV", "NPV", "AUROC"], ["GSE17260", "110", "102", "0.927", "0.894", "0.987", "0.964", "0.915", "0.988"], ["GSE44104", "60", "56", "0.933", "1.000", "0.800", "0.909", "1.000", "0.970"], ["GSE51088", "147", "142", "0.966", "0.969", "0.941", "0.992", "0.800", "0.967"], ["TCGA", "395", "357", "0.9038", "0.987", "0.801", "0.862", "0.979", "0.981"]], "row_count": 5, "column_count": 9, "numeric_cells": 35, "header_rows": 1, "locator": "section[13]/table-wrap[2]#tVI-mmr-18-04-3589"}}], "gaps": ["asset:data:geo:GSE17260 not downloaded", "asset:data:geo:GSE17260 licence not read", "asset:data:geo:GSE44104 not downloaded", "asset:data:geo:GSE44104 licence not read", "asset:data:geo:GSE51088 not downloaded", "asset:data:geo:GSE51088 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The SVM classifier was subsequently established to predict OC recurrence based on the expression levels of the screened feature genes."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-3", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "centrality"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 90.4, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": []}, "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": true, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: support_vector_machine."}, "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": ["GSE17260", "GSE44104", "GSE51088"], "resolved_accessions": ["GSE17260", "GSE44104", "GSE51088"], "statements": ["The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request."], "basis": "The paper names GSE17260, GSE44104, GSE51088 in Gene Expression Omnibus and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "assets": ["source:pmid:30106117", "data:geo:GSE17260", "asset:table:pmid:30106117:1", "asset:table:pmid:30106117:2", "asset:table:pmid:30106117:3", "asset:table:pmid:30106117:4", "asset:table:pmid:30106117:5", "asset:table:pmid:30106117:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17260"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:22Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 78377, "completion_tokens": 5104, "cached_tokens": 1568}}, "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:30106117", "type": "paper", "label": "pmid:30106117"}, {"id": "source:pmid:30106117", "type": "manuscript", "label": "PMID 30106117 full text"}, {"id": "data:geo:GSE17260", "type": "dataset", "label": "GEO GSE17260"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30106117", "type": "paper", "label": "pmid:30106117"}, {"id": "source:pmid:30106117", "type": "manuscript", "label": "PMID 30106117 full text"}, {"id": "data:geo:GSE17260", "type": "dataset", "label": "GEO GSE17260"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30106117", "type": "extraction", "used": ["source:pmid:30106117"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17260", "type": "accession_resolution", "used": ["data:geo:GSE17260"], "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:30106117", "parent_hash": "sha256:7a0865e7904d3f7e1dec5337440ea1ea009c71e24b2ab98191f28dd50b983447", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE17260 licence not read", "asset:data:geo:GSE17260 not downloaded", "asset:data:geo:GSE44104 licence not read", "asset:data:geo:GSE44104 not downloaded", "asset:data:geo:GSE51088 licence not read", "asset:data:geo:GSE51088 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["ing of 39 feature genes (including cullin 3, mouse double minute 2 homolog, aurora kinase A, WW"], "order_basis": "paper_text_order:1432", "id": "assay:1"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The SVM classifier was subsequently established to predict OC recurrence based on the expression levels of the screened feature genes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"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":"2026-11-04T03:35:07+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}}}