{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33240201", "kind": "science-record", "revision": 8, "content_hash": "sha256:297fcca16039135ca02983e3bbd5bbb3ad0029393d54321f9aacb7228d61d248", "created_at": "2026-11-01T15:41:17Z", "updated_at": "2026-11-01T22:45:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Machine Learning Analysis of the Cerebrovascular Thrombi Proteome in Human Ischemic Stroke: An Exploratory Study.", "doi": "10.3389/fneur.2020.575376", "pmid": "33240201", "authors": ["Cyril Dargazanli", "Emma Zub", "Jeremy Deverdun", "Mathilde Decourcelle", "Frédéric de Bock", "Julien Labreuche", "Pierre-Henri Lefèvre", "Grégory Gascou", "Imad Derraz", "Carlos Riquelme Bareiro", "Federico Cagnazzo", "Alain Bonafé", "Philippe Marin", "Vincent Costalat", "Nicola Marchi"], "journal": "Frontiers in neurology", "year": 2020, "abstract": "Objective: Mechanical retrieval of thrombotic material from acute ischemic stroke patients provides a unique entry point for translational research investigations. Here, we resolved the proteomes of cardioembolic and atherothrombotic cerebrovascular human thrombi and applied an artificial intelligence routine to examine protein signatures between the two selected groups. Methods: We specifically used n = 32 cardioembolic and n = 28 atherothrombotic diagnosed thrombi from patients suffering from acute stroke and treated by mechanical thrombectomy. Thrombi proteins were successfully separated by gel-electrophoresis. For each thrombi, peptide samples were analyzed by nano-flow liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) to obtain specific proteomes. Relative protein quantification was performed using a label-free LFQ algorithm and all dataset were analyzed using a support-vector-machine (SVM) learning method. Data are available via ProteomeXchange with identifier PXD020398. Clinical data were also analyzed using SVM, alone or in combination with the proteomes. Results: A total of 2,455 proteins were identified by nano-LC-MS/MS in the samples analyzed, with 438 proteins constantly detected in all samples. SVM analysis of LFQ proteomic data delivered combinations of three proteins achieving a maximum of 88.3% for correct classification of the cardioembolic and atherothrombotic samples in our cohort. The coagulation factor XIII appeared in all of the SVM protein trios, associating with cardioembolic thrombi. A combined SVM analysis of the LFQ proteome and clinical data did not deliver a better discriminatory score as compared to the proteome only. Conclusion: Our results advance the portrayal of the human cerebrovascular thrombi proteome. The exploratory SVM analysis outlined sets of proteins for a proof-of-principle characterization of our cohort cardioembolic and atherothrombotic samples. The integrated analysis proposed herein could be further developed and retested on a larger patients population to better understand stroke origin and the associated cerebrovascular pathophysiology.", "claims": [{"id": "claim-method", "statement": "A support-vector machine (SVM) approach was implemented using MATLAB (r2018a, MathWorks, Natick, MA, USA). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33240201", "locator": "sections[9] \"Data Analysis\" paragraph 4", "quote": "A support-vector machine (SVM) approach was implemented using MATLAB (r2018a, MathWorks, Natick, MA, USA)."}, {"asset": "source:pmid:33240201", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33240201", "locator": "sections[20] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33240201"], "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:PXD020398"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "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:PXD020398"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33240201", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fneur.2020.575376", "sha256": 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with the dataset identifier PXD020398.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Support-vector-machine learning analysis of the human cerebrovascular thrombi proteome: an exploratory study", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33240201:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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["Hypercholesterolemia", "10/32 (31.3)", "8/28 (28.6)", "0.82"], ["Current smoking", "6/32 (18.8)", "10/28 (35.7)", "0.14"], ["Alcohol abuse", "3/32 (9.4)", "4/28 (14.3)", "0.70"], ["Coronary artery disease/Myocardial Infarction", "5/32 (15.6)", "3/28 (10.7)", "0.71"], ["Previous stroke or TIA", "8/32 (25.0)", "2/28 (7.1)", "0.088"], ["Cardiac failure", "6/32 (18.8)", "0/28 (0.0)", "0.047"], ["Coronary stent", "1/32 (3.1)", "1/28 (3.6)", "NA"], ["Coronary bypass", "1/32 (3.1)", "1/28 (3.6)", "NA"], ["Carotid endarterectomy", "0/32 (0.0)", "0/28 (0.0)", "NA"], ["Atrial fibrillation", "20/32 (62.5)", "1/28 (3.6)", "<0.001"], ["Previous antithrombotic medications", "20/32 (62.5)", "11/28 (39.3)", "0.073"], ["Aspirin", "10/32 (31.3)", "8/28 (28.6)", "0.82"], ["Clopidogrel", "1/32 (3.1)", "2/28 (14.3)", "NA"], ["Vitamin K Antagonist", "7/32 (21.9)", "0/28 (0.0)", "0.0110"], ["New oral anticoagulant", "3/32 (9.4)", "0/28 (0.0)", "NA"], ["Current stroke event"], ["Systolic blood pressure, 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"Catalyzes the last step of the coagulation cascade by crosslinking fibrin fibers", "0.0022"], ["", "• Eukaryotic translation initiation factor 2 subunit 3", "Involved in the early steps of protein synthesis", "0.0439"], ["", "• Ras GTPase-activating-like protein IQGAP2", "Binds to activated CDC42 and RAC1. Associates with calmodulin", "0.1326"], ["2", "• Coagulation factor XIII", "Catalyzes the last step of the coagulation cascade by crosslinking fibrin fibers", "0.0022"], ["", "• F-actin-capping protein", "Binds to the fast-growing ends of actin filaments in a Ca2+ independent manner", "0.1752"], ["", "• Myosin light chain kinase", "Calcium/calmodulin-dependent kinase implicated in smooth muscle contraction via phosphorylation of myosin light chains", "0.0142"], ["3", "• Coagulation factor XIII", "Catalyzes the last step of the coagulation cascade by crosslinking fibrin fibers", "0.0022"], ["", "• Septin-7", "Filament-forming cytoskeletal GTPase. Required for normal organization of the actin cytoskeleton", "0.1897"], ["", "• Gamma-adducin", "Membrane-cytoskeleton-associated protein that promotes the assembly of the spectrin-actin network.", "0.0589"]], "row_count": 10, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:33240201:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a595d60e38df13304efce0943f9a7a81203d442617d91ea037b1a3bcb3eebb4a", "bytes": 1026, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T3", "version": null, "note": "LFQ (log2 transformed) of single proteins enriched in cardioembolic as compared to atherothrombotic thrombi.", "structure": {"pmcid": "PMC7678741", "section_index": 15, "section_title": "Testing Proteome Using LFQ Statistics", "row_count": 5, "column_count": 7}, "table": {"label": "Table 3", "caption": "LFQ (log2 transformed) of single proteins enriched in cardioembolic as compared to atherothrombotic thrombi.", "rows": [["Gene", "Uniprot Identification (40)", "Protein name", "Main known protein function (40)", "Subcellular Location", "Student's T-test Difference Log2 LFQ intensity Atheroma_Log2 LFQ intensity Cardioembolic", "-log P-value"], ["SLC25A11", "Q02978", "Mitochondrial 2-oxoglutarate/malate carrier protein", "Catalyzes the transport of 2-oxoglutarate at mitochondrial membrane", "Mitochondrion", "−1.278498", "1.94"], ["APOE", "P02649", "Apolipoprotein E", "Lipid transport between organs via the plasma and interstitial fluids", "Extracellular", "−1.34310437", "1.69"], ["PHB", "P35232", "Prohibitin", "Inhibits DNA synthesis", "Mitochondrion", "−1.1333107", "2.46"], ["ATP5A1", "P25705", "ATP synthase subunit alpha", "Produces ATP from ADP", "Mitochondrion, plasma membrane", "−1.1749357", "1.93"]], "row_count": 5, "column_count": 7, "numeric_cells": 17, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:PXD020398 not downloaded", "asset:data:geo:PXD020398 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": "reordered", "quote": "A support-vector machine (SVM) approach was implemented using MATLAB (r2018a, MathWorks, Natick, MA, USA). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398."}}], "targets": [], "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": ["PXD020398"], "resolved_accessions": ["PXD020398"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398."], "basis": "The paper names PXD020398 in ProteomeXchange Consortium via the PRIDE partner repository 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:33240201", "data:geo:PXD020398", "asset:table:pmid:33240201:1", "asset:table:pmid:33240201:2", "asset:table:pmid:33240201:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD020398"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:32Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31653, "completion_tokens": 1295, "cached_tokens": 784}}, "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:33240201", "type": "paper", "label": "pmid:33240201"}, {"id": "source:pmid:33240201", "type": "manuscript", "label": "PMID 33240201 full text"}, {"id": "data:geo:PXD020398", "type": "dataset", "label": "GEO PXD020398"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33240201", "type": "paper", "label": "pmid:33240201"}, {"id": "source:pmid:33240201", "type": "manuscript", "label": "PMID 33240201 full text"}, {"id": "data:geo:PXD020398", "type": "dataset", "label": "GEO PXD020398"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33240201", "type": "extraction", "used": ["source:pmid:33240201"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD020398", "type": "accession_resolution", "used": ["data:geo:PXD020398"], "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:33240201", "parent_hash": "sha256:c8da92aea405933381ea956b2f4cc600cdb89db9caf93edb50f557c6b15b8ca0", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD020398 licence not read", "asset:data:geo:PXD020398 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["flow liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) to obtain specific proteomes", "hy coupled to tandem mass spectrometry (nano-LC-MS/MS) to obtain specific proteomes. Relative prot", "al of 2,455 proteins were identified by nano-LC-MS/MS in the samples analyzed, with 438 proteins c", "the hemoglobin band excised (Figures 1 A–F). Mass spectrometry analysis identified a total of 2,455 protein"], "order_basis": "paper_text_order:792", "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": ["A support-vector machine (SVM) approach was implemented using MATLAB (r2018a, MathWorks, Natick, MA, USA). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD020398."], "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. 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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}}}