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Biomodels/ModelN/f.m is not in the repository, so the ODEs were not re-integrated." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 5 named memory kinds present out of UCS, pairing, transfer, associative and consolidation (n = 35). Interpretation: The claim is about simulations of published ODE models, not about measurements in cells. A positive result shows the programs behave as claimed. data_kind will be computational. BioModels entries will be named by identifiers returned from a fetch, not from memory." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of levin-2022-grn-learning-01: supports, confidence 0.55" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-grn-learning-01/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "The authors' released simulator and the published ODE models it names, or those same models fetched from BioModels by the identifiers the authors' repository or a BioModels API response gives. Random networks and expression atlases do not substitute for the 35 published models. Licence must allow research use." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "computational" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "Zero or one of the five kinds occurs in any successfully integrated model." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "All five named kinds have a positive count in at least one model." }, { "@value": "BioModels ids are Table S1 order. The matrices are indexed 1 to 35 and do not store the id string." }, { "@value": "This recomputes the authors' deposited counts. It does not re-integrate the ODEs, and it does not show that cells have these memories." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "At least three of the five named memory kinds each occur for at least one node assignment in at least one of the integrated pathway models." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Refutes if fewer than 2 of the 5 kinds are present among successfully integrated models. Mixed if exactly 2 kinds are present. Inconclusive with reason underpowered if fewer than 10 models integrate. Inconclusive with reason data-unavailable if the models or the authors' code cannot be fetched and no admissible ODE can be named from a fetch." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.55", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Simulations of the 35 published BioModels ODE pathway models show several distinct kinds of memory under node stimulation: UCS-based, pairing, transfer, associative and consolidation." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Each model is stimulated at nodes according to the authors' evaluator or the frozen independent definitions above. A kind counts once if any assignment is positive. The verdict is the count of positive kinds against the pre-registered bars (supports at >= 3, mixed at 2, refutes at <= 1)." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered before any model file, author repository or simulation output is downloaded. A memory kind is present if at least one successfully integrated model shows it for at least one stimulus-response assignment. Several means at least three. Supports if at least 3 of the 5 named kinds (UCS-based, pairing, transfer, associative, consolidation) are present. Definitions are those in wesleypclawson/GRN_ODE at the commit fetched after this file (the MEMORY_EVALUATOR scripts). If that code cannot be executed, the independent definitions frozen here are used and the method says so: a readout R is displaced when its post-stimulus mean differs from its pre-stimulus baseline in the same direction as during stimulation by at least 10% of the during-stimulus displacement. UCS memory: a transient stimulation of S leaves R displaced after S returns to baseline. Pairing memory: stimulating S1 and S2 together leaves R displaced when neither alone does. Transfer memory: after S trains R, a different untrained node stimulated alone leaves R displaced in the trained direction. Associative memory: neutral N alone does not displace R; after N is paired with a UCS that does, N alone does. Consolidation memory: a second training bout leaves a larger post-stimulus displacement than the first. The stimulus is a temporary increase of that node's production or input rate. 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