https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8/Head https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8/assertion https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8/provenance https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8/pubinfo https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8/assertion https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://purl.org/dc/terms/description Loaded Bin_Memory_Type from ODE_New.mat in the authors' repository at the pinned commit. Columns follow Clean_Results.m, Test_Pairing_Memory.m and AL.m: 1 UCS, 2 pairing, 3 transfer, 4 associative, 7 consolidation. A kind counts as present if at least one of the 35 models has a positive count. Bin_Mem_Prop matches the formula in Clean_Results.m, which checks that the matrix is that program's output rather than a hand-typed summary. Biomodels/ModelN/f.m is not in the repository, so the ODEs were not re-integrated. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://www.w3.org/2000/01/rdf-schema#comment 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. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-grn-learning-01: supports, confidence 0.55 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-grn-learning-01/result.json https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/admissibleDatasets 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Zero or one of the five kinds occurs in any successfully integrated model. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst All five named kinds have a positive count in at least one model. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst BioModels ids are Table S1 order. The matrices are indexed 1 to 35 and do not store the id string. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/expectedObservation 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/failCriterion 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.55 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/hypothesis 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/inferenceMethod 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/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/passCriterion 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. The numeric bar is not edited after outputs are seen. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2022-grn-learning-01 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://purl.org/dc/terms/description authors' MATLAB sources and deposited simulation-count matrices; the ODE right-hand sides are not in this repository https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: GRN_ODE, code and deposited outputs for Biswas, Clawson and Levin 2022 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://github.com/wesleypclawson/GRN_ODE/archive/aaa60c37a49d41b5fa15e09b9a81d098674694fc.tar.gz https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/BreakResis.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/Degree_BioModel.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/DrugResisSensit.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/NewDrugResSensitBreak.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/ODE_New.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/numSp.mat https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://github.com/wesleypclawson/GRN_ODE https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:0f4a71d2fca4c41c1dd91bcb7d1c3107fe754e2d596d8d2c4f4dfa26d402c771 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:384a9740876e19d927593cb75af4b2632691616951f166840d01bc3bb16978db https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:3ae6e7ccb729050f22c4f9f1b8feb587c2e05ab14166506392ab8e331e647574 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:6768dd71632e319eded55cbab072eb79bc1af4510ef489e46be168e4828ac71e https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:9b04ac49abb7ca558728f00f5048237688bf1a4acfd54b29b8c05659124bdffc https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:b954fbb03601a7a4af543bb9c5d905a2b2c24a67995ee5e2f399ea1b8c7baa5e https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:fb03c13849dccbc62a92dd9df087cd06075183e8a79dc391359cf0d6c7d98d6f https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-2 http://purl.org/dc/terms/description BioModels ids in table order; 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