https://w3id.org/np/RAXfBaSAFtrfEc2l2FAJwm_98TeY_ydGFYWHn2pUFBSB8
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-01--claim-test>
a <https://w3id.org/delphi/ontology/Assessment>;
dc: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.";
<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.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of levin-2022-grn-learning-01: supports, confidence 0.55";
<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>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<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/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "computational";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Zero or one of the five kinds occurs in any successfully integrated model.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "All five named kinds have a positive count in at least one model.",
"BioModels ids are Table S1 order. The matrices are indexed 1 to 35 and do not store the id string.",
"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> "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> "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> "0.55"^^xsd:double;
<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/evidence/levin-2022-grn-learning-01--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<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/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/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.";
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a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "authors' MATLAB sources and deposited simulation-count matrices; the ODE right-hand sides are not in this repository";
dc:license "";
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<https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/DrugResisSensit.mat>,
<https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/NewDrugResSensitBreak.mat>,
<https://raw.githubusercontent.com/wesleypclawson/GRN_ODE/aaa60c37a49d41b5fa15e09b9a81d098674694fc/ODE_New.mat>,
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<https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-01--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "BioModels ids in table order; each id was then resolved on the BioModels search API";
dc:license "cc by";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Table S1, list of 35 BioModels ODE networks";
prov:atLocation <https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9820177/supplementaryFiles>;
prov:wasDerivedFrom <https://www.mdpi.com/article/10.3390/ijms24010285/s1>;
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prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/grok-4-7> .
<https://w3id.org/delphi/resource/model/grok-4-7> a <https://w3id.org/delphi/ontology/LanguageModel>;
dc:identifier "grok-4.7" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-grn-learning-01/result.json>;
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sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.872Z"^^xsd:dateTime;
dc:creator <https://orcid.org/0009-0007-4948-9192>;
dc:license <https://creativecommons.org/licenses/by/4.0/>;
npx:hasNanopubType <https://w3id.org/delphi/ontology/Assessment>;
npx:introduces <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/ontology/domain> <https://w3id.org/delphi/resource/domain/levin-papers> .
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