@prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { a ; 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."; "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."; "Claim test of levin-2022-grn-learning-01: supports, confidence 0.55"; ; prov:wasAttributedTo ; "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."; "claim-test/0.1.0"; "computational"; "Zero or one of the five kinds occurs in any successfully integrated model."; "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."; "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."; "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."; "0.55"^^xsd:double; , ; "supports"; "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."; "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)."; "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."; "false"^^xsd:boolean . . a ; dc:description "authors' MATLAB sources and deposited simulation-count matrices; the ODE right-hand sides are not in this repository"; dc:license ""; "Dataset: GRN_ODE, code and deposited outputs for Biswas, Clawson and Levin 2022"; prov:atLocation , , , , , , ; prov:wasDerivedFrom ; "sha256:0f4a71d2fca4c41c1dd91bcb7d1c3107fe754e2d596d8d2c4f4dfa26d402c771", "sha256:384a9740876e19d927593cb75af4b2632691616951f166840d01bc3bb16978db", "sha256:3ae6e7ccb729050f22c4f9f1b8feb587c2e05ab14166506392ab8e331e647574", "sha256:6768dd71632e319eded55cbab072eb79bc1af4510ef489e46be168e4828ac71e", "sha256:9b04ac49abb7ca558728f00f5048237688bf1a4acfd54b29b8c05659124bdffc", "sha256:b954fbb03601a7a4af543bb9c5d905a2b2c24a67995ee5e2f399ea1b8c7baa5e", "sha256:fb03c13849dccbc62a92dd9df087cd06075183e8a79dc391359cf0d6c7d98d6f" . a ; dc:description "BioModels ids in table order; each id was then resolved on the BioModels search API"; dc:license "cc by"; "Dataset: Table S1, list of 35 BioModels ODE networks"; prov:atLocation ; prov:wasDerivedFrom ; "sha256:1ae204459a539a8d52bbde46352c6e7fcbc7b28ae6833dcaa584585c35c7571c" . } sub:provenance { a prov:SoftwareAgent; "delphisci claim tester (grok-4.7; cursor/levin-xenobot-pathway-memory-254b)"; prov:actedOnBehalfOf ; . a ; dc:identifier "grok-4.7" . sub:assertion prov:wasAttributedTo ; prov:wasDerivedFrom ; prov:wasGeneratedBy sub:test . sub:plan prov:hadPlan . sub:test a prov:Activity; prov:qualifiedAssociation sub:plan; prov:wasAssociatedWith . } sub:pubinfo { this: dc:created "2026-11-08T16:24:31.872Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:hasNanopubType ; npx:introduces ; "Claim test of levin-2022-grn-learning-01: supports, confidence 0.55"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB"; npx:hasSignature "Myy4ISRP6dHTZSsAwugPwlUscewWveqMIhD+vFM12pzo7YzGylETFLAwo7XyOplZgWivih+8/O4UERYXHj+ecvd9JhpDchvl1tnJaX6fpg5ei4q37WWI333KhTpAQzrhNa22R1i2uNMjs0SJVrqj8KQTMIzF2mdAfdQcBJNb4FrGPwvTh7LqFWeEBjqyHJT2cMjMF/0OBJ9puHBtw+aSNOsB2hu7xtdG180ozS2miTkXr8TF7b3MSmXGNQ3gurQS363fhQAl8Auohr6JC4XAJ88FRwnSDeC88XPZQ6H73Zx/5oRB5u9dggn6hCMlBleg2Q7RTEUrtE5fviKgwVYyAg=="; npx:hasSignatureTarget this:; npx:signedBy . }