https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/Head https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/assertion https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/provenance https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/pubinfo https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/assertion https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test http://purl.org/dc/terms/description Memory amount is the fraction of counted assignments in ODE_New.mat that fall in one of the five named kinds. Node count is Bin_numSp. Edges are half the sum of the deposited degree vector, mean degree is its mean, and hubness is its maximum divided by its mean, as pre-registered. Each is compared with memory amount by a two-sided Spearman correlation at alpha 0.05 with no multiple-comparison correction. The ODEs were not re-integrated. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--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-06--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.017569332117588564 two-sided Spearman p for memory amount versus node count; all four tests are in extra (n = 35). Interpretation: The correlations are between simulation-derived memory scores and topology of the ODE models. They do not show that cellular memory is independent of network size. data_kind will be computational. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-grn-learning-06: refutes, confidence 0.55 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--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-06/result.json https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--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-06--claim-test https://w3id.org/delphi/ontology/admissibleDatasets The published ODE pathway models used for the memory assay, with topology counted from the same fetched model files that are simulated. A hand-typed table of the paper's correlations is not admissible. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation At least one of those four correlations has two-sided p < 0.05. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Edges (p 0.080) and mean degree (p 0.503) are not significant at 0.05. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Hubness here is maximum degree over mean degree. Two models have a degree vector one shorter than their node count (BIOMD0000000209, BIOMD0000000210). The node-count correlation does not use that vector. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Memory amount correlates with node count (Spearman rho 0.399, two-sided p 0.0176) and with hubness (rho 0.346, p 0.0420). Either one fails the pre-registered rule that every correlation be non-significant. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The ODEs were not re-integrated. Memory amount is a fraction of the deposited assignment counts. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/expectedObservation Spearman correlations of memory amount with node count, edge count, mean degree and hubness are all non-significant at two-sided p >= 0.05. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/failCriterion Refutes if any of the four Spearman p-values is < 0.05. Inconclusive with reason underpowered if fewer than 15 models have a finite memory amount and finite topology measures. Inconclusive with reason data-unavailable if the models cannot be fetched. Mixed is not used. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.55 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/hypothesis Across the surveyed BioModels pathway models, memory amount is not significantly correlated with node count, edge count, degree or hubness. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/inferenceMethod Spearman rank correlation, two-sided, alpha 0.05, uncorrected, one test per measure. Supports only if every test is non-significant. n and each rho and p are reported from the script. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered before any model file or simulation output is downloaded. Memory amount is the fraction of tested stimulus-response pairs that show at least one of the five memory kinds defined in the levin-2022-grn-learning-01 preregistration. Degree is mean node degree. Hubness is maximum degree divided by mean degree, unless the authors' GRN_ODE code defines hubness, in which case that definition is used and named. Edges are the regulatory edges in the fetched model. The test is a two-sided Spearman rank correlation of memory amount with each of the four measures, alpha = 0.05, no multiple-comparison correction (the claim says no significant correlation with any of them, at the ordinary per-test bar). Supports if all four p-values are >= 0.05. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2022-grn-learning-06 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--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-06--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--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-06--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-06--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-06--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-06--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-06--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-06--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-06--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-06--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-06--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-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:0f4a71d2fca4c41c1dd91bcb7d1c3107fe754e2d596d8d2c4f4dfa26d402c771 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:384a9740876e19d927593cb75af4b2632691616951f166840d01bc3bb16978db https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:3ae6e7ccb729050f22c4f9f1b8feb587c2e05ab14166506392ab8e331e647574 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:6768dd71632e319eded55cbab072eb79bc1af4510ef489e46be168e4828ac71e https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:9b04ac49abb7ca558728f00f5048237688bf1a4acfd54b29b8c05659124bdffc https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:b954fbb03601a7a4af543bb9c5d905a2b2c24a67995ee5e2f399ea1b8c7baa5e https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:fb03c13849dccbc62a92dd9df087cd06075183e8a79dc391359cf0d6c7d98d6f https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 http://purl.org/dc/terms/description BioModels ids in table order; each id was then resolved on the BioModels search API https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 http://purl.org/dc/terms/license cc by https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 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-06--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Table S1, list of 35 BioModels ODE networks https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://www.ebi.ac.uk/europepmc/webservices/rest/PMC9820177/supplementaryFiles https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://www.mdpi.com/article/10.3390/ijms24010285/s1 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-06--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:1ae204459a539a8d52bbde46352c6e7fcbc7b28ae6833dcaa584585c35c7571c https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/ns/prov#SoftwareAgent https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (grok-4.7; cursor/levin-xenobot-pathway-memory-254b) https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 http://www.w3.org/ns/prov#actedOnBehalfOf https://orcid.org/0009-0007-4948-9192 https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/ontology/usesModel https://w3id.org/delphi/resource/model/grok-4-7 https://w3id.org/delphi/resource/model/grok-4-7 http://purl.org/dc/terms/identifier grok-4.7 https://w3id.org/delphi/resource/model/grok-4-7 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/LanguageModel https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/assertion http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/assertion http://www.w3.org/ns/prov#wasDerivedFrom https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2022-grn-learning-06/result.json https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/assertion http://www.w3.org/ns/prov#wasGeneratedBy https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/test https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/plan http://www.w3.org/ns/prov#hadPlan https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/test http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/ns/prov#Activity https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/test http://www.w3.org/ns/prov#qualifiedAssociation https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/plan https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/test http://www.w3.org/ns/prov#wasAssociatedWith https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/pubinfo https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://purl.org/dc/terms/created 2026-11-08T16:24:31.873Z https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://purl.org/dc/terms/creator https://orcid.org/0009-0007-4948-9192 https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/ https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://purl.org/nanopub/x/hasNanopubType https://w3id.org/delphi/ontology/Assessment https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://purl.org/nanopub/x/introduces https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-06--claim-test https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-grn-learning-06: refutes, confidence 0.55 https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g https://w3id.org/delphi/ontology/domain https://w3id.org/delphi/resource/domain/levin-papers https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/sig http://purl.org/nanopub/x/hasAlgorithm RSA https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/sig http://purl.org/nanopub/x/hasPublicKey MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/sig http://purl.org/nanopub/x/hasSignature YLk2fxB6V0L3SYB48dpAhrhZNN+9KoxZdgITRNoTo6spK/rv0a0wx4Zfg7itLAiImqXbyO1SpqpwqHd1/qAGweKHOR/jAMkQDzxR8euZuus1Xb8lIk3Q2jL1vIXWxwdvzZOYkwI+XiptxF7xiG8o/r4/nXLBKERbJxbYODWutvX5dsShp2o/CRrw2ls8Oc1g1ok2PMLs4PlVD4aeTleprsmZvLGGdkzZJ+5IfsGp1/ndIBS39BBNpDK6pfRr73NC+uDlmCyscI5m7HA9XBzhek9Czy4QEeaYlAt/qX0uYYqdjaUrCdIYJl+2cJSLB/nmN4qDZgOhlumRvt3nAvft+w== https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/sig http://purl.org/nanopub/x/hasSignatureTarget https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g https://w3id.org/np/RAg6bTElf6hzseDvDG8qcgvJOt-Om1WurPi6PEFfh7l0g/sig http://purl.org/nanopub/x/signedBy https://orcid.org/0009-0007-4948-9192