https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8/Head https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8/assertion https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8/provenance https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8/pubinfo https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA76df9-XqBfP4oGbhuOMy6XGtNt0DWZND3eIZt4xvAu8/assertion https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 http://purl.org/dc/terms/description Downloaded each Table S1 model's public Octave export and integrated it with scipy.integrate.solve_ivp (LSODA, rtol 1e-4, atol 1e-7, max_step 0.5). After a 0–100 relax, every ordered pair of species was driven with six clamped pulses of lengths 50, 60, 70, 80, 90 and 100, each followed by an unclamped relax of the same length. Up-clamp is 100 times the relax maximum; down-clamp is the relax minimum divided by 100. A pair habituates when each successive pulse-mean of the response is at most 1/1.5 of the previous mean and the first mean exceeds 1e-12. The pre-registered rule in pass_criterion and fail_criterion was applied to those counts without a change of threshold. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 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-14--claim-test--pr-117 http://www.w3.org/2000/01/rdf-schema#comment Measured: 15 testable models with at least one habituating pair (n = 33, deterministic given the solver tolerances; no sampling error). Interpretation: The claim calls habituation 'a progressive 50% drop' and the source sentence says 'decrease in expression by 50% (i.e., a ratio of 1:1.5)'. The methods equation is the fraction 1/1.5 applied to successive stimulation-window means (MathML ids mm41 and mm42 in the Europe PMC full text), which is a drop to two-thirds, not to one-half. The verdict uses 1/1.5, because that is the criterion that the stated 27-model count was computed with. A true half-drop (ratio 1/2) is reported beside it and does not decide the verdict. 'Testable' in the claim is the authors' MATLAB subset (27 of 35); here it is every Table S1 model that integrates under the rules in the contract, so T need not equal 27 for a support. The continuous clamp (species held at the target, derivative not applied) is the intervention their MATLAB loop approximated by re-integrating and resetting; the chunk length '(10)' in that workaround is not multiplied into the epoch durations. This is a simulation of published ODE models. It does not measure pharmacoresistance in organisms. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2022-grn-learning-14 (pr-117): refutes, confidence 0.5 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 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-14/pr-117/result.json https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 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-14--claim-test--pr-117 https://w3id.org/delphi/ontology/admissibleDatasets The 35 BioModels identifiers named in Table S1 of Biswas, Clawson and Levin, Int. J. Mol. Sci. 2023, 24, 285 (doi:10.3390/ijms24010285), fetched as public SBML from the BioModels/biomodels.org archive. No author result table, figure, or precomputed trajectory may enter the verdict. Models that do not load, whose initial relax is non-finite, that have more than 40 floating species, or for which fewer than half of attempted pairs return finite means, are not testable; they are excluded from T and are not counted as failures. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/disconfirmingObservation Four or more testable models with no such pair, or a majority of testable models whose habituating share lies outside 1–50%. A single hold-out model, or a minority outside the band, is mixed rather than a refutation, because the integrator is not the authors' MATLAB ode23tb. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/evidenceAgainst Of 33 testable models, 18 had no habituating pair and 4 more had a pair but a share below 1% (0.32% to 0.38%). Eleven models fell inside 1–50%. Engagement held in 32 of 33 models (a first pulse moved some response by at least 1.5-fold), including 17 of the 18 models with zero habituation, so the zeros are not a failure of the clamp to move the network. BIOMD0000000483 had no 1.5-fold response in any pair. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/evidenceAgainst Registration written on 2026-11-01 before any BioModels file was fetched and before the supplement zip was downloaded. The zip URL was checked with an HTTP HEAD only (content-type application/zip, content-length 2886027). Methods formulas were read from the already-vendored paper text and from Europe PMC full text XML PMC9820177, which contains no Table S1 identifiers and no per-model habituation counts. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/evidenceAgainst SBFC writes some assignments on the same line as a % comment, after a tab, and places a few assignment rules after the reactions that use them. Those statements were restored and literal constants were moved above the reactions so the exported file can execute. BIOMD0000000024 contains delay(), which the exporter does not implement, and BIOMD0000000539's export refers to reaction_production_A without defining it. Both are not testable and are not counted as failures. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/evidenceAgainst The continuous clamp replaces the paper's MATLAB loop, which reset the stimulus every short solver call because ode23tb cannot edit a trajectory mid-call. Epoch lengths use the methods' step counts at h = 0.01 (50 to 100 time units), not 5000 separate solver calls. A reading in which each of those steps lasted 10 time units was not run. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/evidenceAgainst This is a simulation of published ODE models. It shows whether the habituation inequality appears in those equations under the stated clamp. It is not a measurement of pharmacoresistance in organisms. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/expectedObservation Every numerically testable model from the paper's Table S1 has at least one up- or down-clamped stimulus–response pair whose six stimulation-window means fall by a factor of at least 1/1.5 at every step, and the share of such pairs in that model is between 1% and 50%. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/failCriterion Pre-registered. If the engagement check fails, the verdict is inconclusive with reason other, whatever the habituation counts are. If fewer than 15 of the Table S1 model files can be downloaded, inconclusive with reason data-unavailable. If files download but T < 20, inconclusive with reason underpowered. If the engagement check passes and T >= 20, refutes if Z >= 4 or more than half of the testable models have a fraction outside [0.01, 0.50]; otherwise, if S3 or S4 fails, the verdict is mixed. A descriptive count of pairs that also meet a stricter successive ratio of 1/2 is recorded and does not decide the verdict. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/hasConfidence 0.5 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/hypothesis If the claim holds, then under the paper's six-pulse habituation protocol every BioModels pathway model that integrates has at least one stimulus–response pair whose mean expression falls by a factor of 1/1.5 at each successive lengthening pulse, and that pair is between 1% and 50% of the pairs tested in that model. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/inferenceMethod Six clamped pulses with durations 50, 60, 70, 80, 90 and 100 model-time units (the methods' 5000-to-10000 steps at the stated output step h = 0.01), each followed by an unclamped relax of the same length. Up-clamp is the species' maximum over the initial 0–100 relax, times 100; down-clamp is that minimum divided by 100 (paper MathML mm39–mm41). Habituation is mean(R) on pulse i+1 <= mean(R) on pulse i times 1/1.5 for all five steps, with every pulse mean finite and the first pulse mean > 1e-12. Fraction = habituating pairs / finite pairs. Engagement check: at least half of testable models have at least one pair whose first-pulse mean of R differs from the mean of R over the last 10 time units of the initial relax by a factor of 1.5 or more. Thresholds are S1–S4 above; no threshold is fit after seeing counts. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/passCriterion Pre-registered, before any BioModels file or the supplement archive was opened. Let T be the number of testable models (defined in test_contract). Let Z be how many of them have zero habituating pairs. A model fraction is the number of habituating pairs divided by the number of finite pairs evaluated. Supports only if all of: (S1) the engagement check passes; (S2) T >= 20; (S3) Z = 0; (S4) every testable model's fraction lies in [0.01, 0.50]. https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2022-grn-learning-14 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2022-grn-learning-14--claim-test--pr-117 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 http://purl.org/dc/terms/description identifies the 35 BioModels IDs; only Table S1 (page 1) was read https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--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-14--claim-test--pr-117--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Table S1 of Biswas, Clawson and Levin 2023 (supplement zip) https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 http://www.w3.org/ns/prov#atLocation https://mdpi-res.com/d_attachment/ijms/ijms-24-00285/article_deploy/ijms-24-00285-s001.zip https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://doi.org/10.3390/ijms24010285 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:292a7f33bcb3a9589614507114de8c1a7a5f5d8bc11e382d546c3d08da381e39 https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-2 http://purl.org/dc/terms/description ODE right-hand sides and initial conditions for the habituation screen https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-2 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--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-14--claim-test--pr-117--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: BioModels Octave exports for the 35 Table S1 identifiers https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-2 http://www.w3.org/ns/prov#atLocation https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000001?filename=BIOMD0000000001.m https://w3id.org/delphi/resource/evidence/levin-2022-grn-learning-14--claim-test--pr-117--dataset-2 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