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The model was not re-integrated, and the paper's reported percentages were not copied into measured." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: null percent of cells matching the French flag at step 200 after the two-column perturbation at step 110 (n = 0, not measured). Interpretation: Simulation-result claim. The paper's conclusion for this section is: \"Thus, we conclude that even though we did not specifically reward for anything other than the single self-organizing property, the cells were able to repair to the target setpoint from multiple starting configurations.\" The tested perturbation is the one stated in the claim: two columns of the red stripe converted to white at step 110. A passing run shows that this program repairs that perturbation. It does not show that tissues do this." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of levin-2023-goals-03: inconclusive, confidence 0.9" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2023-goals-03/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "A numeric cell-state trajectory of this perturbation from the authors' model, produced by their code or deposited as a table. The evolutionary objective must be the 100-step French-flag reward only. A figure image and the paper's prose are not admissible." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "none" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "The tissue is dead at step 200, or fewer than half the cells match the flag." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Scoring the model requires MultiNEAT, Mesa and OpenCV, which are outside the standard tooling for these tests. Importing MultiNEAT failed." }, { "@value": "The committed run.py sets nb_gens = 2. The paper states 250 generations and a population of 350. That evolution was not run." }, { "@value": "The figshare supplement is three figure images (energy initialization, perturbation size, random initialization) and their captions." }, { "@value": "The source files were fetched. They do not contain an evolved genome or a cell-state matrix, so the pre-registered accuracy was not computed." }, { "@value": "This record does not show whether the program forms a French flag, and it does not show that cells do this." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "After the two-column red-to-white perturbation at step 110, the tissue is alive at step 200 with French-flag accuracy at least 90 percent." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered: refutes if the tissue is dead at step 200 or accuracy at step 200 is < 50. Mixed if it is alive and accuracy is >= 50 and < 90. The separate whole-red-stripe perturbation is reported and does not decide the verdict. If the authors' code cannot be executed and no numeric cell-state matrix of this perturbation can be fetched, the verdict is inconclusive with reason data-unavailable. The paper's 95.1 at step 200 is not copied into measured." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.9", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-goals-03--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-goals-03--claim-test--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-goals-03--claim-test--dataset-3" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "inconclusive" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "A tissue selected only to form the French flag within 100 steps restores that pattern after the last two columns of the red stripe are set to white at step 110." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Alive-or-dead at step 200 and accuracy at step 200, with thresholds 90 (pass) and 50 (fail)." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered before opening the supplementary file and before any developmental run. Using a tissue whose evolutionary reward covered only unperturbed self-organization within 100 steps, set the last two columns of the red stripe to white at step 110 and change nothing else. Supports if the tissue is still alive at step 200 and French-flag accuracy at step 200 is >= 90. Accuracy is 100 times the fraction of cells in the target state." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/levin-2023-goals-03--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "authors' released model; nb_gens in run.py is 2 and no evolved genome is included. Not executed. 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