https://w3id.org/np/RApicPByL-4rFuV-hPe3wldkQhRWDBWW6zZrfnNvlABRA
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
@prefix this: <https://w3id.org/np/RApicPByL-4rFuV-hPe3wldkQhRWDBWW6zZrfnNvlABRA> .
@prefix sub: <https://w3id.org/np/RApicPByL-4rFuV-hPe3wldkQhRWDBWW6zZrfnNvlABRA/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix npx: <http://purl.org/nanopub/x/> .
@prefix dc: <http://purl.org/dc/terms/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
}
sub:assertion {
<https://w3id.org/delphi/resource/assessment/levin-2023-goals-01--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "analysis.py downloaded the seven source files at commit bced77dd90e6a5c67bf7a557610b19ee995db729 and the figshare docx, recorded byte size and SHA-256, and searched the docx for a numeric table or a numeric file. The archive contains four images and a caption document with zero Word tables. It then attempted to import MultiNEAT, which raised ModuleNotFoundError. No cell-state trajectory was scored. The model was not re-integrated, and the paper's reported percentages were not copied into measured.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: null percent of cells matching the French flag at developmental step 90 (n = 0, not measured). Interpretation: Simulation-result claim. The abstract sentence is: \"Our system showed the evolution of the much more complex setpoints of cell collectives (tissues) that solve a problem in morphospace: the organization of a body-wide positional information axis (the classic French flag problem in developmental biology).\" Cells are rewarded for energy homeostasis in proportion to stripe match; they are not given a local target label. ES-HyperNEAT evolves the policy. A passing run shows that this program reaches the flag. It does not show that cells do this.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of levin-2023-goals-01: inconclusive, confidence 0.9";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/levin-papers/levin-2023-goals-01/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "A numeric cell-state trajectory from the authors' 2D neural cellular automaton, either emitted by their released code at the pinned commit or deposited as a table. A figure image, a sentence in the paper, and a biological planarian count are not admissible. Re-scoring a deposited matrix must be labelled as not a re-integration of the model.";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "none";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "At step 90, fewer than half the cells match the target.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Scoring the model requires MultiNEAT, Mesa and OpenCV, which are outside the standard tooling for these tests. Importing MultiNEAT failed.",
"The committed run.py sets nb_gens = 2. The paper states 250 generations and a population of 350. That evolution was not run.",
"The figshare supplement is three figure images (energy initialization, perturbation size, random initialization) and their captions.",
"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.",
"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> "At developmental step 90, at least 90 percent of cells match the French-flag target.";
<https://w3id.org/delphi/ontology/failCriterion> "Pre-registered: refutes if accuracy at step 90 is < 50. Mixed if accuracy is >= 50 and < 90. If the authors' code cannot be executed and no numeric cell-state matrix from a run can be fetched, the verdict is inconclusive with reason data-unavailable, and the paper's 95.1 is not copied into measured.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.9"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-2>,
<https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-3>;
<https://w3id.org/delphi/ontology/hasVerdict> "inconclusive";
<https://w3id.org/delphi/ontology/hypothesis> "A 2D neural cellular automaton whose cells pursue only energy homeostasis, with that reward tied to how well the tissue matches a stripe pattern, and whose policy is evolved by ES-HyperNEAT, reaches a French-flag pattern by developmental step 90.";
<https://w3id.org/delphi/ontology/inferenceMethod> "Accuracy = 100 * (cells in the target state) / (number of cells), at step 90, compared with 90 (pass) and 50 (fail).";
<https://w3id.org/delphi/ontology/passCriterion> "Pre-registered before opening the supplementary file and before any developmental run. Pattern accuracy is the percentage of cells whose state equals the French-flag target at that position. Supports if a tissue produced by the authors' ES-HyperNEAT setup, started from the homogeneous initial state and scored at developmental step 90, has accuracy >= 90. The 90 threshold is the paper's own cutoff for the evolutions it treated as having solved the flag. The representative 95.1 percent at step 90 is recorded if recomputed, and is not required.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/levin-2023-goals-01> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/levin-2023-goals-01--claim-test> .
<https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "authors' released model; nb_gens in run.py is 2 and no evolved genome is included. Not executed. The paper states 250 generations and population 350.";
dc:license "";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Pio-Lopez and Levin neural cellular automaton source, ES-HyperNEAT French-flag experiment";
prov:atLocation <https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/analysis.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/multicellularity/agents.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/multicellularity/model_for_analysis.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/multicellularity/schedule.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/multicellularity/server.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/multicellularity/visualize.py>,
<https://raw.githubusercontent.com/LPioL/scalefreecognition/bced77dd90e6a5c67bf7a557610b19ee995db729/run.py>;
prov:wasDerivedFrom <https://github.com/LPioL/scalefreecognition>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:0340609bbda69b0a77fb171332d18a24664ca72281437e213850d08d581cc42f",
"sha256:80007d10f78613bff14db5eac62443c59369d714f25385ba964bcd5c80662546", "sha256:bf05e91b35b0400842855cebf108d4036d15236554aa8362eaac25d09bbaa751",
"sha256:ca94cb5e472c94a7b77f10c6e152c5c04d75498b3da29caab15c3c299ebc87bc", "sha256:e9b4b6fc59a884b119a686e521f2f8a31e6e76fa735130ecca4d1022f5e16a3b",
"sha256:ebd87f69e0cda6a4939fc1c5e876e5d48cb505f52b213262e1314ba45c535a85", "sha256:f2889d99911b3e424b794e8bc4369a665b68504f2e7b6264baef9f1b12fc0de1" .
<https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "checked for a deposited cell-state or stress matrix; none present";
dc:license "";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Electronic supplementary material for Interface Focus 2023 rsfs.2022.0072";
prov:atLocation <https://ndownloader.figshare.com/files/39538311>;
prov:wasDerivedFrom <https://doi.org/10.6084/m9.figshare.c.6463335>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:e3b27beb1fbf133c719d36174dd56a663214e93c184b6cee2f601a272ba0c6be" .
<https://w3id.org/delphi/resource/evidence/levin-2023-goals-01--claim-test--dataset-3>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "claim text and the stated experimental parameters; not used as the measurement";
dc:license "CC BY";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Pio-Lopez L, Bischof J, LaPalme JV, Levin M (2023) The scaling of goals from cellular to anatomical homeostasis";
prov:wasDerivedFrom <https://doi.org/10.1098/rsfs.2022.0072> .
}
sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7> a prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (grok-4.7; cursor/levin-competency-goals-363e)";
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-2023-goals-01/result.json>;
prov:wasGeneratedBy sub:test .
sub:plan prov:hadPlan <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md> .
sub:test a prov:Activity;
prov:qualifiedAssociation sub:plan;
prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.881Z"^^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-2023-goals-01--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of levin-2023-goals-01: inconclusive, confidence 0.9";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/levin-papers> .
sub:sig npx:hasAlgorithm "RSA";
npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB";
npx:hasSignature "n+jw1xrTAzPm9OjLR9t+urxtFhK2ac9yOo1MHj8fEPqYHWG5KhfCGbKs0TipbwnQ0TSA2/aJoZOWS0ATC1MD8mZjjbx4WzdRkzpwBTqfG/NI9SfZqAukfBpU+mm6hOpdccP8Oe0Ptl5LyyNVJ74eETbZetAz91SgaDdCYvv2WgYoj1k9cGzTbd5R1+l9cOliGs5eQMza/o1QaKG8rVIvXBhyY9MYTCb88vNzS6b8qalf9IBUiBoGeOkVYa40e3l7HrAoUzaS9Yjs9wTcw3wHZZofh4jYSolXjEnUZQkXAlqjjE3k2z0BYLLf3jV2pU7BMKtLl+fjVHR8mlW4HFFm9g==";
npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}