https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s/Head https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s/assertion https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s/provenance https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s/pubinfo https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAyGJhTUmonwkZxSkeEVwBN4U1vGHt0FL903E3QANV56s/assertion https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test http://purl.org/dc/terms/description analysis.py runs the same 20-seed, 32-bin simulations as levin-2015-place-01 for both initial-expectation spreads, deterministic plus a process-noise copy. For each run it records t_m, t_d, the free-energy trajectory and step-32 identity resolution, and counts runs meeting all pre-registered conditions. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--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-2015-place-05--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 10 median differentiation step (file initialisation randn/8) (n = 20, range 9-14 over 20 seeds). Interpretation: MATLAB is unavailable, so the test uses an independent numpy re-implementation (levin-2015-place-01/morphogenesis.py) of DEM_morphogenesis.m. Re-implemented exactly from the file: the 8-cell target (matrix T for L = 2; four cell types coded by signals 1-4), sensations of position (the exogenous linear gradient), intrinsic signal and extracellular signal (monoexponential decay, k = 1, scaled by the sensitivity ramp 1 - exp(-2t) with t = iY/32 as set by spm_ADEM), softmax identity expectations, model sensory precision exp(3), prior precision exp(-2) on identities, action precision exp(2) with action restricted to each cell's own sensations, and initial action equal to the t = 0 prediction (all cells near the centroid). Not re-implemented: spm_ADEM's generalised filter (embedding order 2, local-linearisation update). Instead each of the 32 bins integrates the gradient flow of the Laplace free energy for one time unit (dt = 1, 200 Euler sub-steps; 400 and 800 sub-steps give identical results to 3 decimals). Free energy is spm_ADEM's -J (E'iS E/2 - logdet(qu.c) - logdet(iS)/2) without generalised-motion terms, so only its changes are comparable to the paper's. The paper says initial expectations had 'a log precision of minus four' (sd = e^2 = 7.4), but the file uses randn(n,n)/8 (log precision about +4.2), which matches the paper's 'small random expectations' and 'undifferentiated'. The rule fixed before any baseline run was to run both and call the claim supported only if both pass, and mixed if they disagree. Assessor note checked: the current SPM file's header comment says 16 cells, but its default target (L = 2) has exactly 8 cells, the paper's head-body-tail form, identical in SPM12 r7679 and current main. SPLIT = 0, so the bisection path is off by default, as noted. 'Migrate rapidly' is the step t_m at which mean distance to the best-assigned targets has halved. 'Differentiate at about the eighth step' is the step t_d at which at least 6/8 cells are correctly typed and mean max identity probability exceeds 0.5, accepted in [4, 16]. 'Resolve ambiguity' means that at step 32 mean max identity probability exceeds 0.5 with at least 7/8 cells correctly typed. Context dependence is built into the model, since each cell senses only other cells' signals and the exogenous gradient. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of levin-2015-place-05: mixed, confidence 0.6 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--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-2015-place-05/result.json https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/admissibleDatasets The generative model and parameters of the paper and its public SPM implementation. MATLAB is unavailable, so an independent Python re-implementation (gradient descent on Laplace free energy for internal states and action, not SPM's generalized filter spm_ADEM) is used; its time step is matched to the SPM loop (one time step = one update of the 32-step schedule of the extracellular-sensitivity ramp). 8-cell head-body-tail target as in the paper. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/dataKind computational https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Differentiation precedes migration, occurs far from step 8 or never, free energy does not fall, or identities stay ambiguous at step 32 in most runs. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst After seeing the deterministic results, a disclosed sensitivity condition added the SPM generative process's sensory noise (precision exp(16)), which the pre-registered re-implementation omits. It did not change any count by more than one run. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Cell types use the file's encoding (T values 2, 1, 4, 3 from left to right along the body axis). The paper's head/body/tail labels map onto these four signal codes. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Independent re-implementation, not the published MATLAB solver. spm_ADEM's generalised filtering in generalised coordinates can follow a different path through the same free-energy landscape. Nothing was run in MATLAB or Octave. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Seeds are numpy default_rng(0..19). The paper reports one run with MATLAB rng('default'), which cannot be matched outside MATLAB. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Under the file's initialisation the reported sequence reproduces closely in 19/20 runs: migration halves the distance by step 4 (median), differentiation follows at median step 10 (range 9-14), free energy peaks at step 2 and then falls (the paper notes an initial increase), and identities resolve. Under the paper's literal 'log precision -4', 0/20 runs qualify: cells begin with random near-one-hot identities, so median 'differentiation' is step 6.5, before migration (median t_m 17, and in some runs distance never halves). That is the opposite order, and it drives the mixed verdict. The literal reading contradicts the paper's own description of the start as 'undifferentiated'. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/expectedObservation Mean distance to targets halves before cells commit to identities; identities commit near step 8 (between 4 and 16); free energy falls; identities end resolved and correct in most seeded runs. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: in fewer than 10 of 20 runs the conditions hold, or in the majority of runs differentiation precedes or coincides with migration (t_d <= t_m), or the median t_d is outside [2, 24] or never reached. Between 10 and 15 qualifying runs is 'mixed'. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.6 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-4 https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/hypothesis In the paper's eight-cell active-inference model started from identical co-located undifferentiated cells, migration toward target locations happens first and fast, differentiation into head/body/tail types follows at around the eighth time step, ensemble free energy falls as identities resolve, and identities end resolved even though each cell's identity depends on signals from other equally ambiguous cells. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/inferenceMethod Per-run t_m, t_d, free-energy change and final identity resolution; count of qualifying runs against 16 (pass) and 10 (fail) out of 20; median t_d reported. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered, over 20 random seeds (initial expectations with log precision -4), 32 steps: define migration time t_m as the first step at which the mean distance of cells to their best-assigned target positions falls below 50% of its value at step 0, and differentiation time t_d as the first step at which at least 6 of 8 cells have a most-probable identity of the type encoded at their assigned target and mean max identity probability exceeds 0.5. The claim is supported if, in at least 16 of 20 runs: t_m < t_d; t_d lies in [4, 16] (within a factor of 2 of the reported eighth step); ensemble free energy at step 32 is below step 1; and at step 32 mean max identity probability exceeds 0.5 with at least 7/8 cells correctly typed. https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/levin-2015-place-05 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/levin-2015-place-05--claim-test https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-1 http://purl.org/dc/terms/description generative model, generative process, precisions, target morphology (L = 2), initial conditions and SPLIT procedure re-implemented in Python https://w3id.org/delphi/resource/evidence/levin-2015-place-05--claim-test--dataset-1 http://purl.org/dc/terms/license GPL-2.0 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