{"artifact_id":"L1-409","layer":"L1","title":"Phylogenetic Likelihood Inference","domain":"Computational Biology","sub_domain":"Molecular evolution","physics_fingerprint":{"L_DAG":4.5,"title":"Phylogenetic Likelihood Inference","domain":"Computational Biology","carrier":"N/A","primitives":["N.pointwise","S.mcmc.tree_space_bayesian","O.atr.total_tree_likelihood"],"sub_domain":"Molecular evolution","noise_model":"multinomial","problem_class":"nonlinear_inverse","solution_space":"phylogenetic_tree_topology","difficulty_delta":5,"integration_axis":"phylogenetic_tree","sensing_mechanism":"molecular_sequence_alignment"},"observable_profile":{"metric":"Robinson_Foulds_distance","regime":"Existence of the recovered phylogenetic_tree_topology is guaranteed within the declared Omega bounds. Uniqueness holds on the measurement-supported subspace; out-of-support modes are controlled by declared priors. Stability is conditionally stable (kappa_eff ~= 2000); model_misspecification_substitution dominates the stability cliff; the remaining mismatch parameters contribute higher-order bias terms. Multinomial sets the irreducible data-fidelity floor.","secondary":"branch_length_RMSE"},"size_tiers":{"center_spec":{"omega":{"N_taxa":50,"N_sites":5000,"divergence_time_My":100,"mutation_rate_per_site_yr":1e-09},"input_format":"measurement_only","problem_class":"nonlinear_inverse","forward_operator":"molecular_sequence_alignment","epsilon_fn_center":"5 Robinson_Foulds_distance"},"omega_bounds":{"N_taxa":[4,10000],"N_sites":[100,100000],"divergence_time_My":[1,1000],"mutation_rate_per_site_yr":[1e-10,1e-07]},"epsilon_bounds":{"Robinson_Foulds_distance":[0,20]},"allowed_problem_classes":["nonlinear_inverse"],"allowed_omega_dimensions":["N_taxa","N_sites","divergence_time_My","mutation_rate_per_site_yr"],"allowed_forward_operators":["molecular_sequence_alignment"]},"hardness_fn":{"type":"epsilon_fn","delta":5,"kappa":100000.0,"metric":"Robinson_Foulds_distance"},"initiator_dataset":[{"name":"primary","weight":1.0,"ipfs_cid":null,"license_hash":null}],"status":"testnet","staked_pwm":0.0,"chain_hash":"0x89d3fb6cb7267412f3fd12ba45b4705b67200fc24e7b93d4c5cde61fbfa2b4e3","chain_tx_hash":"0x820f0c2cd9fc9212901c8779f0a5ac0601dd802d9870bd446a567b786268b0f9","chain_block":41555219}