{"artifact_id":"L1-413","layer":"L1","title":"HMM Sequence Alignment and Profile Inference","domain":"Computational Biology","sub_domain":"Computational genomics","physics_fingerprint":{"L_DAG":3.5,"title":"HMM Sequence Alignment and Profile Inference","domain":"Computational Biology","carrier":"N/A","primitives":["N.pointwise","S.viterbi.alignment","O.baum_welch.em_training"],"sub_domain":"Computational genomics","noise_model":"multinomial","problem_class":"statistical_inverse","solution_space":"HMM_profile_parameter_matrix","difficulty_delta":5,"integration_axis":"sequence_positions","sensing_mechanism":"sequence_emission_probability"},"observable_profile":{"metric":"alignment_sensitivity_percent","regime":"Existence of the recovered HMM_profile_parameter_matrix 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 ~= 500); sequence_divergence_too_high dominates the stability cliff; the remaining mismatch parameters contribute higher-order bias terms. Multinomial sets the irreducible data-fidelity floor.","secondary":"specificity_percent"},"size_tiers":{"center_spec":{"omega":{"N_sequences":100,"M_model_states":200,"L_alignment_length":200,"sequence_identity_percent":40},"input_format":"measurement_only","problem_class":"statistical_inverse","forward_operator":"sequence_emission_probability","epsilon_fn_center":"80 alignment_sensitivity_percent"},"omega_bounds":{"N_sequences":[5,10000],"M_model_states":[10,2000],"L_alignment_length":[20,5000],"sequence_identity_percent":[5,100]},"epsilon_bounds":{"alignment_sensitivity_percent":[30,100]},"allowed_problem_classes":["statistical_inverse"],"allowed_omega_dimensions":["N_sequences","L_alignment_length","sequence_identity_percent","M_model_states"],"allowed_forward_operators":["sequence_emission_probability"]},"hardness_fn":{"type":"epsilon_fn","delta":5,"kappa":10000.0,"metric":"alignment_sensitivity_percent"},"initiator_dataset":[{"name":"primary","weight":1.0,"ipfs_cid":null,"license_hash":null}],"status":"testnet","staked_pwm":0.0,"chain_hash":"0xf98f8579912e154da9fd2f93ff45db2c8a33fd2ce25458ca1bfa9cd3c29fc578","chain_tx_hash":"0xd95947e49ead7244913ccaea703b95ecdd11c9bbf6365b5a263ac302a158f87f","chain_block":41555220}