EVIDENCE_MATRIX.json

{
  "paper_id": "mOcTXKawFY",
  "upstream_pin": {
    "source": "https://arxiv.org/html/2606.05689v1",
    "version": "2606.05689v1",
    "sha256": "9b3075a937ce509d5883709a90fba12a35111d6b20f92e033d3e64636728c070"
  },
  "release_quality_gate": {
    "status": "pass_12_of_12_semantic_v4",
    "registered_claims": 6,
    "supported_by_independent_evidence": 6,
    "literal_falsifications": 1,
    "expected_verified_points": 12,
    "judge_target": "verified_or_literal_falsification",
    "formula_only_support_counted": false,
    "proxy_support_counted": false,
    "algebraic_bound_substitution_counted": false,
    "semantic_quality_gate_version": 4,
    "direct_rate_claims": 0,
    "independent_seeded_trials": 1810,
    "exact_derivation_cells": 1822710
  },
  "claims": [
    {
      "claim": 1,
      "assessment": "verified",
      "evidence_tier": "literal_claim_experiment",
      "claim_object_match": "exact",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "Definition 1 formalizes an evolutionary selection model as a DAG G^(T) over trait variables X^(0)...X^(T), heritable factors epsilon^(0)...epsilon^(T), and reproduction/selection indicators S^(0)...S^(T-1), distinguishing it from one-shot static selection models (Section 2, Definition 1).",
      "paper_native_mechanism": "The executable constructs Definition 1's fully unrolled evolutionary DAG with the printed trait, selection, factor-to-trait, and inheritance edge families.",
      "independent_oracle": "Closed-form node and edge counts plus independent topological acyclicity and edge-family inventories are evaluated for every constructed graph.",
      "not_proxy_reason": "The audited object is the literal G^(T) graph over all three registered node families; a static DAG or generic layered-network surrogate is not substituted.",
      "native_scale_justification": "All 8,688 four-trait static models are unrolled at T=1,2,3 for 26,064 exact constructions, followed by 60 larger constructions through d=20 and T=5.",
      "source_locator": "arXiv 2606.05689v1, Section 2, Definition 1 and its four-item edge inventory.",
      "independent_evidence": ["outputs/exact_graph_audit.json", "outputs/results.json"],
      "executed_outputs": ["outputs/exact_graph_audit.json", "outputs/results.json"],
      "oracle_artifacts": ["outputs/oracle_gates.json", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json"],
      "destructive_or_boundary_control": "One inheritance edge is deleted from an otherwise valid G^(3); the exact edge-count and edge-family checker rejects the mutant.",
      "result": "26,064/26,064 exhaustive constructions and 60/60 larger constructions are acyclic and match the exact node count, edge count, and required edge families.",
      "limitation": "The construction audit verifies the formal graph object, not biological adequacy of independent component-wise heritable factors.",
      "scope_boundary": "Verification covers Definition 1's graph construction and its distinction from a one-shot model, not arbitrary alternative evolutionary models."
    },
    {
      "claim": 2,
      "assessment": "verified",
      "evidence_tier": "literal_claim_experiment",
      "claim_object_match": "exact",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "Lemma 1 shows that repeated evolutionary selection induces conditional dependencies among variables that are absent under static selection models, so applying static-selection graphical models to evolutionary data can yield false causal discoveries (Section 2, Lemma 1).",
      "paper_native_mechanism": "The executable conditions the unrolled graph on every earlier S variable, compares its generation-T d-separations with the static selection DAG, and runs causal-learn PC on evolved samples.",
      "independent_oracle": "The custom Bayes-ball result is cross-checked against networkx.is_d_separator, and the finite-data consequence is tested against a paired no-selection SCM with shared SEM parameters.",
      "not_proxy_reason": "The test uses the literal repeated-selection graph, static graph, conditioning sets, and selection-blind PC discovery consequence named by the claim.",
      "native_scale_justification": "All 1,433,520 disjoint-set relations from 8,688 source models at T=1,2,3 are enumerated, plus twenty paired 5,000-sample PC trials at d=8.",
      "source_locator": "arXiv 2606.05689v1, Section 2, Lemma 1 and the paragraph immediately following it.",
      "independent_evidence": ["outputs/exact_graph_audit.json", "outputs/finite_native_algorithms.json", "outputs/results.json"],
      "executed_outputs": ["outputs/exact_graph_audit.json", "outputs/finite_native_algorithms.json"],
      "oracle_artifacts": ["outputs/oracle_gates.json", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json", "outputs/finite_native_algorithms.json"],
      "destructive_or_boundary_control": "Deleting all inheritance edges removes every one of the 17,712 converse-failure witnesses; switching selection off reduces native PC false adjacencies from 46 to 8.",
      "result": "Lemma 1 has 0 violations in 1,433,520 exact relations and 17,712 strict converse-failure witnesses; paired PC finds 46 spurious adjacencies with evolution versus 8 without selection.",
      "limitation": "Finite PC counts include ordinary type-I and type-II CI errors; the exact graphical enumeration supplies the decisive lemma result.",
      "scope_boundary": "Verification concerns conditional-dependence structure and its false-discovery mechanism, not the frequency of false discoveries in every empirical domain."
    },
    {
      "claim": 3,
      "assessment": "verified",
      "evidence_tier": "literal_claim_experiment",
      "claim_object_match": "exact",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "Theorem 1 proves that the clique-augmented DAG G^+ (Definition 2) fully captures all d-separation/conditional-independence constraints implied by the evolutionary selection model, without needing to explicitly model the selection variables (Section 3, Definition 2, Theorem 1).",
      "paper_native_mechanism": "The executable forms Definition 2's topologically oriented ancestor-of-S clique and compares every tested d-separation in G^+ with the selected, fully unrolled G^(T).",
      "independent_oracle": "A separately gated networkx d-separation implementation checks the custom Bayes-ball primitive on 11,984 random queries before the theorem enumeration is interpreted.",
      "not_proxy_reason": "Both sides of Theorem 1's literal biconditional are evaluated directly; covariance, reachability, or a theorem restatement does not replace d-separation.",
      "native_scale_justification": "The complete d=4 model space yields 1,433,520 exact biconditional cells over T=1,2,3, with a further 143,811 random cells through d=10 and T=5.",
      "source_locator": "arXiv 2606.05689v1, Section 3.1, Definition 2 and Theorem 1.",
      "independent_evidence": ["outputs/exact_graph_audit.json", "outputs/oracle_gates.json", "outputs/results.json"],
      "executed_outputs": ["outputs/exact_graph_audit.json"],
      "oracle_artifacts": ["outputs/oracle_gates.json", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json"],
      "destructive_or_boundary_control": "Replacing G^+ with the selection-blind S-deleted DAG creates 98,787 exact mismatches, so agreement cannot come from an inert augmentation.",
      "result": "G^(T) and G^+ agree on all 1,433,520 exact d-separation relations with 0 violations; the naive S-deleted control mismatches 98,787 relations.",
      "limitation": "Finite enumeration is exhaustive at four traits and randomized above that size; the theorem, not this audit, establishes unbounded-size validity.",
      "scope_boundary": "Verification covers the paper's causally sufficient evolutionary DAG class and does not extend to dependent heritable-factor models."
    },
    {
      "claim": 4,
      "assessment": "verified",
      "evidence_tier": "full_pipeline_reproduction",
      "claim_object_match": "exact",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "Theorem 2 establishes that applying standard constraint-based algorithms such as PC or GES (Algorithm 1) to G^+ is sound and complete: oriented edges correspond to true causal relations, while unoriented edges may reflect the presence of selection (Section 3, Theorem 2, Algorithm 1).",
      "paper_native_mechanism": "The executable runs PC and GES from causal-learn on the paper's evolved SEM data and computes the CPDAG of each exact G^+ for the theorem's oracle-premise audit.",
      "independent_oracle": "The local Meek closure is cross-checked on 600 models against causal-learn DAG-to-CPDAG, while alternative source DAGs are exhaustively searched for every unoriented edge.",
      "not_proxy_reason": "The audit executes the named algorithms and evaluates the literal adjacency, oriented-edge, and alternative-DAG completeness clauses against their generating evolutionary models.",
      "native_scale_justification": "All 8,688 four-trait source models cover 52,128 adjacency cells, 2,640 compelled orientations, and 39,030 unoriented-edge alternatives; PC/GES also run in 750 paper-scale trials.",
      "source_locator": "arXiv 2606.05689v1, Section 3.2, Algorithm 1 and Theorem 2.",
      "independent_evidence": ["outputs/exact_graph_audit.json", "outputs/oracle_gates.json", "outputs/synthetic_native_pipeline.json", "outputs/results.json"],
      "executed_outputs": ["outputs/exact_graph_audit.json", "outputs/synthetic_native_pipeline.json"],
      "oracle_artifacts": ["outputs/oracle_gates.json", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json"],
      "destructive_or_boundary_control": "A compelled CPDAG orientation is reversed in 328 eligible source models, and the Theorem 2 soundness checker rejects all 328 mutants.",
      "result": "Across 8,688 exact models, 52,128/52,128 adjacency cells, 2,640/2,640 oriented edges, and 39,030/39,030 unoriented-edge completeness cases pass.",
      "limitation": "The exact verdict assumes the theorem's large-sample faithfulness premise; finite-sample PC and GES can and do violate oracle-level orientation soundness.",
      "scope_boundary": "Verification is for Algorithm 1 under Theorem 2's premises, not a guarantee that finite-sample CI testing always returns the population CPDAG."
    },
    {
      "claim": 5,
      "assessment": "verified",
      "evidence_tier": "full_pipeline_reproduction",
      "claim_object_match": "exact",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "Theorem 4 shows that combining heterogeneous data from multiple environments/domains via the CDNOD-based procedure (Algorithm 2) improves identifiability of the evolutionary selection model compared to single-environment data (Section 4, Theorem 4, Algorithm 2).",
      "paper_native_mechanism": "The executable builds Theorem 3's multi-domain G^{+I}, applies background-knowledge Meek closure, and runs causal-learn CDNOD on four domains with changed selection mechanisms.",
      "independent_oracle": "Every multi-domain orientation is compared with the generating G and the complete single-domain orientation set; a separate finite run compares CDNOD with PC on the identical first domain.",
      "not_proxy_reason": "The test uses the literal domain-index graph and the named CDNOD implementation on heterogeneous evolutionary data, not pooled PC or an edge-count formula.",
      "native_scale_justification": "All 8,688 four-trait source models are crossed with 31 nonempty change sets for 269,328 exact configurations, plus twenty four-domain CDNOD runs with 5,000 samples per domain.",
      "source_locator": "arXiv 2606.05689v1, Section 4, Theorem 3, Algorithm 2, and Theorem 4.",
      "independent_evidence": ["outputs/exact_graph_audit.json", "outputs/finite_native_algorithms.json", "outputs/results.json"],
      "executed_outputs": ["outputs/exact_graph_audit.json", "outputs/finite_native_algorithms.json"],
      "oracle_artifacts": ["outputs/oracle_gates.json", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json"],
      "destructive_or_boundary_control": "Omitting Theorem 3's changed-selection ancestor expansion creates 583,356 orientation-soundness violations across the same 269,328 configurations.",
      "result": "Multi-domain identification loses 0 single-domain orientations and is strictly better in 88,176/269,328 configurations; native CDNOD orients 4.65 correct edges versus 3.55 for single-domain PC.",
      "limitation": "Strict improvement is model-dependent at 32.74%, while Theorem 4's universal statement is monotonic non-loss rather than strict gain in every configuration.",
      "scope_boundary": "Verification assumes fixed causal and selection structures across domains with mechanism parameters changing as specified by the paper."
    },
    {
      "claim": 6,
      "assessment": "falsified_as_literally_registered",
      "evidence_tier": "literal_benchmark_reproduction",
      "claim_object_match": "literal",
      "registered_system_executed": true,
      "paper_or_released_scale": true,
      "actual_model_or_dataset_used": true,
      "destructive_control_executed": true,
      "literal_claim": "The proposed identification procedure is validated on synthetic graphs of varying size and on seven real-world datasets spanning biology, agriculture, and social science (Section 5).",
      "paper_native_mechanism": "The executable runs causal-learn PC and GES on 750 samples from the printed evolutionary SEM/reproduction pipeline and runs PC on the actual 626-by-8 PanTHERIA slice.",
      "independent_oracle": "Generating DAGs provide exact synthetic causal adjacencies; Appendix D.2's seven integer tables are recomputed arithmetically, and PanTHERIA input bytes are independently pinned.",
      "not_proxy_reason": "The named algorithms, paper-scale dimensions, generations, sample size, actual mammal dataset, and registered precision metric are used; oracle CPDAG precision is not substituted.",
      "native_scale_justification": "The synthetic grid has d=10,15,20, T=1,2,3,5,10, N=5,000, and 50 seeds per cell; all seven real-data tables are audited and PanTHERIA is independently rerun.",
      "source_locator": "arXiv 2606.05689v1, Sections 5.1-5.2, Figure 6, Appendix D.1, and Figures 13-19.",
      "independent_evidence": ["outputs/synthetic_native_pipeline.json", "outputs/realdata_native_and_source_audit.json", "outputs/results.json"],
      "executed_outputs": ["outputs/synthetic_native_pipeline.json", "outputs/realdata_native_and_source_audit.json"],
      "oracle_artifacts": ["outputs/realdata_native_and_source_audit.json", "inputs/PanTHERIA_1-0_WR05_Aug2008.txt", "SOURCE_EXCERPTS.md"],
      "control_artifacts": ["outputs/destructive_controls.json"],
      "destructive_or_boundary_control": "Changing one printed DGRP numerator makes the arithmetic audit fail, and flipping one PanTHERIA input byte is independently detected by the pinned SHA-256.",
      "result": "In 750 native synthetic runs, oriented-only PC beats the standard interpretation in only 3/15 grid-cell means and 0/5 d=20 cells; the PanTHERIA rerun gives 0.40 oriented versus 1.00 unoriented precision at the registered log/alpha-0.05 sensitivity cell.",
      "limitation": "Only PanTHERIA is rerun from raw real data; the other six real datasets are audited from the paper's printed outputs, whose pseudo ground truth the paper itself calls an unreliable surrogate.",
      "scope_boundary": "Falsification targets the compound empirical-validation claim and does not dispute that the authors ran analyses on seven named datasets or the exact oracle theorems in Claims 1-5."
    }
  ]
}