{ "engine": "bio-suite dca-compare (Mean-Field Direct Coupling Analysis mfDCA Precision Matrix + APC)", "benchmark_id": "TOOL-BENCHMARK-23-DCA-COEVO-VS-SCIPY", "validation_set_id": "VAL-SET-012-DCA-COEVOLUTION-12COHORT", "external_reference": "SciPy v1.18.1 (scipy.linalg.inv Regularized Covariance Inversion) + NumPy v2.5.4 + Morcos et al. (2011) mfDCA", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "gen1_mean_mi_top3_precision": 1.0, "calibrated_mean_dca_top3_precision": 1.0, "dev_mean_f_apc_abs_diff": 0.0, "reserve_mean_f_apc_abs_diff": 0.0, "overall_f_apc_pearson_r": 1.0, "mean_direct_to_indirect_ratio": 692.2833, "regime_concordance_pct": 100.0, "total_native_ms": 1.3776, "total_scipy_ms": 124.9193, "speedup_factor": 90.6789, "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "name": "Bacterial 23S rRNA Domain V Peptidyl Transferase Center (A2058-U2611 Triad)", "biological_system": "Prokaryotic 50S Ribosome Macrolide Resistance Epistasis", "accession_or_pdb": "NC_000913.3 (rrlB) / PDB 4V9D", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 6.7548, "scipy_top_direct_f_apc": 6.7548, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 675.48, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 6.7548 vs. F_trap = 0.0000, 675.48x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "DEV-02", "split": "Development", "name": "Klebsiella pneumoniae SHV-1 Beta-Lactamase Ser70-Lys73-Glu166 Catalytic Network", "biological_system": "Class A Serine Beta-Lactamase Omega-Loop Epistasis", "accession_or_pdb": "PDB 4ZAM (blaSHV-1)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 11.5228, "scipy_top_direct_f_apc": 11.5228, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 1.714, "scipy_indirect_trap_f_apc": 1.714, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 6.7228, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 11.5228 vs. F_trap = 1.7140, 6.72x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "DEV-03", "split": "Development", "name": "E. coli Dihydrofolate Reductase (DHFR) Met20-FG Loop Allosteric Bridge", "biological_system": "Folate Pathway Catalytic Loop Co-Evolution (Asp27-Trp22-Gly121)", "accession_or_pdb": "PDB 1RX2 (folA)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 7.3387, "scipy_top_direct_f_apc": 7.3387, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 733.87, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 7.3387 vs. F_trap = 0.0000, 733.87x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "DEV-04", "split": "Development", "name": "Bacterial 16S rRNA Helix 44 Decoding Site (A1408-C1494 Aminoglycoside Clamp)", "biological_system": "30S Ribosomal Decoding Center Watson-Crick Stem Epistasis", "accession_or_pdb": "NC_000913.3 (rrsA) / PDB 4V5D", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 7.4444, "scipy_top_direct_f_apc": 7.4444, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 744.44, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 7.4444 vs. F_trap = 0.0000, 744.44x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "DEV-05", "split": "Development", "name": "Human HSP90-Alpha Bergerat ATP-Lid Salt-Bridge Network", "biological_system": "Eukaryotic Molecular Chaperone N-Domain Co-Evolution", "accession_or_pdb": "PDB 1UYD (HSP90AA1)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 8.0471, "scipy_top_direct_f_apc": 8.0471, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 804.71, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 8.0471 vs. F_trap = 0.0000, 804.71x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "DEV-06", "split": "Development", "name": "Column-Permuted Independent Alignment Control (0-Beaker Gate)", "biological_system": "0🧪 Shuffled Column-Independent Alignment Control", "accession_or_pdb": "SIM-COLPERM-DEV06", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 0.0, "scipy_top_direct_f_apc": 0.0, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 1.0, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "0-Beaker Independent/Neutral Control Rejected (Max F_APC = 0.0000 < 0.08 Gate)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-01", "split": "Reserve", "name": "Eukaryotic ITS2 Helix III Compensatory Base Change (CBC) Stem-Loop", "biological_system": "Fungal/Plant Ribosomal ITS2 Helix III CBC Speciation Marker", "accession_or_pdb": "NR_111007.1 (ITS2 Helix III)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 7.401, "scipy_top_direct_f_apc": 7.401, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 740.1, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 7.4010 vs. F_trap = 0.0000, 740.10x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-02", "split": "Reserve", "name": "Human Mitochondrial 16S rRNA (MT-RNR2) A1555G-1494C Ototoxicity Stem", "biological_system": "Mitochondrial Mitoribosome Decoding Stem Pharmacogenomics", "accession_or_pdb": "NC_012920.1 (MT-RNR2)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 9.897, "scipy_top_direct_f_apc": 9.897, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 989.7, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 9.8970 vs. F_trap = 0.0000, 989.70x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-03", "split": "Reserve", "name": "S. aureus Topoisomerase IV ParE GHKL ATP-Binding Pocket Network", "biological_system": "Gram-Positive Fluoroquinolone/Aminobenzimidazole Target Epistasis", "accession_or_pdb": "PDB 4URL (parE)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 7.9441, "scipy_top_direct_f_apc": 7.9441, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 794.41, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 7.9441 vs. F_trap = 0.0000, 794.41x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-04", "split": "Reserve", "name": "Human Bruton's Tyrosine Kinase (BTK) Gatekeeper Thr474-Cys481 Network", "biological_system": "Tec-Family Kinase Active-Site Covalent Inhibitor Epistasis", "accession_or_pdb": "PDB 6X3P (BTK)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 6.4988, "scipy_top_direct_f_apc": 6.4988, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 649.88, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 6.4988 vs. F_trap = 0.0000, 649.88x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-05", "split": "Reserve", "name": "Human Estrogen Receptor Alpha (ESR1) Helix-12 Agonist Clamp", "biological_system": "Nuclear Hormone Receptor Ligand-Binding Pocket Co-Evolution", "accession_or_pdb": "PDB 1G50 (ESR1)", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 7.8352, "scipy_top_direct_f_apc": 7.8352, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 783.52, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "Direct Contacts Resolved & Indirect Trap Suppressed (F_direct = 7.8352 vs. F_trap = 0.0000, 783.52x, Top-3 = 100.0%)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 }, { "cohort_id": "RES-06", "split": "Reserve", "name": "Clonal Neutral Drift Star-Phylogeny Decoy (0-Beaker Gate)", "biological_system": "0🧪 Clonal Neutral Drift Alignment Without Epistatic Selection", "accession_or_pdb": "SIM-CLONAL-RES06", "num_seqs": 160, "num_cols": 12, "gen1_mi_indirect_false_positive_rate": 0.0, "gen1_mi_top3_precision": 1.0, "native_top_direct_f_apc": 0.0, "scipy_top_direct_f_apc": 0.0, "abs_diff_top_f_apc": 0.0, "native_indirect_trap_f_apc": 0.0, "scipy_indirect_trap_f_apc": 0.0, "abs_diff_indirect_f_apc": 0.0, "direct_to_indirect_suppression_ratio": 1.0, "native_top3_contact_precision": 1.0, "scipy_top3_contact_precision": 1.0, "regime_classification": "0-Beaker Independent/Neutral Control Rejected (Max F_APC = 0.0000 < 0.08 Gate)", "concordant_with_scipy": true, "native_runtime_ms": 0.1148, "scipy_runtime_ms": 10.4099 } ], "ascii_summary_table": "========================================================================================================================================================\n TOOL BENCHMARK #23: Native Mean-Field Direct Coupling Analysis (mfDCA + APC) vs. Live SciPy v1.18.1 (linalg.inv)\n========================================================================================================================================================\nCohort Split NSeq NCol MI_Prec DCA_Prec Nat_DirF Sci_DirF |ΔDirF| Nat_TrapF Sci_TrapF Dir/Trap Match\n--------------------------------------------------------------------------------------------------------------------------------------------------------\nDEV-01 Development 160 12 100.0% 100.0% 6.7548 6.7548 0.0000 0.0000 0.0000 675.48x YES (100%)\nDEV-02 Development 160 12 100.0% 100.0% 11.5228 11.5228 0.0000 1.7140 1.7140 6.72x YES (100%)\nDEV-03 Development 160 12 100.0% 100.0% 7.3387 7.3387 0.0000 0.0000 0.0000 733.87x YES (100%)\nDEV-04 Development 160 12 100.0% 100.0% 7.4444 7.4444 0.0000 0.0000 0.0000 744.44x YES (100%)\nDEV-05 Development 160 12 100.0% 100.0% 8.0471 8.0471 0.0000 0.0000 0.0000 804.71x YES (100%)\nDEV-06 Development 160 12 100.0% 100.0% 0.0000 0.0000 0.0000 0.0000 0.0000 1.00x YES (100%)\nRES-01 Reserve 160 12 100.0% 100.0% 7.4010 7.4010 0.0000 0.0000 0.0000 740.10x YES (100%)\nRES-02 Reserve 160 12 100.0% 100.0% 9.8970 9.8970 0.0000 0.0000 0.0000 989.70x YES (100%)\nRES-03 Reserve 160 12 100.0% 100.0% 7.9441 7.9441 0.0000 0.0000 0.0000 794.41x YES (100%)\nRES-04 Reserve 160 12 100.0% 100.0% 6.4988 6.4988 0.0000 0.0000 0.0000 649.88x YES (100%)\nRES-05 Reserve 160 12 100.0% 100.0% 7.8352 7.8352 0.0000 0.0000 0.0000 783.52x YES (100%)\nRES-06 Reserve 160 12 100.0% 100.0% 0.0000 0.0000 0.0000 0.0000 0.0000 1.00x YES (100%)\n--------------------------------------------------------------------------------------------------------------------------------------------------------\n" }