{ "claim_boundary": { "mode": "B_reverse_loop_small_must_separate", "pipeline": [ "veto", "complement", "verify" ], "not_claimed": [ "Mode_A_residual_stream_as_field", "layer_Jacobian", "in_silico_gene_perturbs", "fusion_audit", "clinical" ], "true_adt_events_note": "complement (b) admits true ADT as typed evidence for this probe only; production path keeps holdout ADT verifier-only" }, "inputs": { "pairs_path": "/Users/tianchichen/Documents/GitHub/teddy_mm/outputs/anm_cite_bridge/reverse_step1/must_separate_pairs.jsonl", "n_pairs": 5000, "n_unique_cells": 2872, "z_path": "/Users/tianchichen/Documents/GitHub/teddy_mm/outputs/anm_cite_bridge/z_rna_512.npy", "panel": [ "CD19", "CD72", "CD22", "CD3", "CD2", "CD5", "CD16", "CD11c", "CD36" ] }, "veto": { "claim": "z_512 (mean-pool last-layer @ ctx 1024, L2 512-D) is INSUFFICIENT to separate these must-pairs: near-identical z carries disagreeing true ADT lineage / protein labels. Downstream readout must abstain, rewrite observer, or admit a complement evidence channel.", "n_pairs_written": 5000, "flag_counts": { "diff_adt_lineage": 2059, "diff_protein_profile": 4639, "diff_key_marker_lineage": 3287, "diff_coarse_cell_type": 790 }, "lineage_confusion": { "myeloid|t_lineage": 1490, "b_lineage|t_lineage": 375, "abstain|t_lineage": 213, "b_lineage|myeloid": 194, "abstain|myeloid": 168, "abstain|b_lineage": 24 }, "n_myeloid_t_pairs": 1490, "frac_myeloid_t": 0.298, "myeloid_t_cos_sim_quantiles": { "min": 0.9800012707710266, "q25": 0.9810009449720383, "q50": 0.9822191596031189, "q75": 0.983788788318634, "max": 0.990542471408844 }, "myeloid_t_focus_protein_deltas": { "CD5": { "n": 1490, "mean_abs_delta": 0.7155161401769459, "median_abs_delta": 0.40774770081043243, "q75_abs_delta": 1.0865748226642609 }, "CD3": { "n": 1490, "mean_abs_delta": 0.6981261888506428, "median_abs_delta": 0.3616558760404587, "q75_abs_delta": 0.8664438873529434 }, "CD16": { "n": 1490, "mean_abs_delta": 1.0650999203649343, "median_abs_delta": 0.907050609588623, "q75_abs_delta": 1.776064932346344 } }, "veto": true, "mode": "B_sufficiency_for_readout", "not_mode_a": true, "baseline_pred_O0_myeloid_t": { "false_agreement_rate_among_both_decided": 0.8536754507628294, "soft_separation_rate": 0.1738255033557047, "Q_among_decided": 0.7409695817490495 } }, "complements": { "a_observer": [ "complement_a_O1_abstain", "complement_a_O2_observer" ], "b_true_adt": [ "complement_b_true_ADT_O0", "complement_b_true_ADT_O1" ], "c_zplus": { "n_myeloid_t_pairs": 1490, "held_lineage": "myeloid", "held_proteins": [ "CD16", "CD11c", "CD36" ], "zplus_proteins": [ "CD19", "CD72", "CD22", "CD3", "CD2", "CD5" ], "cos_z512": { "mean": 0.9826505275780723, "median": 0.9822191596031189, "frac_still_ge_0_98": 1.0, "frac_dropped_below_0_95": 0.0 }, "cos_zplus_true_complement": { "mean": 0.8255820943005133, "median": 0.8865448236465454, "frac_still_ge_0_98": 0.09395973154362416, "frac_dropped_below_0_95": 0.7208053691275168 }, "cos_zplus_pred_complement": { "mean": 0.9877049229289061, "median": 0.9969751238822937, "frac_still_ge_0_98": 0.8348993288590604, "frac_dropped_below_0_95": 0.07583892617449664 }, "prior_global_relative_must_reduction_vs_z512": { "zplus_adt_true_complement": -0.27272456550677143, "zplus_adt_pred_complement": -0.27353544257798595, "zplus_adt_pred_all9_leakcheck": -0.2508802113539737 }, "prior_note": "Prior global z\u207a probe (held myeloid) relative_must_reduction primary=-0.27272456550677143; NEGATIVE => z\u207a alone worsens must-rate among near.", "interpretation": "On FIXED myeloid\u2194T must-pairs: true-ADT z\u207a lowers cosine (frac still \u22650.98 = 0.09395973154362416; frac <0.95 = 0.7208053691275168), so geometry can separate this fixed set. Pred z\u207a does NOT (frac still \u22650.98 = 0.8348993288590604). Prior GLOBAL probe still found z\u207a worsens must-rate among its own near neighborhoods (relative_must_reduction primary=-0.27272456550677143). Decision winner remains true-ADT typed evidence + O1, not z\u207a alone.", "decision_vs_geometry_note": "z\u207a true geometry helps on fixed pairs but is not the winning decision complement; prior z\u207a alone worsened global must-rate. Pred z\u207a fails fixed-pair separation." }, "variants_run": [ "baseline_pred_O0", "complement_a_O1_abstain", "complement_a_O2_observer", "complement_b_true_ADT_O0", "complement_b_true_ADT_O1" ] }, "verify": { "all_written_pairs": { "baseline_pred_O0": { "n_pairs": 5000, "both_decided": 4666, "same_action_among_both_decided": 4165, "differ_action_among_both_decided": 501, "false_agreement_rate_among_both_decided": 0.8926275182168881, "any_abstain": 334, "both_abstain": 142, "abstain_pair_frac": 0.0668, "soft_separation_rate": 0.167, "correct_separation_rate": 0.0416, "n_decided_cell_slots": 9524, "mean_Q_among_decided_defined": 0.8081765087605451, "n_Q_defined": 7705, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 7705, "Q_among_decided": 0.8081765087605451, "mean_Q_recomputed": 0.8081765087605451 }, "complement_a_O1_abstain": { "n_pairs": 5000, "both_decided": 4462, "same_action_among_both_decided": 4031, "differ_action_among_both_decided": 431, "false_agreement_rate_among_both_decided": 0.9034065441506051, "any_abstain": 538, "both_abstain": 496, "abstain_pair_frac": 0.1076, "soft_separation_rate": 0.1938, "correct_separation_rate": 0.0114, "n_decided_cell_slots": 8966, "mean_Q_among_decided_defined": 0.8665363426337302, "n_Q_defined": 5627, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 5627, "Q_among_decided": 0.8665363426337302, "mean_Q_recomputed": 0.8665363426337302 }, "complement_a_O2_observer": { "n_pairs": 5000, "both_decided": 2582, "same_action_among_both_decided": 2027, "differ_action_among_both_decided": 555, "false_agreement_rate_among_both_decided": 0.7850503485670023, "any_abstain": 2418, "both_abstain": 1969, "abstain_pair_frac": 0.4836, "soft_separation_rate": 0.5946, "correct_separation_rate": 0.087, "n_decided_cell_slots": 5613, "mean_Q_among_decided_defined": 0.8514386376981797, "n_Q_defined": 5109, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 5109, "Q_among_decided": 0.8514386376981797, "mean_Q_recomputed": 0.8514386376981797 }, "complement_b_true_ADT_O0": { "n_pairs": 5000, "both_decided": 4905, "same_action_among_both_decided": 2963, "differ_action_among_both_decided": 1942, "false_agreement_rate_among_both_decided": 0.6040774719673803, "any_abstain": 95, "both_abstain": 0, "abstain_pair_frac": 0.019, "soft_separation_rate": 0.4074, "correct_separation_rate": 0.2226, "n_decided_cell_slots": 9905, "mean_Q_among_decided_defined": 0.9567061759201497, "n_Q_defined": 8015, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 8015, "Q_among_decided": 0.9567061759201497, "mean_Q_recomputed": 0.9567061759201497 }, "complement_b_true_ADT_O1": { "n_pairs": 5000, "both_decided": 4529, "same_action_among_both_decided": 2653, "differ_action_among_both_decided": 1876, "false_agreement_rate_among_both_decided": 0.5857805255023184, "any_abstain": 471, "both_abstain": 116, "abstain_pair_frac": 0.0942, "soft_separation_rate": 0.4694, "correct_separation_rate": 0.1092, "n_decided_cell_slots": 9413, "mean_Q_among_decided_defined": 0.9899108794350092, "n_Q_defined": 5947, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 5947, "Q_among_decided": 0.9899108794350092, "mean_Q_recomputed": 0.9899108794350092 } }, "myeloid_t_focus": { "baseline_pred_O0": { "n_pairs": 1490, "both_decided": 1442, "same_action_among_both_decided": 1231, "differ_action_among_both_decided": 211, "false_agreement_rate_among_both_decided": 0.8536754507628294, "any_abstain": 48, "both_abstain": 17, "abstain_pair_frac": 0.032214765100671144, "soft_separation_rate": 0.1738255033557047, "correct_separation_rate": 0.08389261744966443, "n_decided_cell_slots": 2915, "mean_Q_among_decided_defined": 0.7409695817490495, "n_Q_defined": 2104, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 2104, "Q_among_decided": 0.7409695817490495, "mean_Q_recomputed": 0.7409695817490495 }, "complement_a_O1_abstain": { "n_pairs": 1490, "both_decided": 1391, "same_action_among_both_decided": 1156, "differ_action_among_both_decided": 235, "false_agreement_rate_among_both_decided": 0.8310567936736161, "any_abstain": 99, "both_abstain": 83, "abstain_pair_frac": 0.06644295302013423, "soft_separation_rate": 0.22416107382550335, "correct_separation_rate": 0.032214765100671144, "n_decided_cell_slots": 2798, "mean_Q_among_decided_defined": 0.7777777777777778, "n_Q_defined": 1332, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 1332, "Q_among_decided": 0.7777777777777778, "mean_Q_recomputed": 0.7777777777777778 }, "complement_a_O2_observer": { "n_pairs": 1490, "both_decided": 1109, "same_action_among_both_decided": 935, "differ_action_among_both_decided": 174, "false_agreement_rate_among_both_decided": 0.8431018935978359, "any_abstain": 381, "both_abstain": 330, "abstain_pair_frac": 0.2557046979865772, "soft_separation_rate": 0.3724832214765101, "correct_separation_rate": 0.08389261744966443, "n_decided_cell_slots": 2269, "mean_Q_among_decided_defined": 0.8824110671936759, "n_Q_defined": 2024, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 2024, "Q_among_decided": 0.8824110671936759, "mean_Q_recomputed": 0.8824110671936759 }, "complement_b_true_ADT_O0": { "n_pairs": 1490, "both_decided": 1475, "same_action_among_both_decided": 674, "differ_action_among_both_decided": 801, "false_agreement_rate_among_both_decided": 0.4569491525423729, "any_abstain": 15, "both_abstain": 0, "abstain_pair_frac": 0.010067114093959731, "soft_separation_rate": 0.5476510067114094, "correct_separation_rate": 0.36845637583892615, "n_decided_cell_slots": 2965, "mean_Q_among_decided_defined": 0.9716981132075472, "n_Q_defined": 2120, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 2120, "Q_among_decided": 0.9716981132075472, "mean_Q_recomputed": 0.9716981132075472 }, "complement_b_true_ADT_O1": { "n_pairs": 1490, "both_decided": 1407, "same_action_among_both_decided": 558, "differ_action_among_both_decided": 849, "false_agreement_rate_among_both_decided": 0.39658848614072495, "any_abstain": 83, "both_abstain": 17, "abstain_pair_frac": 0.05570469798657718, "soft_separation_rate": 0.625503355704698, "correct_separation_rate": 0.17248322147651007, "n_decided_cell_slots": 2880, "mean_Q_among_decided_defined": 0.9868421052631579, "n_Q_defined": 1368, "match_expected_among_decided_with_expected": null, "n_decided_with_expected": 1368, "Q_among_decided": 0.9868421052631579, "mean_Q_recomputed": 0.9868421052631579 }, "complement_c_zplus_geometry": { "n_pairs": 1490, "soft_separation_rate": 0.7208053691275168, "correct_separation_rate": null, "false_agreement_rate_among_both_decided": 0.09395973154362416, "abstain_pair_frac": null, "Q_among_decided": null, "note": "geometry only: soft_sep\u2248frac cos dropped <0.95; false_agree\u2248frac still \u22650.98" } } }, "winner": { "winner": "complement_b_true_ADT_O1", "winner_row": { "complement": "complement_b_true_ADT_O1", "score": 2.8412603305318287, "soft_separation_rate": 0.625503355704698, "Q_among_decided": 0.9868421052631579, "false_agreement_rate_among_both_decided": 0.39658848614072495, "correct_separation_rate": 0.17248322147651007, "abstain_pair_frac": 0.05570469798657718 }, "ranking": [ { "complement": "complement_b_true_ADT_O1", "score": 2.8412603305318287, "soft_separation_rate": 0.625503355704698, "Q_among_decided": 0.9868421052631579, "false_agreement_rate_among_both_decided": 0.39658848614072495, "correct_separation_rate": 0.17248322147651007, "abstain_pair_frac": 0.05570469798657718 }, { "complement": "complement_b_true_ADT_O0", "score": 2.610050974087993, "soft_separation_rate": 0.5476510067114094, "Q_among_decided": 0.9716981132075472, "false_agreement_rate_among_both_decided": 0.4569491525423729, "correct_separation_rate": 0.36845637583892615, "abstain_pair_frac": 0.010067114093959731 }, { "complement": "complement_c_zplus_geometry", "score": 2.3476510067114096, "soft_separation_rate": 0.7208053691275168, "Q_among_decided": null, "false_agreement_rate_among_both_decided": 0.09395973154362416, "correct_separation_rate": null, "abstain_pair_frac": null }, { "complement": "complement_a_O2_observer", "score": 1.78427561654886, "soft_separation_rate": 0.3724832214765101, "Q_among_decided": 0.8824110671936759, "false_agreement_rate_among_both_decided": 0.8431018935978359, "correct_separation_rate": 0.08389261744966443, "abstain_pair_frac": 0.2557046979865772 }, { "complement": "complement_a_O1_abstain", "score": 1.3950431317551684, "soft_separation_rate": 0.22416107382550335, "Q_among_decided": 0.7777777777777778, "false_agreement_rate_among_both_decided": 0.8310567936736161, "correct_separation_rate": 0.032214765100671144, "abstain_pair_frac": 0.06644295302013423 }, { "complement": "baseline_pred_O0", "score": 1.2349451376976295, "soft_separation_rate": 0.1738255033557047, "Q_among_decided": 0.7409695817490495, "false_agreement_rate_among_both_decided": 0.8536754507628294, "correct_separation_rate": 0.08389261744966443, "abstain_pair_frac": 0.032214765100671144 } ], "note": "Winner = best Mode B decision complement on myeloid\u2194T must-pairs (soft_separation + Q_among_decided \u2212 false_agreement). z\u207a geometry reported separately; prior showed it worsens global must-rate." }, "wall_seconds": 2.169034004211426 }