{ "gate_run_id": "gate_20260901T100219Z", "created_utc": "2026-09-01T10:02:20.060589+00:00", "reps": 5, "mode": "live_fred", "basis_path": "/home/singh/sim/corpus/seed/precedents/comparability_basis.json", "backend_identity": { "schema": "sim.gate_backend_identity.v3", "captured": true, "captured_at_utc": "2026-09-01T10:02:19.764088+00:00", "label": "CONFIGURATION OBSERVED AT RUN TIME, NOT VERIFIED MODEL IDENTITY", "container": { "name": "compound2-fred-v020", "resolved_by": "port binding 127.0.0.1:8102, not by name (R30)", "image": "fred:v0.2.0.dev0", "image_id": "sha256:1a6ad32d6c47d3d53f8b02d1d7b2b45e1bc28cdca71311fbab3a5a808d9a07f4", "repo_digests": "[fred@sha256:1a6ad32d6c47d3d53f8b02d1d7b2b45e1bc28cdca71311fbab3a5a808d9a07f4]", "repo_digest_is_registry_verifiable": false, "repo_digest_note": "RepoDigest equals local ImageID: locally built, digest is not verifiable against any registry", "created": "2026-08-06T17:31:25.774913691Z" }, "image_digest_pins": "the fred HARNESS container, NOT the reasoning model. The model is served from outside this image; the digest attests neither which model answered nor that the tag was stable across the gate.", "fred_model_configured_tag": "kimi-k2.6:cloud", "fred_model_tag_note": "the tag CONFIGURED on the container, not a record of what answered. A remote tag can move under a fixed name.", "ollama_base_url": "http://host.docker.internal:11434/v1", "other_env_names_only": [], "env_filter": { "applied": "^(FRED_MODEL|OLLAMA_BASE_URL|[A-Za-z0-9_]*_HOST)=", "superseded": "(FRED_MODEL|OLLAMA_BASE_URL|.*_HOST)=", "deviation_reason": "the superseded pattern is unanchored on the right; '.*_HOST=' can match on the VALUE side and record a secret in full (R32)", "values_recorded_for": [ "FRED_MODEL", "OLLAMA_BASE_URL" ] }, "health": { "wire_version": "1.1", "status": "ok", "fred_version": "0.2.0.dev0", "current_run_id": null }, "health_note": "/v1/health carries no model field, so it corroborates that fred is up and which fred_version is running --- not which model answered.", "code_state": { "captured": true, "repo": "/home/singh/sim", "head": "4f9d0098ce247009baa75f9195b2237460375776", "dirty": false, "dirty_paths_count": 0, "note": "the commit checked out when the gate started. If dirty is true this sha does NOT describe the code that ran." }, "model_probe": { "endpoint_base": "http://127.0.0.1:11434", "queried_tag": "kimi-k2.6:cloud", "tags": { "reachable": true, "name": "kimi-k2.6:cloud", "model": "kimi-k2.6:cloud", "remote_model": "kimi-k2.6", "remote_host": "https://ollama.com:443", "digest": "a90cd0d1590c53b9f9f4e0f66218e4c514d190652b8bed2842528e2530e34dc6", "modified_at": "2026-04-24T20:00:03.980908081+01:00", "details": { "parent_model": "", "format": "", "family": "kimi-k2", "families": [ "kimi-k2" ], "parameter_size": "1T", "quantization_level": "int4" }, "size_bytes": 384 }, "show": { "reachable": true, "capabilities": [ "vision", "thinking", "completion", "tools" ], "details": { "parent_model": "kimi-k2.6", "format": "", "family": "kimi-k2", "families": null, "parameter_size": "1042000000000", "quantization_level": "INT4" }, "model_info": { "general.architecture": "kimi-k2", "general.parameter_count": 1042000000000, "kimi-k2.context_length": 262144, "kimi-k2.embedding_length": 2048 }, "modified_at": "2026-04-20T00:00:00Z" }, "modified_at_agree": false, "parameter_size_agree": false, "note": "the LOCAL POINTER and the remote's DECLARED metadata, captured at gate start. A size of a few hundred bytes shows the local entry is a pointer, not weights. NEITHER modified_at attests which weights answered and neither is a model file's mtime. A remote tag can move mid-gate; a start-time probe does not cover the gate's duration. parameter_size_agree can read false for a difference of representation alone." }, "tool_inventory": { "schema": "sim.fred_tool_inventory.v1", "url": "http://127.0.0.1:8102/v1/tools", "reachable": true, "wire_version": "1.1", "tool_count": 10, "tool_names": [ "brave_search", "check_lipinski", "get_compound_properties", "get_protein_info", "get_target_info", "read_file", "search_compounds", "search_pathways", "search_publications", "write_file" ], "tool_args": { "read_file": [ "path" ], "write_file": [ "content", "path" ], "brave_search": [ "max_results", "query" ], "search_compounds": [ "max_results", "query" ], "get_compound_properties": [ "cid", "name" ], "check_lipinski": [ "properties" ], "get_protein_info": [ "identifier", "max_results", "organism_id" ], "search_pathways": [ "max_results", "query", "species" ], "get_target_info": [ "identifier" ], "search_publications": [ "max_results", "query" ] }, "body_bytes": 6860, "body_sha256": "e39f7479b846d16142b69b49ebb011ec12e4cb901f67bc713c9f552cb0bd2c68", "reason": null, "note": "ENUMERATED AT GATE START FROM THE RUNNING SERVICE, NEVER FROM A CONSTANT. It records what fred OFFERED, not what any run called. A tool absent from tool_names that appears in a call is an UNKNOWN TOOL and must be reported as one rather than defaulted. fred is frozen: SIM enumerates and buckets, and never edits or removes a tool. NO JUDGEMENT IS RECORDED HERE -- not which tools return literature, not which matter, and no order." } }, "claims_requested": [ "target_engagement", "selectivity", "cns_penetrance", "in_vivo_efficacy", "admet_pk_hepatic", "developability" ], "claims_excluded": [], "exclusion_rule": "A readout with no authored liability (payload.known_flaw absent, null, or blank) produces NO CLAIM, not a repaired sentence. cns_penetrance is exempt: its claim_text is the Part 5 constant and does not derive from known_flaw.", "claims": [ { "readout": "target_engagement", "status": "resolved", "claim_label": "target_engagement_sufficiency", "claim_text": "On the Target engagement / potency (NLRP3-driven IL-1beta release) readout, the noted liability -- potency here is a peripheral-compartment measure only: the whole-blood IC50 evidences engagement in blood and carries no evidence of central engagement, and the declared microglial secondary assay was never reported; the estimate itself rests on 2 of 4 replicates after two exclusions (cv_over_threshold, ref_cpd_out_of_range); against a Kp,uu of 0.22 the question of whether central NLRP3 engagement can be inferred from this panel at all is a judgment call at this gate -- is sufficient to support advancing the candidate to in-vivo AD-efficacy studies at the commit-to-animal gate.", "claim_text_source": "templated_from_readout", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.target_engagement", "synthetic": true, "dataset": "Target engagement / potency (NLRP3-driven IL-1beta release)", "value": { "assay": "whole human blood IL-1beta release, NLRP3-primed", "IC50_nM": 17.7, "secondary_assay": "primed macrophage/microglia IL-1beta" }, "assay_basis": { "assay_type": "in vitro whole-blood and primed macrophage IL-1beta release", "units": "nM (IC50)", "reference_conditions": "NLRP3-specific priming (LPS) + activation (nigericin/ATP); IL-1beta by immunoassay", "secondary_assay_status": "no_raw_authored; no derived value; not reported" }, "numeric_provenance": { "raw_source": "raw/candidate/readouts_raw.json#readout.target_engagement", "measurement_type": "IC50", "canonical_unit": "nM", "replicates_total": 4, "dropped": [ { "run": 3, "reasons": [ "cv_over_threshold_25.0" ] }, { "run": 4, "reasons": [ "ref_cpd_out_of_range" ] } ], "excluded_run_ids": [ 3, 4 ], "outliers": [], "aggregation": "geometric_mean", "n_used": 2, "estimate": 17.727944043232995, "display_value": 17.7, "spread": { "geo_sd": 1.1359443802126525, "ddof": 1 }, "censored": false, "derivation": null, "stat_test": null, "divergence_from_target": { "asserted": 18, "derived": 17.727944043232995, "rel_diff": 0.015114219820389173, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 12, "joined": 12, "joined_refs": [ "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 12, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 5, "malformed": [ { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 11, "supplied_ids": [ "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_target_engagement_sufficiency_20260901T100220Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_target_engagement_sufficiency_20260901T100220Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_target_engagement_sufficiency_20260901T100220Z/fred", "any_low_confidence": false, "verdict_sequence": [ "B", "B", "B", "B", "B" ], "counts": { "A": 0, "B": 5, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 }, { "readout": "selectivity", "status": "resolved", "claim_label": "selectivity_sufficiency", "claim_text": "On the Selectivity panel (NLRP3 vs related NLRs and off-targets) readout, the noted liability -- a subtle selectivity liability (modest hepatic-transporter activity) that a scientist must weigh alongside the hepatic-safety readout -- is sufficient to support advancing the candidate to in-vivo AD-efficacy studies at the commit-to-animal gate.", "claim_text_source": "templated_from_readout", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.selectivity", "synthetic": true, "dataset": "Selectivity panel (NLRP3 vs related NLRs and off-targets)", "value": { "NLRP3_IC50_nM": 17.9, "AIM2_IC50_nM": ">10000", "NLRC4_IC50_nM": ">10000", "NLRP1_IC50_nM": ">10000", "note": "subtle off-target: modest activity at one hepatic transporter flagged for the ADMET readout" }, "assay_basis": { "assay_type": "inflammasome-sensor selectivity panel + off-target screen", "units": "nM (IC50)", "reference_conditions": "matched activation conditions per sensor" }, "numeric_provenance": { "raw_source": "raw/candidate/readouts_raw.json#readout.selectivity", "measurement_type": "IC50_selectivity_panel", "canonical_unit": "nM", "targets": [ { "target": "NLRP3", "field": "NLRP3_IC50_nM", "replicates_total": 2, "dropped": [], "excluded_run_ids": [], "aggregation": "geometric_mean", "n_used": 2, "estimate": 17.92986335698072, "display_value": 17.9, "censored": false, "divergence_from_target": { "asserted": 18, "derived": 17.92986335698072, "rel_diff": 0.0038964801677376926, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } }, { "target": "AIM2", "field": "AIM2_IC50_nM", "replicates_total": 2, "dropped": [], "excluded_run_ids": [], "aggregation": "censored_preserved", "n_used": 2, "estimate": ">10000", "display_value": ">10000", "censored": true, "divergence_from_target": { "asserted": ">10000", "derived": ">10000", "material": false, "reason": "non_numeric_not_comparable" } }, { "target": "NLRC4", "field": "NLRC4_IC50_nM", "replicates_total": 1, "dropped": [], "excluded_run_ids": [], "aggregation": "censored_preserved", "n_used": 1, "estimate": ">10000", "display_value": ">10000", "censored": true, "divergence_from_target": { "asserted": ">10000", "derived": ">10000", "material": false, "reason": "non_numeric_not_comparable" } }, { "target": "NLRP1", "field": "NLRP1_IC50_nM", "replicates_total": 1, "dropped": [], "excluded_run_ids": [], "aggregation": "censored_preserved", "n_used": 1, "estimate": ">10000", "display_value": ">10000", "censored": true, "divergence_from_target": { "asserted": ">10000", "derived": ">10000", "material": false, "reason": "non_numeric_not_comparable" } } ], "derivation": null, "stat_test": null } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 12, "joined": 12, "joined_refs": [ "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 12, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 5, "malformed": [ { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 11, "supplied_ids": [ "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_selectivity_sufficiency_20260901T110353Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_selectivity_sufficiency_20260901T110353Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_selectivity_sufficiency_20260901T110353Z/fred", "any_low_confidence": false, "verdict_sequence": [ "B", "B", "B", "B", "A" ], "counts": { "A": 1, "B": 4, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 }, { "readout": "cns_penetrance", "status": "resolved_low_conf", "claim_label": "cns_penetrance_sufficiency", "claim_text": "The candidate's borderline brain exposure (Kp,uu ~0.22 with P-gp efflux) is sufficient to support advancing to in-vivo AD-efficacy studies, on the strength of the dapansutrile APP/PS1 cognitive-rescue precedent.", "claim_text_source": "part5_centerpiece_constant", "basis_alignment": "centerpiece", "readout_fields_dropped": [ "flaw_must_be_flagged", "is_centerpiece_flaw", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.cns_penetrance", "synthetic": true, "dataset": "CNS penetrance / brain exposure (Kp,uu, brain:plasma, P-gp efflux)", "value": { "Kp_uu_brain": 0.22, "brain_plasma_total_ratio": 0.6, "Pgp_efflux_ratio": 4.8, "note": "unbound brain exposure borderline; P-gp efflux liability material" }, "assay_basis": { "assay_type": "rodent brain:plasma PK + MDCK-MDR1 efflux", "units": "Kp,uu (unitless), efflux ratio (unitless)", "reference_conditions": "steady-state unbound fractions in brain and plasma; MDR1-overexpressing monolayer" }, "numeric_provenance": { "raw_source": "raw/candidate/readouts_raw.json#readout.cns_penetrance", "measurement_type": "cns_penetrance_composite", "quantities": { "Kp_uu_brain": { "raw_source": "raw/candidate/readouts_raw.json#readout.cns_penetrance", "measurement_type": "Kp_uu", "canonical_unit": "unitless", "replicates_total": 3, "dropped": [], "excluded_run_ids": [], "outliers": [], "aggregation": "arithmetic_mean", "n_used": 3, "estimate": 0.22, "display_value": 0.22, "spread": { "sd": 0.01999999999999999, "ddof": 1 }, "censored": false, "derivation": null, "stat_test": null, "divergence_from_target": { "asserted": 0.22, "derived": 0.22, "rel_diff": 0.0, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } }, "brain_plasma_total_ratio": { "raw_source": "raw/candidate/readouts_raw.json#readout.cns_penetrance", "measurement_type": "ratio_linear", "canonical_unit": "unitless", "replicates_total": 2, "dropped": [], "excluded_run_ids": [], "outliers": [], "aggregation": "arithmetic_mean", "n_used": 2, "estimate": 0.6, "display_value": 0.6, "spread": { "sd": 0.028284271247461926, "ddof": 1 }, "censored": false, "derivation": null, "stat_test": null, "divergence_from_target": { "asserted": 0.6, "derived": 0.6, "rel_diff": 0.0, "material": false, "threshold_rel": 0.15, "boundary_rule": "material iff rel_diff strictly greater than threshold" } }, "Pgp_efflux_ratio": { "raw_source": "raw/candidate/readouts_raw.json#readout.cns_penetrance", "measurement_type": "efflux_ratio_derived", "canonical_unit": "unitless", "derivation": { "formula": "ER = Papp_BA / Papp_AB", "method": "first_order_delta_propagation", "assumptions": "independent BA/AB; 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It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 12, "joined": 12, "joined_refs": [ "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 12, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 5, "malformed": [ { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 11, "supplied_ids": [ "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_admet_pk_hepatic_sufficiency_20260901T143632Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_admet_pk_hepatic_sufficiency_20260901T143632Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_admet_pk_hepatic_sufficiency_20260901T143632Z/fred", "any_low_confidence": false, "verdict_sequence": [ "A", "B", "B", "A", "B" ], "counts": { "A": 2, "B": 3, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 }, { "readout": "developability", "status": "resolved", "claim_label": "developability_sufficiency", "claim_text": "On the Developability (oral CNS small molecule flags) readout, the noted liability -- the exposure that any in-vivo package would rest on depends on an enabling amorphous dispersion that has not been made: an amorphous form is metastable and can recrystallize in the matrix or out of the supersaturated solution it generates, so exposure achieved in an efficacy study may not be reproducible in the form carried into toxicology, and dose escalation may be form-limited rather than tolerability-limited; with a borderline CNS-MPO-like score and the P-gp efflux already noted, whether this is developable as an oral CNS agent is unresolved at this gate -- is sufficient to support advancing the candidate to in-vivo AD-efficacy studies at the commit-to-animal gate.", "claim_text_source": "templated_from_readout", "basis_alignment": "shared_basis_not_claim_specific", "readout_fields_dropped": [ "flaw_must_be_flagged", "known_flaw" ], "readout_inputs": { "supplied": { "id": "readout.developability", "synthetic": true, "dataset": "Developability (oral CNS small molecule flags)", "value": { "solubility": "moderate; formulation-dependent", "permeability": "high passive; offset by P-gp efflux (see cns_penetrance)", "formulation_flags": "amorphous dispersion likely needed for exposure", "cns_mpo_like_score": "borderline" }, "assay_basis": { "assay_type": "developability profiling for oral CNS small molecule", "units": "qualitative flags + CNS-MPO-like score", "reference_conditions": "standard developability cascade" }, "numeric_provenance": { "cleaned": false, "reason": "qualitative_readout_no_numerics" } }, "withheld_by_decision": { "flaw_must_be_flagged": "an instruction to flag a liability, not evidence of one; crossing it supplies the conclusion the adversarial loop exists to reach", "known_flaw": "authored characterization of the candidate's flaw. THE EARLIER REASON HERE SAID IT WAS ALREADY CARRIED VERBATIM IN THE CLAIM TEXT AND THAT WAS MEASURED FALSE: the string occurs verbatim nowhere in the corpus outside its own readout file. It is not a duplicate, so crossing it would be ADDITIVE authored prose in front of the arms, which is a stronger reason to withhold than the one it replaces" }, "unallowed_unexplained": [], "allowed_fields": [ "assay_basis", "dataset", "numeric_provenance", "value" ] }, "retrieval": { "source": "/home/singh/sim/corpus/index/retrievable.json", "seed_dir": "/home/singh/sim/corpus/seed/precedents", "offered": 12, "joined": 12, "joined_refs": [ "ClinicalTrials:NCT06556173", "PMID:34219728", "DOI:10.1016/j.isci.2024.109733", "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "DOI:10.1038/s44400-025-00011-5", "PMID:31207457", "PMID:31748742; PMID:23254930; PMID:30381407", "ClinicalTrials:NCT05932069", "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "PMC:13132802", "PMID:37577847; ClinicalTrials:NCT05981040", "PMID:40792655; PMID:37874905" ], "join_misses": [], "public_ref_namespaces": { "total": 12, "well_formed_by_namespace": { "ClinicalTrials": 2, "PMID": 2, "DOI": 2, "PMC": 1 }, "malformed_count": 5, "malformed": [ { "citation": "ISRCTN:85338453; DOI:10.15252/embj.2018101064", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:31748742; PMID:23254930; PMID:30381407", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:33257576; PMC:PMC7749353; DOI:10.1073/pnas.2009680117", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:37577847; ClinicalTrials:NCT05981040", "reason": "string carries more than one accession; not split here" }, { "citation": "PMID:40792655; PMID:37874905", "reason": "string carries more than one accession; not split here" } ], "syntax_only": true, "note": "well_formed is a SYNTAX claim over the five seed namespaces; it is never a claim that an accession resolves or exists" }, "deduped": [ "precedent_pc7b071" ], "supplied": 11, "supplied_ids": [ "precedent_p12682b", "precedent_p17d8f1", "precedent_p26a1fb", "precedent_p340e7b", "precedent_p57a9d7", "precedent_p5bb765", "precedent_p7bbc38", "precedent_p8a117d", "precedent_pcf4b44", "precedent_pdeb9af", "precedent_peb7226" ], "supplied_refs": [ { "id": "precedent_p12682b", "public_ref": "ClinicalTrials:NCT06556173" }, { "id": "precedent_p17d8f1", "public_ref": "PMID:34219728" }, { "id": "precedent_p26a1fb", "public_ref": "DOI:10.1016/j.isci.2024.109733" }, { "id": "precedent_p340e7b", "public_ref": "ISRCTN:85338453; DOI:10.15252/embj.2018101064" }, { "id": "precedent_p57a9d7", "public_ref": "DOI:10.1038/s44400-025-00011-5" }, { "id": "precedent_p5bb765", "public_ref": "PMID:31207457" }, { "id": "precedent_p7bbc38", "public_ref": "PMID:31748742; PMID:23254930; PMID:30381407" }, { "id": "precedent_p8a117d", "public_ref": "ClinicalTrials:NCT05932069" }, { "id": "precedent_pcf4b44", "public_ref": "PMC:13132802" }, { "id": "precedent_pdeb9af", "public_ref": "PMID:37577847; ClinicalTrials:NCT05981040" }, { "id": "precedent_peb7226", "public_ref": "PMID:40792655; PMID:37874905" } ], "fields_dropped_vs_precedent_view": [ "penetrance_status", "verification_tier", "precedent_numerics" ], "note": "surfaced precedent crosses as flat text (molecule + mechanistic_record) PLUS the public_ref joined from its seed record; the paired precedent still crosses as a structured firewalled record" }, "run_id": "sim_developability_sufficiency_20260901T153445Z", "run_dir": "/home/singh/sim/corpus/runtime/outputs/sim_developability_sufficiency_20260901T153445Z", "validation_dir": "/home/singh/sim/corpus/runtime/validation/sim_developability_sufficiency_20260901T153445Z/fred", "any_low_confidence": false, "verdict_sequence": [ "B", "B", "B", "B", "B" ], "counts": { "A": 0, "B": 5, "both": 0, "neither": 0, "unresolved": 0 }, "counts_no_verdict": 0 } ], "sc3_pre_inventory": { "state": "VERIFIED", "path": "/home/singh/sim_patches/sc3_inventory/inventory_pre_20260901T110048.json", "sha256": "8e1ddf8ed3acede093077bde3334213ced744fc7b9005ed66a3a64d13c8bae8c", "entries_sha256": "f5dd15004d8a35393936d792bb11327570c05d24aeea96c5d9260c51e4e09a27", "entry_count": 4330, "root": "/home/singh/compound2/fred-workspace-v020", "inventory_mtime_utc": "2026-09-01T10:00:48.462212+00:00", "launch_utc": "2026-09-01T10:02:19.763392+00:00", "age_seconds": 91, "note": "R284, procedural. The workspace state at launch is KNOWN because it was inventoried and the artifact's digest is recorded here. THIS DOES NOT ESTABLISH THAT THE STATE WAS ACCEPTABLE, CLEAN OR FRESH. Freshness is not enforced; age_seconds is recorded so staleness is auditable rather than assumed. The inventory sees names and metadata only and cannot see an id inside a file." }, "orchestrator_log": "orchestrator.log" }