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Source papers, claims, scoring, and embedding config are recovered; generation-time metadata (exact git commit at gen time, host, exact command) is not recoverable.","source_papers":[{"doi":"10.1007/s00401-023-02564-2","pmid":"36966244","year":2023,"roles":["mediator_outcome"],"title":"TREM2 gene expression associations with Alzheimer’s disease neuropathology are region-specific: implications for cortical versus subcortical microglia","journal":"Acta Neuropathol","work_id":62708,"publication_date":"2023-03-25"},{"doi":"10.1016/j.etap.2023.104090","pmid":"36870407","year":2023,"roles":["drug_mediator"],"title":"Prenatally VPA exposure is likely to cause autistic-like behavior in the rats offspring via TREM2 down-regulation to affect the microglial activation and synapse alterations","journal":"Environ Toxicol Pharmacol","work_id":32495,"publication_date":"2023-03-02"},{"doi":"10.1084/jem.20220654","pmid":"36219197","year":2022,"roles":["mediator_outcome"],"title":"Chronic TREM2 activation exacerbates Aβ-associated tau seeding and spreading","journal":"J Exp Med","work_id":60601,"publication_date":"2022-10-11"},{"doi":"10.1038/s41588-022-01208-7","pmid":"36411364","year":2022,"roles":["mediator_outcome"],"title":"Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s disease","journal":"Nat Genet","work_id":60321,"publication_date":"2022-11-21"},{"doi":"10.2174/1567205018666211105140732","pmid":"34749609","year":2021,"roles":["mediator_outcome"],"title":"Microglia and its Genetics in Alzheimer's Disease","journal":"Curr Alzheimer Res","work_id":63117,"publication_date":"2021-08-01"},{"doi":"10.1016/j.celrep.2021.108739","pmid":"33567283","year":2021,"roles":["mediator_outcome"],"title":"Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease","journal":"Cell Rep","work_id":61534,"publication_date":"2021-02-01"}],"source_paper_count":6,"extracted_claims":[{"side":"drug_mediator","object":"TREM2","context":"prenatal exposure in rat offspring","subject":"VPA","work_id":32495,"claim_id":16412,"polarity":"positive","predicate":"downregulates","confidence":0.95,"extraction_run_id":14},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"exome sequencing of 32,558 individuals (16,036 AD cases and 16,522 controls)","subject":"TREM2","work_id":60321,"claim_id":37456,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"late-onset","subject":"TREM2","work_id":60601,"claim_id":38247,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"human AD studies","subject":"Trem2","work_id":61534,"claim_id":40521,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"in dorsolateral prefrontal cortex and posterior cingulate cortex","subject":"TREM2","work_id":62708,"claim_id":43352,"polarity":"positive","predicate":"correlates_with","confidence":0.9,"extraction_run_id":16},{"side":"mediator_outcome","object":"Alzheimer's disease","context":"microglia","subject":"TREM2","work_id":63117,"claim_id":44281,"polarity":"positive","predicate":"associated_with","confidence":0.9,"extraction_run_id":16}],"extracted_claim_count":6,"extraction":{"model":"deepseek-v4-flash","model_source":"configured","prompt_version":"v1_2026_05_07","run_ids":[14,16]},"bridge":{"a_to_b_predicate":"downregulates","b_to_c_predicate":"associated_with","a_to_b_evidence_count":1,"b_to_c_evidence_count":5,"edge_support_log_ab":0.6931471805599453,"edge_support_log_bc":1.791759469228055,"novelty_factor":1.0,"direct_a_to_c_count":0},"embedding":{"model":"bge-m3","dim":1024,"max_length":8192,"similarity_scores":{}},"scoring":{"method":"swanson_abc_log_evidence_with_novelty_penalty","formula":"score = min((log(ab+1) + log(bc+1)) * novelty / 10, 1.0); novelty = 1.0 if direct==0 else 0.7 / (direct+1)","score_raw":0.24849066497880004,"score":0.24849066497880004,"quality_tier":"mid","quality_reason":null},"pipeline_run":{"id":4,"run_uuid":"eb8b7730-d92e-4cd5-95dd-95f6c5d62cc2","command":"scripts/backfill_provenance_v2.py:v2_2026_05_12","status":"completed","git_commit":"9996ffaa56e9b7cd5f677bd8203624c2c18aa000","host":"MacBook-Pro-Daniel96.local","started_at":"2026-05-12T21:35:53.363326+00:00","ended_at":"2026-05-12T21:43:41.903387+00:00","notes":"Retroactive provenance backfill on 2026-05-13 for snapshot v2_2026_05_12. Synthetic pipeline_runs row — original generation run records are lost (pre-date provenance schema). All recoverable fields populated from current DB state (claims, works, repurposing_hypotheses); pipeline_run record is synthetic, hence completeness='partial_backfill'.\nBackfilled 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.\nRefreshed 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.\nRefreshed 1,618 provenance rows. Source papers: avg=3.73, zero=0. Claims matched: avg=4.09, zero=0.","domains":["als","alzheimer","depression","epilepsy","glioblastoma","inflammatory_bowel_disease","multiple_sclerosis","pancreatic_cancer","rheumatoid_arthritis","type_2_diabetes"]},"generated_at":"2026-05-12T21:43:39.496175+00:00"}