Kemal Yaylali
e76ae847a1
A review of the ranking's arithmetic found four things wrong, all of which made the score look better informed than it was. Measurements below are from this repo, not estimates. **Components now abstain instead of inventing a number.** A run without a VEP cache returns no allele frequencies, and rarity_score(None) read that as "absent from gnomAD, therefore maximally rare" and awarded every variant a free 0.25. jobs.has_frequencies / has_effect_scores record what the run actually produced, absent components are dropped from the weighted mean, and the remaining weights are renormalised so the score keeps its meaning. The UI shows "not looked up" rather than a bar, and the funnel stops calling a step "rare" when nothing was filtered. **Allele frequency is no longer a model feature.** It dominated: the same missense variant scored 0.887 at AF 0 and 0.0003 at AF 0.01. That double- counted, because the ranking already scores frequency explicitly, putting ~45% of every rank on one measurement; and it was circular, because ACMG assigns ClinVar's benign labels using frequency (BA1/BS1). Retraining without it moves missense AUROC from 0.872 to 0.500 — exactly random. The old figure was allele frequency, not variant-effect knowledge. The model therefore abstains unless CADD or AlphaMissense is present, since otherwise it only restates the consequence class. **Phenotype matching is weighted by information content** and HPO annotations are propagated up the ontology. Counting terms alike let "global developmental delay" (IC 0.93) count as much as "dilated left subclavian artery" (IC 7.88). **A real bug in the propagation, found by checking it.** The ancestor walk read a pre-order DFS backwards, which on a DAG lets a term resolve before one of its parents and inherit that parent alone instead of its lineage. It dropped 399 terms out of the phenotype branch, Camptodactyly and Chiari malformation among them. Now a true post-order, tested against a reference transitive closure. The ontology arithmetic moved to rarelens_ml.hpo so it is covered by tests, and rarelens_ml.benchmark measures the whole thing: across 10,178 published cases the causal gene ranks first 45.9-81.0% of the time against 5,269 genes, versus 0.02% for chance. docs/data.md reports that with its contamination (HPO's annotations come from these same case reports), and includes the measurement showing information-content weighting earns its place while propagation does not - kept anyway, for a reason the docs argue rather than assume.
63 lines
1.9 KiB
Python
63 lines
1.9 KiB
Python
"""Loader tests. DB tests use DATABASE_URL (CI's Postgres service) or a throwaway pgserver."""
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import os
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import sys
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import tempfile
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from collections.abc import Iterator
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from pathlib import Path
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import pytest
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sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "bin"))
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# The subset of the Alembic schema (api/alembic/versions) that the loader writes to.
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SCHEMA = """
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CREATE TYPE jobstatus AS ENUM ('queued', 'running', 'succeeded', 'failed');
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CREATE TABLE jobs (
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id uuid PRIMARY KEY,
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status jobstatus NOT NULL,
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vep_version text,
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has_frequencies boolean NOT NULL DEFAULT false,
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has_effect_scores boolean NOT NULL DEFAULT false,
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log text,
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finished_at timestamptz
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);
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CREATE TABLE variants (
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id serial PRIMARY KEY,
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job_id uuid NOT NULL,
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chrom text NOT NULL, pos integer NOT NULL, ref text NOT NULL, alt text NOT NULL,
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gene text, consequence text, impact text, hgvsc text, hgvsp text,
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gnomad_af double precision, clinvar_sig text, annotations jsonb NOT NULL
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);
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"""
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_server = None
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def _url() -> str | None:
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global _server
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if url := os.environ.get("DATABASE_URL"):
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return url
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try:
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import pgserver
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except ImportError:
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return None
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_server = pgserver.get_server(tempfile.mkdtemp(prefix="loader-pg-"), cleanup_mode="delete")
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return "postgresql://postgres@/postgres?host=" + _server.get_uri().split("host=", 1)[1]
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@pytest.fixture
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def engine() -> Iterator:
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url = _url()
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if not url:
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if os.environ.get("REQUIRE_DB"):
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pytest.fail("REQUIRE_DB is set but no database is available")
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pytest.skip("no DATABASE_URL and pgserver is not installed")
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from load_db import engine_for
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eng = engine_for(url)
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with eng.begin() as conn:
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conn.exec_driver_sql("DROP TABLE IF EXISTS variants, jobs; DROP TYPE IF EXISTS jobstatus")
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conn.exec_driver_sql(SCHEMA)
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yield eng
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eng.dispose()
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