Variant Effect Viewer

Interactive browser for Evo2 ClinVar probe predictions. Visualizes pathogenicity scores, per-head disruption/effect profiles, UMAP embeddings, nearest neighbors, and VEP annotations for ~230K ClinVar variants.

Quick start

uv sync
uv run python build.py           # builds to webapp/build/ (~2 min on H200)
python -m http.server -d webapp/build/ 8080

Pipeline

The viewer consumes artifacts produced by the probe pipeline:

harvest          Extract Evo2 bidir activations (SLURM array)
    |
extract          Stream activations through probe -> embeddings + scores
finalize         Merge shard scores into scores.feather
    |
eval             AUROC/AUPRC with bootstrap CIs
    |
build.py         Generate static site (global.json, search.json, per-variant JSONs)

Run the full extract-finalize-eval chain: bash probe/pipeline.sh /path/to/probe

Architecture

File	Role
build.py	Static site generator: loads scores + metadata, computes UMAP + neighbors, writes JSON
display.py	Head display names and category grouping (standalone, no deps)
streaming.py	Streaming iteration over chunked activation datasets
index.html	Single-page frontend (vanilla JS, no build step)
probe/	Probe weights, extraction scripts, eval
pipeline/	Production pipeline (frozen)
SCHEMA.md	Data contract between build.py and the frontend

Data requirements

Expects probe artifacts under the shared artifact directory:

• clinvar_evo2_deconfounded_full/{probe}/scores.feather — labeled variant scores
• clinvar_evo2_vus/{probe}/scores.feather — VUS scores
• clinvar_evo2_deconfounded_full/{probe}/embeddings/ — probe embeddings (chunked)
• clinvar_evo2_deconfounded_full/{probe}/config.json — probe head definitions
• clinvar_evo2_labeled/variant_annotations/ — VEP annotations (per-chromosome parquet)

See SCHEMA.md for the full data contract.