Spaces:
Running
Running
Commit History
-
§3 VEP: replace variant set with audited 8-pick spread
Old set: 6 variants, two disagreed with ClinVar at the 4 kb scoring window, one was effectively invisible, one had a contested clinical classification (TP53 Pro72Arg). Replaced with 8 picks (6 Pathogenic + 1 Risk + 1 Benign), all checked against Carbon-3B at the demo's window length: HBB, BRCA2, TP53 c.712T>A, F9, LDLR splice donor, VHL stop, LRRK2 G2019S, VHL 3' UTR benign. The two VHL rows are paired by design as the narrative payoff (same gene, opposite verdicts: −323 nats vs ≈0). Regenerated data/variants.json end to end via fetch_variants.py + precompute_vep against the live /score endpoint; rewrote GENE_INFO / VARIANT_DESC for the new genes; updated the VEP takeaway to point at the VHL pair instead of the retired sign-disagreement framing. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>41739ad
-
Carry over §2 Variant rework + §1/§4 polish dropped by the -s ours merge
The previous merge (32c9c3a) used -s ours to keep the local tree intact while preserving Leandro's two upstream commits (57bce37 §2 Variant rework, 176caed banner wordmark) in the history for attribution. Most of those changes had already been adapted locally to the new modular CSS/JS split, but the actual content carry-over wasn't yet committed. This commit applies the remaining ports on top of the merge. §3 VEP (was §2 in Leandro's tree) — refonte complète - 4 kb scoring window: fetch_variants.py WINDOW 60 → 4002 (well below the 8 kb eval recipe but enough that all 3 pathogenic variants land on the correct side of zero). data/variants.json regenerated. - Two-row sequence display: original above, click-editable mutation below, with arrows on every base that differs from the original. Click cycles A → C → G → T, debounced 500 ms rescore against /score. - Per-row log-likelihood score on the right (green if more likely, red if less likely); mutation score blanks to '—' while a…1d3e72f
-
Add tabbed Demo / Model / Sandbox page (default = Sandbox)
New /demo route serves a single-page app with three tabs: - Demo: 4 interactive sections (gene completion, VEP, likelihood track, cross-species) plus folding/UMAP placeholders - Model: tokenizer, training objective (CE→FNS), data, architecture - Sandbox: the existing DNA continuation playground (default tab) Server-side: new /score endpoint (echo-logprobs), /genes /variants /species data routes, /img static mount, and left-padding for prompts that aren't a multiple of 6 bases (avoids phantom-A artifacts at the prompt boundary). Includes data fetchers (Ensembl REST) for genes / variants / species and a precompute script that bakes per-token logprobs and ref-vs-alt window scores into the JSON files so the page renders instantly without round-tripping the inference endpoint on first paint. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>971b586