evo2 dashboard: ColoredSequence + GeneUMAPView + 500-gene precompute

Two new visualizations for the SAE interpretability dashboard, plus the
offline pipeline that produces the gene-UMAP precompute bundle.

scripts/generate_fake_genes.py
  500-row genes.tsv stand-in (gene_symbol, species, sequence) until a real
  curated catalog lands. Realistic-ish distributions across 7 species.

scripts/gene_umap_precompute.py
  End-to-end offline pipeline: genes.tsv -> Evo2 1B layer-20 -> TopK SAE
  encode -> mean per gene -> UMAP (cosine) -> HDBSCAN clusters -> per-feature
  firing stats. Writes G.npz, genes_umap.parquet, feature_stats.parquet,
  manifest.json. Reuses predict_evo2 via torchrun subprocess; aggregates
  .pt files by seq_idx + pad_mask. Idempotent (skips predict if .pt
  files exist).

src/ColoredSequence.jsx
  React component: paste a DNA sequence -> each base background-colored
  by its top-firing SAE feature, opacity scaled by activation strength.
  Two modes: top-feature (default), single-feature lookup. Builds mock
  activations internally when no `analysis` prop is supplied so the
  component works standalone before the /analyze backend is wired.
  Tableau-10 colorblind palette, hover tooltip with top-5 features,
  legend sorted by per-color position count.

src/GeneUMAPView.jsx
  Renders the 500-gene UMAP via canvas. Loads G.bin (raw float32),
  genes_meta.json, feature_stats.json from public/gene_umap/. Click a
  feature in the sidebar -> instant recolor by activation strength
  (no recompute). Click Reorganize -> re-runs UMAP client-side with
  feature-weighted vectors (umap-js, ~2-5s at N=500), animates the
  transition with ease-in-out cubic. Hover shows gene metadata + top 5
  firing features.

src/Preview.jsx + src/index.jsx
  Tabbed entry at /#preview: "Main" (the existing dashboard, untouched),
  "ColoredSequence", "Gene UMAP". Hash-gated so /  still goes to the
  unchanged production layout. The ColoredSequence tab includes a paste
  textarea so users can drop their own sequences in.

public/gene_umap/
  Precomputed bundle for the GeneUMAPView (G.bin 30 MB, plus small JSON
  metadata + per-feature stats filtered to n_firing >= 10).

Dep change: umap-js for client-side reorganize. Generated genes are
synthetic; replace fake_genes.tsv with a real curated 500-gene list and
re-run the precompute when one is available.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: polinabinder1

bionemo-recipes/interpretability/sparse_autoencoders/recipes/evo2/evo2_dashboard_mockup/package.json

@@ -15,7 +15,8 @@
     "embedding-atlas": "^0.16.1",
     "lucide-react": "^0.577.0",
     "react": "^18.2.0",
-    "react-dom": "^18.2.0"
+    "react-dom": "^18.2.0",
+    "umap-js": "^1.4.0"
   },
   "devDependencies": {
     "@vitejs/plugin-react": "^4.2.0",