Clarify UniRef50 lookup histogram

Wire Twin UniRef50 FAISS lookup

Merge CRISPR lookup and unknown characterization

Expand benchmark interpretation text

Avoid blocking Space tab load

Update CRISPR benchmark page

Benchmark tab: add Cas-only Pfam-verified reference section

Characterize: add ESM2-vs-Twin-MF signal-strength panel for unknowns

Characterize tab: pre-computed gallery of 24 uncharacterised proteins

Add Twin-MF embeddings + UMAP coords for Characterize tab (force past *.npy gitignore)

Add Characterize tab: verdict + top-10 + UMAP placement for unknown proteins

Benchmark: UMAP first, Twin-MF as primary, drop emojis, professional tone

Benchmark: replace ROC with silhouette; add URL-hash tab deep-linking

Extend Benchmark tab: UMAP, ROC, and BP-vs-CC-vs-MF aspect comparison

Fix Benchmark tab crash: drop show_download_button (unsupported in this Gradio)

Add Benchmark tab: CRISPR clustering comparison ESM2 vs Twin-BP

Add crispr_reference/embeddings_esm2.npy (force past *.npy gitignore)

Add Method selector (ESM2 vs genomenet-twin) on Lookup tab

Lookup: drop k slider, fixed 25, stacked histogram with context pool

Drop the "available once Step 6 build completes" note in Lookup tab

Add crispr_reference/embeddings.npy (force through *.npy gitignore)

Wire CRISPR reference (Twin-BP) into the Lookup tab

Lookup: show top-k AND bottom-k + SVG histogram; widen slider to 5-50

Add CRISPR example queries to Lookup tab

Render Lookup hits with per-row similarity gradient bars + scale legend

Redesign Compare tab as Lookup; add UniRef metadata; update header

Accept long sequences; truncate to ESM2 max len with visible note

CRISPR-themed default sequences and example pairs on Distance tab

Swap cosine-similarity bar for cosine-distance for consistent direction

Add visual bars for L2 distance and cosine similarity

Distance tab first, with example pairs and loading indicator

Add Distance tab for Twin pairwise distance prediction

Re-add FAISS fallback so missing index doesn't break all panels

Switch Twin to aspect-specific checkpoints with runtime switcher

Fix Twin embedding dim: 1024 -> 512 (projection_dim=256 in checkpoint)

Remove Twin and FAISS fallbacks; let failures surface explicitly

Add FAISS nearest-neighbor search and real Twin model inference

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initial commit