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FNS base-level decoder both modes; recovery 31.5/38.9 euk, 40.9/54.1 bacteria (Carbon's actual decoder)
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Match Carbon FNS BpLogitsProcessor decoding
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Stats: base-pair FNS likelihood 1.88 vs 1.79; bacteria recovery 35.3%
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Default generation = base-pair (FNS), marginalized per-base sampling
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FNS base-pair-level decode + per-base score() (Carbon's factorized-nucleotide method)
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stats: bits/base 1.79 (prok round2, trailing +0.0427)
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Switch sampled decoder to nucleus/top-p (Carbon's decoder) instead of top-k — escapes low-complexity loops
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Apply repetition penalty + no-repeat block to greedy/argmax (was sampled-only) — fixes argmax repeat-collapse
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real 570bp example sequences (were 240bp snippets)
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sampled default; long (570bp) examples
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Feed FULL sequence as context to the specialist (was seq[-48:]); argmax default
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Generation now matches offline tests: full frame-aligned context (len%6==0, cap 1020), not seq[-48:]
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Fix Examples decode value to match new radio choices (sampled default)
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Default decoding back to sampled; fix unreadable (dark-mode black) radio/checkbox options
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Per-domain auto decoding: argmax for euk/prok/splice, sampled for mrna (default 'auto'); manual override kept
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Add DECODING toggle (greedy argmax default / sampled); argmax shows coding ATG-start frames
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Add greedy/argmax decoding to generate_stream
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Restore raw-sequence text box (copy-paste) below the helix + token tracks during generation
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Stats: routing 99.8%, bits/base 1.80; splice now beats Carbon
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Add tokenization tracks (our take on carbon-tokenization-02): per-base color track + real 6-mer token strip below the helix; align nucleotide palette
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Add live 2D double-helix viz (our own take on carbon-helix-2d): base-by-base SVG strand, cream palette, routed-accent strands
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Update seq-recovery stats to re-measured values (euk 31.0%, bacteria 36.5%)
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Stats: routing 98.3%, bits/base 1.81 (mrna round, mean trailing +0.0573)
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Stats: routing 98.0%, bits/base 1.84 (eukaryote round)
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Fix Examples dataset rows rendering black (override table row-fill vars)
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Fix readability: pin paper palette for dark-mode + force light theme (text was white-on-cream)
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Restyle: Carbon-demo editorial paper aesthetic (cream/ink/green + JetBrains Mono), DaisyChain hero banner + chain motif
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Update stats: routing 94.8% -> 96.2%, bits/base 1.86 -> 1.85 (prokaryote distill round)
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initial commit
