Final paper and small tokenizer fix - #8
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- Skip malformed sequences during training instead of aborting the run, and map malformed input to <unk> at encode time so it stays detectable via unk_rate rather than raising mid-batch. - Debit both constituents when a merge is applied so *_freq.json reflects accurate post-merge counts; primitive keys are retained for coverage. - Drop the per-merge full copy of pair_counts (never read) and reuse untouched sequences by reference during rebuild. Output is unchanged; merge order stays pinned for reproducibility. - Document that encoding is greedy longest-match, not a replay of learned merge order, and that both phases share it. - Remove dead two-letter metal branches from SMILES_RE (always bracketed in canonical SMILES); verified identical splits on the shipped vocab. - Correct the misleading "unbalanced parens = defect" comment: boundary- crossing SMILES tokens are inherent to APE and match the paper. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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