From afcda09d154a285cd366135f98ffc1d357f7ddbd Mon Sep 17 00:00:00 2001
From: Kashif Rasul <kashif.rasul@gmail.com>
Date: Fri, 22 May 2026 11:17:31 +0200
Subject: [PATCH] vocab : fix HybridDNA tokenizer (#23466)
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* vocab : mark hybriddna k-mers to avoid BPE token collisions

* improved loop

---------

Co-authored-by: Sigbjørn Skjæret <sigbjorn.skjaeret@scala.com>
---
 conversion/base.py  |  5 +++++
 src/llama-vocab.cpp | 50 +++++++++++++++++++++++++++------------------
 2 files changed, 35 insertions(+), 20 deletions(-)

diff --git a/conversion/base.py b/conversion/base.py
index 8e12af6c5..d8f050ed3 100644
--- a/conversion/base.py
+++ b/conversion/base.py
@@ -1617,6 +1617,11 @@ class TextModel(ModelBase):
         assert max(tokenizer.vocab.values()) < vocab_size  # ty: ignore[unresolved-attribute]
 
         reverse_vocab = {id_: encoded_tok for encoded_tok, id_ in tokenizer.vocab.items()}  # ty: ignore[unresolved-attribute]
+        # k-mers can share text with a base-vocab BPE token (e.g. CCCCCC) and get
+        # dropped by get_vocab(); a reserved marker suffix (U+E000) keeps each
+        # k-mer's own id (llama.cpp strips it on detokenization)
+        for kmer in tokenizer.kmers:  # ty: ignore[unresolved-attribute]
+            reverse_vocab[tokenizer.dna_token_to_id[kmer]] = kmer + "\ue000"  # ty: ignore[unresolved-attribute]
         added_vocab = tokenizer.get_added_vocab()  # ty: ignore[unresolved-attribute]
         added_tokens_decoder = tokenizer.added_tokens_decoder  # ty: ignore[unresolved-attribute]
 
diff --git a/src/llama-vocab.cpp b/src/llama-vocab.cpp
index acf832d05..a5cf148b2 100644
--- a/src/llama-vocab.cpp
+++ b/src/llama-vocab.cpp
@@ -1581,6 +1581,11 @@ private:
     const llm_tokenizer_plamo2 & tokenizer;
 };
 
+// reserved suffix (U+E000) that keeps DNA k-mers distinct from identical
+// base-vocab BPE tokens (e.g. CCCCCC) in token_to_id; erased from id_to_token
+// text at load
+static const std::string dna_kmer_marker = "\xee\x80\x80";
+
 struct llm_tokenizer_hybriddna_session : llm_tokenizer_bpe_session {
     llm_tokenizer_hybriddna_session(const llama_vocab & vocab, const llm_tokenizer_bpe & tokenizer) : llm_tokenizer_bpe_session{vocab, tokenizer}, vocab{vocab} {}
 
@@ -1636,34 +1641,22 @@ private:
                 c = char(c - 32);
             }
         }
-        auto is_valid_kmer = [](const std::string & s) {
-            for (char c : s) {
-                if (c != 'A' && c != 'C' && c != 'G' && c != 'T') {
-                    return false;
-                }
-            }
-            return true;
+
+        // k-mers carry the reserved marker suffix; a non-ACGT k-mer simply
+        // isn't in the vocab and falls back to <oov>
+        auto kmer_token = [&](const std::string & kmer) {
+            const auto tok = vocab.text_to_token(kmer + dna_kmer_marker);
+            return tok != LLAMA_TOKEN_NULL ? tok : oov_id;
         };
 
         size_t i = 0;
         for (; i + k <= seq.size(); i += k) {
-            const std::string kmer = seq.substr(i, k);
-            if (is_valid_kmer(kmer)) {
-                const auto tok = vocab.text_to_token(kmer);
-                output.push_back(tok != LLAMA_TOKEN_NULL ? tok : oov_id);
-            } else {
-                output.push_back(oov_id);
-            }
+            output.push_back(kmer_token(seq.substr(i, k)));
         }
         if (i < seq.size()) {
             std::string kmer = seq.substr(i);
             kmer.append(k - kmer.size(), 'A');
-            if (is_valid_kmer(kmer)) {
-                const auto tok = vocab.text_to_token(kmer);
-                output.push_back(tok != LLAMA_TOKEN_NULL ? tok : oov_id);
-            } else {
-                output.push_back(oov_id);
-            }
+            output.push_back(kmer_token(kmer));
         }
     }
 
@@ -2357,6 +2350,23 @@ void llama_vocab::impl::load(llama_model_loader & ml, const LLM_KV & kv) {
     }
     GGML_ASSERT(id_to_token.size() == token_to_id.size());
 
+    // hybriddna: the marker suffix kept k-mer ids distinct in token_to_id; erase
+    // it from id_to_token so the k-mers detokenize to the bare DNA sequence. The
+    // k-mers are the block right after <oov>, so only scan from there.
+    if (tokenizer_model == "hybriddna") {
+        const auto idx = token_to_id.find("<oov>");
+        if (idx != token_to_id.end()) {
+            auto it = id_to_token.begin() + idx->second + 1;
+            for (; it != id_to_token.end(); ++it) {
+                std::string & text = it->text;
+                if (text.size() > dna_kmer_marker.size()
+                        && text.compare(text.size() - dna_kmer_marker.size(), dna_kmer_marker.size(), dna_kmer_marker) == 0) {
+                    text.erase(text.size() - dna_kmer_marker.size());
+                }
+            }
+        }
+    }
+
     init_tokenizer(type);
 
     // determine the newline token: LLaMA "<0x0A>" == 10 == '\n', Falcon 193 == '\n'