commit 88254424c254b5faf668388cc455ef7232e4abca
Author: ModelHub XC <noreply@modelhub.org.cn>
Date:   Thu Aug 13 21:19:17 2026 +0800

    初始化项目，由ModelHub XC社区提供模型
    
    Model: khairi/qwen3-0.6b-protein-vocab-v0
    Source: Original Platform

diff --git a/.gitattributes b/.gitattributes
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+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
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+*.pt filter=lfs diff=lfs merge=lfs -text
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+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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+tokenizer.json filter=lfs diff=lfs merge=lfs -text
diff --git a/README.md b/README.md
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+---
+base_model: Qwen/Qwen3-0.6B
+tags:
+  - protein
+  - tokenizer-extension
+  - not-yet-trained
+---
+
+# qwen3-0.6b-protein-vocab-v0
+
+`Qwen/Qwen3-0.6B` with its tokenizer extended by a protein-sequence BPE
+vocabulary (+9,568 new tokens plus `<protein>`/`</protein>` special tokens),
+and input/output embeddings resized to match (new rows mean/covariance-
+initialized from the existing embedding distribution).
+
+**This checkpoint has not been trained on any protein data.** It's a
+starting point ("V0") for LoRA continued-pretraining, not a usable protein
+language model yet. All of Qwen3's original pretrained weights and special
+tokens (`<|im_start|>`, `<|im_end|>`, `<think>`, etc.) are unchanged and
+keep their original ids.
+
+Built with [`eshmun-vocab`](https://github.com/) via:
+
+```bash
+python scripts/extend_tokenizer.py \
+  --protein-tokenizer data/tokenizers/tokenizer_c100_10k/tokenizer.json \
+  --llm-tokenizer Qwen/Qwen3-0.6B \
+  --output data/tokenizers/qwen3_0.6b_protein_extended
+
+python scripts/build_vocab_extended_model.py \
+  --base-model Qwen/Qwen3-0.6B \
+  --tokenizer-path data/tokenizers/qwen3_0.6b_protein_extended \
+  --output models/Qwen3-0.6B-V0
+```
diff --git a/chat_template.jinja b/chat_template.jinja
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+{%- if tools %}
+    {{- '<|im_start|>system\n' }}
+    {%- if messages[0].role == 'system' %}
+        {{- messages[0].content + '\n\n' }}
+    {%- endif %}
+    {{- "# Tools\n\nYou may call one or more functions to assist with the user query.\n\nYou are provided with function signatures within <tools></tools> XML tags:\n<tools>" }}
+    {%- for tool in tools %}
+        {{- "\n" }}
+        {{- tool | tojson }}
+    {%- endfor %}
+    {{- "\n</tools>\n\nFor each function call, return a json object with function name and arguments within <tool_call></tool_call> XML tags:\n<tool_call>\n{\"name\": <function-name>, \"arguments\": <args-json-object>}\n</tool_call><|im_end|>\n" }}
+{%- else %}
+    {%- if messages[0].role == 'system' %}
+        {{- '<|im_start|>system\n' + messages[0].content + '<|im_end|>\n' }}
+    {%- endif %}
+{%- endif %}
+{%- set ns = namespace(multi_step_tool=true, last_query_index=messages|length - 1) %}
+{%- for message in messages[::-1] %}
+    {%- set index = (messages|length - 1) - loop.index0 %}
+    {%- if ns.multi_step_tool and message.role == "user" and message.content is string and not(message.content.startswith('<tool_response>') and message.content.endswith('</tool_response>')) %}
+        {%- set ns.multi_step_tool = false %}
+        {%- set ns.last_query_index = index %}
+    {%- endif %}
+{%- endfor %}
+{%- for message in messages %}
+    {%- if message.content is string %}
+        {%- set content = message.content %}
+    {%- else %}
+        {%- set content = '' %}
+    {%- endif %}
+    {%- if (message.role == "user") or (message.role == "system" and not loop.first) %}
+        {{- '<|im_start|>' + message.role + '\n' + content + '<|im_end|>' + '\n' }}
+    {%- elif message.role == "assistant" %}
+        {%- set reasoning_content = '' %}
+        {%- if message.reasoning_content is string %}
+            {%- set reasoning_content = message.reasoning_content %}
+        {%- else %}
+            {%- if '</think>' in content %}
+                {%- set reasoning_content = content.split('</think>')[0].rstrip('\n').split('<think>')[-1].lstrip('\n') %}
+                {%- set content = content.split('</think>')[-1].lstrip('\n') %}
+            {%- endif %}
+        {%- endif %}
+        {%- if loop.index0 > ns.last_query_index %}
+            {%- if loop.last or (not loop.last and reasoning_content) %}
+                {{- '<|im_start|>' + message.role + '\n<think>\n' + reasoning_content.strip('\n') + '\n</think>\n\n' + content.lstrip('\n') }}
+            {%- else %}
+                {{- '<|im_start|>' + message.role + '\n' + content }}
+            {%- endif %}
+        {%- else %}
+            {{- '<|im_start|>' + message.role + '\n' + content }}
+        {%- endif %}
+        {%- if message.tool_calls %}
+            {%- for tool_call in message.tool_calls %}
+                {%- if (loop.first and content) or (not loop.first) %}
+                    {{- '\n' }}
+                {%- endif %}
+                {%- if tool_call.function %}
+                    {%- set tool_call = tool_call.function %}
+                {%- endif %}
+                {{- '<tool_call>\n{"name": "' }}
+                {{- tool_call.name }}
+                {{- '", "arguments": ' }}
+                {%- if tool_call.arguments is string %}
+                    {{- tool_call.arguments }}
+                {%- else %}
+                    {{- tool_call.arguments | tojson }}
+                {%- endif %}
+                {{- '}\n</tool_call>' }}
+            {%- endfor %}
+        {%- endif %}
+        {{- '<|im_end|>\n' }}
+    {%- elif message.role == "tool" %}
+        {%- if loop.first or (messages[loop.index0 - 1].role != "tool") %}
+            {{- '<|im_start|>user' }}
+        {%- endif %}
+        {{- '\n<tool_response>\n' }}
+        {{- content }}
+        {{- '\n</tool_response>' }}
+        {%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
+            {{- '<|im_end|>\n' }}
+        {%- endif %}
+    {%- endif %}
+{%- endfor %}
+{%- if add_generation_prompt %}
+    {{- '<|im_start|>assistant\n' }}
+    {%- if enable_thinking is defined and enable_thinking is false %}
+        {{- '<think>\n\n</think>\n\n' }}
+    {%- endif %}
+{%- endif %}
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diff --git a/config.json b/config.json
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+++ b/config.json
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+{
+  "architectures": [
+    "Qwen3ForCausalLM"
+  ],
+  "attention_bias": false,
+  "attention_dropout": 0.0,
+  "bos_token_id": 151643,
+  "dtype": "bfloat16",
+  "eos_token_id": 151645,
+  "head_dim": 128,
+  "hidden_act": "silu",
+  "hidden_size": 1024,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_types": [
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention",
+    "full_attention"
+  ],
+  "max_position_embeddings": 40960,
+  "max_window_layers": 28,
+  "model_type": "qwen3",
+  "num_attention_heads": 16,
+  "num_hidden_layers": 28,
+  "num_key_value_heads": 8,
+  "pad_token_id": null,
+  "rms_norm_eps": 1e-06,
+  "rope_parameters": {
+    "rope_theta": 1000000,
+    "rope_type": "default"
+  },
+  "sliding_window": null,
+  "tie_word_embeddings": true,
+  "transformers_version": "5.8.1",
+  "use_cache": true,
+  "use_sliding_window": false,
+  "vocab_size": 161239
+}
diff --git a/generation_config.json b/generation_config.json
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+++ b/generation_config.json
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+{
+  "bos_token_id": 151643,
+  "do_sample": true,
+  "eos_token_id": [
+    151645,
+    151643
+  ],
+  "pad_token_id": 151643,
+  "temperature": 0.6,
+  "top_k": 20,
+  "top_p": 0.95,
+  "transformers_version": "5.8.1"
+}
diff --git a/model.safetensors b/model.safetensors
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+++ b/model.safetensors
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+version https://git-lfs.github.com/spec/v1
+oid sha256:ceb9356e61a4c50c8269bdd8d324e9a04587f8192898ac7f5fa7a1e90b26a6aa
+size 1211187656
diff --git a/tokenizer.json b/tokenizer.json
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--- /dev/null
+++ b/tokenizer.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:97790f03782ea2086eced06c8f2ab2aeb299986aad2153afeb76a6f746856d7c
+size 12049680
diff --git a/tokenizer_config.json b/tokenizer_config.json
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+++ b/tokenizer_config.json
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+{
+  "backend": "tokenizers",
+  "eos_token": "<|im_end|>",
+  "extra_special_tokens": [
+    "<protein>",
+    "</protein>",
+    "<think>",
+    "</think>"
+  ],
+  "is_local": true,
+  "local_files_only": false,
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "<|endoftext|>",
+  "tokenizer_class": "TokenizersBackend"
+}
diff --git a/vocab_extension.json b/vocab_extension.json
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+++ b/vocab_extension.json
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+{
+  "base_vocab_size": 151669,
+  "new_token_start_id": 151669,
+  "new_tokens_added": 9568,
+  "final_vocab_size": 161237,
+  "required_special_tokens": [
+    "<protein>",
+    "</protein>",
+    "<think>",
+    "</think>"
+  ]
+}
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