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@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+tokenizer.json filter=lfs diff=lfs merge=lfs -text

LICENSE

@@ -0,0 +1,202 @@
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README.md

@@ -0,0 +1,79 @@
+---
+license: apache-2.0
+language:
+  - en
+library_name: transformers
+tags:
+  - genomics
+  - tool-calling
+  - function-calling
+  - qwen3.5
+  - qwen
+pipeline_tag: text-generation
+base_model: Qwen/Qwen3.5-4B
+pretty_name: CodeXomics-ToolAgent-4B-v1
+---
+
+# CodeXomics-ToolAgent-4B-v1
+
+**CodeXomics-ToolAgent-4B-v1** (internally `qwen3.5:4b-codexomics-tools-v5`) is a 4.2B-parameter
+tool-calling model fine-tuned from `Qwen/Qwen3.5-4B` for the CodeXomics genomics workbench. It
+performs native function calling against the CodeXomics tool registry (file loading, navigation,
+sequence analysis, annotation, track control, export, BLAST, primer design, database/protein
+retrieval, task management, and UI control).
+
+## Fine-tuning
+
+- Method: QLoRA (rank 16, scale 32.0, dropout 0.05, 4 layers) with MLX-LM 0.31.2 / MLX 0.32.0
+- Trainable parameters: 4.058M (0.096%)
+- Optimizer: AdamW, learning rate 1.0e-5, effective batch size 4, 200 iterations
+- Maximum sequence length: 3,072 tokens; prompt masking enabled
+- Hardware: Apple M3 Max; peak memory 191 GB (including swap)
+- Checkpoint selection: iteration 75 (validation loss 0.020); test loss 0.074 (perplexity 1.077)
+- Training data: CodeXomics-ToolCalling-v1 (373/123/30 train/validation/test examples)
+
+## Evaluation
+
+On the CodeXomics Benchmark (172 automatic tests: 143 single-operation, 29 multi-step), evaluated
+in the real application loop with task-completion scoring plus execution evidence:
+
+| Suite | Passed / Total |
+| --- | --- |
+| Simple | 143/143 |
+| Complex | 29/29 |
+| **Total** | **172/172 (100%)** |
+
+100% was achieved in multiple independent complete sessions (simple: 2026-08-04 and 2026-08-07;
+complex: 2026-08-04 and 2026-08-10). Inference settings: temperature 0, thinking enabled.
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+
+model = AutoModelForCausalLM.from_pretrained("CodeXomics-ToolAgent-4B-v1")
+tokenizer = AutoTokenizer.from_pretrained("CodeXomics-ToolAgent-4B-v1")
+```
+
+For deployment in CodeXomics, the model is served through Ollama as `qwen3.5:4b-codexomics-tools-v5`
+(Q4_K_M, 2.7 GB) with native tool calling and thinking enabled.
+
+## Limitations
+
+- Multi-step workflows can occasionally stop before the final verification step, causing minor
+  run-to-run variance on the complex suite (27–29/29 across complete sessions).
+- The model is specialized for CodeXomics genomic workflows; generalization to other tool-calling
+  domains was not evaluated.
+
+## Citation
+
+```bibtex
+@software{codexomics-toolagent-v1,
+  title = {CodeXomics-ToolAgent-4B-v1},
+  author = {Song, Lifu},
+  year = {2026},
+  license = {Apache-2.0},
+  publisher = {Hugging Face},
+  base_model = {Qwen/Qwen3.5-4B}
+}
+```

chat_template.jinja

@@ -0,0 +1,154 @@
+{%- set image_count = namespace(value=0) %}
+{%- set video_count = namespace(value=0) %}
+{%- macro render_content(content, do_vision_count, is_system_content=false) %}
+    {%- if content is string %}
+        {{- content }}
+    {%- elif content is iterable and content is not mapping %}
+        {%- for item in content %}
+            {%- if 'image' in item or 'image_url' in item or item.type == 'image' %}
+                {%- if is_system_content %}
+                    {{- raise_exception('System message cannot contain images.') }}
+                {%- endif %}
+                {%- if do_vision_count %}
+                    {%- set image_count.value = image_count.value + 1 %}
+                {%- endif %}
+                {%- if add_vision_id %}
+                    {{- 'Picture ' ~ image_count.value ~ ': ' }}
+                {%- endif %}
+                {{- '<|vision_start|><|image_pad|><|vision_end|>' }}
+            {%- elif 'video' in item or item.type == 'video' %}
+                {%- if is_system_content %}
+                    {{- raise_exception('System message cannot contain videos.') }}
+                {%- endif %}
+                {%- if do_vision_count %}
+                    {%- set video_count.value = video_count.value + 1 %}
+                {%- endif %}
+                {%- if add_vision_id %}
+                    {{- 'Video ' ~ video_count.value ~ ': ' }}
+                {%- endif %}
+                {{- '<|vision_start|><|video_pad|><|vision_end|>' }}
+            {%- elif 'text' in item %}
+                {{- item.text }}
+            {%- else %}
+                {{- raise_exception('Unexpected item type in content.') }}
+            {%- endif %}
+        {%- endfor %}
+    {%- elif content is none or content is undefined %}
+        {{- '' }}
+    {%- else %}
+        {{- raise_exception('Unexpected content type.') }}
+    {%- endif %}
+{%- endmacro %}
+{%- if not messages %}
+    {{- raise_exception('No messages provided.') }}
+{%- endif %}
+{%- if tools and tools is iterable and tools is not mapping %}
+    {{- '<|im_start|>system\n' }}
+    {{- "# Tools\n\nYou have access to the following functions:\n\n<tools>" }}
+    {%- for tool in tools %}
+        {{- "\n" }}
+        {{- tool | tojson }}
+    {%- endfor %}
+    {{- "\n</tools>" }}
+    {{- '\n\nIf you choose to call a function ONLY reply in the following format with NO suffix:\n\n<tool_call>\n<function=example_function_name>\n<parameter=example_parameter_1>\nvalue_1\n</parameter>\n<parameter=example_parameter_2>\nThis is the value for the second parameter\nthat can span\nmultiple lines\n</parameter>\n</function>\n</tool_call>\n\n<IMPORTANT>\nReminder:\n- Function calls MUST follow the specified format: an inner <function=...></function> block must be nested within <tool_call></tool_call> XML tags\n- Required parameters MUST be specified\n- You may provide optional reasoning for your function call in natural language BEFORE the function call, but NOT after\n- If there is no function call available, answer the question like normal with your current knowledge and do not tell the user about function calls\n</IMPORTANT>' }}
+    {%- if messages[0].role == 'system' %}
+        {%- set content = render_content(messages[0].content, false, true)|trim %}
+        {%- if content %}
+            {{- '\n\n' + content }}
+        {%- endif %}
+    {%- endif %}
+    {{- '<|im_end|>\n' }}
+{%- else %}
+    {%- if messages[0].role == 'system' %}
+        {%- set content = render_content(messages[0].content, false, true)|trim %}
+        {{- '<|im_start|>system\n' + 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" %}
+        {%- set content = render_content(message.content, false)|trim %}
+        {%- if not(content.startswith('<tool_response>') and content.endswith('</tool_response>')) %}
+            {%- set ns.multi_step_tool = false %}
+            {%- set ns.last_query_index = index %}
+        {%- endif %}
+    {%- endif %}
+{%- endfor %}
+{%- if ns.multi_step_tool %}
+    {{- raise_exception('No user query found in messages.') }}
+{%- endif %}
+{%- for message in messages %}
+    {%- set content = render_content(message.content, true)|trim %}
+    {%- if message.role == "system" %}
+        {%- if not loop.first %}
+            {{- raise_exception('System message must be at the beginning.') }}
+        {%- endif %}
+    {%- elif message.role == "user" %}
+        {{- '<|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 %}
+        {%- set reasoning_content = reasoning_content|trim %}
+        {%- if loop.index0 > ns.last_query_index %}
+            {{- '<|im_start|>' + message.role + '\n<think>\n' + reasoning_content + '\n</think>\n\n' + content }}
+        {%- else %}
+            {{- '<|im_start|>' + message.role + '\n' + content }}
+        {%- endif %}
+        {%- if message.tool_calls and message.tool_calls is iterable and message.tool_calls is not mapping %}
+            {%- for tool_call in message.tool_calls %}
+                {%- if tool_call.function is defined %}
+                    {%- set tool_call = tool_call.function %}
+                {%- endif %}
+                {%- if loop.first %}
+                    {%- if content|trim %}
+                        {{- '\n\n<tool_call>\n<function=' + tool_call.name + '>\n' }}
+                    {%- else %}
+                        {{- '<tool_call>\n<function=' + tool_call.name + '>\n' }}
+                    {%- endif %}
+                {%- else %}
+                    {{- '\n<tool_call>\n<function=' + tool_call.name + '>\n' }}
+                {%- endif %}
+                {%- if tool_call.arguments is defined %}
+                    {%- for args_name, args_value in tool_call.arguments|items %}
+                        {{- '<parameter=' + args_name + '>\n' }}
+                        {%- set args_value = args_value | tojson | safe if args_value is mapping or (args_value is sequence and args_value is not string) else args_value | string %}
+                        {{- args_value }}
+                        {{- '\n</parameter>\n' }}
+                    {%- endfor %}
+                {%- endif %}
+                {{- '</function>\n</tool_call>' }}
+            {%- endfor %}
+        {%- endif %}
+        {{- '<|im_end|>\n' }}
+    {%- elif message.role == "tool" %}
+        {%- if loop.previtem and loop.previtem.role != "tool" %}
+            {{- '<|im_start|>user' }}
+        {%- endif %}
+        {{- '\n<tool_response>\n' }}
+        {{- content }}
+        {{- '\n</tool_response>' }}
+        {%- if not loop.last and loop.nextitem.role != "tool" %}
+            {{- '<|im_end|>\n' }}
+        {%- elif loop.last %}
+            {{- '<|im_end|>\n' }}
+        {%- endif %}
+    {%- else %}
+        {{- raise_exception('Unexpected message role.') }}
+    {%- 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' }}
+    {%- else %}
+        {{- '<think>\n' }}
+    {%- endif %}
+{%- endif %}

config.json

@@ -0,0 +1,84 @@
+{
+  "architectures": [
+    "Qwen3_5ForConditionalGeneration"
+  ],
+  "model_type": "qwen3_5",
+  "text_config": {
+    "attention_bias": false,
+    "attention_dropout": 0.0,
+    "attn_output_gate": true,
+    "dtype": "bfloat16",
+    "eos_token_id": 248044,
+    "full_attention_interval": 4,
+    "head_dim": 256,
+    "hidden_act": "silu",
+    "hidden_size": 2560,
+    "initializer_range": 0.02,
+    "intermediate_size": 9216,
+    "layer_types": [
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention",
+      "linear_attention",
+      "linear_attention",
+      "linear_attention",
+      "full_attention"
+    ],
+    "linear_conv_kernel_dim": 4,
+    "linear_key_head_dim": 128,
+    "linear_num_key_heads": 16,
+    "linear_num_value_heads": 32,
+    "linear_value_head_dim": 128,
+    "max_position_embeddings": 262144,
+    "mlp_only_layers": [],
+    "model_type": "qwen3_5_text",
+    "mtp_num_hidden_layers": 0,
+    "mtp_use_dedicated_embeddings": false,
+    "num_attention_heads": 16,
+    "num_hidden_layers": 32,
+    "num_key_value_heads": 4,
+    "rms_norm_eps": 1e-06,
+    "tie_word_embeddings": true,
+    "use_cache": true,
+    "vocab_size": 248320,
+    "mamba_ssm_dtype": "float32",
+    "rope_parameters": {
+      "mrope_interleaved": true,
+      "mrope_section": [
+        11,
+        11,
+        10
+      ],
+      "rope_theta": 10000000,
+      "partial_rotary_factor": 0.25,
+      "type": "default"
+    }
+  },
+  "tie_word_embeddings": true,
+  "transformers_version": "4.57.0.dev0"
+}

export-manifest.json

@@ -0,0 +1,10 @@
+{
+  "schema_version": "1.0",
+  "architecture": "Qwen3_5ForConditionalGeneration",
+  "model_type": "qwen3_5",
+  "tensor_count": 426,
+  "total_size": 8411504128,
+  "shards": 2,
+  "quantization": null,
+  "mtp_num_hidden_layers": 0
+}

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model.safetensors.index.json

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+    "model.language_model.layers.9.mlp.down_proj.weight": "model-00001-of-00002.safetensors",
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tokenizer_config.json

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