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Model: khazarai/Bio-8B-it Source: Original Platform
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127
README.md
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---
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base_model: unsloth/Qwen3-8B
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tags:
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- text-generation-inference
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- transformers
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- unsloth
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- qwen3
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- sft
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license: apache-2.0
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language:
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- en
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datasets:
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- bio-nlp-umass/bioinstruct
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pipeline_tag: text-generation
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library_name: transformers
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---
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# khazarai/Bio-8B-it
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## Model Description
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Bio-8B-it is an 8B parameter biomedical instruction-tuned language model built on top of Qwen 3-8B.
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The model was fine-tuned using Supervised Fine-Tuning (SFT) with QLoRA via the PEFT framework.
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This model is optimized for biomedical and clinical NLP instruction-following tasks, including:
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- Biomedical question answering
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- Clinical text summarization
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- Information extraction
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- Clinical trial eligibility assessment
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- Differential diagnosis reasoning
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**Base Model**
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- Base: Qwen3-8B
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- Architecture: Decoder-only Transformer
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- Parameter count: 8B
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**Fine-Tuning Method**
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- Technique: Supervised Fine-Tuning (SFT)
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- Parameter-efficient tuning: QLoRA (PEFT)
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- Base model loading: 4-bit / 8-bit quantization during training
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- Final merged model: 16-bit full-precision weights
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- Training objective: Instruction-following adaptation for biomedical tasks
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- QLoRA enables efficient fine-tuning by freezing base weights and training low-rank adapters, which are later merged into the full model.
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## Dataset Overview
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- Total samples: 25,000 instruction–response pairs
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- Generation method: GPT-4 generated synthetic instruction tuning dataset
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- Inspired by: Self-Instruct methodology
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- Seed tasks: 80 manually constructed biomedical tasks
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- The dataset was automatically expanded by prompting GPT-4 with randomly selected seed examples to generate diverse biomedical instruction data.
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### Intended Use
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This model is intended for:
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- Biomedical NLP research
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- Clinical text processing experiments
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- Instruction-following biomedical assistants
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- Academic evaluation on BioMedical NLP tasks
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### Out-of-Scope Use
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This model is not intended for:
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- Direct clinical decision-making
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- Real-world medical diagnosis
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- Prescribing medication
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- Deployment in safety-critical healthcare systems
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- It should not replace licensed medical professionals.
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### How to Get Started with the Model
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```python
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from transformers import AutoTokenizer, AutoModelForCausalLM
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tokenizer = AutoTokenizer.from_pretrained("khazarai/Bio-8B-it")
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model = AutoModelForCausalLM.from_pretrained(
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"khazarai/Bio-8B-it",
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device_map={"": 0}
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)
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question = """
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Describe how to properly perform a hand hygiene using an alcohol-based hand sanitizer.
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"""
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messages = [
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{"role" : "user", "content" : question}
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]
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text = tokenizer.apply_chat_template(
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messages,
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tokenize = False,
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add_generation_prompt = True,
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enable_thinking = False,
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)
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from transformers import TextStreamer
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_ = model.generate(
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**tokenizer(text, return_tensors = "pt").to("cuda"),
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max_new_tokens = 1400,
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temperature = 0.7,
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top_p = 0.8,
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top_k = 20,
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streamer = TextStreamer(tokenizer, skip_prompt = True),
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)
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```
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Citation
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If you use this model, please cite the original BioInstruct paper:
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```
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@article{Tran2024Bioinstruct,
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author = {Tran, Hieu and Yang, Zhichao and Yao, Zonghai and Yu, Hong},
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title = {BioInstruct: instruction tuning of large language models for biomedical natural language processing},
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journal = {Journal of the American Medical Informatics Association},
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year = {2024},
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doi = {10.1093/jamia/ocae122}
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}
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```
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28
added_tokens.json
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added_tokens.json
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{
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"</think>": 151668,
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"</tool_response>": 151666,
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"<think>": 151667,
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"<tool_response>": 151665,
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"<|endoftext|>": 151643,
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}
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chat_template.jinja
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chat_template.jinja
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{%- if tools %}
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{{- '<|im_start|>system\n' }}
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{%- if messages[0].role == 'system' %}
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{{- messages[0].content + '\n\n' }}
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{%- endif %}
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{{- "# 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>" }}
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{%- for tool in tools %}
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{{- "\n" }}
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{{- tool | tojson }}
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{%- endfor %}
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{{- "\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" }}
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{%- else %}
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{%- if messages[0].role == 'system' %}
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{{- '<|im_start|>system\n' + messages[0].content + '<|im_end|>\n' }}
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{%- endif %}
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{%- endif %}
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{%- set ns = namespace(multi_step_tool=true, last_query_index=messages|length - 1) %}
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{%- for forward_message in messages %}
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{%- set index = (messages|length - 1) - loop.index0 %}
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{%- set message = messages[index] %}
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{%- set current_content = message.content if message.content is not none else '' %}
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{%- set tool_start = '<tool_response>' %}
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{%- set tool_start_length = tool_start|length %}
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{%- set start_of_message = current_content[:tool_start_length] %}
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{%- set tool_end = '</tool_response>' %}
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{%- set tool_end_length = tool_end|length %}
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{%- set start_pos = (current_content|length) - tool_end_length %}
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{%- if start_pos < 0 %}
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{%- set start_pos = 0 %}
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{%- endif %}
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{%- set end_of_message = current_content[start_pos:] %}
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{%- if ns.multi_step_tool and message.role == "user" and not(start_of_message == tool_start and end_of_message == tool_end) %}
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{%- set ns.multi_step_tool = false %}
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{%- set ns.last_query_index = index %}
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{%- endif %}
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{%- endfor %}
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{%- for message in messages %}
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{%- if (message.role == "user") or (message.role == "system" and not loop.first) %}
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{{- '<|im_start|>' + message.role + '\n' + message.content + '<|im_end|>' + '\n' }}
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{%- elif message.role == "assistant" %}
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{%- set content = message.content %}
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{%- set reasoning_content = '' %}
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{%- if message.reasoning_content is defined and message.reasoning_content is not none %}
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{%- set reasoning_content = message.reasoning_content %}
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{%- else %}
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{%- if '</think>' in message.content %}
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{%- set content = (message.content.split('</think>')|last).lstrip('\n') %}
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{%- set reasoning_content = (message.content.split('</think>')|first).rstrip('\n') %}
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{%- set reasoning_content = (reasoning_content.split('<think>')|last).lstrip('\n') %}
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{%- endif %}
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{%- endif %}
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{%- if loop.index0 > ns.last_query_index %}
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{%- if loop.last or (not loop.last and reasoning_content) %}
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{{- '<|im_start|>' + message.role + '\n<think>\n' + reasoning_content.strip('\n') + '\n</think>\n\n' + content.lstrip('\n') }}
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{%- else %}
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{{- '<|im_start|>' + message.role + '\n' + content }}
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{%- endif %}
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{%- else %}
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{{- '<|im_start|>' + message.role + '\n' + content }}
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{%- endif %}
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{%- if message.tool_calls %}
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{%- for tool_call in message.tool_calls %}
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{%- if (loop.first and content) or (not loop.first) %}
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{{- '\n' }}
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{%- endif %}
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||||
{%- if tool_call.function %}
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||||
{%- set tool_call = tool_call.function %}
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||||
{%- endif %}
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{{- '<tool_call>\n{"name": "' }}
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{{- tool_call.name }}
|
||||
{{- '", "arguments": ' }}
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{%- if tool_call.arguments is string %}
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||||
{{- tool_call.arguments }}
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{%- else %}
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{{- tool_call.arguments | tojson }}
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{%- endif %}
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{{- '}\n</tool_call>' }}
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{%- endfor %}
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{%- endif %}
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{{- '<|im_end|>\n' }}
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{%- elif message.role == "tool" %}
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||||
{%- if loop.first or (messages[loop.index0 - 1].role != "tool") %}
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{{- '<|im_start|>user' }}
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{%- endif %}
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{{- '\n<tool_response>\n' }}
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{{- message.content }}
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{{- '\n</tool_response>' }}
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{%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
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{{- '<|im_end|>\n' }}
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{%- endif %}
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{%- endif %}
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{%- endfor %}
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{%- if add_generation_prompt %}
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{{- '<|im_start|>assistant\n' }}
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{%- if enable_thinking is defined and enable_thinking is false %}
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{{- '<think>\n\n</think>\n\n' }}
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{%- endif %}
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{%- endif %}
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config.json
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config.json
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{
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"architectures": [
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"Qwen3ForCausalLM"
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"head_dim": 128,
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|
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|
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|
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"max_position_embeddings": 40960,
|
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"max_window_layers": 36,
|
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"model_type": "qwen3",
|
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"num_attention_heads": 32,
|
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|
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|
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"rms_norm_eps": 1e-06,
|
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|
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"sliding_window": null,
|
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"tie_word_embeddings": false,
|
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"torch_dtype": "float16",
|
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"transformers_version": "4.57.1",
|
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"unsloth_fixed": true,
|
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"use_cache": true,
|
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"use_sliding_window": false,
|
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"vocab_size": 151936
|
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}
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generation_config.json
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generation_config.json
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{
|
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"bos_token_id": 151643,
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"do_sample": true,
|
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"eos_token_id": [
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151645,
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],
|
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"max_length": 40960,
|
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|
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"temperature": 0.6,
|
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"top_k": 20,
|
||||
"top_p": 0.95,
|
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"transformers_version": "4.57.1"
|
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}
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31
special_tokens_map.json
Normal file
31
special_tokens_map.json
Normal file
@@ -0,0 +1,31 @@
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||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
},
|
||||
"pad_token": {
|
||||
"content": "<|vision_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
}
|
||||
}
|
||||
3
tokenizer.json
Normal file
3
tokenizer.json
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:aeb13307a71acd8fe81861d94ad54ab689df773318809eed3cbe794b4492dae4
|
||||
size 11422654
|
||||
241
tokenizer_config.json
Normal file
241
tokenizer_config.json
Normal file
@@ -0,0 +1,241 @@
|
||||
{
|
||||
"add_bos_token": false,
|
||||
"add_prefix_space": false,
|
||||
"added_tokens_decoder": {
|
||||
"151643": {
|
||||
"content": "<|endoftext|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151644": {
|
||||
"content": "<|im_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151645": {
|
||||
"content": "<|im_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151646": {
|
||||
"content": "<|object_ref_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151647": {
|
||||
"content": "<|object_ref_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151648": {
|
||||
"content": "<|box_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151649": {
|
||||
"content": "<|box_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151650": {
|
||||
"content": "<|quad_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151651": {
|
||||
"content": "<|quad_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151652": {
|
||||
"content": "<|vision_start|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151653": {
|
||||
"content": "<|vision_end|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151654": {
|
||||
"content": "<|vision_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151655": {
|
||||
"content": "<|image_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151656": {
|
||||
"content": "<|video_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": true
|
||||
},
|
||||
"151657": {
|
||||
"content": "<tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151658": {
|
||||
"content": "</tool_call>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151659": {
|
||||
"content": "<|fim_prefix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151660": {
|
||||
"content": "<|fim_middle|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151661": {
|
||||
"content": "<|fim_suffix|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151662": {
|
||||
"content": "<|fim_pad|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151663": {
|
||||
"content": "<|repo_name|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151664": {
|
||||
"content": "<|file_sep|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151665": {
|
||||
"content": "<tool_response>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151666": {
|
||||
"content": "</tool_response>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151667": {
|
||||
"content": "<think>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
},
|
||||
"151668": {
|
||||
"content": "</think>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false,
|
||||
"special": false
|
||||
}
|
||||
},
|
||||
"additional_special_tokens": [
|
||||
"<|im_start|>",
|
||||
"<|im_end|>",
|
||||
"<|object_ref_start|>",
|
||||
"<|object_ref_end|>",
|
||||
"<|box_start|>",
|
||||
"<|box_end|>",
|
||||
"<|quad_start|>",
|
||||
"<|quad_end|>",
|
||||
"<|vision_start|>",
|
||||
"<|vision_end|>",
|
||||
"<|vision_pad|>",
|
||||
"<|image_pad|>",
|
||||
"<|video_pad|>"
|
||||
],
|
||||
"bos_token": null,
|
||||
"clean_up_tokenization_spaces": false,
|
||||
"eos_token": "<|im_end|>",
|
||||
"errors": "replace",
|
||||
"extra_special_tokens": {},
|
||||
"model_max_length": 40960,
|
||||
"pad_token": "<|vision_pad|>",
|
||||
"padding_side": "right",
|
||||
"split_special_tokens": false,
|
||||
"tokenizer_class": "Qwen2Tokenizer",
|
||||
"unk_token": null,
|
||||
"chat_template": "{%- if tools %}\n {{- '<|im_start|>system\\n' }}\n {%- if messages[0].role == 'system' %}\n {{- messages[0].content + '\\n\\n' }}\n {%- endif %}\n {{- \"# 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>\" }}\n {%- for tool in tools %}\n {{- \"\\n\" }}\n {{- tool | tojson }}\n {%- endfor %}\n {{- \"\\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\" }}\n{%- else %}\n {%- if messages[0].role == 'system' %}\n {{- '<|im_start|>system\\n' + messages[0].content + '<|im_end|>\\n' }}\n {%- endif %}\n{%- endif %}\n{%- set ns = namespace(multi_step_tool=true, last_query_index=messages|length - 1) %}\n{%- for forward_message in messages %}\n {%- set index = (messages|length - 1) - loop.index0 %}\n {%- set message = messages[index] %}\n {%- set current_content = message.content if message.content is not none else '' %}\n {%- set tool_start = '<tool_response>' %}\n {%- set tool_start_length = tool_start|length %}\n {%- set start_of_message = current_content[:tool_start_length] %}\n {%- set tool_end = '</tool_response>' %}\n {%- set tool_end_length = tool_end|length %}\n {%- set start_pos = (current_content|length) - tool_end_length %}\n {%- if start_pos < 0 %}\n {%- set start_pos = 0 %}\n {%- endif %}\n {%- set end_of_message = current_content[start_pos:] %}\n {%- if ns.multi_step_tool and message.role == \"user\" and not(start_of_message == tool_start and end_of_message == tool_end) %}\n {%- set ns.multi_step_tool = false %}\n {%- set ns.last_query_index = index %}\n {%- endif %}\n{%- endfor %}\n{%- for message in messages %}\n {%- if (message.role == \"user\") or (message.role == \"system\" and not loop.first) %}\n {{- '<|im_start|>' + message.role + '\\n' + message.content + '<|im_end|>' + '\\n' }}\n {%- elif message.role == \"assistant\" %}\n {%- set content = message.content %}\n {%- set reasoning_content = '' %}\n {%- if message.reasoning_content is defined and message.reasoning_content is not none %}\n {%- set reasoning_content = message.reasoning_content %}\n {%- else %}\n {%- if '</think>' in message.content %}\n {%- set content = (message.content.split('</think>')|last).lstrip('\\n') %}\n {%- set reasoning_content = (message.content.split('</think>')|first).rstrip('\\n') %}\n {%- set reasoning_content = (reasoning_content.split('<think>')|last).lstrip('\\n') %}\n {%- endif %}\n {%- endif %}\n {%- if loop.index0 > ns.last_query_index %}\n {%- if loop.last or (not loop.last and reasoning_content) %}\n {{- '<|im_start|>' + message.role + '\\n<think>\\n' + reasoning_content.strip('\\n') + '\\n</think>\\n\\n' + content.lstrip('\\n') }}\n {%- else %}\n {{- '<|im_start|>' + message.role + '\\n' + content }}\n {%- endif %}\n {%- else %}\n {{- '<|im_start|>' + message.role + '\\n' + content }}\n {%- endif %}\n {%- if message.tool_calls %}\n {%- for tool_call in message.tool_calls %}\n {%- if (loop.first and content) or (not loop.first) %}\n {{- '\\n' }}\n {%- endif %}\n {%- if tool_call.function %}\n {%- set tool_call = tool_call.function %}\n {%- endif %}\n {{- '<tool_call>\\n{\"name\": \"' }}\n {{- tool_call.name }}\n {{- '\", \"arguments\": ' }}\n {%- if tool_call.arguments is string %}\n {{- tool_call.arguments }}\n {%- else %}\n {{- tool_call.arguments | tojson }}\n {%- endif %}\n {{- '}\\n</tool_call>' }}\n {%- endfor %}\n {%- endif %}\n {{- '<|im_end|>\\n' }}\n {%- elif message.role == \"tool\" %}\n {%- if loop.first or (messages[loop.index0 - 1].role != \"tool\") %}\n {{- '<|im_start|>user' }}\n {%- endif %}\n {{- '\\n<tool_response>\\n' }}\n {{- message.content }}\n {{- '\\n</tool_response>' }}\n {%- if loop.last or (messages[loop.index0 + 1].role != \"tool\") %}\n {{- '<|im_end|>\\n' }}\n {%- endif %}\n {%- endif %}\n{%- endfor %}\n{%- if add_generation_prompt %}\n {{- '<|im_start|>assistant\\n' }}\n {%- if enable_thinking is defined and enable_thinking is false %}\n {{- '<think>\\n\\n</think>\\n\\n' }}\n {%- endif %}\n{%- endif %}"
|
||||
}
|
||||
1
vocab.json
Normal file
1
vocab.json
Normal file
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user