初始化项目，由ModelHub XC社区提供模型
Model: khazarai/BioGenesis-ToT Source: Original Platform
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README.md
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README.md
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---
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library_name: transformers
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tags:
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- sft
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- reasoning
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- unsloth
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license: apache-2.0
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language:
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- en
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metrics:
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- accuracy
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base_model:
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- unsloth/Qwen3-1.7B
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pipeline_tag: text-generation
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---
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# Model Card for BioGenesis-ToT
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- **Overall Success Rate**:
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- khazarai/BioGenesis-ToT: **51.45**
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- Qwen/Qwen3-1.7B: **46.82**
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- **Benchmark**: [emre/TARA_Turkish_LLM_Benchmark](https://huggingface.co/datasets/emre/TARA_Turkish_LLM_Benchmark)
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BioGenesis-ToT is a fine-tuned version of Qwen3-1.7B, optimized for mechanistic reasoning and explanatory understanding in biology.
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This model has been trained on the [moremilk/ToT-Biology](https://huggingface.co/datasets/moremilk/ToT-Biology) dataset — a reasoning-rich collection of biology questions emphasizing why and how processes occur, rather than simply what happens.
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The model demonstrates strong capabilities in:
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- Structured biological explanation generation
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- Logical and causal reasoning
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- Chain-of-thought (ToT) reasoning in scientific contexts
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- Interdisciplinary biological analysis (e.g., bioengineering, medicine, ecology)
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## Uses
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### 🚀 Intended Use
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- Educational and scientific explanation generation
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- Biological reasoning and tutoring applications
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- Model interpretability research
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- Training datasets for reasoning-focused LLMs
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### ⚠️ Limitations
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- Not a replacement for expert biological judgment
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- May occasionally over-generalize or simplify complex phenomena
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- Limited to reasoning quality within biological contexts (not trained for creative writing or coding)
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## How to Get Started with the Model
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Use the code below 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/BioGenesis-ToT")
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model = AutoModelForCausalLM.from_pretrained(
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"khazarai/BioGenesis-ToT",
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device_map={"": 0}
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)
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question = """
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Describe the composition of the plasma membrane and explain how its structure relates to its function of selective permeability.
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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 = True,
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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 = 2200,
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temperature = 0.6,
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top_p = 0.95,
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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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## 🧪 Dataset: moremilk/ToT-Biology
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The ToT-Biology dataset emphasizes mechanistic understanding and explanatory reasoning within biology.
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It’s designed to help AI models develop interpretable, step-by-step reasoning abilities for complex biological systems.
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It spans a wide range of biological subdomains:
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- Foundational biology: Cell biology, genetics, evolution, and ecology
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- Advanced topics: Systems biology, synthetic biology, computational biophysics
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- Applied domains: Medicine, agriculture, bioengineering, and environmental science
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Dataset features include:
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- 🧩 Logical reasoning styles — deductive, inductive, abductive, causal, and analogical
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- 🧠 Problem-solving techniques — decomposition, elimination, systems thinking, trade-off analysis
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- 🔬 Real-world problem contexts — experiment design, pathway mapping, and data interpretation
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- 🌍 Practical relevance — bridging theoretical reasoning and applied biological insight
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- 🎓 Educational focus — for both AI training and human learning in scientific reasoning
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## 🧭 Objective
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This fine-tuning project aims to build an interpretable reasoning model capable of:
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- Explaining biological mechanisms clearly and coherently
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- Demonstrating transparent, step-by-step thought processes
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- Applying logical reasoning techniques to biological and interdisciplinary problems
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- Supporting educational and research use cases where reasoning transparency matters
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## Citation
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**BibTeX:**
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```bibtex
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@model{khazarai/BioGenesis-ToT,
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title = {BioGenesis-ToT: A Fine-Tuned Model for Explanatory Biological Reasoning},
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author = {Rustam Shiriyev},
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year = {2025},
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publisher = {Hugging Face},
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base_model = {Qwen3-1.7B},
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dataset = {moremilk/ToT-Biology},
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license = {MIT}
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}
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```
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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_call>": 151658,
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"</tool_response>": 151666,
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"<think>": 151667,
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"<tool_call>": 151657,
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"<tool_response>": 151665,
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"<|box_end|>": 151649,
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"<|endoftext|>": 151643,
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"<|file_sep|>": 151664,
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"<|fim_middle|>": 151660,
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"<|fim_pad|>": 151662,
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"<|fim_prefix|>": 151659,
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"<|vision_pad|>": 151654,
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"<|vision_start|>": 151652
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}
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BIN
benchmark/BioGenesis-ToT.png
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benchmark/BioGenesis-ToT.png
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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 }}
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{{- '", "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' }}
|
||||
{%- 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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64
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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],
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"attention_bias": false,
|
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"attention_dropout": 0.0,
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"bos_token_id": null,
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"dtype": "bfloat16",
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"eos_token_id": 151645,
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"head_dim": 128,
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"hidden_act": "silu",
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"hidden_size": 2048,
|
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"initializer_range": 0.02,
|
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"intermediate_size": 6144,
|
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"layer_types": [
|
||||
"full_attention",
|
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"full_attention",
|
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"full_attention",
|
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"full_attention",
|
||||
"full_attention",
|
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"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
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"full_attention",
|
||||
"full_attention",
|
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"full_attention",
|
||||
"full_attention",
|
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"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": 151654,
|
||||
"rms_norm_eps": 1e-06,
|
||||
"rope_parameters": {
|
||||
"rope_theta": 1000000,
|
||||
"rope_type": "default"
|
||||
},
|
||||
"sliding_window": null,
|
||||
"tie_word_embeddings": true,
|
||||
"transformers_version": "5.0.0",
|
||||
"unsloth_fixed": true,
|
||||
"use_cache": true,
|
||||
"use_sliding_window": false,
|
||||
"vocab_size": 151936
|
||||
}
|
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generation_config.json
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generation_config.json
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{
|
||||
"bos_token_id": 151643,
|
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"do_sample": true,
|
||||
"eos_token_id": [
|
||||
151645,
|
||||
151643
|
||||
],
|
||||
"max_length": 40960,
|
||||
"pad_token_id": 151654,
|
||||
"temperature": 0.6,
|
||||
"top_k": 20,
|
||||
"top_p": 0.95,
|
||||
"transformers_version": "5.0.0"
|
||||
}
|
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151388
merges.txt
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merges.txt
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3
model.safetensors
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model.safetensors
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version https://git-lfs.github.com/spec/v1
|
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oid sha256:0e981de07cdfee9642f1a6edbbb03f8509848954668611041b4a98c92c56a417
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size 3441185608
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special_tokens_map.json
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special_tokens_map.json
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|
||||
{
|
||||
"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|>"
|
||||
],
|
||||
"eos_token": {
|
||||
"content": "<|im_end|>",
|
||||
"lstrip": false,
|
||||
"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:be75606093db2094d7cd20f3c2f385c212750648bd6ea4fb2bf507a6a4c55506
|
||||
size 11422650
|
||||
240
tokenizer_config.json
Normal file
240
tokenizer_config.json
Normal file
@@ -0,0 +1,240 @@
|
||||
{
|
||||
"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": "left",
|
||||
"split_special_tokens": false,
|
||||
"tokenizer_class": "Qwen2Tokenizer",
|
||||
"unk_token": null
|
||||
}
|
||||
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