chemAi2025

Qwen3-Max generated image

Meet chemAi2025, a fine tuned chemistry model that was based on the Qwen3-4B-Thinking-2507 model.

It was trained on a custom dataset consisting of scientific chemistry papers from archivex from january to july of 2025. The created dataset was merged and shuffled with camel-ai/chemistry dataset and used for LoRa training.

The aim with this model was to create a chemistry model that was trained on current data from 2025. Of course, it will be a few months out of date since data processing and dataset creation takes significant time as a solo developer.

The following sections are either copied as they were from the onieth/chemAI2025 page or slightly modified. I didn't want to make it seem like I just ripped them off.

Model Overview

chemAi2025 has the same model features as Qwen3-4B-Thinking-2507. Which are:

• Type: Causal Language Models
• Training Stage: Pretraining & Post-training
• Number of Parameters: 4.0B
• Number of Paramaters (Non-Embedding): 3.6B
• Number of Layers: 36
• Number of Attention Heads (GQA): 32 for Q and 8 for KV
• Context Length: 262,144 natively.

NOTE: This model supports only thinking mode. Meanwhile, specifying enable_thinking=True is no longer required.

Additionally, to enforce model thinking, the default chat template automatically includes <think>. Therefore, it is normal for the model's output to contain only </think> without an explicit opening <think> tag.

Quickstart

The code of Qwen3 has been in the latest Hugging Face transformers and we advise you to use the latest version of transformers.

With transformers<4.51.0, you will encounter the following error:

KeyError: 'qwen3'

The following contains a code snippet illustrating how to use the model generate content based on given inputs.

from transformers import AutoModelForCausalLM, AutoTokenizer

model_name = "onieth/chemAI2025"

# load the tokenizer and the model
tokenizer = AutoTokenizer.from_pretrained(model_name)
model = AutoModelForCausalLM.from_pretrained(
    model_name,
    torch_dtype="auto",
    device_map="auto"
)

# prepare the model input
prompt = "Give me a short introduction to large language model."
messages = [
    {"role": "user", "content": prompt}
]
text = tokenizer.apply_chat_template(
    messages,
    tokenize=False,
    add_generation_prompt=True,
)
model_inputs = tokenizer([text], return_tensors="pt").to(model.device)

# conduct text completion
generated_ids = model.generate(
    **model_inputs,
    max_new_tokens=32768
)
output_ids = generated_ids[0][len(model_inputs.input_ids[0]):].tolist() 

# parsing thinking content
try:
    # rindex finding 151668 (</think>)
    index = len(output_ids) - output_ids[::-1].index(151668)
except ValueError:
    index = 0

thinking_content = tokenizer.decode(output_ids[:index], skip_special_tokens=True).strip("\n")
content = tokenizer.decode(output_ids[index:], skip_special_tokens=True).strip("\n")

print("thinking content:", thinking_content) # no opening <think> tag
print("content:", content)

For deployment, you can use sglang>=0.4.6.post1 or vllm>=0.8.5 or to create an OpenAI-compatible API endpoint:

• SGLang:

  python -m sglang.launch_server --model-path onieth/chemAI2025 --context-length 262144  --reasoning-parser deepseek-r1
  

• vLLM:

  vllm serve onieth/chemAI2025 --max-model-len 262144 --enable-reasoning --reasoning-parser deepseek_r1
  

Note: If you encounter out-of-memory (OOM) issues, you may consider reducing the context length to a smaller value. However, since the model may require longer token sequences for reasoning, we strongly recommend using a context length greater than 131,072 when possible.

For local use, applications such as Ollama, LMStudio, MLX-LM, llama.cpp, and KTransformers have also supported Qwen3.

Agentic Use

Qwen3 excels in tool calling capabilities. We recommend using Qwen-Agent to make the best use of agentic ability of Qwen3. Qwen-Agent encapsulates tool-calling templates and tool-calling parsers internally, greatly reducing coding complexity.

To define the available tools, you can use the MCP configuration file, use the integrated tool of Qwen-Agent, or integrate other tools by yourself.

from qwen_agent.agents import Assistant

# Define LLM
# Using OpenAI-compatible API endpoint. It is recommended to disable the reasoning and the tool call parsing
# functionality of the deployment frameworks and let Qwen-Agent automate the related operations. For example, 
# `VLLM_USE_MODELSCOPE=true vllm serve onieth/chemAI2025 --served-model-name onieth/chemAI2025 --max-model-len 262144`.
llm_cfg = {
    'model': 'onieth/chemAI2025',

    # Use a custom endpoint compatible with OpenAI API:
    'model_server': 'http://localhost:8000/v1',  # api_base without reasoning and tool call parsing
    'api_key': 'EMPTY',
    'generate_cfg': {
        'thought_in_content': True,
    },
}

# Define Tools
tools = [
    {'mcpServers': {  # You can specify the MCP configuration file
            'time': {
                'command': 'uvx',
                'args': ['mcp-server-time', '--local-timezone=Asia/Shanghai']
            },
            "fetch": {
                "command": "uvx",
                "args": ["mcp-server-fetch"]
            }
        }
    },
  'code_interpreter',  # Built-in tools
]

# Define Agent
bot = Assistant(llm=llm_cfg, function_list=tools)

# Streaming generation
messages = [{'role': 'user', 'content': 'https://qwenlm.github.io/blog/ Introduce the latest developments of Qwen'}]
for responses in bot.run(messages=messages):
    pass
print(responses)

Best Practices

To achieve optimal performance, we recommend the following settings:

1. Sampling Parameters:

   • We suggest using Temperature=0.6, TopP=0.95, TopK=20, and MinP=0.
   • For supported frameworks, you can adjust the presence_penalty parameter between 0 and 2 to reduce endless repetitions. However, using a higher value may occasionally result in language mixing and a slight decrease in model performance.

2. Adequate Output Length: We recommend using an output length of 32,768 tokens for most queries. For benchmarking on highly complex problems, such as those found in math and programming competitions, we suggest setting the max output length to 81,920 tokens. This provides the model with sufficient space to generate detailed and comprehensive responses, thereby enhancing its overall performance.

3. Standardize Output Format: We recommend using prompts to standardize model outputs when benchmarking.

   • Math Problems: Include "Please reason step by step, and put your final answer within \boxed{}." in the prompt.
   • Multiple-Choice Questions: Add the following JSON structure to the prompt to standardize responses: "Please show your choice in the answer field with only the choice letter, e.g., "answer": "C"."

4. No Thinking Content in History: In multi-turn conversations, the historical model output should only include the final output part and does not need to include the thinking content. It is implemented in the provided chat template in Jinja2. However, for frameworks that do not directly use the Jinja2 chat template, it is up to the developers to ensure that the best practice is followed.

Citation

If you use this model or find it helpful, please cite the original Qwen3 work:

@misc{qwen3technicalreport,
      title={Qwen3 Technical Report}, 
      author={Qwen Team},
      year={2025},
      eprint={2505.09388},
      archivePrefix={arXiv},
      primaryClass={cs.CL},
      url={https://arxiv.org/abs/2505.09388}, 
}