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Model: mims-harvard/ATHENA-R1-Qwen3-8B Source: Original Platform
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README.md
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README.md
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---
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license: mit
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language:
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- en
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base_model: Qwen/Qwen3-8B
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library_name: transformers
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pipeline_tag: text-generation
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tags:
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- agent
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- biomedical
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- treatment-reasoning
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- tool-use
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- reinforcement-learning
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- qwen3
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---
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# ATHENA-R1-Qwen3-8B
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**Project page:** [athena.openscientist.ai](https://athena.openscientist.ai/) · **Code:** [mims-harvard/ATHENA](https://github.com/mims-harvard/ATHENA)
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**ATHENA-R1** is an AI agent for treatment reasoning, trained through
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reinforcement learning over a universe of 212 biomedical tools. It performs
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*multi-step* reasoning — identifying what evidence is needed, selecting tools,
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and incorporating retrieved evidence into subsequent steps — with tool calls
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served through the
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[ToolUniverse](https://github.com/mims-harvard/ToolUniverse) (FDA labeling,
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Open Targets, ChEMBL, EuropePMC, etc.).
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Given a clinical question, the model performs *multi-step* tool calls,
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synthesises the evidence, and returns a free-form answer grounded in
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authoritative biomedical sources.
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## Quick start
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The model is exposed through the
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[`athena-r1`](https://github.com/mims-harvard/ATHENA) Python package,
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which handles the tool-call protocol and conversation management. Two
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services back the agent: vLLM (model server) and ToolUniverse (tool server).
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```bash
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# 1. Install
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pip install "athena-r1[vllm,web] @ git+https://github.com/mims-harvard/ATHENA.git"
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# 2. Start backing services
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bash scripts/launch_tooluniverse.sh # → :8080
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bash scripts/launch_vllm.sh 8000 mims-harvard/ATHENA-R1-Qwen3-8B
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# 3. Run the agent (Python)
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python -c "
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from athena_r1 import AthenaR1
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agent = AthenaR1(
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model='mims-harvard/ATHENA-R1-Qwen3-8B',
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vllm_url='http://0.0.0.0:8000/v1',
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tool_server='http://0.0.0.0:8080',
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)
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print(agent.answer('Dose adjustment for metformin in CKD eGFR 35?').answer)
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"
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```
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For a chat UI (bundled browser demo with live-streamed reasoning):
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```bash
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python web/agui_server.py # → http://localhost:8090/ (AG-UI server + demo)
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```
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For an OpenAI-compatible API endpoint:
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```bash
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python web/openai_server.py # → http://localhost:9000/v1/chat/completions
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```
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## Inference settings (paper-canonical)
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| Parameter | Value |
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|---|---|
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| temperature | 0.7 |
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| top_p | 0.95 |
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| top_k | 20 |
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| min_p | 0.0 |
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| presence_penalty | 0 |
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| max_round | 40 |
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| concurrent Qs | 4 |
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## Evaluation
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Open-ended setting: each question is answered free-form, then mapped to one of
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the original answer choices.
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| Benchmark | n | ATHENA-R1 | GPT-5 |
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|---|---|---|---|
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| DrugPC (open-ended drug reasoning) | 3,168 | **94.7%** | 76.9% |
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| TreatmentPC (patient-specific treatment) | 456 | **82.9%** | 72.2% |
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ATHENA-R1 exceeds GPT-5 by 17.8 points on DrugPC and 10.7 on TreatmentPC.
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See the
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[`docs/eval_results.md`](https://github.com/mims-harvard/ATHENA/blob/main/docs/eval_results.md)
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file in the code repo for the full benchmark tables and the two-level
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self-learning ablation.
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## How it works
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1. **Stage 1 — multi-step tool reasoning**: the model emits
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`<tool_call>...</tool_call>` blocks; the runtime dispatches them through
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ToolUniverse, appends results to the conversation, and re-prompts. Loop
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continues until `[FinalAnswer]` or `max_round` is hit.
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2. **Stage 2 (eval only) — option mapping**: a *separate* function call
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maps the free-form answer to an MCQ letter. Two backends supported:
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the local ATHENA-R1 model (self-extraction) or Azure GPT-5
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(external reader).
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## Intended use
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ATHENA-R1 is a research artifact for treatment-reasoning research and
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decision support. It is not a medical device and must not be used for direct
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patient care.
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## Citation
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```bibtex
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@article{gao2026athena,
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title = {An AI agent for treatment reasoning over a biomedical tool universe},
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author = {Gao, Shanghua and ... and Zitnik, Marinka},
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journal = {arXiv preprint},
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year = {2026}
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}
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```
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## License
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MIT.
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## Acknowledgements
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Evidence retrieval is powered by
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[ToolUniverse](https://github.com/mims-harvard/ToolUniverse), a library of
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curated biomedical tools.
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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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"<|quad_start|>": 151650,
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"<|repo_name|>": 151663,
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"<|video_pad|>": 151656,
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"<|vision_end|>": 151653,
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"<|vision_pad|>": 151654,
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"<|vision_start|>": 151652
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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
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' }}
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{%- if messages[0].role == 'system' %}
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{{- messages[0].content + '
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' }}
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{%- endif %}
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{{- "# Tools
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You may call one or more functions to assist with the user query.
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You are provided with function signatures within <tools></tools> XML tags:
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<tools>" }}
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{%- for tool in tools %}
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{{- "
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" }}
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{{- tool }}
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{%- endfor %}
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{{- "
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</tools>
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For each function call, return a json object with function name and arguments within <tool_call></tool_call> XML tags:
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<tool_call>
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" }}
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{{- '{"name": <function-name>, "arguments": <args-json-object>}
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</tool_call><|im_end|>
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' }}
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{%- else %}
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{%- if messages[0].role == 'system' %}
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{{- '<|im_start|>system
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' + messages[0].content + '<|im_end|>
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' }}
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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 message in messages[::-1] %}
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{%- set index = (messages|length - 1) - loop.index0 %}
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{%- 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>')) %}
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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.content is string %}
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{%- set content = message.content %}
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{%- else %}
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{%- set content = '' %}
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{%- endif %}
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{%- if (message.role == "user") or (message.role == "system" and not loop.first) %}
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{{- '<|im_start|>' + message.role + '
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' + content + '<|im_end|>' + '
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' }}
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{%- elif message.role == "assistant" %}
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{%- set reasoning_content = '' %}
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{%- if message.reasoning_content is string %}
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{%- set reasoning_content = message.reasoning_content %}
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{%- else %}
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{%- if '</think>' in content %}
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{%- set reasoning_content = content.split('</think>')[0].rstrip('
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').split('<think>')[-1].lstrip('
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') %}
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{%- set content = content.split('</think>')[-1].lstrip('
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') %}
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{%- endif %}
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{%- endif %}
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{%- if loop.last or (not loop.last and reasoning_content) %}
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{{- '<|im_start|>' + message.role + '
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<think>
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' + reasoning_content.strip('
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') + '
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</think>
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' + content.lstrip('
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') }}
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{%- else %}
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{{- '<|im_start|>' + message.role + '
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' + 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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{{- '
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' }}
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{%- endif %}
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{%- set raw_tool_call = tool_call %}
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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>
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' }}
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{# --- 解析成功：按原有 JSON 格式输出 --- #}
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{%- if (tool_call is mapping) and ('name' in tool_call) and ('arguments' in tool_call) %}
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{"name": "{{ tool_call.name }}", "arguments": {%- if tool_call.arguments is string -%}{{ tool_call.arguments }}{%- else -%}{{ tool_call.arguments | tojson }}{%- endif -%}}
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{# --- 解析失败：把原始输入原样塞进 <tool_call> --- #}
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{%- else %}
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{%- if raw_tool_call is string -%}{{ raw_tool_call }}{%- else -%}{{ raw_tool_call | tojson }}{%- endif -%}
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{%- endif %}
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{{- '
|
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</tool_call>' }}
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{%- endfor %}
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{%- endif %}
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{{- '<|im_end|>
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' }}
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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' }}
|
||||
{%- endif %}
|
||||
{{- '
|
||||
<tool_response>
|
||||
' }}
|
||||
{{- content }}
|
||||
{{- '
|
||||
</tool_response>' }}
|
||||
{%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
|
||||
{{- '<|im_end|>
|
||||
' }}
|
||||
{%- endif %}
|
||||
{%- endif %}
|
||||
{%- endfor %}
|
||||
{%- if add_generation_prompt %}
|
||||
{{- '<|im_start|>assistant
|
||||
' }}
|
||||
{%- if enable_thinking is defined and enable_thinking is false %}
|
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{{- '<think>
|
||||
|
||||
</think>
|
||||
|
||||
' }}
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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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{
|
||||
"architectures": [
|
||||
"Qwen3ForCausalLM"
|
||||
],
|
||||
"attention_bias": false,
|
||||
"attention_dropout": 0.0,
|
||||
"dtype": "bfloat16",
|
||||
"eos_token_id": 151645,
|
||||
"head_dim": 128,
|
||||
"hidden_act": "silu",
|
||||
"hidden_size": 4096,
|
||||
"initializer_range": 0.02,
|
||||
"intermediate_size": 12288,
|
||||
"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",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention"
|
||||
],
|
||||
"max_position_embeddings": 40960,
|
||||
"max_window_layers": 36,
|
||||
"model_type": "qwen3",
|
||||
"num_attention_heads": 32,
|
||||
"num_hidden_layers": 36,
|
||||
"num_key_value_heads": 8,
|
||||
"pad_token_id": 151643,
|
||||
"rms_norm_eps": 1e-06,
|
||||
"rope_scaling": null,
|
||||
"rope_theta": 1000000,
|
||||
"sliding_window": null,
|
||||
"tie_word_embeddings": false,
|
||||
"torch_dtype": "bfloat16",
|
||||
"transformers_version": "4.52.0",
|
||||
"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,
|
||||
"do_sample": true,
|
||||
"eos_token_id": [
|
||||
151645,
|
||||
151643
|
||||
],
|
||||
"pad_token_id": 151643,
|
||||
"temperature": 0.7,
|
||||
"top_k": 20,
|
||||
"top_p": 0.95,
|
||||
"transformers_version": "4.52.0"
|
||||
}
|
||||
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merges.txt
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151388
merges.txt
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model-00001-of-00004.safetensors
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model-00001-of-00004.safetensors
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version https://git-lfs.github.com/spec/v1
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size 4944232808
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version https://git-lfs.github.com/spec/v1
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oid sha256:781ac00356ab57fc2b03bc2249ae1a8af5d306d211177901d86879c6f879374e
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size 4957903872
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"model.layers.8.self_attn.k_norm.weight": "model-00003-of-00004.safetensors",
|
||||
"model.layers.8.self_attn.k_proj.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.8.self_attn.o_proj.weight": "model-00004-of-00004.safetensors",
|
||||
"model.layers.8.self_attn.q_norm.weight": "model-00004-of-00004.safetensors",
|
||||
"model.layers.8.self_attn.q_proj.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.8.self_attn.v_proj.weight": "model-00001-of-00004.safetensors",
|
||||
"model.layers.9.input_layernorm.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.9.mlp.down_proj.weight": "model-00001-of-00004.safetensors",
|
||||
"model.layers.9.mlp.gate_proj.weight": "model-00003-of-00004.safetensors",
|
||||
"model.layers.9.mlp.up_proj.weight": "model-00003-of-00004.safetensors",
|
||||
"model.layers.9.post_attention_layernorm.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.k_norm.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.k_proj.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.o_proj.weight": "model-00001-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.q_norm.weight": "model-00002-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.q_proj.weight": "model-00001-of-00004.safetensors",
|
||||
"model.layers.9.self_attn.v_proj.weight": "model-00001-of-00004.safetensors",
|
||||
"model.norm.weight": "model-00001-of-00004.safetensors"
|
||||
}
|
||||
}
|
||||
31
special_tokens_map.json
Normal file
31
special_tokens_map.json
Normal file
@@ -0,0 +1,31 @@
|
||||
{
|
||||
"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": "<|endoftext|>",
|
||||
"lstrip": false,
|
||||
"normalized": false,
|
||||
"rstrip": false,
|
||||
"single_word": false
|
||||
}
|
||||
}
|
||||
BIN
tokenizer.json
(Stored with Git LFS)
Normal file
BIN
tokenizer.json
(Stored with Git LFS)
Normal file
Binary file not shown.
239
tokenizer_config.json
Normal file
239
tokenizer_config.json
Normal file
@@ -0,0 +1,239 @@
|
||||
{
|
||||
"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": 131072,
|
||||
"pad_token": "<|endoftext|>",
|
||||
"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