# Improving Medical Calculation of LLMs with Embedded Coding

arXiv: https://arxiv.org/abs/2609.31908 · HTML: https://mlsanity.com/paper/2609.31908/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 26 references that are in the map.
- First posted on arXiv 25 Sep 2026.

## Builds on (most cited first, 18 of 18)

- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Program of Thoughts Prompting: Disentangling Computation from Reasoning for Numerical Reasoning Tasks](https://mlsanity.com/paper/2211.12588/) (2022)
- [Solving Challenging Math Word Problems Using GPT-4 Code Interpreter with Code-based Self-Verification](https://mlsanity.com/paper/2308.07921/) (2023)
- [Provably Robust DPO: Aligning Language Models with Noisy Feedback](https://mlsanity.com/paper/2403.00409/) (2024)
- [Chain of Code: Reasoning with a Language Model-Augmented Code Emulator](https://mlsanity.com/paper/2312.04474/) (2023)
- [LLM Hallucinations in Practical Code Generation: Phenomena, Mechanism, and Mitigation](https://mlsanity.com/paper/2409.20550/) (2024)
- [HuatuoGPT-II, One-stage Training for Medical Adaption of LLMs](https://mlsanity.com/paper/2311.09774/) (2023)
- [MedCalc-Bench: Evaluating Large Language Models for Medical Calculations](https://mlsanity.com/paper/2406.12036/) (2024)
- [LLM Agents Making Agent Tools](https://mlsanity.com/paper/2502.11705/) (2025)
- [Taiyi: A Bilingual Fine-Tuned Large Language Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2311.11608/) (2023)
- [OphGLM: Training an Ophthalmology Large Language-and-Vision Assistant based on Instructions and Dialogue](https://mlsanity.com/paper/2306.12174/) (2023)
- [AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning](https://mlsanity.com/paper/2402.13225/) (2024)
- [Leveraging Medical Knowledge Graphs Into Large Language Models for Diagnosis Prediction: Design and Application Study](https://mlsanity.com/paper/2308.14321/) (2023)
- [ReflecTool: Towards Reflection-Aware Tool-Augmented Clinical Agents](https://mlsanity.com/paper/2410.17657/) (2024)

## Abstract (arXiv)

Large Language Models (LLMs) perform well on medical examinations and question-answering benchmarks, but remain unreliable on medical calculation tasks that require exact numerical outputs. These calculations support high-stakes decisions such as medication dosing, organ-function assessment, and prognostic scoring, for which even small errors can have serious clinical consequences. We introduce MedCode, a framework that improves medical calculation by training LLMs to generate embedded executable code. Given a clinical context, the model identifies the relevant calculator, extracts its input variables, and produces a script that delegates arithmetic operations to a deterministic interpreter. Executing the script returns the calculated value together with an explanation and the appropriate unit. We construct supervised fine-tuning (SFT) and preference datasets from the MedCalc benchmark and additionally curate a dataset for calculation tasks in Intensive Care Unit (ICU) scenarios. We further propose weighted Direct Preference Optimization (wDPO), which adaptively emphasizes preference pairs that are difficult for the model to distinguish. Experiments with LLaMA3-8B, Qwen2.5-7B, and Mistral-7B show absolute accuracy gains of 20--30 percentage points, demonstrating the effectiveness of embedded code generation for medical calculation.