With the remarkable performance of large language models (LLMs) in medicine, particularly their ability to support clinical decision-making in medical dialogues, a key limitation remains: the static reasoning patterns derived from human expert experience are often inadequate for the dynamic and diverse nature of real-world multi-turn conversations. While recent large reasoning models (such as R1) enable deeper and more complex thought processes to address such challenges, they also introduce significant redundancy. Meanwhile, recent studies on reusing atomic thoughts demonstrate a practical pathway toward dynamic and precise reasoning in general domains. In this paper, we investigate the role of atomic thought-based experience in medical dialogue tasks. First, we collect human expert clinical experience. Then, we propose a novel distillation framework that extracts atomic thoughts from teacher models and reuses them to guide reasoning and generate responses. Based on this framework, we construct training data from ReMeDi and fine-tune student models, which demonstrate enhanced performance in both static and interactive medical dialogue scenarios. Furthermore, we examine the impact of experience across various models, datasets, and scenarios. Crucially, transferring this experience empowers weaker models to generate high-quality reasoning data, matching the annotation capabilities of stronger LLMs while significantly reducing costs. The code is available in this repository https://github.com/VioletAmethystLunar/Atomic-Thoughts-Medical-Dialogue.

Large language models (LLMs) have been widely adopted in healthcare, yet they still encounter significant challenges in complex clinical decision-making scenarios. Existing benchmarks primarily assess LLM performance in single-course settings and lack systematic evaluation in multi-course scenarios, where a patient’s condition evolves over time. To address this gap, we propose ClinicalMC, a benchmark for multi-course clinical decision-making. It includes 1,275 Chinese and 5,804 English samples across four stages from admission to discharge. These stages cover triage, first-course examination/diagnosis/treatment, subsequent multi-course examination/assessment/treatment, and final diagnosis. In ClinicalMC, patients in the English dataset undergo an average of 5.11 clinical courses, whereas those in the Chinese dataset undergo 3.42. To assess LLM performance, we construct a multi-agent evaluation framework that includes patient, examiner, and doctor agents. Based on the benchmark and framework, we design two experimental settings—a single-turn static setting and a multi-turn dynamic setting—and assess three categories of LLMs: 1) closed-source LLMs like GPT-4o-mini; 2) open-source LLMs like DeepSeek-V3, and 3) medical LLMs like HuatuoGPT-o1. Through extensive evaluation, we aim to better understand LLM performance in the medical domain and support its effective deployment in healthcare.

Large language models (LLMs) offer a new paradigm for molecular property prediction (MPP), yet a semantic gap between natural language and molecular representations limits LLMs’ ability to capture structure–activity relationships (SAR). Recent approaches have explored injecting structure-level information into LLMs, primarily modeling associations based on statistical regularities. However, these methods are prone to misinterpreting coincidental associations as general principles, imposing a bottleneck on predictive performance. To tackle the challenges above, we propose MCLE-Mol, an ML–LLM–Rule collaborative framework for MPP. It bridges the semantic gap by injecting ML-derived substructure attribution values into LLMs, utilizing Context-Calibrated Substructure Attribution Rules (CCSAR) to calibrate these attributions under specific chemical contexts to mitigate such misinterpretation. In addition, MCLE-Mol introduces a low-cost continual evolution strategy that updates CCSAR with frozen model parameters to adapt to dynamic chemical spaces. Experiments on multiple benchmark datasets demonstrate that MCLE-Mol outperforms all baselines, successfully resolving the trade-off between predictive performance and interpretability.

Instruction tuning plays a crucial role in enhancing large language models (LLMs) to better understand complex user instructions. While various data selection and revision methods have been explored to optimize instruction tuning datasets, they face two main challenges: unreasonable pruning of potentially valuable low-quality data and the persistence of noise or semantic drift during revision. To address these issues, we propose a novel automated iterative framework for instruction data optimization. Our framework introduces Instruction Quality Differentiation to identify valuable high-quality and low-quality data across multiple dimensions. For low-quality data, we propose a Feedback-driven Iterative Refinement mechanism with an "evaluate-refine-review" process and design an Output Alignment module to improve data quality. Experiments on seven public benchmark datasets show that our framework outperforms state-of-the-art methods, achieving 2.09% and 2.60% improvements on the Alpaca and Dolly datasets, respectively, with high data efficiency. Our code and data are available at the anonymous link https://github.com/surihuhang/From-Selection-to-Refinement–Iterative-Optimization-for-Instruction-Data.

Many current studies focus on extracting tests or treatments when constructing clinical pathways, often neglecting the patient’s symptoms and diagnosis, leading to incomplete diagnostic and therapeutic logic. Therefore, this paper aims to extract clinical pathways from electronic medical records that encompass complete diagnostic and therapeutic logic, including temporal information, patient symptoms, diagnosis, and tests or treatments. To achieve this objective, we propose a novel clinical pathway representation: the clinical status pathway. We also design a LLM-based pipeline framework for extracting clinical status pathway from electronic medical records, with the core concept being to improve extraction accuracy by modeling the diagnostic and treatment processes. In our experiments, we apply this framework to construct a comprehensive breast cancer-specific clinical status pathway and evaluate its performance on medical question-answering and decision-support tasks, demonstrating significant improvements over traditional clinical pathways. The code is publicly available at https://github.com/finnchen11/EMRs2CSP.

Medical quality control indicators are essential to assess the qualifications of healthcare institutions for medical services. With the impressive performance of large language models (LLMs) like GPT-4 in the medical field, leveraging these technologies for the Medical Quality Control Indicator Calculation (MQCIC) presents a promising approach. In this work, (1) we introduce a real-world task MQCIC and propose an open-source Chinese electronic medical records (EMRs)-based dataset (CMQCIC-Bench) comprising 785 instances and 76 indicators. (2) We propose a semi-automatic method to enhance the rule representation. Then we propose the Clinical Facts-based Inferential Rule (CF-IR) method that disentangles the clinical fact verification and inferential rule reasoning actions. (3) We conduct comprehensive experiments on 20 representative LLMs, covering general and medical models. Our findings reveal that CF-IR outperforms Chain-of-Thought methods in MQCIC tasks. (4) We conduct an error analysis and investigate the capabilities of clinical fact verification and inferential rule reasoning, providing insights to improve performance in the MQCIC further. The dataset and code is available in this repository https://github.com/YuY-2001/C-MQCIC.

Elasticsearch (ES) is a distributed RESTful search engine optimized for large-scale and long-text search scenarios. Recent research on text-to-Query has explored using large language models (LLMs) to convert user query intent to executable code, making it an increasingly popular research topic. To our knowledge, we are the first to introduce the novel semantic parsing task text-to-ES. To bridge the gap between LLM and ES, in detail, we leverage LLMs and employ domain experts to generate ES query bodies, which are Domain-Specific Language (DSL), along with the corresponding post-processing code to support multi-index ES queries. Consequently, we propose the text-to-ES benchmark that consists of two datasets: Large Elasticsearch Dataset (LED), containing 26,207 text-ES pairs derived from a 224.9GB schema-free database, and ElasticSearch (BirdES)with 10,926 pairs sourced from the Bird dataset on a 33.4GB schema-fixed database. Compared with fourteen advanced LLMs and six code-based LLMs, the model we trained outperformed DeepSeek-R1 by 15.64% on the LED dataset, setting a new state-of-the-art, and achieved 78% of DeepSeek-R1’s performance on the BirdES dataset. Additionally, we provide in-depth experimental analyses and suggest future research directions for this task. Our datasets are available at https://huggingface.co/datasets/Barry1915/Text-to-ES.