CodeClinic: Evaluating Automation of Coding Skills for Clinical Reasoning Agents

Clinical reasoning agents based on large language models (LLMs) aim to automate tasks such as intensive care unit (ICU) monitoring and patient state tracking from electronic health records (EHRs). Existing systems typically rely on manually curated clinical tools or skills for concepts such as sepsis detection and organ failure assessment. However, maintaining these tool libraries requires substantial expert effort, while zero-shot querying or code generation often produces inefficient and unreliable reasoning chains, especially under institution-specific clinical policies. We introduce CodeClinic, a benchmark built on MIMIC-IV for evaluating whether LLM agents can synthesize and compose reusable clinical skills instead of relying on fixed toolboxes. The benchmark contains two complementary tasks: longitudinal ICU surveillance and compositional information seeking. The longitudinal setting simulates monitoring patient trajectories with structured decisions every four hours across 25 findings and eight clinical families, while the compositional setting spans 63k instances across 259 tasks in nine domains and is stratified by compositional dependency depth to evaluate increasingly complex multi-step reasoning. We further propose an offline autoformalization pipeline that converts natural-language clinical guidelines into reusable and verified Python skill libraries through iterative LLM refinement. Compared with zero-shot code generation, the resulting libraries improve consistency while reducing per-query token usage by up to 40%.

LogosKG: Hardware-Optimized Scalable and Interpretable Knowledge Graph Retrieval

Knowledge graphs (KGs) are increasingly integrated with large language models (LLMs) to provide structured, verifiable reasoning. A core operation in this integration is multi-hop retrieval, yet existing systems struggle to balance efficiency, scalability, and interpretability. We introduce LogosKG, a novel, hardware-aligned framework that enables scalable and interpretable k-hop retrieval on large KGs by building on symbolic KG formulations and executing traversal as hardware-efficient operations over decomposed subject, object, and relation representations. To scale to billion-edge graphs, LogosKG integrates degree-aware partitioning, cross-graph routing, and on-demand caching. Experiments show substantial efficiency gains over CPU and GPU baselines without loss of retrieval fidelity. With proven performance in KG retrieval, a downstream two-round KG-LLM interaction demonstrates how LogosKG enables large-scale, evidence-grounded analysis of how KG topology, such as hop distribution and connectivity, shapes the alignment between structured biomedical knowledge and LLM diagnostic reasoning, thereby opening the door for next-generation KG-LLM integration. The source code is publicly available at https://github.com/LARK-NLP-Lab/LogosKG, and an online demo is available at https://lark-nlp-lab-logoskg.hf.space/.

CLSGen: A Dual-Head Fine-Tuning Framework for Joint Probabilistic Classification and Verbalized Explanation

With the recent progress of Large Language Models (LLMs), there is a growing interest in applying these models to solve complex and challenging problems. Modern LLMs, capable of processing long contexts and generating verbalized explanations, offer significant potential in addressing real-world applications. However, a critical hurdle in deploying LLMs for practical decision-making is their inability to provide reliable, quantitative probabilities. While task-specific fine-tuning of LLMs using traditional discriminative objectives (similar to encoder-only models) can yield probability estimates, this often leads to catastrophic forgetting and linguistic collapse. Consequently, the model loses its ability to generate explanations, severely undermining its interpretability and usability. To address this challenge, we propose CLSGen, a novel LLM fine-tuning framework designed for binary classification tasks. The CLSGen framework encompasses a new model architecture, training methodology, and data construction strategy to enable robust probability estimation without sacrificing the model's inherent explanation-generation capabilities. Experimental results across multiple benchmark datasets demonstrate that models fine-tuned with CLSGen outperform existing baselines in classification metrics (AUROC and F1-score). Regarding explanation, the results showed strong alignment between predicted labels and generated justifications, as well as high readability.

Evaluating Retrieval-Augmented Generation vs. Long-Context Input for Clinical Reasoning over EHRs

Electronic health records (EHRs) are long, noisy, and often redundant, posing a major challenge for the clinicians who must navigate them. Large language models (LLMs) offer a promising solution for extracting and reasoning over this unstructured text, but the length of clinical notes often exceeds even state-of-the-art models' extended context windows. Retrieval-augmented generation (RAG) offers an alternative by retrieving task-relevant passages from across the entire EHR, potentially reducing the amount of required input tokens. In this work, we propose three clinical tasks designed to be replicable across health systems with minimal effort: 1) extracting imaging procedures, 2) generating timelines of antibiotic use, and 3) identifying key diagnoses. Using EHRs from actual hospitalized patients, we test three state-of-the-art LLMs with varying amounts of provided context, using either targeted text retrieval or the most recent clinical notes. We find that RAG closely matches or exceeds the performance of using recent notes, and approaches the performance of using the models' full context while requiring drastically fewer input tokens. Our results suggest that RAG remains a competitive and efficient approach even as newer models become capable of handling increasingly longer amounts of text.

MoMA: A Mixture-of-Multimodal-Agents Architecture for Enhancing Clinical Prediction Modelling

Multimodal electronic health record (EHR) data provide richer, complementary insights into patient health compared to single-modality data. However, effectively integrating diverse data modalities for clinical prediction modeling remains challenging due to the substantial data requirements. We introduce a novel architecture, Mixture-of-Multimodal-Agents (MoMA), designed to leverage multiple large language model (LLM) agents for clinical prediction tasks using multimodal EHR data. MoMA employs specialized LLM agents ("specialist agents") to convert non-textual modalities, such as medical images and laboratory results, into structured textual summaries. These summaries, together with clinical notes, are combined by another LLM ("aggregator agent") to generate a unified multimodal summary, which is then used by a third LLM ("predictor agent") to produce clinical predictions. Evaluating MoMA on three prediction tasks using real-world datasets with different modality combinations and prediction settings, MoMA outperforms current state-of-the-art methods, highlighting its enhanced accuracy and flexibility across various tasks.

An Information-Theoretic Perspective on Multi-LLM Uncertainty Estimation

Large language models (LLMs) often behave inconsistently across inputs, indicating uncertainty and motivating the need for its quantification in high-stakes settings. Prior work on calibration and uncertainty quantification often focuses on individual models, overlooking the potential of model diversity. We hypothesize that LLMs make complementary predictions due to differences in training and the Zipfian nature of language, and that aggregating their outputs leads to more reliable uncertainty estimates. To leverage this, we propose MUSE (Multi-LLM Uncertainty via Subset Ensembles), a simple information-theoretic method that uses Jensen-Shannon Divergence to identify and aggregate well-calibrated subsets of LLMs. Experiments on binary prediction tasks demonstrate improved calibration and predictive performance compared to single-model and naive ensemble baselines.

Development and Validation of the Provider Documentation Summarization Quality Instrument for Large Language Models

As Large Language Models (LLMs) are integrated into electronic health record (EHR) workflows, validated instruments are essential to evaluate their performance before implementation. Existing instruments for provider documentation quality are often unsuitable for the complexities of LLM-generated text and lack validation on real-world data. The Provider Documentation Summarization Quality Instrument (PDSQI-9) was developed to evaluate LLM-generated clinical summaries. Multi-document summaries were generated from real-world EHR data across multiple specialties using several LLMs (GPT-4o, Mixtral 8x7b, and Llama 3-8b). Validation included Pearson correlation for substantive validity, factor analysis and Cronbach's alpha for structural validity, inter-rater reliability (ICC and Krippendorff's alpha) for generalizability, a semi-Delphi process for content validity, and comparisons of high- versus low-quality summaries for discriminant validity. Seven physician raters evaluated 779 summaries and answered 8,329 questions, achieving over 80% power for inter-rater reliability. The PDSQI-9 demonstrated strong internal consistency (Cronbach's alpha = 0.879; 95% CI: 0.867-0.891) and high inter-rater reliability (ICC = 0.867; 95% CI: 0.867-0.868), supporting structural validity and generalizability. Factor analysis identified a 4-factor model explaining 58% of the variance, representing organization, clarity, accuracy, and utility. Substantive validity was supported by correlations between note length and scores for Succinct (rho = -0.200, p = 0.029) and Organized (rho = -0.190, p = 0.037). Discriminant validity distinguished high- from low-quality summaries (p < 0.001). The PDSQI-9 demonstrates robust construct validity, supporting its use in clinical practice to evaluate LLM-generated summaries and facilitate safer integration of LLMs into healthcare workflows.

Position Paper On Diagnostic Uncertainty Estimation from Large Language Models: Next-Word Probability Is Not Pre-test Probability

Large language models (LLMs) are being explored for diagnostic decision support, yet their ability to estimate pre-test probabilities, vital for clinical decision-making, remains limited. This study evaluates two LLMs, Mistral-7B and Llama3-70B, using structured electronic health record data on three diagnosis tasks. We examined three current methods of extracting LLM probability estimations and revealed their limitations. We aim to highlight the need for improved techniques in LLM confidence estimation.

When Raw Data Prevails: Are Large Language Model Embeddings Effective in Numerical Data Representation for Medical Machine Learning Applications?

The introduction of Large Language Models (LLMs) has advanced data representation and analysis, bringing significant progress in their use for medical questions and answering. Despite these advancements, integrating tabular data, especially numerical data pivotal in clinical contexts, into LLM paradigms has not been thoroughly explored. In this study, we examine the effectiveness of vector representations from last hidden states of LLMs for medical diagnostics and prognostics using electronic health record (EHR) data. We compare the performance of these embeddings with that of raw numerical EHR data when used as feature inputs to traditional machine learning (ML) algorithms that excel at tabular data learning, such as eXtreme Gradient Boosting. We focus on instruction-tuned LLMs in a zero-shot setting to represent abnormal physiological data and evaluating their utilities as feature extractors to enhance ML classifiers for predicting diagnoses, length of stay, and mortality. Furthermore, we examine prompt engineering techniques on zero-shot and few-shot LLM embeddings to measure their impact comprehensively. Although findings suggest the raw data features still prevails in medical ML tasks, zero-shot LLM embeddings demonstrate competitive results, suggesting a promising avenue for future research in medical applications.

Improving Clinical NLP Performance through Language Model-Generated Synthetic Clinical Data

Generative models have been showing potential for producing data in mass. This study explores the enhancement of clinical natural language processing performance by utilizing synthetic data generated from advanced language models. Promising results show feasible applications in such a high-stakes domain.