Jifan Gao

Jifan Gao, Michael Rosenthal, Brian Wolpin et al.

Structured electronic health records (EHR) are essential for clinical prediction. While count-based learners continue to perform strongly on such data, no benchmarking has directly compared them against more recent mixture-of-agents LLM pipelines, which have been reported to outperform single LLMs in various NLP tasks. In this study, we evaluated three categories of methodologies for EHR prediction using the EHRSHOT dataset: count-based models built from ontology roll-ups with two time bins, based on LightGBM and the tabular foundation model TabPFN; a pretrained sequential transformer (CLMBR); and a mixture-of-agents pipeline that converts tabular histories to natural-language summaries followed by a text classifier. We assessed eight outcomes using the EHRSHOT dataset. Across the eight evaluation tasks, head-to-head wins were largely split between the count-based and the mixture-of-agents methods. Given their simplicity and interpretability, count-based models remain a strong candidate for structured EHR benchmarking. The source code is available at: https://github.com/cristea-lab/Structured_EHR_Benchmark.

Jifan Gao, Mahmudur Rahman, John Caskey et al.

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.

Jifan Gao, Guanhua Chen

Causal concept effect estimation is gaining increasing interest in the field of interpretable machine learning. This general approach explains the behaviors of machine learning models by estimating the causal effect of human-understandable concepts, which represent high-level knowledge more comprehensibly than raw inputs like tokens. However, existing causal concept effect explanation methods assume complete observation of all concepts involved within the dataset, which can fail in practice due to incomplete annotations or missing concept data. We theoretically demonstrate that unobserved concepts can bias the estimation of the causal effects of observed concepts. To address this limitation, we introduce the Missingness-aware Causal Concept Explainer (MCCE), a novel framework specifically designed to estimate causal concept effects when not all concepts are observable. Our framework learns to account for residual bias resulting from missing concepts and utilizes a linear predictor to model the relationships between these concepts and the outputs of black-box machine learning models. It can offer explanations on both local and global levels. We conduct validations using a real-world dataset, demonstrating that MCCE achieves promising performance compared to state-of-the-art explanation methods in causal concept effect estimation.