Accurate prediction of clinical outcomes using Electronic Health Records (EHRs) is critical for early intervention, efficient resource allocation, and improved patient care. EHRs contain multimodal data, including both structured data and unstructured clinical notes that provide rich, context-specific information. In this work, we introduce a unified framework that seamlessly integrates these diverse modalities, leveraging all relevant available information through a two-stage architecture for clinical risk prediction. In the first stage, a fine-tuned Large Language Model (LLM) extracts crucial, task-relevant information from clinical notes, which is enhanced by graph-based retrieval of external domain knowledge from sources such as a medical corpus like PubMed, grounding the LLM's understanding. The second stage combines both unstructured representations and features derived from the structured data to generate the final predictions. This approach supports a wide range of clinical tasks. Here, we demonstrate its effectiveness on 30-day readmission and in-hospital mortality prediction. Experimental results show that our framework achieves strong performance, with AUC scores of $0.84$ and $0.92$, respectively, despite these tasks involving severely imbalanced datasets, with positive rates ranging from approximately $4\%$ to $13\%$. Moreover, it outperforms all existing baselines and clinical practices, including established risk scoring systems. To the best of our knowledge, this is one of the first frameworks for healthcare prediction which enhances the power of an LLM-based graph-guided knowledge retrieval method by combining it with structured data for improved clinical outcome prediction.

We present a comparative analysis of the parseability of structured outputs generated by small language models for open attribute-value extraction from clinical notes. We evaluate three widely used serialization formats: JSON, YAML, and XML, and find that JSON consistently yields the highest parseability. Structural robustness improves with targeted prompting and larger models, but declines for longer documents and certain note types. Our error analysis identifies recurring format-specific failure patterns. These findings offer practical guidance for selecting serialization formats and designing prompts when deploying language models in privacy-sensitive clinical settings.

Clinician notes are a rich source of patient information but often contain inconsistencies due to varied writing styles, colloquialisms, abbreviations, medical jargon, grammatical errors, and non-standard formatting. These inconsistencies hinder the extraction of meaningful data from electronic health records (EHRs), posing challenges for quality improvement, population health, precision medicine, decision support, and research. We present a large language model approach to standardizing a corpus of 1,618 clinical notes. Standardization corrected an average of $4.9 +/- 1.8$ grammatical errors, $3.3 +/- 5.2$ spelling errors, converted $3.1 +/- 3.0$ non-standard terms to standard terminology, and expanded $15.8 +/- 9.1$ abbreviations and acronyms per note. Additionally, notes were re-organized into canonical sections with standardized headings. This process prepared notes for key concept extraction, mapping to medical ontologies, and conversion to interoperable data formats such as FHIR. Expert review of randomly sampled notes found no significant data loss after standardization. This proof-of-concept study demonstrates that standardization of clinical notes can improve their readability, consistency, and usability, while also facilitating their conversion into interoperable data formats.

High-throughput phenotyping, the automated mapping of patient signs and symptoms to standardized ontology concepts, is essential to gaining value from electronic health records (EHR) in the support of precision medicine. Despite technological advances, high-throughput phenotyping remains a challenge. This study compares three computational approaches to high-throughput phenotyping: a Large Language Model (LLM) incorporating generative AI, a Natural Language Processing (NLP) approach utilizing deep learning for span categorization, and a hybrid approach combining word vectors with machine learning. The approach that implemented GPT-4 (a Large Language Model) demonstrated superior performance, suggesting that Large Language Models are poised to be the preferred method for high-throughput phenotyping of physician notes.

Deep phenotyping is the detailed description of patient signs and symptoms using concepts from an ontology. The deep phenotyping of the numerous physician notes in electronic health records requires high throughput methods. Over the past thirty years, progress toward making high throughput phenotyping feasible. In this study, we demonstrate that a large language model and a hybrid NLP model (combining word vectors with a machine learning classifier) can perform high throughput phenotyping on physician notes with high accuracy. Large language models will likely emerge as the preferred method for high throughput deep phenotyping of physician notes.

Anginal symptoms can connote increased cardiac risk and a need for change in cardiovascular management. This study evaluated the potential to extract these symptoms from physician notes using the Bidirectional Encoder from Transformers language model fine-tuned on a domain-specific corpus. The history of present illness section of 459 expert annotated primary care physician notes from consecutive patients referred for cardiac testing without known atherosclerotic cardiovascular disease were included. Notes were annotated for positive and negative mentions of chest pain and shortness of breath characterization. The results demonstrate high sensitivity and specificity for the detection of chest pain or discomfort, substernal chest pain, shortness of breath, and dyspnea on exertion. Small sample size limited extracting factors related to provocation and palliation of chest pain. This study provides a promising starting point for the natural language processing of physician notes to characterize clinically actionable anginal symptoms. Introduction Angina pectoris is a constellation of symptoms that portends inadequate oxygenation of cardiac muscle due to either a decrease in coronary blood supply, an increase in myocardial oxygen demand, or both.