Progress notes are among the most clinically meaningful artifacts in an Electronic Health Record (EHR), offering temporally grounded insights into a patient's evolving condition, treatments, and care decisions. Despite their importance, they are severely underrepresented in large-scale EHR datasets. For instance, in the widely used Medical Information Mart for Intensive Care III (MIMIC-III) dataset, only about $8.56\%$ of hospital visits include progress notes, leaving gaps in longitudinal patient narratives. In contrast, the dataset contains a diverse array of other note types, each capturing different aspects of care. We present DENSE (Documenting Evolving Progress Notes from Scattered Evidence), a system designed to align with clinical documentation workflows by simulating how physicians reference past encounters while drafting progress notes. The system introduces a fine-grained note categorization and a temporal alignment mechanism that organizes heterogeneous notes across visits into structured, chronological inputs. At its core, DENSE leverages a clinically informed retrieval strategy to identify temporally and semantically relevant content from both current and prior visits. This retrieved evidence is used to prompt a large language model (LLM) to generate clinically coherent and temporally aware progress notes. We evaluate DENSE on a curated cohort of patients with multiple visits and complete progress note documentation. The generated notes demonstrate strong longitudinal fidelity, achieving a temporal alignment ratio of $1.089$, surpassing the continuity observed in original notes. By restoring narrative coherence across fragmented documentation, our system supports improved downstream tasks such as summarization, predictive modeling, and clinical decision support, offering a scalable solution for LLM-driven note synthesis in real-world healthcare settings.

Large language models (LLMs), including zero-shot and few-shot paradigms, have shown promising capabilities in clinical text generation. However, real-world applications face two key challenges: (1) patient data is highly unstructured, heterogeneous, and scattered across multiple note types and (2) clinical notes are often long and semantically dense, making naive prompting infeasible due to context length constraints and the risk of omitting clinically relevant information. We introduce CLI-RAG (Clinically Informed Retrieval-Augmented Generation), a domain-specific framework for structured and clinically grounded text generation using LLMs. It incorporates a novel hierarchical chunking strategy that respects clinical document structure and introduces a task-specific dual-stage retrieval mechanism. The global stage identifies relevant note types using evidence-based queries, while the local stage extracts high-value content within those notes creating relevance at both document and section levels. We apply the system to generate structured progress notes for individual hospital visits using 15 clinical note types from the MIMIC-III dataset. Experiments show that it preserves temporal and semantic alignment across visits, achieving an average alignment score of 87.7%, surpassing the 80.7% baseline from real clinician-authored notes. The generated outputs also demonstrate high consistency across LLMs, reinforcing deterministic behavior essential for reproducibility, reliability, and clinical trust.

Electronic Health Records (EHRs) and routine documentation practices play a vital role in patients' daily care, providing a holistic record of health, diagnoses, and treatment. However, complex and verbose EHR narratives overload healthcare providers, risking diagnostic inaccuracies. While Large Language Models (LLMs) have showcased their potential in diverse language tasks, their application in the healthcare arena needs to ensure the minimization of diagnostic errors and the prevention of patient harm. In this paper, we outline an innovative approach for augmenting the proficiency of LLMs in the realm of automated diagnosis generation, achieved through the incorporation of a medical knowledge graph (KG) and a novel graph model: Dr.Knows, inspired by the clinical diagnostic reasoning process. We derive the KG from the National Library of Medicine's Unified Medical Language System (UMLS), a robust repository of biomedical knowledge. Our method negates the need for pre-training and instead leverages the KG as an auxiliary instrument aiding in the interpretation and summarization of complex medical concepts. Using real-world hospital datasets, our experimental results demonstrate that the proposed approach of combining LLMs with KG has the potential to improve the accuracy of automated diagnosis generation. More importantly, our approach offers an explainable diagnostic pathway, edging us closer to the realization of AI-augmented diagnostic decision support systems.

Background: Data collected in controlled settings typically results in high-quality datasets. However, in real-world applications, the quality of data collection is often compromised. It is well established that the quality of a dataset significantly impacts the performance of machine learning models. Methods: A rudimentary error rate metric was developed to evaluate textual dataset quality at the token level. Mixtral Large Language Model (LLM) was used to quantify and correct errors in low quality datasets. The study analyzed two healthcare datasets: the high-quality MIMIC-III public hospital dataset and a lower-quality private dataset from Australian aged care homes. Errors were systematically introduced into MIMIC at varying rates, while the ACH dataset quality was improved using the LLM. Results: For the sampled 35,774 and 6,336 patients from the MIMIC and ACH datasets respectively, we used Mixtral to introduce errors in MIMIC and correct errors in ACH. Mixtral correctly detected errors in 63% of progress notes, with 17% containing a single token misclassified due to medical terminology. LLMs demonstrated potential for improving progress note quality by addressing various errors. Under varying error rates, feature representation performance was tolerant to lower error rates (<10%) but declined significantly at higher rates. Conclusions: The study revealed that models performed relatively well on datasets with lower error rates (<10%), but their performance declined significantly as error rates increased (>=10%). Therefore, it is crucial to evaluate the quality of a dataset before utilizing it for machine learning tasks. For datasets with higher error rates, implementing corrective measures is essential to ensure the reliability and effectiveness of machine learning models.

Recent advancements in large language models (LLMs) have shown potential for transforming data processing in healthcare, particularly in understanding complex clinical narratives. This study evaluates the efficacy of zero-shot LLMs in summarizing long clinical texts that require temporal reasoning, a critical aspect for comprehensively capturing patient histories and treatment trajectories. We applied a series of advanced zero-shot LLMs to extensive clinical documents, assessing their ability to integrate and accurately reflect temporal dynamics without prior task-specific training. While the models efficiently identified key temporal events, they struggled with chronological coherence over prolonged narratives. The evaluation, combining quantitative and qualitative methods, highlights the strengths and limitations of zero-shot LLMs in clinical text summarization. The results suggest that while promising, zero-shot LLMs require further refinement to effectively support clinical decision-making processes, underscoring the need for enhanced model training approaches that better capture the nuances of temporal information in long context medical documents.

Extracting sections from clinical notes is crucial for downstream analysis but is challenging due to variability in formatting and labor-intensive nature of manual sectioning. While proprietary large language models (LLMs) have shown promise, privacy concerns limit their accessibility. This study develops a pipeline for automated note sectioning using open-source LLMs, focusing on three sections: History of Present Illness, Interval History, and Assessment and Plan. We fine-tuned three open-source LLMs to extract sections using a curated dataset of 487 progress notes, comparing results relative to proprietary models (GPT-4o, GPT-4o mini). Internal and external validity were assessed via precision, recall and F1 score. Fine-tuned Llama 3.1 8B outperformed GPT-4o (F1=0.92). On the external validity test set, performance remained high (F1= 0.85). Fine-tuned open-source LLMs can surpass proprietary models in clinical note sectioning, offering advantages in cost, performance, and accessibility.

We introduce LLMD, a large language model designed to analyze a patient's medical history based on their medical records. Along with domain knowledge, LLMD is trained on a large corpus of records collected over time and across facilities, as well as tasks and labels that make nuanced connections among them. This approach is critical to an accurate picture of patient health, and has distinctive advantages over models trained on knowledge alone, unlabeled records, structured EHR data, or records from a single health system. The recipe for LLMD continues pretraining a foundational model on both domain knowledge and the contents of millions of records. These span an average of 10 years of care and as many as 140 care sites per patient. LLMD is then instruction fine-tuned on structuring and abstraction tasks. The former jointly identify and normalize document metadata, provenance information, clinical named-entities, and ontology mappings, while the latter roll these into higher-level representations, such a continuous era of time a patient was on a medication. LLMD is deployed within a layered validation system that includes continual random audits and review by experts, e.g. based on uncertainty, disease-specific rules, or use-case. LLMD exhibits large gains over both more-powerful generalized models and domain-specific models. On medical knowledge benchmarks, LLMD-8B achieves state of the art accuracy on PubMedQA text responses, besting orders-of-magnitude larger models. On production tasks, we show that LLMD significantly outperforms all other models evaluated, and among alternatives, large general purpose LLMs like GPT-4o are more accurate than models emphasizing medical knowledge. We find strong evidence that accuracy on today's medical benchmarks is not the most significant factor when analyzing real-world patient data, an insight with implications for future medical LLMs.'

Regular documentation of progress notes is one of the main contributors to clinician burden. The abundance of structured chart information in medical records further exacerbates the burden, however, it also presents an opportunity to automate the generation of progress notes. In this paper, we propose a task to automate progress note generation using structured or tabular information present in electronic health records. To this end, we present a novel framework and a large dataset, ChartPNG, for the task which contains $7089$ annotation instances (each having a pair of progress notes and interim structured chart data) across $1616$ patients. We establish baselines on the dataset using large language models from general and biomedical domains. We perform both automated (where the best performing Biomistral model achieved a BERTScore F1 of $80.53$ and MEDCON score of $19.61$) and manual (where we found that the model was able to leverage relevant structured data with $76.9\%$ accuracy) analyses to identify the challenges with the proposed task and opportunities for future research.

The large amount of time clinicians spend sifting through patient notes and documenting in electronic health records (EHRs) is a leading cause of clinician burnout. By proactively and dynamically retrieving relevant notes during the documentation process, we can reduce the effort required to find relevant patient history. In this work, we conceptualize the use of EHR audit logs for machine learning as a source of supervision of note relevance in a specific clinical context, at a particular point in time. Our evaluation focuses on the dynamic retrieval in the emergency department, a high acuity setting with unique patterns of information retrieval and note writing. We show that our methods can achieve an AUC of 0.963 for predicting which notes will be read in an individual note writing session. We additionally conduct a user study with several clinicians and find that our framework can help clinicians retrieve relevant information more efficiently. Demonstrating that our framework and methods can perform well in this demanding setting is a promising proof of concept that they will translate to other clinical settings and data modalities (e.g., labs, medications, imaging).

Generative artificial intelligence (AI) is a promising direction for augmenting clinical diagnostic decision support and reducing diagnostic errors, a leading contributor to medical errors. To further the development of clinical AI systems, the Diagnostic Reasoning Benchmark (DR.BENCH) was introduced as a comprehensive generative AI framework, comprised of six tasks representing key components in clinical reasoning. We present a comparative analysis of in-domain versus out-of-domain language models as well as multi-task versus single task training with a focus on the problem summarization task in DR.BENCH (Gao et al., 2023). We demonstrate that a multi-task, clinically trained language model outperforms its general domain counterpart by a large margin, establishing a new state-of-the-art performance, with a ROUGE-L score of 28.55. This research underscores the value of domain-specific training for optimizing clinical diagnostic reasoning tasks.