Physicians spend significant time documenting clinical encounters, a burden that contributes to professional burnout. To address this, robust automation tools for medical documentation are crucial. We introduce MedSynth -- a novel dataset of synthetic medical dialogues and notes designed to advance the Dialogue-to-Note (Dial-2-Note) and Note-to-Dialogue (Note-2-Dial) tasks. Informed by an extensive analysis of disease distributions, this dataset includes over 10,000 dialogue-note pairs covering over 2000 ICD-10 codes. We demonstrate that our dataset markedly enhances the performance of models in generating medical notes from dialogues, and dialogues from medical notes. The dataset provides a valuable resource in a field where open-access, privacy-compliant, and diverse training data are scarce. Code is available at https://github.com/ahmadrezarm/MedSynth/tree/main and the dataset is available at https://huggingface.co/datasets/Ahmad0067/MedSynth.

OpenNotes enables patients to access EHR notes, but medical jargon can hinder comprehension. To improve understanding, we evaluated closed- and open-source LLMs for extracting and prioritizing key medical terms using prompting, fine-tuning, and data augmentation. We assessed LLMs on 106 expert-annotated EHR notes, experimenting with (i) general vs. structured prompts, (ii) zero-shot vs. few-shot prompting, (iii) fine-tuning, and (iv) data augmentation. To enhance open-source models in low-resource settings, we used ChatGPT for data augmentation and applied ranking techniques. We incrementally increased the augmented dataset size (10 to 10,000) and conducted 5-fold cross-validation, reporting F1 score and Mean Reciprocal Rank (MRR). Our result show that fine-tuning and data augmentation improved performance over other strategies. GPT-4 Turbo achieved the highest F1 (0.433), while Mistral7B with data augmentation had the highest MRR (0.746). Open-source models, when fine-tuned or augmented, outperformed closed-source models. Notably, the best F1 and MRR scores did not always align. Few-shot prompting outperformed zero-shot in vanilla models, and structured prompts yielded different preferences across models. Fine-tuning improved zero-shot performance but sometimes degraded few-shot performance. Data augmentation performed comparably or better than other methods. Our evaluation highlights the effectiveness of prompting, fine-tuning, and data augmentation in improving model performance for medical jargon extraction in low-resource scenarios.

Large language models (LLMs) have shown remarkable performance in vision-language tasks, but their application in the medical field remains underexplored, particularly for integrating structured time series data with unstructured clinical notes. In clinical practice, dynamic time series data such as lab test results capture critical temporal patterns, while clinical notes provide rich semantic context. Merging these modalities is challenging due to the inherent differences between continuous signals and discrete text. To bridge this gap, we introduce ProMedTS, a novel self-supervised multimodal framework that employs prompt-guided learning to unify these heterogeneous data types. Our approach leverages lightweight anomaly detection to generate anomaly captions that serve as prompts, guiding the encoding of raw time series data into informative embeddings. These embeddings are aligned with textual representations in a shared latent space, preserving fine-grained temporal nuances alongside semantic insights. Furthermore, our framework incorporates tailored self-supervised objectives to enhance both intra- and inter-modal alignment. We evaluate ProMedTS on disease diagnosis tasks using real-world datasets, and the results demonstrate that our method consistently outperforms state-of-the-art approaches.

Accurate diagnostic coding of medical notes is crucial for enhancing patient care, medical research, and error-free billing in healthcare organizations. Manual coding is a time-consuming task for providers, and diagnostic codes often exhibit low sensitivity and specificity, whereas the free text in medical notes can be a more precise description of a patients status. Thus, accurate automated diagnostic coding of medical notes has become critical for a learning healthcare system. Recent developments in long-document transformer architectures have enabled attention-based deep-learning models to adjudicate medical notes. In addition, contrastive loss functions have been used to jointly pre-train large language and image models with noisy labels. To further improve the automated adjudication of medical notes, we developed an approach based on i) models for ICD-10 diagnostic code sequences using a large real-world data set, ii) large language models for medical notes, and iii) contrastive pre-training to build an integrated model of both ICD-10 diagnostic codes and corresponding medical text. We demonstrate that a contrastive approach for pre-training improves performance over prior state-of-the-art models for the MIMIC-III-50, MIMIC-III-rare50, and MIMIC-III-full diagnostic coding tasks.

Clinical rationales play a pivotal role in accurate disease diagnosis; however, many models predominantly use discriminative methods and overlook the importance of generating supportive rationales. Rationale distillation is a process that transfers knowledge from large language models (LLMs) to smaller language models (SLMs), thereby enhancing the latter's ability to break down complex tasks. Despite its benefits, rationale distillation alone is inadequate for addressing domain knowledge limitations in tasks requiring specialized expertise, such as disease diagnosis. Effectively embedding domain knowledge in SLMs poses a significant challenge. While current LLMs are primarily geared toward processing textual data, multimodal LLMs that incorporate time series data, especially electronic health records (EHRs), are still evolving. To tackle these limitations, we introduce ClinRaGen, an SLM optimized for multimodal rationale generation in disease diagnosis. ClinRaGen incorporates a unique knowledge-augmented attention mechanism to merge domain knowledge with time series EHR data, utilizing a stepwise rationale distillation strategy to produce both textual and time series-based clinical rationales. Our evaluations show that ClinRaGen markedly improves the SLM's capability to interpret multimodal EHR data and generate accurate clinical rationales, supporting more reliable disease diagnosis, advancing LLM applications in healthcare, and narrowing the performance divide between LLMs and SLMs.

Although rapid advancements in Large Language Models (LLMs) are facilitating the integration of artificial intelligence-based applications and services in healthcare, limited research has focused on the systematic evaluation of medical notes for guideline adherence. This paper introduces GuidelineGuard, an agentic framework powered by LLMs that autonomously analyzes medical notes, such as hospital discharge and office visit notes, to ensure compliance with established healthcare guidelines. By identifying deviations from recommended practices and providing evidence-based suggestions, GuidelineGuard helps clinicians adhere to the latest standards from organizations like the WHO and CDC. This framework offers a novel approach to improving documentation quality and reducing clinical errors.

ICD(International Classification of Diseases) coding involves assigning ICD codes to patients visit based on their medical notes. Considering ICD coding as a multi-label text classification task, researchers have developed sophisticated methods. Despite progress, these models often suffer from label imbalance and may develop spurious correlations with demographic factors. Additionally, while human coders assign ICD codes, the inclusion of irrelevant information from unrelated experts introduces biases. To combat these issues, we propose a novel method to mitigate Demographic and Expert biases in ICD coding through Causal Inference (DECI). We provide a novel causality-based interpretation in ICD Coding that models make predictions by three distinct pathways. And based counterfactual reasoning, DECI mitigate demographic and expert biases. Experimental results show that DECI outperforms state-of-the-art models, offering a significant advancement in accurate and unbiased ICD coding.

Social Determinants of Health (SDOH) play a significant role in patient health outcomes. The Center of Disease Control (CDC) introduced a subset of ICD-10 codes called Z-codes in an attempt to officially recognize and measure SDOH in the health care system. However, these codes are rarely annotated in a patient's Electronic Health Record (EHR), and instead, in many cases, need to be inferred from clinical notes. Previous research has shown that large language models (LLMs) show promise on extracting unstructured data from EHRs. However, with thousands of models to choose from with unique architectures and training sets, it's difficult to choose one model that performs the best on coding tasks. Further, clinical notes contain trusted health information making the use of closed-source language models from commercial vendors difficult, so the identification of open source LLMs that can be run within health organizations and exhibits high performance on SDOH tasks is an urgent problem. Here, we introduce an intelligent routing system for SDOH coding that uses a language model router to direct medical record data to open source LLMs that demonstrate optimal performance on specific SDOH codes. The intelligent routing system exhibits state of the art performance of 97.4% accuracy averaged across 5 codes, including homelessness and food insecurity, on par with closed models such as GPT-4o. In order to train the routing system and validate models, we also introduce a synthetic data generation and validation paradigm to increase the scale of training data without needing privacy protected medical records. Together, we demonstrate an architecture for intelligent routing of inputs to task-optimal language models to achieve high performance across a set of medical coding sub-tasks.

ICD(International Classification of Diseases) coding involves assigning ICD codes to patients visit based on their medical notes. ICD coding is a challenging multilabel text classification problem due to noisy medical document inputs. Recent advancements in automated ICD coding have enhanced performance by integrating additional data and knowledge bases with the encoding of medical notes and codes. However, most of them ignore the code hierarchy, leading to improper code assignments. To address these problems, we propose a novel framework based on associated and hierarchical code description distillation (AHDD) for better code representation learning and avoidance of improper code assignment.we utilize the code description and the hierarchical structure inherent to the ICD codes. Therefore, in this paper, we leverage the code description and the hierarchical structure inherent to the ICD codes. The code description is also applied to aware the attention layer and output layer. Experimental results on the benchmark dataset show the superiority of the proposed framework over several state-of-the-art baselines.

LLMs are revolutionizing NLP tasks. However, the use of the most advanced LLMs, such as GPT-4, is often prohibitively expensive for most specialized fields. We introduce HEAL, the first continuously trained 13B LLaMA2-based LLM that is purpose-built for medical conversations and measured on automated scribing. Our results demonstrate that HEAL outperforms GPT-4 and PMC-LLaMA in PubMedQA, with an accuracy of 78.4\%. It also achieves parity with GPT-4 in generating medical notes. Remarkably, HEAL surpasses GPT-4 and Med-PaLM 2 in identifying more correct medical concepts and exceeds the performance of human scribes and other comparable models in correctness and completeness.