The advancement of natural language processing (NLP) systems in healthcare hinges on language models’ ability to interpret the intricate information contained within clinical notes. This process often requires integrating information from various time points in a patient’s medical history. However, most earlier clinical language models were pretrained with a context length limited to roughly one clinical document. In this study, We introduce ClinicalMamba, a specialized version of the Mamba language model, pretrained on a vast corpus of longitudinal clinical notes to address the unique linguistic characteristics and information processing needs of the medical domain. ClinicalMamba models, with 130 million and 2.8 billion parameters, demonstrate superior performance in modeling clinical language across extended text lengths compared to Mamba and other clinical models based on longformer and Llama. With few-shot learning, ClinicalMamba achieves notable benchmarks in speed and performance, outperforming existing clinical language models and large language models like GPT-4 in longitudinal clinical tasks.

This paper presents our team’s participation in the MEDIQA-ClinicalNLP 2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show it’s superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

This study examines the effect of prompt engineering on the performance of Large Language Models (LLMs) in clinical note generation. We introduce an Automatic Prompt Optimization (APO) framework to refine initial prompts and compare the outputs of medical experts, non-medical experts, and APO-enhanced GPT3.5 and GPT4. Results highlight GPT4-APO’s superior performance in standardizing prompt quality across clinical note sections. A human-in-the-loop approach shows that experts maintain content quality post-APO, with a preference for their own modifications, suggesting the value of expert customization. We recommend a two-phase optimization process, leveraging APO-GPT4 for consistency and expert input for personalization.

We introduce NoteChat, a novel cooperative multi-agent framework leveraging Large Language Models (LLMs) to generate patient-physician dialogues. NoteChat embodies the principle that an ensemble of role-specific LLMs, through structured role-play and strategic prompting, can perform their assigned roles more effectively. The synergy among these role-playing LLMs results in a cohesive and efficient dialogue generation. Evaluation on MTS-dialogue, a benchmark dataset for patient-physician dialogues-note pairs, shows that models trained with the augmented synthetic patient-physician dialogues by NoteChat outperforms other state-of-the-art models for generating clinical notes. Our comprehensive automatic and human evaluation demonstrates that NoteChat substantially surpasses state-of-the-art models like ChatGPT and GPT-4 up to 22.78% by domain experts in generating superior synthetic patient-physician dialogues based on clinical notes. NoteChat has the potential to engage patients directly and help clinical documentation, a leading cause of physician burnout.

This paper presents UMASS_BioNLP team participation in the MEDIQA-Chat 2023 shared task for Task-A and Task-C. We focus especially on Task-C and propose a novel LLMs cooperation system named a doctor-patient loop to generate high-quality conversation data sets. The experiment results demonstrate that our approaches yield reasonable performance as evaluated by automatic metrics such as ROUGE, medical concept recall, BLEU, and Self-BLEU. Furthermore, we conducted a comparative analysis between our proposed method and ChatGPT and GPT-4. This analysis also investigates the potential of utilizing cooperation LLMs to generate high-quality datasets.

Visual Word Sense Disambiguation (VWSD) is a task to find the image that most accurately depicts the correct sense of the target word for the given context. Previously, image-text matching models often suffered from recognizing polysemous words. This paper introduces an unsupervised VWSD approach that uses gloss information of an external lexical knowledge-base, especially the sense definitions. Specifically, we suggest employing Bayesian inference to incorporate the sense definitions when sense information of the answer is not provided. In addition, to ameliorate the out-of-dictionary (OOD) issue, we propose a context-aware definition generation with GPT-3. Experimental results show that the VWSD performance significantly increased with our Bayesian inference-based approach. In addition, our context-aware definition generation achieved prominent performance improvement in OOD examples exhibiting better performance than the existing definition generation method.

Solutions to math word problems (MWPs) with step-by-step explanations are valuable, especially in education, to help students better comprehend problem-solving strategies. Most existing approaches only focus on obtaining the final correct answer. A few recent approaches leverage intermediate solution steps to improve final answer correctness but often cannot generate coherent steps with a clear solution strategy. Contrary to existing work, we focus on improving the correctness and coherence of the intermediate solutions steps. We propose a step-by-step planning approach for intermediate solution generation, which strategically plans the generation of the next solution step based on the MWP and the previous solution steps. Our approach first plans the next step by predicting the necessary math operation needed to proceed, given history steps, then generates the next step, token-by-token, by prompting a language model with the predicted math operation. Experiments on the GSM8K dataset demonstrate that our approach improves the accuracy and interpretability of the solution on both automatic metrics and human evaluation.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

One of the fundamental goals of artificial intelligence is to build computer-based expert systems. Inferring clinical diagnoses to generate a clinical assessment during a patient encounter is a crucial step towards building a medical diagnostic system. Previous works were mainly based on either medical domain-specific knowledge, or patients’ prior diagnoses and clinical encounters. In this paper, we propose a novel model for automated clinical assessment generation (MCAG). MCAG is built on an innovative graph neural network, where rich clinical knowledge is incorporated into an end-to-end corpus-learning system. Our evaluation results against physician generated gold standard show that MCAG significantly improves the BLEU and rouge score compared with competitive baseline models. Further, physicians’ evaluation showed that MCAG could generate high-quality assessments.

Classical Chinese poetry is a jewel in the treasure house of Chinese culture. Previous poem generation models only allow users to employ keywords to interfere the meaning of generated poems, leaving the dominion of generation to the model. In this paper, we propose a novel task of generating classical Chinese poems from vernacular, which allows users to have more control over the semantic of generated poems. We adapt the approach of unsupervised machine translation (UMT) to our task. We use segmentation-based padding and reinforcement learning to address under-translation and over-translation respectively. According to experiments, our approach significantly improve the perplexity and BLEU compared with typical UMT models. Furthermore, we explored guidelines on how to write the input vernacular to generate better poems. Human evaluation showed our approach can generate high-quality poems which are comparable to amateur poems.