Onco-Retriever: Generative Classifier for Retrieval of EHR Records in Oncology

Retrieving information from EHR systems is essential for answering specific questions about patient journeys and improving the delivery of clinical care. Despite this fact, most EHR systems still rely on keyword-based searches. With the advent of generative large language models (LLMs), retrieving information can lead to better search and summarization capabilities. Such retrievers can also feed Retrieval-augmented generation (RAG) pipelines to answer any query. However, the task of retrieving information from EHR real-world clinical data contained within EHR systems in order to solve several downstream use cases is challenging due to the difficulty in creating query-document support pairs. We provide a blueprint for creating such datasets in an affordable manner using large language models. Our method results in a retriever that is 30-50 F-1 points better than propriety counterparts such as Ada and Mistral for oncology data elements. We further compare our model, called Onco-Retriever, against fine-tuned PubMedBERT model as well. We conduct an extensive manual evaluation on real-world EHR data along with latency analysis of the different models and provide a path forward for healthcare organizations to build domain-specific retrievers.

Distilling Large Language Models for Matching Patients to Clinical Trials

The recent success of large language models (LLMs) has paved the way for their adoption in the high-stakes domain of healthcare. Specifically, the application of LLMs in patient-trial matching, which involves assessing patient eligibility against clinical trial's nuanced inclusion and exclusion criteria, has shown promise. Recent research has shown that GPT-3.5, a widely recognized LLM developed by OpenAI, can outperform existing methods with minimal 'variable engineering' by simply comparing clinical trial information against patient summaries. However, there are significant challenges associated with using closed-source proprietary LLMs like GPT-3.5 in practical healthcare applications, such as cost, privacy and reproducibility concerns. To address these issues, this study presents the first systematic examination of the efficacy of both proprietary (GPT-3.5, and GPT-4) and open-source LLMs (LLAMA 7B,13B, and 70B) for the task of patient-trial matching. Employing a multifaceted evaluation framework, we conducted extensive automated and human-centric assessments coupled with a detailed error analysis for each model. To enhance the adaptability of open-source LLMs, we have created a specialized synthetic dataset utilizing GPT-4, enabling effective fine-tuning under constrained data conditions. Our findings reveal that open-source LLMs, when fine-tuned on this limited and synthetic dataset, demonstrate performance parity with their proprietary counterparts. This presents a massive opportunity for their deployment in real-world healthcare applications. To foster further research and applications in this field, we release both the annotated evaluation dataset along with the fine-tuned LLM -- Trial-LLAMA -- for public use.

Placing (Historical) Facts on a Timeline: A Classification cum Coref Resolution Approach

A timeline provides one of the most effective ways to visualize the important historical facts that occurred over a period of time, presenting the insights that may not be so apparent from reading the equivalent information in textual form. By leveraging generative adversarial learning for important sentence classification and by assimilating knowledge based tags for improving the performance of event coreference resolution we introduce a two staged system for event timeline generation from multiple (historical) text documents. We demonstrate our results on two manually annotated historical text documents. Our results can be extremely helpful for historians, in advancing research in history and in understanding the socio-political landscape of a country as reflected in the writings of famous personas.