Yuhang Jiang

Yuhang Jiang, Ramakanth Kavuluru

Combination drug therapies are treatment regimens that involve two or more drugs, administered more commonly for patients with cancer, HIV, malaria, or tuberculosis. Currently there are over 350K articles in PubMed that use the "combination drug therapy" MeSH heading with at least 10K articles published per year over the past two decades. Extracting combination therapies from scientific literature inherently constitutes an $n$-ary relation extraction problem. Unlike in the general $n$-ary setting where $n$ is fixed (e.g., drug-gene-mutation relations where $n=3$), extracting combination therapies is a special setting where $n \geq 2$ is dynamic, depending on each instance. Recently, Tiktinsky et al. (NAACL 2022) introduced a first of its kind dataset, CombDrugExt, for extracting such therapies from literature. Here, we use a sequence-to-sequence style end-to-end extraction method to achieve an F1-Score of $66.7\%$ on the CombDrugExt test set for positive (or effective) combinations. This is an absolute $\approx 5\%$ F1-score improvement even over the prior best relation classification score with spotted drug entities (hence, not end-to-end). Thus our effort introduces a state-of-the-art first model for end-to-end extraction that is already superior to the best prior non end-to-end model for this task. Our model seamlessly extracts all drug entities and relations in a single pass and is highly suitable for dynamic $n$-ary extraction scenarios.

Aviv Brokman, Xuguang Ai, Yuhang Jiang et al.

Objective: Zero-shot methodology promises to cut down on costs of dataset annotation and domain expertise needed to make use of NLP. Generative large language models trained to align with human goals have achieved high zero-shot performance across a wide variety of tasks. As of yet, it is unclear how well these models perform on biomedical relation extraction (RE). To address this knowledge gap, we explore patterns in the performance of OpenAI LLMs across a diverse sampling of RE tasks. Methods: We use OpenAI GPT-4-turbo and OpenAI's reasoning models o1 and GPT-OSS to conduct end-to-end RE experiments on seven datasets. We use the JSON generation capabilities of GPT models to generate structured output in two ways: (1) by defining an explicit schema describing the structure of relations, and (2) using a setting that infers the structure from the prompt language. Results: Our work is the first to study and compare the performance of the GPT-4, o1 and GPT-OSS for the end-to-end zero-shot biomedical RE task across a broad array of datasets. We found the zero-shot performances to be proximal to that of fine-tuned methods. The limitations of this approach are that it performs poorly on instances containing many relations and errs on the boundaries of textual mentions. Conclusion: LLMs exhibit promising zero-shot capabilities in complex biomedical RE tasks, offering competitive performance with reduced dataset curation costs and NLP modeling needs but with increased perpetual compute costs. Addressing the limitations we identify could further boost reliability. The code, data, and prompts for all our experiments are publicly available for additional benchmarking by the community: https://github.com/bionlproc/ZeroShotRE

Shuoling Liu, Gaoguo Jia, Yuhang Jiang et al.

Large Language Models (LLMs) have achieved remarkable success recently, displaying exceptional capabilities in creating understandable and organized text. These LLMs have been utilized in diverse fields, such as clinical research, where domain-specific models like Med-Palm have achieved human-level performance. Recently, researchers have employed advanced prompt engineering to enhance the general reasoning ability of LLMs. Despite the remarkable success of zero-shot Chain-of-Thoughts (CoT) in solving general reasoning tasks, the potential of these methods still remains paid limited attention in the financial reasoning task.To address this issue, we explore multiple prompt strategies and incorporated semantic news information to improve LLMs' performance on financial reasoning tasks.To the best of our knowledge, we are the first to explore this important issue by applying ChatGPT to the gold investment.In this work, our aim is to investigate the financial reasoning capabilities of LLMs and their capacity to generate logical and persuasive investment opinions. We will use ChatGPT, one of the most powerful LLMs recently, and prompt engineering to achieve this goal. Our research will focus on understanding the ability of LLMs in sophisticated analysis and reasoning within the context of investment decision-making. Our study finds that ChatGPT with CoT prompt can provide more explainable predictions and overcome behavioral biases, which is crucial in finance-related tasks and can achieve higher investment returns.