Yongfeng Zhang

Juntao Tan, Yongfeng Zhang

This paper presents ExplainableFold, an explainable AI framework for protein structure prediction. Despite the success of AI-based methods such as AlphaFold in this field, the underlying reasons for their predictions remain unclear due to the black-box nature of deep learning models. To address this, we propose a counterfactual learning framework inspired by biological principles to generate counterfactual explanations for protein structure prediction, enabling a dry-lab experimentation approach. Our experimental results demonstrate the ability of ExplainableFold to generate high-quality explanations for AlphaFold's predictions, providing near-experimental understanding of the effects of amino acids on 3D protein structure. This framework has the potential to facilitate a deeper understanding of protein structures.

Wenyue Hua, Ollie Liu, Lingyao Li et al.

This paper investigates the rationality of large language models (LLMs) in strategic decision-making contexts, specifically within the framework of game theory. We evaluate several state-of-the-art LLMs across a spectrum of complete-information and incomplete-information games. Our findings reveal that LLMs frequently deviate from rational strategies, particularly as the complexity of the game increases with larger payoff matrices or deeper sequential trees. To address these limitations, we design multiple game-theoretic workflows that guide the reasoning and decision-making processes of LLMs. These workflows aim to enhance the models' ability to compute Nash Equilibria and make rational choices, even under conditions of uncertainty and incomplete information. Experimental results demonstrate that the adoption of these workflows significantly improves the rationality and robustness of LLMs in game-theoretic tasks. Specifically, with the workflow, LLMs exhibit marked improvements in identifying optimal strategies, achieving near-optimal allocations in negotiation scenarios, and reducing susceptibility to exploitation during negotiations. Furthermore, we explore the meta-strategic considerations of whether it is rational for agents to adopt such workflows, recognizing that the decision to use or forgo the workflow constitutes a game-theoretic issue in itself. Our research contributes to a deeper understanding of LLMs' decision-making capabilities in strategic contexts and provides insights into enhancing their rationality through structured workflows. The findings have implications for the development of more robust and strategically sound AI agents capable of navigating complex interactive environments. Code and data supporting this study are available at \url{https://github.com/Wenyueh/game_theory}.

Kai Mei, Wujiang Xu, Shuhang Lin et al.

Large language models (LLMs) deliver superior performance but require substantial computational resources and operate with relatively low efficiency, while smaller models can efficiently handle simpler tasks with fewer resources. LLM routing is a crucial paradigm that dynamically selects the most suitable large language models from a pool of candidates to process diverse inputs, ensuring optimal resource utilization while maintaining response quality. Existing routing frameworks typically model this as a locally optimal decision-making problem, selecting the presumed best-fit LLM for each query individually, which overlook global budget constraints, resulting in ineffective resource allocation. To tackle this problem, we introduce OmniRouter, a fundamentally controllable routing framework for multi-LLM serving. Instead of making per-query greedy choices, OmniRouter models the routing task as a constrained optimization problem, assigning models that minimize total cost while ensuring the required performance level. Specifically, a hybrid retrieval-augmented predictor is designed to predict the capabilities and costs of LLMs and a constrained optimizer is employed to control globally optimal query-model allocation. Experiments show that OmniRouter achieves up to 6.30% improvement in response accuracy while simultaneously reducing computational costs by at least 10.15% compared to competitive router baselines. The code and the dataset are available at https://github.com/agiresearch/OmniRouter.

Huizi Yu, Lizhou Fan, Lingyao Li et al.

Large Language Models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), enabling new ways to analyze data, treat patients, and conduct research. This study aims to provide a comprehensive overview of LLM applications in BHI, highlighting their transformative potential and addressing the associated ethical and practical challenges. We reviewed 1,698 research articles from January 2022 to December 2023, categorizing them by research themes and diagnostic categories. Additionally, we conducted network analysis to map scholarly collaborations and research dynamics. Our findings reveal a substantial increase in the potential applications of LLMs to a variety of BHI tasks, including clinical decision support, patient interaction, and medical document analysis. Notably, LLMs are expected to be instrumental in enhancing the accuracy of diagnostic tools and patient care protocols. The network analysis highlights dense and dynamically evolving collaborations across institutions, underscoring the interdisciplinary nature of LLM research in BHI. A significant trend was the application of LLMs in managing specific disease categories such as mental health and neurological disorders, demonstrating their potential to influence personalized medicine and public health strategies. LLMs hold promising potential to further transform biomedical research and healthcare delivery. While promising, the ethical implications and challenges of model validation call for rigorous scrutiny to optimize their benefits in clinical settings. This survey serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI.