Yijia Xiao

Yijia Xiao, Edward Sun, Tianyu Liu et al.

We propose LogicVista, an evaluation benchmark that assesses the integrated logical reasoning capabilities of multimodal large language models (MLLMs) in Visual contexts. Recent advancements in MLLMs have demonstrated various fascinating abilities, from crafting poetry based on an image to performing mathematical reasoning. However, there is still a lack of systematic evaluation of MLLMs' proficiency in logical reasoning tasks, which are essential for activities like navigation and puzzle-solving. Thus we evaluate general logical cognition abilities across 5 logical reasoning tasks encompassing 9 different capabilities, using a sample of 448 multiple-choice questions. Each question is annotated with the correct answer and the human-written reasoning behind the selection, enabling both open-ended and multiple-choice evaluation. A total of 8 MLLMs are comprehensively evaluated using LogicVista. Code and Data Available at https://github.com/Yijia-Xiao/LogicVista.

Yijia Xiao, Edward Sun, Yiqiao Jin et al.

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research. To streamline this process, we introduce ProteinGPT, a state-of-the-art multimodal large language model for proteins that enables users to upload protein sequences and/or structures for comprehensive analysis and responsive inquiries. ProteinGPT integrates protein sequence and structure encoders with linear projection layers to ensure precise representation adaptation and leverages a large language model (LLM) to generate accurate, contextually relevant responses. To train ProteinGPT, we constructed a large-scale dataset of 132,092 proteins, each annotated with 20-30 property tags and 5-10 QA pairs per protein, and optimized the instruction-tuning process using GPT-4o. Experiments demonstrate that ProteinGPT effectively generates informative responses to protein-related questions, achieving high performance on both semantic and lexical metrics and significantly outperforming baseline models and general-purpose LLMs in understanding and responding to protein-related queries. Our code and data are available at https://github.com/ProteinGPT/ProteinGPT.

Yiqiao Jin, Qinlin Zhao, Yiyang Wang et al.

Peer review is fundamental to the integrity and advancement of scientific publication. Traditional methods of peer review analyses often rely on exploration and statistics of existing peer review data, which do not adequately address the multivariate nature of the process, account for the latent variables, and are further constrained by privacy concerns due to the sensitive nature of the data. We introduce AgentReview, the first large language model (LLM) based peer review simulation framework, which effectively disentangles the impacts of multiple latent factors and addresses the privacy issue. Our study reveals significant insights, including a notable 37.1% variation in paper decisions due to reviewers' biases, supported by sociological theories such as the social influence theory, altruism fatigue, and authority bias. We believe that this study could offer valuable insights to improve the design of peer review mechanisms. Our code is available at https://github.com/Ahren09/AgentReview.