Jiayi Li

Jiyue Jiang, Zikang Wang, Yuheng Shan et al.

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis and synthesis, attracting widespread attention from academics and medicine. In this paper, we systematically investigate the application of prompt-based methods with LLMs to biological sequences, including DNA, RNA, proteins, and drug discovery tasks. Specifically, we focus on how prompt engineering enables LLMs to tackle domain-specific problems, such as promoter sequence prediction, protein structure modeling, and drug-target binding affinity prediction, often with limited labeled data. Furthermore, our discussion highlights the transformative potential of prompting in bioinformatics while addressing key challenges such as data scarcity, multimodal fusion, and computational resource limitations. Our aim is for this paper to function both as a foundational primer for newcomers and a catalyst for continued innovation within this dynamic field of study.

Xinyu Wang, Jiayi Li, Sarah Rajtmajer

Social media users drive the spread of misinformation online by sharing posts that include erroneous information or commenting on controversial topics with unsubstantiated arguments often in earnest. Work on echo chambers has suggested that users' perspectives are reinforced through repeated interactions with like-minded peers, promoted by homophily and bias in information diffusion. Building on long-standing interest in the social bases of language and linguistic underpinnings of social behavior, this work explores how conversations around misinformation are mediated through language use. We compare a number of linguistic measures, e.g., in-/out-group cues, readability, and discourse connectives, within and across topics of conversation and user communities. Our findings reveal increased presence of group identity signals and processing fluency within echo chambers during discussions of misinformation. We discuss the specific character of these broader trends across topics and examine contextual influences.

Yanting Li, Jiyue Jiang, Zikang Wang et al.

Inverse Protein Folding (IPF) is a critical subtask in the field of protein design, aiming to engineer amino acid sequences capable of folding correctly into a specified three-dimensional (3D) conformation. Although substantial progress has been achieved in recent years, existing methods generally rely on either backbone coordinates or molecular surface features alone, which restricts their ability to fully capture the complex chemical and geometric constraints necessary for precise sequence prediction. To address this limitation, we present DS-ProGen, a dual-structure deep language model for functional protein design, which integrates both backbone geometry and surface-level representations. By incorporating backbone coordinates as well as surface chemical and geometric descriptors into a next-amino-acid prediction paradigm, DS-ProGen is able to generate functionally relevant and structurally stable sequences while satisfying both global and local conformational constraints. On the PRIDE dataset, DS-ProGen attains the current state-of-the-art recovery rate of 61.47%, demonstrating the synergistic advantage of multi-modal structural encoding in protein design. Furthermore, DS-ProGen excels in predicting interactions with a variety of biological partners, including ligands, ions, and RNA, confirming its robust functional retention capabilities.