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Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, structure, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery.…

Machine Learning · Computer Science 2026-03-04 Darshan Patil , Pranshu Malviya , Mathieu Reymond , Quentin Fournier , Sarath Chandar

Large Language Models (LLMs) have shown remarkable performance in various basic natural language tasks. For completing the complex task, we still need a plan for the task to guide LLMs to generate the specific solutions step by step. LLMs…

Computation and Language · Computer Science 2023-12-14 Yiduo Guo , Yaobo Liang , Chenfei Wu , Wenshan Wu , Dongyan Zhao , Nan Duan

The trade-off between expressiveness and interpretability remains a core challenge when building human-centric predictive models for classification and decision-making. While symbolic rules offer interpretability, they often lack…

Artificial Intelligence · Computer Science 2024-06-26 Ruochen Wang , Si Si , Felix Yu , Dorothea Wiesmann , Cho-Jui Hsieh , Inderjit Dhillon

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the…

Machine Learning · Computer Science 2024-08-20 Tianyu Zhang , Yuxiang Ren , Chengbin Hou , Hairong Lv , Xuegong Zhang

Effective protein representation learning is crucial for predicting protein functions. Traditional methods often pretrain protein language models on large, unlabeled amino acid sequences, followed by finetuning on labeled data. While…

Biomolecules · Quantitative Biology 2024-09-05 Jiangbin Zheng , Stan Z. Li

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Computation and Language · Computer Science 2025-04-24 Gilchan Park , Byung-Jun Yoon , Xihaier Luo , Vanessa López-Marrero , Shinjae Yoo , Shantenu Jha

In order for large language model (LLM)-based assistants to effectively adapt to evolving information needs, it must be possible to update their factual knowledge through continued training on new data. The standard recipe for doing so…

Computation and Language · Computer Science 2024-05-28 Zhengbao Jiang , Zhiqing Sun , Weijia Shi , Pedro Rodriguez , Chunting Zhou , Graham Neubig , Xi Victoria Lin , Wen-tau Yih , Srinivasan Iyer

Virtual Reality (VR) has emerged as a powerful tool for workforce training, offering immersive, interactive, and risk-free environments that enhance skill acquisition, decision-making, and confidence. Despite its advantages, developing VR…

Computer Vision and Pattern Recognition · Computer Science 2025-08-07 Subin Raj Peter

With the rapid advancement of Large Language Models (LLMs), the demand for robust instruction-following capabilities in code generation tasks has grown significantly. Code generation not only facilitates faster prototyping and automated…

Software Engineering · Computer Science 2025-08-05 Kaiwen Yan , Hongcheng Guo , Xuanqing Shi , Shaosheng Cao , Donglin Di , Zhoujun Li

Large Language Models (LLMs) trained on petabytes of data are highly compressed repositories of a significant proportion of the knowledge accumulated and distilled so far. In this paper we study techniques to elicit this knowledge in the…

Artificial Intelligence · Computer Science 2025-02-14 Paul Tarau

The evolution of web applications relies on iterative code modifications, a process that is traditionally manual and time-consuming. While Large Language Models (LLMs) can generate UI code, their ability to edit existing code from new…

Software Engineering · Computer Science 2025-10-31 Truong Hai Dang , Jingyu Xiao , Yintong Huo

Effective text generation and chat interfaces for low-resource languages (LRLs) remain a challenge for state-of-the-art large language models (LLMs) to support. This is mainly due to the difficulty of curating high-quality instruction…

Machine Learning · Computer Science 2026-02-09 Mamadou K. Keita , Sebastien Diarra , Christopher Homan , Seydou Diallo

Large language models (LLMs) have demonstrated strong capabilities across various language tasks, notably through instruction-tuning methods. However, LLMs face challenges in visualizing complex, real-world data through charts and plots.…

Machine Learning · Computer Science 2025-02-18 Fatemeh Pesaran Zadeh , Juyeon Kim , Jin-Hwa Kim , Gunhee Kim

Large vision language models (LVLMs) have demonstrated impressive performance across a wide range of tasks. These capabilities largely stem from visual instruction tuning, which fine-tunes models on datasets consisting of curated…

Computer Vision and Pattern Recognition · Computer Science 2026-04-28 Myeongkyun Kang , Soopil Kim , Xiaoxiao Li , Sang Hyun Park

In recent years, instruction tuning has gained increasing attention and emerged as a crucial technique to enhance the capabilities of Large Language Models (LLMs). To construct high-quality instruction datasets, many instruction processing…

Computation and Language · Computer Science 2024-06-25 Yixin Ou , Ningyu Zhang , Honghao Gui , Ziwen Xu , Shuofei Qiao , Yida Xue , Runnan Fang , Kangwei Liu , Lei Li , Zhen Bi , Guozhou Zheng , Huajun Chen

Large language models (LLMs) are a promising venue for natural language understanding and generation tasks. However, current LLMs are far from reliable: they are prone to generate non-factual information and, more crucially, to contradict…

Machine Learning · Computer Science 2024-04-22 Diego Calanzone , Stefano Teso , Antonio Vergari

Linking (aligning) biomedical concepts across diverse data sources enables various integrative analyses, but it is challenging due to the discrepancies in concept naming conventions. Various strategies have been developed to overcome this…

Information Retrieval · Computer Science 2024-05-14 Yuzhang Xie , Jiaying Lu , Joyce Ho , Fadi Nahab , Xiao Hu , Carl Yang

Multi-turn instruction following is essential for building intelligent conversational systems that can consistently adhere to instructions across dialogue turns. However, existing approaches to enhancing multi-turn instruction following…

Computation and Language · Computer Science 2026-03-26 Zhenhe Li , Can Lin , Ling Zheng , Wen-Da Wei , Junli Liang , Qi Song

Domain models are central to software engineering, as they enable a shared understanding, guide implementation, and support automated analyses and model-driven development. Yet, despite these benefits, practitioners often skip modeling…

Software Engineering · Computer Science 2025-12-16 Gökberk Çelikmasat , Atay Özgövde , Fatma Başak Aydemir

Knowledge editing for large language models can offer an efficient solution to alter a model's behavior without negatively impacting the overall performance. However, the current approaches encounter issues with limited generalizability…

Computation and Language · Computer Science 2024-04-30 Ningyu Zhang , Bozhong Tian , Siyuan Cheng , Xiaozhuan Liang , Yi Hu , Kouying Xue , Yanjie Gou , Xi Chen , Huajun Chen