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Large language models (LLMs) have emerged as powerful tools for knowledge-intensive tasks across domains. In materials science, to find novel materials for various energy efficient devices for various real-world applications, requires…

Large Language Models (LLMs) are becoming increasingly popular in pervasive computing due to their versatility and strong performance. However, despite their ubiquitous use, the exact mechanisms underlying their outstanding performance…

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured…

Novel research ideas play a critical role in advancing scientific inquiries. Recent advancements in Large Language Models (LLMs) have demonstrated their potential to generate novel research ideas by leveraging large-scale scientific…

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…

Despite their remarkable natural language understanding capabilities, Large Language Models (LLMs) have been underutilized for retrieval tasks. We present Search-R3, a novel framework that addresses this limitation by adapting LLMs to…

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or…

Large language models (LLMs) have recently been proposed as general-purpose agents for experimental design, with claims that they can perform in-context experimental design. We evaluate this hypothesis using both open- and closed-source…

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language…

Efficient inference in large language models (LLMs) has become a critical focus as their scale and complexity grow. Traditional autoregressive decoding, while effective, suffers from computational inefficiencies due to its sequential token…

Large Language Models (LLMs) have rapidly transformed the landscape of artificial intelligence, enabling natural language interfaces and dynamic orchestration of software components. However, their reliance on probabilistic inference limits…

Molecule design is a multifaceted approach that leverages computational methods and experiments to optimize molecular properties, fast-tracking new drug discoveries, innovative material development, and more efficient chemical processes.…

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…

Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug…

Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs),…

Large Language Models (LLMs) have recently developed new advanced functionalities. Their effectiveness relies on statistical learning and generalization capabilities. However, they face limitations in internalizing the data they process and…

LLM Ensemble -- which involves the comprehensive use of multiple large language models (LLMs), each aimed at handling user queries during downstream inference, to benefit from their individual strengths -- has gained substantial attention…

Large Language Models (LLMs) have exhibited impressive generation capabilities, but they suffer from hallucinations when solely relying on their internal knowledge, especially when answering questions that require less commonly known…

Structure-based drug design (SBDD) is crucial for developing specific and effective therapeutics against protein targets but remains challenging due to complex protein-ligand interactions and vast chemical space. Although language models…

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…