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Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However,…

Molecular generative models, often employing GPT-style language modeling on molecular string representations, have shown promising capabilities when scaled to large datasets and model sizes. However, it remains unclear and subject to debate…

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Unlocking the potential of Large Language Models (LLMs) in data classification represents a promising frontier in natural language processing. In this work, we evaluate the performance of different LLMs in comparison with state-of-the-art…

Large language models (LLM) not only have revolutionized the field of natural language processing (NLP) but also have the potential to reshape many other fields, e.g., recommender systems (RS). However, most of the related work treats an…

Predicting enzymatic reactions is crucial for applications in biocatalysis, metabolic engineering, and drug discovery, yet it remains a complex and resource-intensive task. Large Language Models (LLMs) have recently demonstrated remarkable…

This groundbreaking study explores the expanse of Large Language Models (LLMs), such as Generative Pre-Trained Transformer (GPT) and Bidirectional Encoder Representations from Transformers (BERT) across varied domains ranging from…

Multimodal Large Language Models (MLLMs) have advanced open-world action understanding and can be adapted as generative classifiers for closed-set settings by autoregressively generating action labels as text. However, this approach is…

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the…

Large language models (LLMs) such as those embedded in 'chatbots' are accelerating and democratizing research by providing comprehensible information and expertise from many different fields. However, these models may also confer easy…

Antimicrobial resistance is an important public health concern that has implications in the practice of medicine worldwide. Accurately predicting resistance phenotypes from genome sequences shows great promise in promoting better use of…

Large language models (LLMs) are increasingly seen as assistants, copilots, and consultants, capable of supporting a wide range of tasks through natural conversation. However, most systems remain constrained by a linear request-response…

While large language models (LLMs) show great potential in temporal reasoning, most existing work focuses heavily on enhancing performance, often neglecting the explainable reasoning processes underlying the results. To address this gap, we…

Large language models (LLMs) offer new opportunities for automated data extraction and property prediction across materials science, yet their use in superconductivity research remains limited. Here we construct a large experimental…

In recent years, large language models (LLM) have emerged as powerful tools for diverse natural language processing tasks. However, their potential for recommender systems under the generative recommendation paradigm remains relatively…

Large, pre-trained transformer-based language models such as BERT have drastically changed the Natural Language Processing (NLP) field. We present a survey of recent work that uses these large language models to solve NLP tasks via…

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an…

The advent of Large Language Models (LLMs) has significantly transformed the fields of natural and social sciences. Generative Agent-Based Models (GABMs), which utilize large language models in place of real subjects, are gaining increasing…

Natural language processing (NLP) has been traditionally applied to medicine, and generative large language models (LLMs) have become prominent recently. However, the differences between them across different medical tasks remain…

Despite the inherent limitations of existing Large Language Models in directly reading and interpreting single-cell omics data, they demonstrate significant potential and flexibility as the Foundation Model. This research focuses on how to…