Related papers: Lomics: Generation of Pathways and Gene Sets using…

Interpreting transcriptomic data is one of the most common analytical tasks in modern biology. Yet most current models either consume expression profiles without producing natural-language biological explanations, or reason in language…

The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting…

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…

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…

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,…

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

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…

This study applies Large Language Models (LLMs) to two foundational Electronic Health Record (EHR) data science tasks: structured data querying (using programmatic languages, Python/Pandas) and information extraction from unstructured…

In practice, clinicians achieve a diagnosis by following a sequence of steps, such as laboratory exams, observations, or imaging. The pathways to reach diagnosis decisions are documented by guidelines authored by expert organizations, which…

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent…

While Genetic Improvement (GI) is a useful paradigm to improve functional and nonfunctional aspects of software, existing techniques tended to use the same set of mutation operators for differing objectives, due to the difficulty of writing…

Large language models (LLMs) are beginning to reshape how chemists plan and run reactions in organic synthesis. Trained on millions of reported transformations, these text-based models can propose synthetic routes, forecast reaction…

Real-world path planning tasks typically involve multiple constraints beyond simple route optimization, such as the number of routes, maximum route length, depot locations, and task-specific requirements. Traditional approaches rely on…

Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale…

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose…

The use of generative artificial intelligence (AI) models is becoming ubiquitous in many fields. Though progress continues to be made, general purpose large language AI models (LLM) show a tendency to deliver creative answers, often called…

Large language models (LLMs) have shown impressive promise in code generation, yet their progress remains limited by the shortage of large-scale datasets that are both diverse and well-aligned with human reasoning. Most existing resources…

Large language models (LLMs) have recently attracted considerable interest for their ability to perform complex reasoning tasks, such as chain-of-thought (CoT) reasoning. However, most of the existing approaches to enhance this ability rely…

Microwell microfluidics has been utilized for single-cell analysis to reveal heterogeneity in gene expression, signaling pathways, and phenotypic responses for identifying rare cell types, understanding disease progression, and developing…