Related papers: Large Language Model is Secretly a Protein Sequenc…

Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified…

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…

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…

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 paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential…

Protein sequence design, determined by amino acid sequences, are essential to protein engineering problems in drug discovery. Prior approaches have resorted to evolutionary strategies or Monte-Carlo methods for protein design, but often…

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,…

Large Language Models (LLMs) exhibit world knowledge and inference capabilities, making them powerful tools for various applications. This paper proposes a feedback loop mechanism that leverages these capabilities to tune Evolution…

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…

Algorithms that use Large Language Models (LLMs) to evolve code arrived on the Genetic Programming (GP) scene very recently. We present LLM GP, a formalized LLM-based evolutionary algorithm designed to evolve code. Like GP, it uses…

Language is essentially a complex, intricate system of human expressions governed by grammatical rules. It poses a significant challenge to develop capable AI algorithms for comprehending and grasping a language. As a major approach,…

Large Language Models (LLMs) have revolutionized the field of Natural Language Processing (NLP) by automating traditional labor-intensive tasks and consequently accelerated the development of computer-aided applications. As researchers…

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…

Evolutionary algorithms excel in solving complex optimization problems, especially those with multiple objectives. However, their stochastic nature can sometimes hinder rapid convergence to the global optima, particularly in scenarios…

Prompt engineering is a new paradigm for enhancing the performance of trained neural network models. For optimizing text-style prompts, existing methods usually individually operate small portions of a text step by step, which either breaks…

Large Language Models (LLMs) have demonstrated great promise in generating code, especially when used inside an evolutionary computation framework to iteratively optimize the generated algorithms. However, in some cases they fail to…

Designing proteins de novo with tailored structural, physicochemical, and functional properties remains a grand challenge in biotechnology, medicine, and materials science, due to the vastness of sequence space and the complex coupling…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Large Language Models (LLMs) possess substantial reasoning capabilities and are increasingly applied to optimization tasks, particularly in synergy with evolutionary computation. However, while recent surveys have explored specific aspects…

Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the…