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Evolution, the engine behind the survival and growth of life on Earth, operates through the population-based process of reproduction. Inspired by this principle, this paper formally defines a newly emerging problem -- the population-based…

The ability of Large Language Models (LLMs) to perform reasoning tasks such as deduction has been widely investigated in recent years. Yet, their capacity to generate proofs-faithful, human-readable explanations of why conclusions…

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,…

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training…

This paper proposes a novel conceptualization of Large Language Models (LLMs) as externalized informational substrates that function analogously to DNA for human cultural dynamics. Rather than viewing LLMs as either autonomous intelligence…

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) have unveiled remarkable capabilities in understanding and generating both natural language and code, but LLM reasoning is prone to hallucination and struggle with complex, novel scenarios, often getting stuck…

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…

Research on long non-coding RNAs (lncRNAs) has garnered significant attention due to their critical roles in gene regulation and disease mechanisms. However, the complexity and diversity of lncRNA sequences, along with the limited knowledge…

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…

Feature transformation aims to reconstruct the feature space of raw features to enhance the performance of downstream models. However, the exponential growth in the combinations of features and operations poses a challenge, making it…

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…

Pre-trained large language models (LLMs) exhibit powerful capabilities for generating natural text. Evolutionary algorithms (EAs) can discover diverse solutions to complex real-world problems. Motivated by the common collective and…

Large Language Models (LLMs) represent a class of deep learning models adept at understanding natural language and generating coherent responses to various prompts or queries. These models far exceed the complexity of conventional neural…

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes…

The rapid advancement of artificial intelligence, particularly with the development of Large Language Models (LLMs) built on the transformer architecture, has redefined the capabilities of natural language processing. These models now…

Large Language Models (LLMs) have revolutionized natural language processing through their state of art reasoning capabilities. This paper explores the convergence of LLM reasoning techniques and feature generation for machine learning…

Large language models (LLMs) have led to breakthroughs in language tasks, yet the internal mechanisms that enable their remarkable generalization and reasoning abilities remain opaque. This lack of transparency presents challenges such as…

Evolutionary methods have long been useful for analysis and explanation in genetics, biology, ecology, and related fields. In this work, we extend these methods to neural networks, specifically large language models (LLMs), to better…