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In recent years, many design automation methods have been developed to routinely create approximate implementations of circuits and programs that show excellent trade-offs between the quality of output and required resources. This paper…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
Coreset selection targets the challenge of finding a small, representative subset of a large dataset that preserves essential patterns for effective machine learning. Although several surveys have examined data reduction strategies before,…
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps…
Evolutionary algorithms (EAs) are population-based metaheuristics, originally inspired by aspects of natural evolution. Modern varieties incorporate a broad mixture of search mechanisms, and tend to blend inspiration from nature with…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Single-cell analysis is an increasingly relevant approach in "omics'' studies. In the last decade, it has been applied to various fields, including cancer biology, neuroscience, and, especially, developmental biology. This rise in…
For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unbiased measurements that reveal phenotypic patterns powerful…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
Evolutionary algorithms are metaheuristic techniques that derive inspiration from the natural process of evolution. They can efficiently solve (generate acceptable quality of solution in reasonable time) complex optimization (NP-Hard)…
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…
Recently, there has been a resurgence of interest in rigorous algorithms for the inference of cancer progression from genomic data. The motivations are manifold: (i) growing NGS and single cell data from cancer patients, (ii) need for novel…
Feature selection is one of the most challenging issues in machine learning, especially while working with high dimensional data. In this paper, we address the problem of feature selection and propose a new approach called Evolving Fast and…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
Evolutionary modeling applications are the best way to provide full information to support in-depth understanding of evaluation of organisms. These applications mainly depend on identifying the evolutionary history of existing organisms and…
Evolutionary processes proved very useful for solving optimization problems. In this work, we build a formalization of the notion of cooperation and competition of multiple systems working toward a common optimization goal of the population…
Document retrieval is one of the best established information retrieval activities since the sixties, pervading all search engines. Its aim is to obtain, from a collection of text documents, those most relevant to a pattern query. Current…
In computer interfaces in general, especially in information retrieval tasks, it is important to be able to quickly find and retrieve information. State of the art approach, used, for example, in search engines, is not effective as it…