Related papers: A genetic algorithm to discover flexible motifs wi…
Genetic algorithms are a powerful tool in optimization for single and multi-modal functions. This paper provides an overview of their fundamentals with some analytical examples. In addition, we explore how they can be used as a parameter…
Networks are a fundamental tool for modeling complex systems in a variety of domains including social and communication networks as well as biology and neuroscience. Small subgraph patterns in networks, called network motifs, are crucial to…
The standard methods for detecting differential gene expression are mostly designed for analyzing a single gene expression experiment. When data from multiple related gene expression studies are available, separately analyzing each study is…
Current genomic foundation models (GFMs) rely on extensive neural computation to implicitly approximate conserved biological motifs from single-nucleotide inputs. We propose Gengram, a conditional memory module that introduces an explicit…
We introduce MoTIF, a mode-structured tensor framework for multi-parametric approximation, super-resolution, and temporal forecasting of high-dimensional unsteady systems. The methodology leverages High-Order Singular Value Decomposition…
Genotype-to-phenotype mappings translate genotypic variations such as mutations into phenotypic changes. Neutrality is the observation that some mutations do not lead to phenotypic changes. Studying the search trajectories in genotypic and…
Motivation: Laboratory gene regulatory data for a species are sporadic. Despite the abundance of gene regulatory network algorithms that employ single data sets, few algorithms can combine the vast but disperse sources of data and extract…
One fundamental problem in temporal graph analysis is to count the occurrences of small connected subgraph patterns (i.e., motifs), which benefits a broad range of real-world applications, such as anomaly detection, structure prediction,…
This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
A leitmotif is a recurring theme in literature, movies or music that carries symbolic significance for the piece it is contained in. When this piece can be represented as a multi-dimensional time series (MDTS), such as acoustic or visual…
Graph motif, defined as the microstructure that appears repeatedly in a large graph, reveals important topological characteristics of the large graph and has gained increasing attention in power system analysis regarding reliability,…
In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
Is there a unified framework for graph-based retrosynthesis prediction? Through analysis of full-, semi-, and non-template retrosynthesis methods, we discovered that they strive to strike an optimal balance between combinability and…
Time series prediction is of great significance in many applications and has attracted extensive attention from the data mining community. Existing work suggests that for many problems, the shape in the current time series may correlate an…
A motif is a frequently occurring subgraph of a given directed or undirected graph $G$. Motifs capture higher order organizational structure of $G$ beyond edge relationships, and, therefore, have found wide applications such as in graph…
In this article we provide a comprehensive review of the different evolutionary algorithm techniques used to address multimodal optimization problems, classifying them according to the nature of their approach. On the one hand there are…