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Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Human cancers present a significant public health challenge and require the discovery of novel drugs through translational research. Transcriptomics profiling data that describes molecular activities in tumors and cancer cell lines are…
We propose a new framework for the study of continuous time dynamical systems on networks. We view such dynamical systems as collections of interacting control systems. We show that a class of maps between graphs called graph fibrations…
Motivated by classical communications engineering, early works in molecular communication (MC) largely adopted established modeling and signal processing concepts from wireless electromagnetic communication systems. In the context of the…
Classifying network traffic is the basis for important network applications. Prior research in this area has faced challenges on the availability of representative datasets, and many of the results cannot be readily reproduced. Such a…
Self-generated gradients have atttracted a lot of attention in the recent biological literature. It is considered as a robust strategy for a group of cells to find its way during a long journey. This note is intended to discuss various…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…
Structure and dynamics of complex networks usually deal with degree distributions, clustering, shortest path lengths and other graph properties. Although these concepts have been analysed for graphs on abstract spaces, many networks happen…
System-centric modeling and analysis are of key significance in planning and optimizing cellular networks. In this paper, we provide a mathematical analysis of performance modeling for LTE networks. The system model characterizes the…
We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Network enrichment analysis methods allow to identify active modules without being biased towards a priori defined pathways. One of mathematical formulations of such analysis is a reduction to a maximum-weight connected subgraph problem. In…
Graph property detection aims to determine whether a graph exhibits certain structural properties, such as being Hamiltonian. Recently, learning-based approaches have shown great promise by leveraging data-driven models to detect graph…
A relatively new set of transport-based transforms (CDT, R-CDT, LOT) have shown their strength and great potential in various image and data processing tasks such as parametric signal estimation, classification, cancer detection among many…
Motivated by the fact that intelligent traffic control systems have become inevitable demand to cope with the risk of traffic congestion in urban areas, this paper develops a distributed control strategy for urban traffic networks. Since…
Classification is a common AI problem, and vector search is a typical solution. This transforms a given body of text into a numerical representation, known as an embedding, and modern improvements to vector search focus on optimising speed…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
Many neural nets appear to represent data as linear combinations of "feature vectors." Algorithms for discovering these vectors have seen impressive recent success. However, we argue that this success is incomplete without an understanding…
Distribution networks -- from vasculature to urban transportation systems -- are prevalent in both the natural and consumer worlds. These systems are intrinsically physical in composition and are embedded into real space, properties that…