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We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…
Network Embedding (NE) methods, which map network nodes to low-dimensional feature vectors, have wide applications in network analysis and bioinformatics. Many existing NE methods rely only on network structure, overlooking other…
Exploring the structural topology of genome-based large-scale metabolic network is essential for investigating possible relations between structure and functionality. Visualization would be helpful for obtaining immediate information about…
Synthetic molecular communication (MC) in the cardiovascular system is a key enabler for many envisioned medical applications inside the human body, such as targeted drug delivery, early disease detection, and continuous health monitoring.…
A novel model-based approach to verify dynamic networks is proposed; the approach consists in formally describing the network topology and dynamic link parameters. A many sorted first order logic formula is constructed to check the model…
Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate,…
This paper addresses the problem of finding cycles in the state transition graphs of synchronous Boolean networks. Synchronous Boolean networks are a class of deterministic finite state machines which are used for the modeling of gene…
In many applications such as color image processing, data has more than one piece of information associated with each spatial coordinate, and in such cases the classical optimal mass transport (OMT) must be generalized to handle…
Modern computer networks support interesting new routing models in which traffic flows from a source s to a destination t can be flexibly steered through a sequence of waypoints, such as (hardware) middleboxes or (virtualized) network…
Optimizing paths on networks is crucial for many applications, from subway traffic to Internet communication. As global path optimization that takes account of all path-choices simultaneously is computationally hard, most existing routing…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
Highly-optimized complex transport networks serve crucial functions in many man-made and natural systems such as power grids and plant or animal vasculature. Often, the relevant optimization functional is non-convex and characterized by…
Molecular dynamics (MD) simulations are increasingly being combined with machine learning (ML) to predict material properties. The molecular configurations obtained from MD are represented by multiple features, such as thermodynamic…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
The notion of synthetic molecular communication (MC) refers to the transmission of information via molecules and is largely foreseen for use within the human body, where traditional electromagnetic wave (EM)-based communication is…
Spectral embedding finds vector representations of the nodes of a network, based on the eigenvectors of a properly constructed matrix, and has found applications throughout science and technology. Many networks are multipartite, meaning…
The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular…
Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various…
In this survey paper, we will present a number of core algorithmic questions concerning several transitive reduction problems on network that have applications in network synthesis and analysis involving cellular processes. Our starting…