Related papers: Mod/Resc Parsimony Inference
Given a network with an ongoing epidemic, the network immunization problem seeks to identify a fixed number of nodes to immunize in order to maximize the number of infections prevented. A fundamental computational challenge in network…
A host-parasite model is considered for a population of cells that can be of two types, A or B, and exhibits unilateral reproduction: while a B-cell always splits into two cells of the same type, the two daughter cells of an A-cell can be…
Gene regulatory networks are collections of genes that interact with one other and with other substances in the cell. By measuring gene expression over time using high-throughput technologies, it may be possible to reverse engineer, or…
Influence maximization in networks is a central problem in machine learning and causal inference, where an intervention on a subset of individuals triggers a diffusion process through the network. Existing approaches typically optimize…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…
Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature,…
We consider a continuum mechanical model of cell invasion through thin membranes. The model consists of a transmission problem for cell volume fraction complemented with continuity of stresses and mass flux across the surfaces of the…
We investigate partially identifiable queries in a class of causal models. We focus on acyclic Structural Causal Models that are quasi-Markovian (that is, each endogenous variable is connected with at most one exogenous confounder). We look…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…
In this paper, we propose a realistic mathematical model taking into account the mutual interference among the interacting populations. This model attempts to describe the control (vaccination) function as a function of the number of…
We propose a mixed integer programming (MIP) model and iterative algorithms based on topological orders to solve optimization problems with acyclic constraints on a directed graph. The proposed MIP model has a significantly lower number of…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
Biologically inspired model (BIM) for image recognition is a robust computational architecture, which has attracted widespread attention. BIM can be described as a four-layer structure based on the mechanisms of the visual cortex. Although…
Sparse representation with respect to an overcomplete dictionary is often used when regularizing inverse problems in signal and image processing. In recent years, the Convolutional Sparse Coding (CSC) model, in which the dictionary consists…
In this letter, we present a genetic algorithm-based approach for image retrieval through a multimode fiber in a reference-less system. Due to mode interference, when an image is illuminated at one side of a multimode fiber, the transmitted…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
Experimental studies are prevalent in Evolutionary Computation (EC), and concerns about the reproducibility and replicability of such studies have increased in recent times, reflecting similar concerns in other scientific fields. In this…
The design of biologically-inspired wireless communication systems using bacteria as the basic element of the system is initially motivated by a phenomenon called \emph{Quorum Sensing}. Due to high randomness in the individual behavior of a…