Related papers: Mod/Resc Parsimony Inference
The human body is able to generate a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design…
Graph clustering is a challenging pattern recognition problem whose goal is to identify vertex partitions with high intra-group connectivity. This paper investigates a bi-objective problem that maximizes the number of intra-cluster edges of…
Inferring microbial interaction networks from abundance patterns is an important approach to advance our understanding of microbial communities in general and the human microbiome in particular. Here we suggest discriminating two levels of…
It is estimated that around 80\% of the world's population live in areas susceptible to at-least one major vector borne disease, and approximately 20% of global communicable diseases are spread by mosquitoes. Furthermore, the outbreaks of…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
We address the problem of two-variable causal inference without intervention. This task is to infer an existing causal relation between two random variables, i.e. $X \rightarrow Y$ or $Y \rightarrow X$ , from purely observational data. As…
Integrative analyses based on statistically relevant associations between genomics and a wealth of intermediary phenotypes (such as imaging) provide vital insights into their clinical relevance in terms of the disease mechanisms. Estimates…
In an implicit combinatorial optimization problem, the constraints are not enumerated explicitly but rather stated implicitly through equations, other constraints or auxiliary algorithms. An important subclass of such problems is the…
We consider a branching model for a population of dividing cells infected by parasites. Each cell receives parasites by inheritance from its mother cell and independent contamination from outside the population. Parasites multiply randomly…
We study the $k$-Submodular Cover ($kSC$) problem, a natural generalization of the classical Submodular Cover problem that arises in artificial intelligence and combinatorial optimization tasks such as influence maximization, resource…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
We consider causal inference in the presence of unobserved confounding. We study the case where a proxy is available for the unobserved confounding in the form of a network connecting the units. For example, the link structure of a social…
Interest in the study of in-host microbial communities has increased in recent years due to our improved understanding of the communities' significant role in host health. As a result, the ability to model these communities using…
In this paper, we investigate a modified Trojan Y chromosome (TYC) strategy aimed at eradicating invasive species from natural habitats. The proposed mathematical model enhances the original TYC framework by ensuring the non-negativity of…
When our immune system encounters foreign antigens (i.e., from pathogens), the B cells that produce our antibodies undergo a cyclic process of proliferation, mutation, and selection, improving their ability to bind to the specific antigen.…
Natural phenomenon of coevolution is the reciprocally induced evolutionary change between two or more species or population. Though this biological occurrence is a natural fact, there are only few attempts to use this as a simile in…
The control of biological systems presents interesting applications such as cell reprogramming or drug target identification. A common type of control strategy consists in a set of interventions that, by fixing the values of some variables,…
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…
We examine a transmission problem driven by a degenerate quasilinear operator with a natural interface condition. Two aspects of the problem entail genuine difficulties in the analysis: the absence of representation formulas for the…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…