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Properly estimating correlations between objects at different spatial scales necessitates $\mathcal{O}(n^2)$ distance calculations. For this reason, most widely adopted packages for estimating correlations use clustering algorithms to…
Permutation resemblance measures the distance of a function from being a permutation. Here we show how to determine the permutation resemblance through linear integer programming techniques. We also present an algorithm for constructing…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Computing the similarity between two probability distributions is a recurring theme across control. We introduce a unified family of distances between the probability distributions of two random variables that is based on the discrepancy…
The separability of clusters is one of the most desired properties in clustering. There is a wide range of settings in which different clusterings of the same data set appear. We are interested in applications where there is a need for an…
We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a universal similarity distance, the normalized compression…
In this work, we analyze if it is possible to distinguish between different clones of the same bacteria species (Klebsiella pneumoniae) based only on microscopic images. It is a challenging task, previously considered impossible due to the…
Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we…
The evolution of encryption algorithms have led to the development of very complicated and highly versatile algorithms that sacrifice efficiency for better and harder to decrypt results. But by the application of a genetic schema to the…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
Two important tasks in the field of Topological Data Analysis are building practical multifiltrations on objects and using TDA to detect the geometry. Motivated by the tasks, we build multiparameter filtrations by operators on images named…
We study the classical metric $k$-median clustering problem over a set of input rankings (i.e., permutations), which has myriad applications, from social-choice theory to web search and databases. A folklore algorithm provides a…
Subset selection is an important component in evolutionary multiobjective optimization (EMO) algorithms. Clustering, as a classic method to group similar data points together, has been used for subset selection in some fields. However,…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
Recent advances in imaging technology now provide us with 3D images of developing organs. These can be used to extract 3D geometries for simulations of organ development. To solve models on growing domains, the displacement fields between…
In this paper, we focus on numerical approximations of Piecewise Diffusion Markov Processes (PDifMPs), particularly when the explicit flow maps are unavailable. Our approach is based on the thinning method for modelling the jump mechanism…
The compact genetic algorithm (cGA) is an non-elitist estimation of distribution algorithm which has shown to be able to deal with difficult multimodal fitness landscapes that are hard to solve by elitist algorithms. In this paper, we…
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In…
The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization. Describing phenomena that cover such…