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Cellular automata are discrete and computational models thatcan be shown as general models of complexity. They are used in varied applications to derive the generalized behavior of the presented model. In this paper we have took one such…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
Clustering of motion trajectories is highly relevant for human-robot interactions as it allows the anticipation of human motions, fast reaction to those, as well as the recognition of explicit gestures. Further, it allows automated analysis…
Gradients of probabilistic model likelihoods with respect to their parameters are essential for modern computational statistics and machine learning. These calculations are readily available for arbitrary models via automatic…
We propose a novel technique for training deep networks with the objective of obtaining feature representations that exist in a Euclidean space and exhibit strong clustering behavior. Our desired features representations have three traits:…
We created two dimensional hexagonal cellular automata to obtain complexity. Considering the game of life rules, Wolfram's works about life-like structures and John von Neumann's self-replication, self-maintenance, self-reproduction…
Mutation rate variation across loci is well known to cause difficulties, notably identifiability issues, in the reconstruction of evolutionary trees from molecular sequences. Here we introduce a new approach for estimating general…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
In order to apply the recent successes of machine learning and automated plant phenotyping on a large scale using agricultural robotics, efficient and general algorithms must be designed to intelligently split crop fields into small, yet…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
Photomosaic images are a type of images consisting of various tiny images. A complete form can be seen clearly by viewing it from a long distance. Small tiny images which replace blocks of the original image can be seen clearly by viewing…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
The claw finding problem has been studied in terms of query complexity as one of the problems closely connected to cryptography. For given two functions, f and g, as an oracle which have domains of size N and M (N<=M), respectively, and the…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Background: How to extract useful information from complex biological networks is a major goal in many fields, especially in genomics and proteomics. We have shown in several works that iterative hierarchical clustering, as implemented in…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…