arXiv subjects

Benny Chor

Publications and source records attributed to Benny Chor.

4 recordsLinked to original sources

arXiv2017

A High Quartets Distance Construction

Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is $\frac{2}{3}\binom{N}{4}$. However, no strongly explicit construction reaching this bound asymptotically was known. We consider complete, balanced binary trees on $N=2^n$ leaves, labeled by $n$ long bit sequences. Ordering the leaves in one tree by the prefix order, and in the other tree by the suffix order, we show that the resulting quartet distance is $\left(\frac{2}{3} + o(1)\right)\binom{N}{4}$, and it always exceeds the $\frac{2}{3}\binom{N}{4}$ bound.

math.CO↗

arXiv2015

Representative Selection in Non Metric Datasets

This paper considers the problem of representative selection: choosing a subset of data points from a dataset that best represents its overall set of elements. This subset needs to inherently reflect the type of information contained in the entire set, while minimizing redundancy. For such purposes, clustering may seem like a natural approach. However, existing clustering methods are not ideally suited for representative selection, especially when dealing with non-metric data, where only a pairwise similarity measure exists. In this paper we propose $δ$-medoids, a novel approach that can be viewed as an extension to the $k$-medoids algorithm and is specifically suited for sample representative selection from non-metric data. We empirically validate $δ$-medoids in two domains, namely music analysis and motion analysis. We also show some theoretical bounds on the performance of $δ$-medoids and the hardness of representative selection in general.

cs.AI↗

arXiv2013

Tree split probabilities determine the branch lengths

The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree determines the tree and its branch lengths. However, the number of patterns is typically much larger than the number of edges, suggesting considerable redundancy in the branch length estimation. In this paper we ask whether the probabilities of just the `edge-specific' patterns (the ones that correspond to a change of state on a single edge) suffice to recover the branch lengths of the tree, under a symmetric 2-state Markov process. We first show that this holds provided the branch lengths are sufficiently short, by applying the inverse function theorem. We then consider whether this restriction to short branch lengths is necessary, and show that for trees with up to four leaves it can be lifted. This leaves open the interesting question of whether this holds in general.

q-bio.PE↗

arXiv2005

Maximum Likelihood Jukes-Cantor Triplets: Analytic Solutions

Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the simplest models - three and four taxa under a molecular clock, with just two state characters. In this work we give, for the first time, analytic solutions for a family of trees with four state characters, like normal DNA or RNA. The model of substitution we use is the Jukes-Cantor model, and the trees are on three taxa under molecular clock, namely rooted triplets. We employ a number of approaches and tools to solve this system: Spectral methods (Hadamard conjugation), a new representation of variables (the path-set spectrum), and algebraic geometry tools (the resultant of two polynomials). All these, combined with heavy application of computer algebra packages (Maple), let us derive the desired solution.

q-bio.PE↗