Related papers: LvD: A New Algorithm for Computing the Likelihood …
We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…
While likelihood is attractive in theory, its estimates by deep generative models (DGMs) are often broken in practice, and perform poorly for out of distribution (OOD) Detection. Various recent works started to consider alternative scores…
Embeddings of graphs into distributions of trees that preserve distances in expectation are a cornerstone of many optimization algorithms. Unfortunately, online or dynamic algorithms which use these embeddings seem inherently randomized and…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
The Tree Evaluation Problem ($\mathsf{TreeEval}$) is a computational problem originally proposed as a candidate to prove a separation between complexity classes $\mathsf{P}$ and $\mathsf{L}$. Recently, this problem has gained significant…
We consider the problem of efficiently computing the maximum likelihood estimator in Generalized Linear Models (GLMs) when the number of observations is much larger than the number of coefficients ($n \gg p \gg 1$). In this regime,…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…
We consider the problem of finding a solution to a multivariate polynomial equation system of degree $d$ in $n$ variables over $\mathbb{F}_2$. For $d=2$, the best-known algorithm for the problem is by Bardet et al. [J. Complexity, 2013] and…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We give an algorithm that takes as input an $n$-vertex graph $G$ and an integer $k$, runs in time $2^{O(k^2)} n^{O(1)}$, and outputs a tree decomposition of $G$ of width at most $k$, if such a decomposition exists. This resolves the…
We present a fast randomized algorithm that computes a low rank LU decomposition. Our algorithm uses random projections type techniques to efficiently compute a low rank approximation of large matrices. The randomized LU algorithm can be…
The quartet distance is a measure of similarity used to compare two unrooted phylogenetic trees on the same set of $n$ leaves, defined as the number of subsets of four leaves related by a different topology in both trees. After a series of…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…
We provide a new algorithm for the treatment of inverse problems which combines the traditional SVD inversion with an appropriate thresholding technique in a well chosen new basis. Our goal is to devise an inversion procedure which has the…
This paper is devoted to proposing a general weighted low-rank recovery model and designing a fast SVD-free computational scheme to solve it. First, our generic weighted low-rank recovery model unifies several existing approaches in the…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
The paper analyzes theoretically and empirically the performance of likelihood weighting (LW) on a subset of nodes in Bayesian networks. The proposed scheme requires fewer samples to converge due to reduction in sampling variance. The…