Related papers: LvD: A New Algorithm for Computing the Likelihood …
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
Modern trends in data collection are bringing current mainstream techniques for database query processing to their limits. Consequently, various novel approaches for efficient query processing are being actively studied. One such approach…
We study computational aspects of the nonparametric maximum likelihood estimator (NPMLE) for the distribution function of bivariate interval censored data. The computation of the NPMLE consists of two steps: a parameter reduction step and…
In this paper, we propose an offline-online strategy based on the Localized Orthogonal Decomposition (LOD) method for elliptic multiscale problems with randomly perturbed diffusion coefficient. We consider a periodic deterministic…
This paper presents "Predictive Pipelined Decoding (PPD)," an approach that speeds up greedy decoding in Large Language Models (LLMs) while maintaining the exact same output as the original decoding. Unlike conventional strategies, PPD…
Least squares (LS) fitting is one of the most fundamental techniques in science and engineering. It is used to estimate parameters from multiple noisy observations. In many problems the parameters are known a-priori to be bounded integer…
The reconstruction of the history of evolutionary genome-wide events among a set of related organisms is of great biological interest. A simplified model that captures only content modifying operations was introduced recently. It allows the…
Diffusion Large Language Models (DLLMs) have emerged as a new paradigm of language modeling beyond autoregressive next-token prediction. Taking advantage of their inherent modeling foundations, DLLMs have the great potential of efficient…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Multivariate linear mixed models (mvLMMs) have been widely used in many areas of genetics, and have attracted considerable recent interest in genome-wide association studies (GWASs). However, fitting mvLMMs is computationally non-trivial,…
We present a randomized $O(m \log^2 n)$ work, $O(\text{polylog } n)$ depth parallel algorithm for minimum cut. This algorithm matches the work bounds of a recent sequential algorithm by Gawrychowski, Mozes, and Weimann [ICALP'20], and…
Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
We show fast deterministic algorithms for fundamental problems on forests in the challenging low-space regime of the well-known Massive Parallel Computation (MPC) model. A recent breakthrough result by Coy and Czumaj [STOC'22] shows that,…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
The problem of learning forest-structured discrete graphical models from i.i.d. samples is considered. An algorithm based on pruning of the Chow-Liu tree through adaptive thresholding is proposed. It is shown that this algorithm is both…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
Sampling from high-dimensional probability distributions is fundamental in machine learning and statistics. As datasets grow larger, computational efficiency becomes increasingly important, particularly in reducing adaptive complexity,…