Related papers: Efficient Parallel Computation of Nearest Neighbor…
We present the first work-optimal polylogarithmic-depth parallel algorithm for the minimum cut problem on non-sparse graphs. For $m\geq n^{1+\epsilon}$ for any constant $\epsilon>0$, our algorithm requires $O(m \log n)$ work and $O(\log^3…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
Let G be a directed graph with n vertices and non-negative weights in its directed edges, embedded on a surface of genus g, and let f be an arbitrary face of G. We describe a randomized algorithm to preprocess the graph in O(gn log n) time…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Let $G$ be an $n$-node simple directed planar graph with nonnegative edge weights. We study the fundamental problems of computing (1) a global cut of $G$ with minimum weight and (2) a~cycle of $G$ with minimum weight. The best previously…
Computing the similarity between two data points plays a vital role in many machine learning algorithms. Metric learning has the aim of learning a good metric automatically from data. Most existing studies on metric learning for…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
We compare the performance of three nearest neighbor search algorithms: the Orchard, ball tree, and VP-tree algorithms. These algorithms are commonly used for nearest-neighbor searches and are known for their efficiency in large datasets.…
We present four novel approximation algorithms for finding triangulation of minimum treewidth. Two of the algorithms improve on the running times of algorithms by Robertson and Seymour, and Becker and Geiger that approximate the optimum by…
Existing parallel algorithms for wavelet tree construction have a work complexity of $O(n\log\sigma)$. This paper presents parallel algorithms for the problem with improved work complexity. Our first algorithm is based on parallel integer…
Optimal Transport is a popular distance metric for measuring similarity between distributions. Exact algorithms for computing Optimal Transport can be slow, which has motivated the development of approximate numerical solvers (e.g. Sinkhorn…
We present the first near optimal approximation schemes for the maximum weighted (uncapacitated or capacitated) $b$--matching problems for non-bipartite graphs that run in time (near) linear in the number of edges. For any…
A nearest-neighbor-interchange (NNI) walk is a sequence of unrooted phylogenetic trees, T_0, T_1, T_2,... where each consecutive pair of trees differ by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
Uniform cost-distance Steiner trees minimize the sum of the total length and weighted path lengths from a dedicated root to the other terminals. They are applied when the tree is intended for signal transmission, e.g. in chip design or…
Relative Nearest Neighbor Descent (RNN-Descent) is a state-of-the-art algorithm for constructing sparse approximate nearest neighbor (ANN) graphs by combining the iterative refinement of NN-Descent with the edge-pruning rules of the…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Terrain Guarding Problem(TGP), which is known to be NP-complete, asks to find a smallest set of guard locations on a terrain $T$ such that every point on $T$ is visible by a guard. Here, we study this problem on 1.5D orthogonal terrains…
Finding an optimal assignment between two sets of objects is a fundamental problem arising in many applications, including the matching of `bag-of-words' representations in natural language processing and computer vision. Solving the…