Related papers: A Duality Based 2-Approximation Algorithm for Maxi…
Computing and storing probabilities is a hard problem as soon as one has to deal with complex distributions over multiple random variables. The problem of efficient representation of probability distributions is central in term of…
Decision tree optimization is fundamental to interpretable machine learning. The most popular approach is to greedily search for the best feature at every decision point, which is fast but provably suboptimal. Recent approaches find the…
We develop fast approximation algorithms for the minimum-cost version of the Bounded-Degree MST problem (BD-MST) and its generalization the Crossing Spanning Tree problem (Crossing-ST). We solve the underlying LP to within a $(1+\epsilon)$…
This paper studies a 4-approximation algorithm for k-prize collecting Steiner tree problems. This problem generalizes both k-minimum spanning tree problems and prize collecting Steiner tree problems. Our proposed algorithm employs two…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
We present a general method for obtaining strong bounds for discrete optimization problems that is based on a concept of branching duality. It can be applied when no useful integer programming model is available, and we illustrate this with…
We consider an incremental variant of the rooted prize-collecting Steiner-tree problem with a growing budget constraint. While no incremental solution exists that simultaneously approximates the optimum for all budgets, we show that a…
A merge tree is a fundamental topological structure used to capture the sub-level set (and similarly, super-level set) topology in scalar data analysis. The interleaving distance is a theoretically sound, stable metric for comparing merge…
This paper summarizes the work on implementing few solutions for the Steiner Tree problem which we undertook in the PAAL project. The main focus of the project is the development of generic implementations of approximation algorithms…
Given two sets of points in the plane, $P$ of $n$ terminals and $S$ of $m$ Steiner points, a Steiner tree of $P$ is a tree spanning all points of $P$ and some (or none or all) points of $S$. A Steiner tree with length of longest edge…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
We propose a doubly stochastic primal-dual coordinate optimization algorithm for empirical risk minimization, which can be formulated as a bilinear saddle-point problem. In each iteration, our method randomly samples a block of coordinates…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
Given a set $P$ of terminals in the plane and a partition of $P$ into $k$ subsets $P_1, ..., P_k$, a two-level rectilinear Steiner tree consists of a rectilinear Steiner tree $T_i$ connecting the terminals in each set $P_i$ ($i=1,...,k$)…
We achieve a (randomized) polynomial-time approximation scheme (PTAS) for the Steiner Forest Problem in doubling metrics. Before our work, a PTAS is given only for the Euclidean plane in [FOCS 2008: Borradaile, Klein and Mathieu]. Our PTAS…