Related papers: Tree trace reconstruction using subtraces

Consider an information source generating a symbol at the root of a tree network whose links correspond to noisy communication channels, and broadcasting it through the network. We study the problem of reconstructing the transmitted symbol…

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…

Work introduces a hierarchical binary tree-based reduction that replaces standard self-attention. The core idea is to use a recursive Gated Linear Unit merge operation, achieving O(n) total merge operations O(log n) parallel depth O(n d^2)…

We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…

We establish finite-sample guarantees for efficient proper learning of bounded-degree polytrees, a rich class of high-dimensional probability distributions and a subclass of Bayesian networks, a widely-studied type of graphical model.…

We revisit the \textsc{$k$-Secluded Tree} problem. Given a vertex-weighted undirected graph $G$, its objective is to find a maximum-weight induced subtree $T$ whose open neighborhood has size at most $k$. We present a fixed-parameter…

In the trace reconstruction problem, an unknown bit string ${\bf x}\in\{0,1 \}^n$ is sent through a deletion channel where each bit is deleted independently with some probability $q\in(0,1)$, yielding a contracted string $\widetilde{\bf…

We consider the model of random trees introduced by Devroye [SIAM J. Comput. 28 (1999) 409-432]. The model encompasses many important randomized algorithms and data structures. The pieces of data (items) are stored in a randomized fashion…

In this paper, we investigate adaptive nonlinear regression and introduce tree based piecewise linear regression algorithms that are highly efficient and provide significantly improved performance with guaranteed upper bounds in an…

We use a sign-reversing involution to show that trees on the vertex set [n], considered to be rooted at 1, in which no vertex has exactly one child are counted by 1/n sum_{k=1}^{n} (-1)^(n-k) {n}-choose-{k} (n-1)!/(k-1)! k^(k-1). This…

This paper gives a new algorithm for sampling tree-weighted partitions of a large class of planar graphs. Formally, the tree-weighted distribution on $k$-partitions of a graph weights $k$-partitions proportional to the product of the number…

We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…

In this paper we investigate the use of the concept of tree dimension in Horn clause analysis and verification. The dimension of a tree is a measure of its non-linearity - for example a list of any length has dimension zero while a complete…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

We consider the in-plane motion of elastic strings on tree-like network, observed from the 'leaves'. We investigate the inverse problem of recovering not only the physical properties i.e. the 'optical lengths' of each string, but also the…

We propose a novel technique, termed compact shape trees, for computing correspondences of single-boundary 2-D shapes in O(n2) time. Together with zero or more features defined at each of n sample points on the shape's boundary, the compact…

In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…

The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…

A relaxed $k$-ary tree is an ordered directed acyclic graph with a unique source and sink in which every node has out-degree $k$. These objects arise in the compression of trees in which some repeated subtrees are factored and repeated…