Related papers: Compact Ancestry Labeling Schemes for Trees of Sma…
Genealogy research is the study of family history using available resources such as historical records. Ancestry provides its customers with one of the world's largest online genealogical index with billions of records from a wide range of…
We address the problem of summarizing embedded tree patterns extracted from large data trees. We do so by defining and mining closed and maximal embedded unordered tree patterns from a single large data tree. We design an embedded frequent…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
Over the past decade, a long line of research has investigated the distributed complexity landscape of locally checkable labeling (LCL) problems on bounded-degree graphs, culminating in an almost-complete classification on general graphs…
The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…
Suppose we label the vertices of a tree by positive integers. The weight of an edge is defined by a monotonically increasing function of the absolute value of the difference of the labels of its endpoints. We define the total cost of the…
A new family of codes, called clustering-correcting codes, is presented in this paper. This family of codes is motivated by the special structure of data that is stored in DNA-based storage systems. The data stored in these systems has the…
Most of the attention in statistical compression is given to the space used by the compressed sequence, a problem completely solved with optimal prefix codes. However, in many applications, the storage space used to represent the prefix…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
A subtree of a tree is any induced subgraph that is again a tree (i.e., connected). The mean subtree order of a tree is the average number of vertices of its subtrees. This invariant was first analyzed in the 1980s by Jamison. An intriguing…
This paper addresses the basic question of how well can a tree approximate distances of a metric space or a graph. Given a graph, the problem of constructing a spanning tree in a graph which strongly preserves distances in the graph is a…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
An optimal binary search tree for an access sequence on elements is a static tree that minimizes the total search cost. Constructing perfectly optimal binary search trees is expensive so the most efficient algorithms construct almost…
Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context schemes: a method that allows the unambiguous recognition of a…
We propose an extension of tree-based space-partitioning indexing structures for data with low intrinsic dimensionality embedded in a high dimensional space. We call this extension an Angle Tree. Our extension can be applied to both…
Knuth and Moore presented a theoretical lower bound on the number of leaves that any fixed-depth minimax tree-search algorithm traversing a uniform tree must explore, the so-called minimal tree. Since real-life minimax trees are not…
Regularization is essential for avoiding over-fitting to training data in network optimization, leading to better generalization of the trained networks. The label noise provides a strong implicit regularization by replacing the target…
A fault-tolerant distance labeling scheme assigns a label to each vertex and edge of an undirected weighted graph $G$ with $n$ vertices so that, for any edge set $F$ of size $|F| \leq f$, one can approximate the distance between $p$ and $q$…
Suppose we have n keys, n access probabilities for the keys, and n+1 access probabilities for the gaps between the keys. Let h_min(n) be the minimal height of a binary search tree for n keys. We consider the problem to construct an optimal…