Related papers: Relative Suffix Trees
Random Forests (RF) is a popular machine learning method for classification and regression problems. It involves a bagging application to decision tree models. One of the primary advantages of the Random Forests model is the reduction in…
The need for scalable concurrent ordered set data structures with linearizable range query support is increasing due to the rise of multicore computers, data processing platforms and in-memory databases. This paper presents a new concurrent…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
The Binary Search Tree (BST) is average in computer science which supports a compact data structure in memory and oneself even conducts a row of quick algorithms, by which people often apply it in dynamical circumstance. Besides these…
We propose a data structure that stores, in a compressed way, object trajectories, which at the same time, allow to efficiently response queries without the need to decompress the data. We use a data structure, called $k^{2}$-tree, to store…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Traditionally, data compression deals with the problem of concisely representing a data source, e.g. a sequence of letters, for the purpose of eventual reproduction (either exact or approximate). In this work we are interested in the case…
Let $A$ be a static array storing $n$ elements from a totally ordered set. We present a data structure of optimal size at most $n\log_2(3+2\sqrt{2})+o(n)$ bits that allows us to answer the following queries on $A$ in constant time, without…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
In this paper we will describe a new approach on the well-known suffix-array algorithm using Big Table Data Technology. We will demonstrate how it is possible to refactor a well-known algorithm coupled by taking advantage of an…
Given a gene tree and a species tree, ancestral configurations represent the combinatorially distinct sets of gene lineages that can reach a given node of the species tree. They have been introduced as a data structure for use in the…
Trees can accelerate queries that search or aggregate values over large collections. They achieve this by storing metadata that enables quick pruning (or inclusion) of subtrees when predicates on that metadata can prove that none (or all)…
Consider the case where consecutive blocks of N letters of a semi-infinite individual sequence X over a finite-alphabet are being compressed into binary sequences by some one-to-one mapping. No a-priori information about X is available at…
The longest common extension (LCE) of two indices in a string is the length of the longest identical substrings starting at these two indices. The LCE problem asks to preprocess a string into a compact data structure that supports fast LCE…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
One of the central problems in the classification of individual test sequences (e.g. genetic analysis), is that of checking for the similarity of sample test sequences as compared with a set of much longer training sequences. This is done…
Large spatial datasets often represent a number of spatial point processes generated by distinct entities or classes of events. When crossed with covariates, such as discrete time buckets, this can quickly result in a data set with millions…
Sequence representations supporting queries $access$, $select$ and $rank$ are at the core of many data structures. There is a considerable gap between the various upper bounds and the few lower bounds known for such representations, and how…