Related papers: Simpler O(1) Query Algorithm for Level Ancestors
We describe a framework for maintaining forest algebra representations that are of logarithmic height for unranked trees. Such representations can be computed in O(n) time and updated in O(log(n)) time. The framework is of potential…
We describe a method that will reconstruct an unrooted binary phylogenetic level-1 network on n taxa from the set of all quartets containing a certain fixed taxon, in O(n^3) time. We also present a more general method which can handle more…
Consider a pair of plane straight-line graphs, whose edges are colored red and blue, respectively, and let n be the total complexity of both graphs. We present a O(n log n)-time O(n)-space technique to preprocess such pair of graphs, that…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We present an algorithm that generates multiset permutations in O(1) time for each permutation, that is, by a loop-less algorithm with O(n) extra memory requirement. There already exist several such algorithms that generate multiset…
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…
We introduce a structured quantum search algorithm that leverages entanglement maps and a fixed-point method to minimize oracle query complexity in unsorted datasets. By partitioning qubits into rows based on their entanglement order, the…
Chaining algorithms aim to form a semi-global alignment of two sequences based on a set of anchoring local alignments as input. Depending on the optimization criteria and the exact definition of a chain, there are several $O(n \log n)$ time…
Understanding how the time-complexity of evolutionary algorithms (EAs) depend on their parameter settings and characteristics of fitness landscapes is a fundamental problem in evolutionary computation. Most rigorous results were derived…
We present space-efficient parallel strategies for two fundamental combinatorial search problems, namely, backtrack search and branch-and-bound, both involving the visit of an $n$-node tree of height $h$ under the assumption that a node can…
Tree path minimum query problem is a fundamental problem while processing trees, and is used widely in minimum spanning tree verification and randomized minimum spanning tree algorithms. In this paper, we study the possibility of building…
The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We propose Hercules, a parallel tree-based technique for exact similarity search on massive disk-based data series collections. We present novel index construction and query answering algorithms that leverage different summarization…
Consider observation data, comprised of n observation vectors with values on a set of attributes. This gives us n points in attribute space. Having data structured as a tree, implied by having our observations embedded in an ultrametric…
Time series are ubiquitous in domains ranging from medicine to marketing and finance. Frequent Pattern Mining (FPM) from a time series has thus received much attention. Recently, it has been studied under the order-preserving (OP) matching…
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
We show that any quantum algorithm searching an ordered list of n elements needs to examine at least 1/12 log n-O(1) of them. Classically, log n queries are both necessary and sufficient. This shows that quantum algorithms can achieve only…
The nni-distance is a well-known distance measure for phylogenetic trees. We construct an efficient parallel approximation algorithm for the nni-distance in the CRCW-PRAM model running in O(log n) time on O(n) processors. Given two…