Related papers: Prefix Sorting DFAs: a Recursive Algorithm
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
The Cover Suffix Tree (CST) of a string $T$ is the suffix tree of $T$ with additional explicit nodes corresponding to halves of square substrings of $T$. In the CST an explicit node corresponding to a substring $C$ of $T$ is annotated with…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears as a subpath of a graph admits a quadratic lower bound under…
A new method for constructing minimum-redundancy binary prefix codes is described. Our method does not explicitly build a Huffman tree; instead it uses a property of optimal prefix codes to compute the codeword lengths corresponding to the…
A complementation operation on a vertex of a digraph changes all outgoing arcs into non-arcs, and outgoing non-arcs into arcs. A partially complemented digraph $\widetilde{G}$ is a digraph obtained from a sequence of vertex complement…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
\begin{abstract} Greedy permutations, also known as Gonzalez Orderings or Farthest Point Traversals are a standard way to approximate $k$-center clustering and have many applications in sampling and approximating metric spaces. A greedy…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
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…
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…
We introduce a novel chart-based algorithm for span-based parsing of discontinuous constituency trees of block degree two, including ill-nested structures. In particular, we show that we can build variants of our parser with smaller search…
We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…
The binary indexed tree, or Fenwick tree, is a data structure that can efficiently update values and calculate prefix sums in an array. It allows both of these operations to be performed in $O(\log_2 N)$ time. Here we present a novel data…
We tackle two long-standing problems related to re-expansions in heuristic search algorithms. For graph search, A* can require $\Omega(2^{n})$ expansions, where $n$ is the number of states within the final $f$ bound. Existing algorithms…
We seek to perform efficient queries for the predecessor among $n$ values stored in $k$ sorted arrays. Evading the $\Omega(n \log k)$ lower bound from merging $k$ arrays, we support predecessor queries in $O(\log n)$ time after $O(n…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
We give algorithms to accelerate the computation of deterministic finite automata (DFA) by calculating the state of a DFA n positions ahead utilizing a reverse scan of the next n characters. Often this requires scanning fewer than n…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…