相关论文: Lyndon Array Construction during Burrows-Wheeler I…

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…

We provide an $O(n \log n)$ algorithm computing the linear maximum induced matching width of a tree and an optimal layout.

We construct fast algorithms for evaluating transforms associated with families of functions which satisfy recurrence relations. These include algorithms both for computing the coefficients in linear combinations of the functions, given the…

We describe an algorithm, implemented in Python, which can enumerate any permutation class with polynomial enumeration from a structural description of the class. In particular, this allows us to find formulas for the number of permutations…

Change-point problems have appeared in a great many applications for example cancer genetics, econometrics and climate change. Modern multiscale type segmentation methods are considered to be a statistically efficient approach for multiple…

A classic data structure problem is to preprocess a string T of length $n$ so that, given a query $q$, we can quickly find all substrings of T with Hamming distance at most $k$ from the query string. Variants of this problem have seen…

In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…

In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…

We consider the classical makespan minimization scheduling problem where $n$ jobs must be scheduled on $m$ identical machines. Using weighted random sampling, we developed two sublinear time approximation schemes: one for the case where $n$…

A universal cycle for a set S of combinatorial objects is a cyclic sequence of length |S| that contains a representative of each element in S exactly once as a substring. Despite the many universal cycle constructions known in the…

The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…

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…

This paper presents a new technique for deterministic length reduction. This technique improves the running time of the algorithm presented in \cite{LR07} for performing fast convolution in sparse data. While the regular fast convolution of…

Linear rules have played an increasing role in structural proof theory in recent years. It has been observed that the set of all sound linear inference rules in Boolean logic is already coNP-complete, i.e. that every Boolean tautology can…

The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…

Recent research has challenged the necessity of complex deep learning architectures for time series forecasting, demonstrating that simple linear models can often outperform sophisticated approaches. Building upon this insight, we introduce…

We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…

We consider the fundamental problem of constructing fast and small circuits for binary addition. We propose a new algorithm with running time $\mathcal O(n \log_2 n)$ for constructing linear-size $n$-bit adder circuits with a significantly…

We consider the following problem: given an unsorted array of $n$ elements, and a sequence of intervals in the array, compute the median in each of the subarrays defined by the intervals. We describe a simple algorithm which uses O(n) space…

We give an algorithm that computes a $(1+\epsilon)$-approximate Steiner forest in near-linear time $n \cdot 2^{(1/\epsilon)^{O(ddim^2)} (\log \log n)^2}$. This is a dramatic improvement upon the best previous result due to Chan et al., who…