相关论文: Linear Time Construction of Indexable Founder Bloc…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Monotonicity is a simple yet significant qualitative characteristic. We consider the problem of segmenting a sequence in up to K segments. We want segments to be as monotonic as possible and to alternate signs. We propose a quality metric…

RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…

We give an $m^{1+o(1)}\beta^{o(1)}$-time algorithm for generating a uniformly random spanning tree in an undirected, weighted graph with max-to-min weight ratio $\beta$. We also give an $m^{1+o(1)}\epsilon^{-o(1)}$-time algorithm for…

Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…

A spanner of a graph is a subgraph that preserves lengths of shortest paths up to a multiplicative distortion. For every $k$, a spanner with size $O(n^{1+1/k})$ and stretch $(2k+1)$ can be constructed by a simple centralized greedy…

Compact and I/O-efficient data representations play an important role in efficient algorithm design, as memory bandwidth and latency can present a significant performance bottleneck, slowing the computation by orders of magnitude. While…

Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…

The Poisson Generalized Linear Model (GLM) is a foundational tool for analyzing neural spike train data. However, standard implementations rely on discretizing spike times into binned count data, limiting temporal resolution and…

In the index coding problem, introduced by Birk and Kol (INFOCOM, 1998), the goal is to broadcast an n bit word to n receivers (one bit per receiver), where the receivers have side information represented by a graph G. The objective is to…

For an arbitrary undirected simple graph G with m edges, we give an algorithm with running time O(m^4 |L|^2) to generate the set L of all minimal edge dominating sets of G. For bipartite graphs we obtain a better result; we show that their…

Several algorithmic meta-theorems on kernelization have appeared in the last years, starting with the result of Bodlaender et al. [FOCS 2009] on graphs of bounded genus, then generalized by Fomin et al. [SODA 2010] to graphs excluding a…

Multi-Agent Path Finding (MAPF) is NP-hard to solve optimally, even on graphs, suggesting no polynomial-time algorithms can compute exact optimal solutions for them. This raises a natural question: How optimal can polynomial-time algorithms…

Most multi-dimensional (more than two dimensions) lattice partitions only form additive quotient groups and lack multiplication operations. This prevents us from constructing lattice codes based on multi-dimensional lattice partitions…

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…

A graph spanner is a fundamental graph structure that faithfully preserves the pairwise distances in the input graph up to a small multiplicative stretch. The common objective in the computation of spanners is to achieve the best-known…

Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…

We describe algorithms, based on Avis and Fukuda's reverse search paradigm, for listing all maximal independent sets in a sparse graph in polynomial time and delay per output. For bounded degree graphs, our algorithms take constant time per…

A new perspective is introduced regarding the analysis of Multiple Sequence Alignments (MSA), representing aligned data defined over a finite alphabet of symbols. The framework is designed to produce a block decomposition of an MSA, where…

We propose an efficient linear-time graph-based divisive cluster analysis approach called Reductive Clustering. The approach tries to reveal the hierarchical structural information through reducing the graph into a more concise one…