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

We study the problem of finding maximal exact matches (MEMs) between a query string $Q$ and a labeled graph $G$. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their…

Constructing a spanning tree of a graph is one of the most basic tasks in graph theory. We consider a relaxed version of this problem in the setting of local algorithms. The relaxation is that the constructed subgraph is a sparse spanning…

Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…

Temporal graph neural networks have shown promising results in learning inductive representations by automatically extracting temporal patterns. However, previous works often rely on complex memory modules or inefficient random walk methods…

Laman graphs naturally arise in structural mechanics and rigidity theory. Specifically, they characterize minimally rigid planar bar-and-joint systems which are frequently needed in robotics, as well as in molecular chemistry and polymer…

We (nearly) settle the time complexity for computing vertex fault-tolerant (VFT) spanners with optimal sparsity (up to polylogarithmic factors). VFT spanners are sparse subgraphs that preserve distance information, up to a small…

This paper settles the computational complexity of model checking of several extensions of the monadic second order (MSO) logic on two classes of graphs: graphs of bounded treewidth and graphs of bounded neighborhood diversity. A classical…

The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets. A novel method that…

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

We study the complexity of finding communication trees with the lowest possible completion time for rooted, irregular gather and scatter collective communication operations in fully connected, $k$-ported communication networks under a…

Bayesian online algorithms for Sum-Product Networks (SPNs) need to update their posterior distribution after seeing one single additional instance. To do so, they must compute moments of the model parameters under this distribution. The…

Modern neural sequence models are designed to meet the dual mandate of parallelizable training and fast sequential inference. Recent developments have given rise to various models, such as Gated Linear Attention (GLA) and Mamba, that…

We obtain an algorithmic meta-theorem for the following optimization problem. Let \phi\ be a Counting Monadic Second Order Logic (CMSO) formula and t be an integer. For a given graph G, the task is to maximize |X| subject to the following:…

Algorithm MLS (Maximal Label Search) is a graph search algorithm which generalizes algorithms MCS, LexBFS, LexDFS and MNS. On a chordal graph, MLS computes a peo (perfect elimination ordering) of the graph. We show how algorithm MLS can be…

The current landscape of balanced graph partitioning is divided into high-quality but expensive multilevel algorithms and cheaper approaches with linear running time, such as single-level algorithms and streaming algorithms. We demonstrate…

In this paper, we present a low-complexity recursive approach for massive and scalable code-domain nonorthogonal multiple access (NOMA) with applications to emerging low-capacity scenarios. The problem definition in this paper is inspired…

Identifying frequent subgraphs, also called network motifs, is crucial in analyzing and predicting properties of real-world networks. However, finding large commonly-occurring motifs remains a challenging problem not only due to its NP-hard…

Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…

Spanners are fundamental graph structures that sparsify graphs at the cost of small stretch. In particular, in recent years, many sequential algorithms constructing additive all-pairs spanners were designed, providing very sparse…

In this paper, we provide a novel enumeration algorithm for the set of all walks of a given length within a directed graph. Our algorithm has worst-case constant delay between outputting succinct representations of such walks, after a…