相关论文: Space-efficient merging of succinct de Bruijn grap…
We study the approximate maximum weight matching (MWM) problem in a fully dynamic graph subject to edge insertions and deletions. We design meta-algorithms that reduce the problem to the unweighted approximate maximum cardinality matching…
A computational graph in a deep neural network (DNN) denotes a specific data flow diagram (DFD) composed of many tensors and operators. Existing toolkits for visualizing computational graphs are not applicable when the structure is highly…
In this paper, we give new auction algorithms for maximum weighted bipartite matching (MWM) and maximum cardinality bipartite $b$-matching (MCbM). Our algorithms run in $O\left(\log n/\varepsilon^8\right)$ and $O\left(\log…
There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very…
Graph matching is a challenging problem with very important applications in a wide range of fields, from image and video analysis to biological and biomedical problems. We propose a robust graph matching algorithm inspired in…
Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the…
Motivated by a geometric problem, we introduce a new non-convex graph partitioning objective where the optimality criterion is given by the sum of the Dirichlet eigenvalues of the partition components. A relaxed formulation is identified…
This article introduces new algorithms for the uniform random generation of labelled planar graphs. Its principles rely on Boltzmann samplers, as recently developed by Duchon, Flajolet, Louchard, and Schaeffer. It combines the Boltzmann…
This paper presents the results of an experimental study of graph partitioning. We describe a new heuristic technique, path optimization, and its application to two variations of graph partitioning: the max_cut problem and the…
Partition of unity methods (PUMs) on graphs are simple and highly adaptive auxiliary tools for graph signal processing. Based on a greedy-type metric clustering and augmentation scheme, we show how a partition of unity can be generated in…
A bipartite graph $G=(U,V,E)$ is convex if the vertices in $V$ can be linearly ordered such that for each vertex $u\in U$, the neighbors of $u$ are consecutive in the ordering of $V$. An induced matching $H$ of $G$ is a matching such that…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
We propose a new succinct representation of labeled trees which represents a tree T using |T|H_k(T) number of bits (plus some smaller order terms), where |T|H_k(T) denotes the k-th order (tree label) entropy, as defined by Ferragina at al.…
A recent surprising result in the implementation of worst-case-optimal (wco) multijoins in graph databases (specifically, basic graph patterns) is that they can be supported on graph representations that take even less space than a plain…
Kautz and de Bruijn graphs have a high degree of connectivity which makes them ideal candidates for massively parallel computer network topologies. In order to realize a practical computer architecture based on these graphs, it is useful to…
Distributed optimization for resource allocation problems is investigated and a sub-optimal continuous-time algorithm is proposed. Our algorithm has lower order dynamics than others to reduce burdens of computation and communication, and is…
A graph $G=(V,E)$ is word-representable if there exists a word $w$ over the alphabet $V$ such that letters $x$ and $y$ alternate in $w$ if and only if $xy\in E$. Word-representable graphs generalize several important classes of graphs such…
Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large…
This paper addresses the challenge of merging hierarchical navigable small world (HNSW) graphs, a critical operation for distributed systems, incremental indexing, and database compaction. We propose three algorithms for this task: Naive…