Related papers: Efficient Algorithms for de novo Assembly of Alter…
The eigendeomposition of nearest-neighbor (NN) graph Laplacian matrices is the main computational bottleneck in spectral clustering. In this work, we introduce a highly-scalable, spectrum-preserving graph sparsification algorithm that…
Improving the scalability of GNNs is critical for large graphs. Existing methods leverage three sampling paradigms including node-wise, layer-wise and subgraph sampling, then design unbiased estimator for scalability. However, the high…
We present a parallel k-clique listing algorithm with improved work bounds (for the same depth) in sparse graphs with low degeneracy or arboricity. We achieve this by introducing and analyzing a new pruning criterion for a backtracking…
Many graph mining applications rely on detecting subgraphs which are near-cliques. There exists a dichotomy between the results in the existing work related to this problem: on the one hand the densest subgraph problem (DSP) which maximizes…
The graph isomorphism problem remains a fundamental challenge in computer science, driving the search for efficient decision algorithms. Due to its ambiguous computational complexity, heuristic approaches such as simulated annealing are…
The Euler Elastica (EE) model with surface curvature can generate artifact-free results compared with the traditional total variation regularization model in image processing. However, strong nonlinearity and singularity due to the…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
We develop a novel parallel decomposition strategy for unweighted, undirected graphs, based on growing disjoint connected clusters from batches of centers progressively selected from yet uncovered nodes. With respect to similar previous…
Chordal decomposition techniques are used to reduce large structured positive semidefinite matrix constraints in semidefinite programs (SDPs). The resulting equivalent problem contains multiple smaller constraints on the nonzero blocks (or…
We present Sketch 'n Solve, an open-source Python package that implements efficient randomized numerical linear algebra (RandNLA) techniques for solving large-scale least squares problems. While sketch-and-solve algorithms have demonstrated…
De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…
Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…
In the field of robotics, event-based cameras are emerging as a promising low-power alternative to traditional frame-based cameras for capturing high-speed motion and high dynamic range scenes. This is due to their sparse and asynchronous…
Streaming computation plays an important role in large-scale data analysis. The sliding window model is a model of streaming computation which also captures the recency of the data. In this model, data arrives one item at a time, but only…
DBSCAN is a popular density-based clustering algorithm. It computes the $\epsilon$-neighborhood graph of a dataset and uses the connected components of the high-degree nodes to decide the clusters. However, the full neighborhood graph may…
In this paper, we propose a fast method for exactly enumerating a very large number of all lower cost solutions for various combinatorial problems. Our method is based on backtracking for a given decision diagram which represents all the…
Recent advances in the development of commercial quantum annealers such as the D-Wave 2X allow solving NP-hard optimization problems that can be expressed as quadratic unconstrained binary programs. However, the relatively small number of…
We introduce a framework for proving lower bounds on computational problems over distributions against algorithms that can be implemented using access to a statistical query oracle. For such algorithms, access to the input distribution is…
In the decremental $(1+\epsilon)$-approximate Single-Source Shortest Path (SSSP) problem, we are given a graph $G=(V,E)$ with $n = |V|, m = |E|$, undergoing edge deletions, and a distinguished source $s \in V$, and we are asked to process…
We consider the Distinct Shortest Walks problem. Given two vertices $s$ and $t$ of a graph database $\mathcal{D}$ and a regular path query, enumerate all walks of minimal length from $s$ to $t$ that carry a label that conforms to the query.…