Related papers: Memory Efficient De Bruijn Graph Construction

We initiate the study of graph algorithms in the streaming setting on massive distributed and parallel systems inspired by practical data processing systems. The objective is to design algorithms that can efficiently process evolving graphs…

In order to support the real-time interaction with LLMs and the instant search or the instant recommendation on social media, it becomes an imminent problem to build a k-NN graph or an indexing graph for the massive number of vectorized…

We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…

We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…

Purpose: A fast data-driven optimization approach, named bias-accelerated subset selection (BASS), is proposed for learning efficacious sampling patterns (SPs) with the purpose of reducing scan time in large-dimensional parallel MRI.…

Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…

The deployment and training of neural networks on edge computing devices pose many challenges. The low memory nature of edge devices is often one of the biggest limiting factors encountered in the deployment of large neural network models.…

Graph Convolutional Networks (GCNs) are extensively utilized for deep learning on graphs. The large data sizes of graphs and their vertex features make scalable training algorithms and distributed memory systems necessary. Since the…

Graph Neural Networks (GNNs) are widely used for learning on graph-structured data, but scaling GNN training to massive graphs remains challenging. To enable scalable distributed training, graphs are divided into smaller partitions that are…

We develop an efficient parallel algorithm for answering shortest-path queries in planar graphs and implement it on a multi-node CPU/GPU clusters. The algorithm uses a divide-and-conquer approach for decomposing the input graph into small…

Contraction Hierarchies is a successful speedup-technique to Dijkstra's seminal shortest path algorithm that has a convenient trade-off between preprocessing and query times. We investigate a shared-memory parallel implementation that uses…

Maps of brain microarchitecture are important for understanding neurological function and behavior, including alterations caused by chronic conditions such as neurodegenerative disease. Techniques such as knife-edge scanning microscopy…

Partitioning a graph into balanced components is important for several applications. For multi-objective problems, it is useful not only to find one solution but also to enumerate all the solutions with good values of objectives. However,…

We consider the problem of finding a minimum common partition of two strings (MCSP). The problem has its application in genome comparison. MCSP problem is proved to be NP-hard. In this paper, we develop an Integer Programming (IP)…

We investigate the problem of compiling the generation of graph states to arbitrarily many distributed homogeneous quantum processing units (QPUs), providing a scalable partitioning algorithm and graph state generation protocol to minimize…

We develop and extensively evaluate highly scalable distributed-memory algorithms for computing minimum spanning trees (MSTs). At the heart of our solutions is a scalable variant of Boruvka's algorithm. For partitioned graphs with many…

The sequence in which a complex product is assembled directly impacts the ease and efficiency of the assembly process, whether executed by a human or a robot. A sequence that gives the assembler the greatest freedom of movement is therefore…

Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double…

The Constraint Shortest Path (CSP) problem is as follows. An $n$-vertex graph is given, each edge/arc assigned two weights. Let us call them "cost" and "length" for definiteness. Finding a min-cost upper-bounded length path between a given…

A central goal of modern magnetic resonance imaging (MRI) is to reduce the time required to produce high-quality images. Efforts have included hardware and software innovations such as parallel imaging, compressed sensing, and deep…