Related papers: An Asynchronous Distributed-Memory Parallel Algori…

This paper presents a novel hybrid tokenization strategy that enhances the performance of DNA Language Models (DLMs) by combining 6-mer tokenization with Byte Pair Encoding (BPE-600). Traditional k-mer tokenization is effective at capturing…

This paper formulates a distributed computation problem, where a master asks $N$ distributed workers to compute a linearly separable function. The task function can be expressed as $K_c$ linear combinations of $K$ messages, where each…

Coded distributed computing (CDC) is a new technique proposed with the purpose of decreasing the intense data exchange required for parallelizing distributed computing systems. Under the famous MapReduce paradigm, this coded approach has…

Distributed Quantum Computing (DQC) enables scalability by interconnecting multiple QPUs. Among various DQC implementations, quantum data centers (QDCs), which utilize reconfigurable optical switch networks to link QPUs across different…

The extraction of $k$-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads classification in genomics and the characterization of RNA-seq datasets. The extraction of all…

Asynchronous distributed algorithms are a popular way to reduce synchronization costs in large-scale optimization, and in particular for neural network training. However, for nonsmooth and nonconvex objectives, few convergence guarantees…

This paper proposes efficient solutions for $k$-core decomposition with high parallelism. The problem of $k$-core decomposition is fundamental in graph analysis and has applications across various domains. However, existing algorithms face…

The persistence diagram, which describes the topological features of a dataset, is a key descriptor in Topological Data Analysis. The "Discrete Morse Sandwich" (DMS) method has been reported to be the most efficient algorithm for computing…

We consider the problem of low-rank approximation of massive dense non-negative tensor data, for example to discover latent patterns in video and imaging applications. As the size of data sets grows, single workstations are hitting…

Triangle counting is a fundamental graph analytic operation that is used extensively in network science and graph mining. As the size of the graphs that needs to be analyzed continues to grow, there is a requirement in developing scalable…

Computing $k$-Nearest Neighbors (KNN) is one of the core kernels used in many machine learning, data mining and scientific computing applications. Although kd-tree based $O(\log n)$ algorithms have been proposed for computing KNN, due to…

In this paper, we investigate the parallelization of $k$-core decomposition, a method used in graph analysis to identify cohesive substructures and assess node centrality. Although efficient sequential algorithms exist for this task, the…

The kernel $k$-means is an effective method for data clustering which extends the commonly-used $k$-means algorithm to work on a similarity matrix over complex data structures. The kernel $k$-means algorithm is however computationally very…

The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…

Distributed quantum computing (DQC) is being actively investigated as a means of scaling the number of qubits across multiple connected quantum devices. This includes quantum circuit compilation and execution management on multiple quantum…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

In this paper, we revisit the problem of indexing multi-dimensional data in memory for the efficient support of multi-dimensional range queries and nearest neighbor queries. This is a classic problem in main-memory databases, where there is…

We design and implement two single-pass semi-streaming algorithms for the maximum weight $k$-disjoint matching ($k$-DM) problem. Given an integer $k$, the $k$-DM problem is to find $k$ pairwise edge-disjoint matchings such that the sum of…

This work explores a distributed computing setting where $K$ nodes are assigned fractions (subtasks) of a computational task in order to perform the computation in parallel. In this setting, a well-known main bottleneck has been the…

For the last thirty years, several Dynamic Memory Managers (DMMs) have been proposed. Such DMMs include first fit, best fit, segregated fit and buddy systems. Since the performance, memory usage and energy consumption of each DMM differs,…