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We present a strategy to speed up Runge-Kutta-based ODE simulations of large systems with nearest-neighbor coupling. We identify the cache/memory bandwidth as the crucial performance bottleneck. To reduce the required bandwidth, we…

Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper,…

Computing-in-memory (CIM) has attracted significant attentions in recent years due to its massive parallelism and low power consumption. However, current CIM designs suffer from large area overhead of small CIM macros and bad programmablity…

We explore the combination of deterministic and Monte Carlo methods to facilitate efficient automatic numerical computation of multidimensional integrals with singular integrands. Two adaptive algorithms are presented that employ recursion…

Mixed integer sets have a strong modeling capacity to describe practical systems. Nevertheless, incorporating a mixed integer set often renders an optimization formulation drastically more challenging to compute. In this paper, we study how…

BDDs are representations of a Boolean expression in the form of a directed acyclic graph. BDDs are widely used in several fields, particularly in model checking and hardware verification. There are several implementations for BDD…

With high computation power and memory bandwidth, graphics processing units (GPUs) lend themselves to accelerate data-intensive analytics, especially when such applications fit the single instruction multiple data (SIMD) model. However,…

The modern CPU's design, which is composed of hierarchical memory and SIMD/vectorization capability, governs the potential for algorithms to be transformed into efficient implementations. The release of the AVX-512 changed things radically,…

We propose to use Digital Memcomputing Machines (DMMs), implemented with self-organizing logic gates (SOLGs), to solve the problem of numerical inversion. Starting from fixed-point scalar inversion we describe the generalization to solving…

In the Subspace Clustering with Missing Data (SCMD) problem, we are given a collection of n partially observed d-dimensional vectors. The data points are assumed to be concentrated near a union of low-dimensional subspaces. The goal of SCMD…

Parallel computing is a standard approach to achieving high-performance computing (HPC). Three commonly used methods to implement parallel computing include: 1) applying multithreading technology on single-core or multi-core CPUs; 2)…

We develop algorithms to turn quotients of rings of rings of integers into effective Euclidean rings by giving polynomial algorithms for all fundamental ring operations. In addition, we study normal forms for modules over such rings and…

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…

Currently, public-key compression of supersingular isogeny Diffie-Hellman (SIDH) and its variant, supersingular isogeny key encapsulation (SIKE) involve pairing computation and discrete logarithm computation. In this paper, we propose novel…

In the last decade, an impressive increase in software adaptions has led to a surge in log data production, making manual log analysis impractical and establishing the necessity for automated methods. Conversely, most automated analysis…

A new fast (real time) sorter of binary numbers by one-dimensional cellular automata is proposed. It sorts a list of n numbers represented by k-bits each in exactly nk steps. This is only one step more than a lower bound.

Two new algorithms are described for matching two dimensional coordinate lists of point sources that are signifcantly faster than previous methods. By matching rarely occurring triangles (or more complex shapes) in the two lists, and by…

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…

Two-stage stochastic mixed-integer programming (SMIP) problems with general integer variables in the second-stage are generally difficult to solve. This paper develops the theory of integer set reduction for characterizing the subset of the…

The ubiquity of variable-length integers in data storage and communication necessitates efficient decoding techniques. In this paper, we present SFVInt, a simple and fast approach to decode the prevalent Little Endian Base-128 (LEB128)…