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The complexity of combustion simulations demands the latest high-performance computing tools to accelerate its time-to-solution results. A current trend on HPC systems is the utilization of CPUs with SIMD or vector extensions to exploit…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Planning under uncertainty for real-world robotics tasks, such as autonomous driving, requires reasoning in enormous high-dimensional belief spaces, rendering the problem computationally intensive. While parallelization offers scalability,…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
Fixed-parameter algorithms have been successfully applied to solve numerous difficult problems within acceptable time bounds on large inputs. However, most fixed-parameter algorithms are inherently \emph{sequential} and, thus, make no use…
AI accelerator processing capabilities and memory constraints largely dictate the scale in which machine learning workloads (e.g., training and inference) can be executed within a desirable time frame. Training a state of the art,…
Sparse coding aims to model data vectors as sparse linear combinations of basis elements, but a majority of related studies are restricted to continuous data without spatial or temporal structure. A new model-based sparse coding (MSC)…
We discuss how string sorting algorithms can be parallelized on modern multi-core shared memory machines. As a synthesis of the best sequential string sorting algorithms and successful parallel sorting algorithms for atomic objects, we…
In the study of network synchronization, an outstanding question of both theoretical and practical significance is how to allocate a given set of heterogenous oscillators on a complex network in order for improving the synchronization…
Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
We study the problem of exact completion for $m \times n$ sized matrix of rank $r$ with the adaptive sampling method. We introduce a relation of the exact completion problem with the sparsest vector of column and row spaces (which we call…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
Many parallel algorithms which solve basic problems in computer science use auxiliary space linear in the input to facilitate conflict-free computation. There has been significant work on improving these parallel algorithms to be in-place,…
Although empirical studies have confirmed the effectiveness of spectrum-based fault localization (SBFL) techniques, their performance may be degraded due to presence of some undesired circumstances such as the existence of coincidental…
We present a novel approximate graph matching algorithm that incorporates seeded data into the graph matching paradigm. Our Joint Optimization of Fidelity and Commensurability (JOFC) algorithm embeds two graphs into a common Euclidean space…
Given two algorithms for the same problem, can we determine whether they are meaningfully different? In full generality, the question is uncomputable, and empirically it is muddied by competing notions of similarity. Yet, in many…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…