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Profiling techniques are used extensively at different parts of the computing stack to achieve many goals. One major goal is to make a piece of software execute more efficiently on a specific hardware platform, where efficiency spans…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…
Word2vec is a widely used algorithm for extracting low-dimensional vector representations of words. State-of-the-art algorithms including those by Mikolov et al. have been parallelized for multi-core CPU architectures, but are based on…
Genetic Programming (GP) is a computationally intensive technique which also has a high degree of natural parallelism. Parallel computing architectures have become commonplace especially with regards Graphics Processing Units (GPU). Hence,…
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
SQL injection attacks, a class of injection flaw in which specially crafted input strings leads to illegal queries to databases, are one of the topmost threats to web applications. A Number of research prototypes and commercial products…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…
With the advent of era of Big Data and Internet of Things, there has been an exponential increase in the availability of large data sets. These data sets require in-depth analysis that provides intelligence for improvements in methods for…
Manycore processors feature a high number of general-purpose cores designed to work in a multithreaded fashion. Recent manycore processors are kept coherent using scalable distributed directories. A paramount example is the Intel Mesh…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
Hyperparameter optimization (HPO) is a necessary step to ensure the best possible performance of Machine Learning (ML) algorithms. Several methods have been developed to perform HPO; most of these are focused on optimizing one performance…
Homomorphic encryption (HE) allows secure computation on encrypted data without revealing the original data, providing significant benefits for privacy-sensitive applications. Many cloud computing applications (e.g., DNA read mapping,…
Although modern supercomputers are composed of multicore machines, one can find scientists that still execute their legacy applications which were developed to monocore cluster where memory hierarchy is dedicated to a sole core. The main…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…
Several statistical approaches based on reproducing kernels have been proposed to detect abrupt changes arising in the full distribution of the observations and not only in the mean or variance. Some of these approaches enjoy good…
The schooling behavior of fish can be studied through simulations involving a large number of interacting particles. In such systems, each individual particle is guided by behavior rules, which include aggregation towards a centroid,…
In this paper, we consider the convergence of a very general asynchronous-parallel algorithm called ARock, that takes many well-known asynchronous algorithms as special cases (gradient descent, proximal gradient, Douglas Rachford, ADMM,…