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We investigate an application in the automatic tuning of computer codes, an area of research that has come to prominence alongside the recent rise of distributed scientific processing and heterogeneity in high-performance computing…

We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…

During the last decade, a large number of different numerical methods have been proposed to tackle the automatic identification and quantification in {\gamma}-ray spectrometry. However, the lack of common benchmarks, including datasets,…

Bam-readcount is a utility for generating low-level information about sequencing data at specific nucleotide positions. Originally designed to help filter genomic mutation calls, the metrics it outputs are useful as input for variant…

Linear models are a core component for statistical software that analyzes treatment effects. They are used in experimentation platforms where analysis is automated, as well as scientific studies where analysis is done locally and manually.…

The problem of optimization of the array size for modern discrete Fourier transform libraries is considered and reformulated as an integer linear programming problem. Acceleration of finding an optimal solution using standard freely…

Randomized experiments is a key part of product development in the tech industry. It is often necessary to run programs of exclusive experiments, i.e., experiments that cannot be run on the same units during the same time. These programs…

Malware lineage studies the evolutionary relationships among malware and has important applications for malware analysis. A persistent limitation of prior malware lineage approaches is to consider every input sample a separate malware…

Percentiles have been established in bibliometrics as an important alternative to mean-based indicators for obtaining a normalized citation impact of publications. Percentiles have a number of advantages over standard bibliometric…

Ultra-large make-on-demand compound libraries now contain billions of readily available compounds. This represents a golden opportunity for in-silico drug discovery. One challenge, however, is the time and computational cost of an…

Boolean formulae compactly encode huge, constrained search spaces. Thus, variability-intensive systems are often encoded with Boolean formulae. The search space of a variability-intensive system is usually too large to explore without…

Software libraries are the elementary building blocks of open source software ecosystems, extending the capabilities of programming languages beyond their standard libraries. Although ecosystem health is often quantified using data on…

There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating…

This paper is the result of a two month research internship on the topic of library version identification. In this paper, ideas and techniques from literature in the area of binary comparison and fingerprinting are outlined and applied to…

The application of machine learning to bioinformatics problems is well established. Less well understood is the application of bioinformatics techniques to machine learning and, in particular, the representation of non-biological data as…

This report showcases the role of, and future directions for, the field of Randomized Numerical Linear Algebra (RNLA) in a selection of scientific applications. These applications span the domains of imaging, genomics and dynamical systems,…

Sparse linear algebra is central to many scientific programs, yet compilers fail to optimize it well. High-performance libraries are available, but adoption costs are significant. Moreover, libraries tie programs into vendor-specific…

Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

Modern software systems are increasingly dependent on third-party libraries. It is widely recognized that using mature and well-tested third-party libraries can improve developers' productivity, reduce time-to-market, and produce more…