On the descriptional complexity of iterative arrays

The descriptional complexity of iterative arrays (lAs) is studied. Iterative arrays are a parallel computational model with a sequential processing of the input. It is shown that lAs when compared to deterministic finite automata or pushdown automata may provide savings in size which are not bounded by any recursive function, so-called non-recursive trade-offs. Additional non-recursive trade-offs are proven to exist between lAs working in linear time and lAs working in real time. Furthermore, the descriptional complexity of lAs is compared with cellular automata (CAs) and non-recursive trade-offs are proven between two restricted classes. Finally, it is shown that many decidability questions for lAs are undecidable and not semidecidable

Parallel data compression

Data compression schemes remove data redundancy in communicated and stored data and increase the effective capacities of communication and storage devices. Parallel algorithms and implementations for textual data compression are surveyed. Related concepts from parallel computation and information theory are briefly discussed. Static and dynamic methods for codeword construction and transmission on various models of parallel computation are described. Included are parallel methods which boost system speed by coding data concurrently, and approaches which employ multiple compression techniques to improve compression ratios. Theoretical and empirical comparisons are reported and areas for future research are suggested

Applying Deep Learning to Fast Radio Burst Classification

Upcoming Fast Radio Burst (FRB) surveys will search $\sim$10\,$^3$ beams on sky with very high duty cycle, generating large numbers of single-pulse candidates. The abundance of false positives presents an intractable problem if candidates are to be inspected by eye, making it a good application for artificial intelligence (AI). We apply deep learning to single pulse classification and develop a hierarchical framework for ranking events by their probability of being true astrophysical transients. We construct a tree-like deep neural network (DNN) that takes multiple or individual data products as input (e.g. dynamic spectra and multi-beam detection information) and trains on them simultaneously. We have built training and test sets using false-positive triggers from real telescopes, along with simulated FRBs, and single pulses from pulsars. Training of the DNN was independently done for two radio telescopes: the CHIME Pathfinder, and Apertif on Westerbork. High accuracy and recall can be achieved with a labelled training set of a few thousand events. Even with high triggering rates, classification can be done very quickly on Graphical Processing Units (GPUs). That speed is essential for selective voltage dumps or issuing real-time VOEvents. Next, we investigate whether dedispersion back-ends could be completely replaced by a real-time DNN classifier. It is shown that a single forward propagation through a moderate convolutional network could be faster than brute-force dedispersion; but the low signal-to-noise per pixel makes such a classifier sub-optimal for this problem. Real-time automated classification may prove useful for bright, unexpected signals, both now and in the era of radio astronomy when data volumes and the searchable parameter spaces further outgrow our ability to manually inspect the data, such as for SKA and ngVLA

Solving for multi-class using orthogonal coding matrices

A common method of generalizing binary to multi-class classification is the error correcting code (ECC). ECCs may be optimized in a number of ways, for instance by making them orthogonal. Here we test two types of orthogonal ECCs on seven different datasets using three types of binary classifier and compare them with three other multi-class methods: 1 vs. 1, one-versus-the-rest and random ECCs. The first type of orthogonal ECC, in which the codes contain no zeros, admits a fast and simple method of solving for the probabilities. Orthogonal ECCs are always more accurate than random ECCs as predicted by recent literature. Improvments in uncertainty coefficient (U.C.) range between 0.4--17.5% (0.004--0.139, absolute), while improvements in Brier score between 0.7--10.7%. Unfortunately, orthogonal ECCs are rarely more accurate than 1 vs. 1. Disparities are worst when the methods are paired with logistic regression, with orthogonal ECCs never beating 1 vs. 1. When the methods are paired with SVM, the losses are less significant, peaking at 1.5%, relative, 0.011 absolute in uncertainty coefficient and 6.5% in Brier scores. Orthogonal ECCs are always the fastest of the five multi-class methods when paired with linear classifiers. When paired with a piecewise linear classifier, whose classification speed does not depend on the number of training samples, classifications using orthogonal ECCs were always more accurate than the the remaining three methods and also faster than 1 vs. 1. Losses against 1 vs. 1 here were higher, peaking at 1.9% (0.017, absolute), in U.C. and 39% in Brier score. Gains in speed ranged between 1.1% and over 100%. Whether the speed increase is worth the penalty in accuracy will depend on the application

Synthesis, structure and power of systolic computations

AbstractA variety of problems related to systolic architectures, systems, models and computations are discussed. The emphases are on theoretical problems of a broader interest. Main motivations and interesting/important applications are also presented. The first part is devoted to problems related to synthesis, transformations and simulations of systolic systems and architectures. In the second part, the power and structure of tree and linear array computations are studied in detail. The goal is to survey main research directions, problems, methods and techniques in not too formal a way

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

API design for machine learning software: experiences from the scikit-learn project

Scikit-learn is an increasingly popular machine learning li- brary. Written in Python, it is designed to be simple and efficient, accessible to non-experts, and reusable in various contexts. In this paper, we present and discuss our design choices for the application programming interface (API) of the project. In particular, we describe the simple and elegant interface shared by all learning and processing units in the library and then discuss its advantages in terms of composition and reusability. The paper also comments on implementation details specific to the Python ecosystem and analyzes obstacles faced by users and developers of the library