BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

A survey on adaptive random testing

Random testing (RT) is a well-studied testing method that has been widely applied to the testing of many applications, including embedded software systems, SQL database systems, and Android applications. Adaptive random testing (ART) aims to enhance RT's failure-detection ability by more evenly spreading the test cases over the input domain. Since its introduction in 2001, there have been many contributions to the development of ART, including various approaches, implementations, assessment and evaluation methods, and applications. This paper provides a comprehensive survey on ART, classifying techniques, summarizing application areas, and analyzing experimental evaluations. This paper also addresses some misconceptions about ART, and identifies open research challenges to be further investigated in the future work

Distributing test cases more evenly in adaptive random testing

Adaptive random testing (ART) has recently been proposed to enhance the failure-detection capability of random testing. In ART, test cases are not only randomly generated, but also evenly spread over the input domain. Various ART algorithms have been developed to evenly spread test cases in different ways. Previous studies have shown that some ART algorithms prefer to select test cases from the edge part of the input domain rather than from the centre part, that is, inputs do not have equal chance to be selected as test cases. Since we do not know where the failure-causing inputs are prior to testing, it is not desirable for inputs to have different chances of being selected as test cases. Therefore, in this paper, we investigate how to enhance some ART algorithms by offsetting the edge preference, and propose a new family of ART algorithms. A series of simulations have been conducted and it is shown that these new algorithms not only select test cases more evenly, but also have better failure detection capabilities

Generative Design in Minecraft (GDMC), Settlement Generation Competition

This paper introduces the settlement generation competition for Minecraft, the first part of the Generative Design in Minecraft challenge. The settlement generation competition is about creating Artificial Intelligence (AI) agents that can produce functional, aesthetically appealing and believable settlements adapted to a given Minecraft map - ideally at a level that can compete with human created designs. The aim of the competition is to advance procedural content generation for games, especially in overcoming the challenges of adaptive and holistic PCG. The paper introduces the technical details of the challenge, but mostly focuses on what challenges this competition provides and why they are scientifically relevant.Comment: 10 pages, 5 figures, Part of the Foundations of Digital Games 2018 proceedings, as part of the workshop on Procedural Content Generatio

One-domain-one-input: adaptive random testing by orthogonal recursive bisection with restriction

One goal of software testing may be the identification or generation of a series of test cases that can detect a fault with as few test executions as possible. Motivated by insights from research into failure-causing regions of input domains, the even-spreading (even distribution) of tests across the input domain has been identified as a useful heuristic to more quickly find failures. This finding has encouraged a shift in focus from traditional random testing (RT) to its enhancement, adaptive random testing (ART), which retains the randomness of test input selection, but also attempts to maintain a more evenly distributed spread of test inputs across the input domain. Given that there are different ways to achieve the even distribution, several different ART methods and approaches have been proposed. This paper presents a new ART method, called ART-ORB, which explores the advantages of repeated geometric bisection of the input domain, combined with restriction regions, to evenly spread test inputs. Experimental results show a better performance in terms of fewer test executions than RT to find failures. Compared with other ART methods, ART-ORB has comparable performance (in terms of required test executions), but incurs lower test input selection overheads, especially in higher dimensional input space. It is recommended that ART-ORB be used in testing situations involving expensive test input execution

Towards Lattice Quantum Chromodynamics on FPGA devices

In this paper we describe a single-node, double precision Field Programmable Gate Array (FPGA) implementation of the Conjugate Gradient algorithm in the context of Lattice Quantum Chromodynamics. As a benchmark of our proposal we invert numerically the Dirac-Wilson operator on a 4-dimensional grid on three Xilinx hardware solutions: Zynq Ultrascale+ evaluation board, the Alveo U250 accelerator and the largest device available on the market, the VU13P device. In our implementation we separate software/hardware parts in such a way that the entire multiplication by the Dirac operator is performed in hardware, and the rest of the algorithm runs on the host. We find out that the FPGA implementation can offer a performance comparable with that obtained using current CPU or Intel's many core Xeon Phi accelerators. A possible multiple node FPGA-based system is discussed and we argue that power-efficient High Performance Computing (HPC) systems can be implemented using FPGA devices only.Comment: 17 pages, 4 figure

Urysohn Forest for Aleatoric Uncertainty Quantification

This paper focuses on building models of stochastic systems with aleatoric uncertainty. The main novelty is an algorithm of boosted ensemble training of multiple models for obtaining a probability distribution of an individual output as a function of the system input. The second novel contribution is a new regression model to be used in the ensemble. The model is a multi-layered tree of hierarchically-connected discrete Urysohn operators (or generalised additive models, which are mathematically equivalent to the discrete Urysohn operators in this case). Since multiple models (trees) are trained in the ensemble, the authors refer them as an Urysohn forest. The source code is freely available online