SInC: An accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data

We report SInC (SNV, Indel and CNV) simulator and read generator, an open-source tool capable of simulating biological variants taking into account a platform-specific error model. SInC is capable of simulating and generating single- and paired-end reads with user-defined insert size with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes. Sinc can be downloaded from https://sourceforge.net/projects/sincsimulator/

Probabilistic Graphical Models on Multi-Core CPUs using Java 8

In this paper, we discuss software design issues related to the development of parallel computational intelligence algorithms on multi-core CPUs, using the new Java 8 functional programming features. In particular, we focus on probabilistic graphical models (PGMs) and present the parallelisation of a collection of algorithms that deal with inference and learning of PGMs from data. Namely, maximum likelihood estimation, importance sampling, and greedy search for solving combinatorial optimisation problems. Through these concrete examples, we tackle the problem of defining efficient data structures for PGMs and parallel processing of same-size batches of data sets using Java 8 features. We also provide straightforward techniques to code parallel algorithms that seamlessly exploit multi-core processors. The experimental analysis, carried out using our open source AMIDST (Analysis of MassIve Data STreams) Java toolbox, shows the merits of the proposed solutions.Comment: Pre-print version of the paper presented in the special issue on Computational Intelligence Software at IEEE Computational Intelligence Magazine journa

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

Identifying component modules

A computer-based system for modelling component dependencies and identifying component modules is presented. A variation of the Dependency Structure Matrix (DSM) representation was used to model component dependencies. The system utilises a two-stage approach towards facilitating the identification of a hierarchical modular structure. The first stage calculates a value for a clustering criterion that may be used to group component dependencies together. A Genetic Algorithm is described to optimise the order of the components within the DSM with the focus of minimising the value of the clustering criterion to identify the most significant component groupings (modules) within the product structure. The second stage utilises a 'Module Strength Indicator' (MSI) function to determine a value representative of the degree of modularity of the component groupings. The application of this function to the DSM produces a 'Module Structure Matrix' (MSM) depicting the relative modularity of available component groupings within it. The approach enabled the identification of hierarchical modularity in the product structure without the requirement for any additional domain specific knowledge within the system. The system supports design by providing mechanisms to explicitly represent and utilise component and dependency knowledge to facilitate the nontrivial task of determining near-optimal component modules and representing product modularity

Better Safe Than Sorry: An Adversarial Approach to Improve Social Bot Detection

The arm race between spambots and spambot-detectors is made of several cycles (or generations): a new wave of spambots is created (and new spam is spread), new spambot filters are derived and old spambots mutate (or evolve) to new species. Recently, with the diffusion of the adversarial learning approach, a new practice is emerging: to manipulate on purpose target samples in order to make stronger detection models. Here, we manipulate generations of Twitter social bots, to obtain - and study - their possible future evolutions, with the aim of eventually deriving more effective detection techniques. In detail, we propose and experiment with a novel genetic algorithm for the synthesis of online accounts. The algorithm allows to create synthetic evolved versions of current state-of-the-art social bots. Results demonstrate that synthetic bots really escape current detection techniques. However, they give all the needed elements to improve such techniques, making possible a proactive approach for the design of social bot detection systems.Comment: This is the pre-final version of a paper accepted @ 11th ACM Conference on Web Science, June 30-July 3, 2019, Boston, U

Telecommunications Network Planning and Maintenance

Telecommunications network operators are on a constant challenge to provide new services which require ubiquitous broadband access. In an attempt to do so, they are faced with many problems such as the network coverage or providing the guaranteed Quality of Service (QoS). Network planning is a multi-objective optimization problem which involves clustering the area of interest by minimizing a cost function which includes relevant parameters, such as installation cost, distance between user and base station, supported traffic, quality of received signal, etc. On the other hand, service assurance deals with the disorders that occur in hardware or software of the managed network. This paper presents a large number of multicriteria techniques that have been developed to deal with different kinds of problems regarding network planning and service assurance. The state of the art presented will help the reader to develop a broader understanding of the problems in the domain