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Register a new userEBIC: an evolutionary-based parallel biclustering algorithm for pattern discover
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Added by
Patryk Orzechowski
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably the first one capable of discovering with accuracy exceeding 50% multiple complex patterns in real gene expression datasets. It is also one of the very few biclustering methods designed for parallel environments with multiple graphics processing units (GPUs). We demonstrate that EBIC outperforms state-of-the-art biclustering methods, in terms of recovery and relevance, on both synthetic and genetic datasets. EBIC also yields results over 12 times faster than the most accurate reference algorithms. The proposed algorithm is anticipated to be added to the repertoire of unsupervised machine learning algorithms for the analysis of datasets, including those from large-scale genomic studies.
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Biclustering is a data mining technique which searches for local patterns in numeric tabular data with main application in bioinformatics. This technique has shown promise in multiple areas, including development of biomarkers for cancer, disease subtype identification, or gene-drug interactions among others. In this paper we introduce EBIC.JL - an implementation of one of the most accurate biclustering algorithms in Julia, a modern highly parallelizable programming language for data science. We show that the new version maintains comparable accuracy to its predecessor EBIC while converging faster for the majority of the problems. We hope that this open source software in a high-level programming language will foster research in this promising field of bioinformatics and expedite development of new biclustering methods for big data.
Motivation: In this paper we present the latest release of EBIC, a next-generation biclustering algorithm for mining genetic data. The major contribution of this paper is adding support for big data, making it possible to efficiently run large genomic data mining analyses. Additional enhancements include integration with R and Bioconductor and an option to remove influence of missing value on the final result. Results: EBIC was applied to datasets of different sizes, including a large DNA methylation dataset with 436,444 rows. For the largest dataset we observed over 6.6 fold speedup in computation time on a cluster of 8 GPUs compared to running the method on a single GPU. This proves high scalability of the algorithm. Availability: The latest version of EBIC could be downloaded from http://github.com/EpistasisLab/ebic . Installation and usage instructions are also available online.
Designing neural networks for object recognition requires considerable architecture engineering. As a remedy, neuro-evolutionary network architecture search, which automatically searches for optimal network architectures using evolutionary algorithms, has recently become very popular. Although very effective, evolutionary algorithms rely heavily on having a large population of individuals (i.e., network architectures) and is therefore memory expensive. In this work, we propose a Regularized Evolutionary Algorithm with low memory footprint to evolve a dynamic image classifier. In details, we introduce novel custom operators that regularize the evolutionary process of a micro-population of 10 individuals. We conduct experiments on three different digits datasets (MNIST, USPS, SVHN) and show that our evolutionary method obtains competitive results with the current state-of-the-art.
The emerging research paradigm coined as multitasking optimization aims to solve multiple optimization tasks concurrently by means of a single search process. For this purpose, the exploitation of complementarities among the tasks to be solved is crucial, which is often achieved via the transfer of genetic material, thereby forging the Transfer Optimization field. In this context, Evolutionary Multitasking addresses this paradigm by resorting to concepts from Evolutionary Computation. Within this specific branch, approaches such as the Multifactorial Evolutionary Algorithm (MFEA) has lately gained a notable momentum when tackling multiple optimization tasks. This work contributes to this trend by proposing the first adaptation of the recently introduced Multifactorial Evolutionary Algorithm II (MFEA-II) to permutation-based discrete optimization environments. For modeling this adaptation, some concepts cannot be directly applied to discrete search spaces, such as parent-centric interactions. In this paper we entirely reformulate such concepts, making them suited to deal with permutation-based search spaces without loosing the inherent benefits of MFEA-II. The performance of the proposed solver has been assessed over 5 different multitasking setups, composed by 8 datasets of the well-known Traveling Salesman (TSP) and Capacitated Vehicle Routing Problems (CVRP). The obtained results and their comparison to those by the discrete version of the MFEA confirm the good performance of the developed dMFEA-II, and concur with the insights drawn in previous studies for continuous optimization.
A pattern matching based tracking algorithm, named MdcPatRec, is used for the reconstruction of charged tracks in the drift chamber of the BESIII detector. This paper addresses the shortage of segment finding in MdcPatRec algorithm. An extended segment construction scheme and the corresponding pattern dictionary are presented. Evaluation with Monte-Carlo and experimental data show that the new method can achieve higher efficiency for low transverse momentum tracks.
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