Biomedical and Bioinformatics Challenges for Computer Science (BBC) Session 3

Time and Date: 14:20 - 16:00 on 14th June 2019

Room: 0.4

Chair: Mario Cannataro

332 Combining Polynomial Chaos Expansions and Genetic Algorithm for the coupling of electrophysiological models [abstract]
Abstract: The number of computational models in cardiac research has grown over the last decades. Every year new models with different assumptions appear in the literature dealing with differences in interspecies cardiac properties. Generally, these new models update the physiological knowledge using new equations which reflect better the molecular basis of process. New equations require the fitting of parameters to previously known experimental data or even, in some cases, simulated data. This work studies and proposes a new method of parameter adjustment based on Polynomial Chaos and Genetic Algorithm to find the best values for the parameters upon changes in the formulation of ionic channels. It minimizes the search space and the computational cost combining it with a Sensitivity Analysis. We use the analysis of different models of L-type calcium channels to see that by reducing the number of parameters, the quality of the Genetic Algorithm dramatically improves. In addition, we test whether the use of the Polynomial Chaos Expansions improves the process of the Genetic Algorithm search. We find that it reduces the Genetic Algorithm execution in an order of 10³ times in the case studied here, maintaining the quality of the results. We conclude that polynomial chaos expansions can improve and reduce the cost of parameter adjustment in the development of new models.
Gustavo Novaes, Joventino Campos, Enrique Alvarez-Lacalle, Sergio Muñoz, Bernardo Rocha and Rodrigo Santos
365 A cloud architecture for the execution of medical imaging biomarkers [abstract]
Abstract: Digital Medical Imaging is increasingly being used in clinical routine and research. As a consequence, the workload in medical imaging departments in hospitals has multiplied by over 20 in the last decade. Medical Image processing requires intensive computing resources not available at hospitals, but which could be provided by public clouds. The article analyses the requirements of processing digital medical images and introduces a cloud-based architecture centred on a DevOps approach to deploying resources on demand, tailored to different types of workloads (based on the request of resources and the expected execution time). Results presented show a low overhead and high flexibility executing a lung disease biomarker on a public cloud.
Sergio López Huguet, Fabio García-Castro, Ángel Alberich-Bayarri and Ignacio Blanquer
371 A Self-Adaptive Local Search Coordination in Multimeme Memetic Algorithm for Molecular Docking [abstract]
Abstract: Molecular Docking is a methodology that deals with the problem of predicting the non-covalent binding of a receptor and a ligand at an atomic level to form a stable complex. Because the search space of possible conformations is vast, molecular docking is classified in computational complexity theory as a NP-hard problem. Because of the high complexity, exact methods are not efficient and several metaheuristics have been proposed. However, these methods are very dependent on parameter settings and search mechanism definitions, which requires approaches able to self-adapt these configurations along the optimization process. We proposed and developed a novel self-adaptive coordination of local search operators in a Multimeme Memetic Algorithm. The approach is based on the Biased Random Key Genetic Algorithm enhanced with four local search algorithms. The self-adaptation of methods and radius perturbation in local improvements works under a proposed probability function, which measures their performance to best guide the search process. The methods have been tested on a test set based on HIV-protease and compared to existing tools. Statistical test performed on the results shows that this approach reaches better results than a non-adaptive algorithm and is competitive with traditional methods.
Pablo Felipe Leonhart, Pedro Henrique Narloch and Marcio Dorn
428 Parallel CT reconstruction for multiple slices studies with SuiteSparseQR factorization package [abstract]
Abstract: Algebraic factorization methods applied to the discipline of Computerized Tomography (CT) Medical Imaging Reconstruction involve a high computational cost. Since these techniques are significantly slower than the traditional analytical ones and time is critical in this field, we need to employ parallel implementations in order to exploit the machine resources and obtain efficient reconstructions. In this paper, we analyze the performance of the sparse QR decomposition implemented on SuiteSparseQR factorization package applied to the CT reconstruction problem. We explore both the parallelism provided by BLAS threads and the use of the Householder reflections to reconstruct multiple slices at once efficiently. Combining both strategies, we can boost the performance of the reconstructions and implement a reliable and competitive method that gets high-quality CT images.
Mónica Chillarón, Vicente Vidal and Gumersindo Verdú Martín