Distributed transformer for high order epistasis detection in large-scale datasets.

Understanding the genetic basis of complex diseases is one of the most important challenges in current precision medicine. To this end, Genome-Wide Association Studies aim to correlate Single Nucleotide Polymorphisms (SNPs) to the presence or absence of certain traits. However, these studies do not consider interactions between several SNPs, known as epistasis, which explain most genetic diseases. Analyzing SNP combinations to detect epistasis is a major computational task, due to the enormous search space. A possible solution is to employ deep learning strategies for genomic prediction, but the lack of explainability derived from the black-box nature of neural networks is a challenge yet to be addressed. Herein, a novel, flexible, portable, and scalable framework for network interpretation based on transformers is proposed to tackle any-order epistasis. The results on various epistasis scenarios show that the proposed framework outperforms state-of-the-art methods for explainability, while being scalable to large datasets and portable to various deep learning accelerators. The proposed framework is validated on three WTCCC datasets, identifying SNPs related to genes known in the literature that have direct relationships with the studied diseases.

Desvendando as raízes dos estudos culturais físicos: das reflexões iniciais à institucionalização acadêmica / Unveiling the roots of physical cultural studies: from initial reflections to academic institutionalization / Desentrañando las raíces de los estudios culturales físicos: desde reflexiones iniciales hasta la institucionalización académica

Este artigo tem como objetivo principal compreender a trajetória de construção dos Estudos Culturais Físicos (ECF) antes de sua institucionalização no meio acadêmico. A problemática central reside na escassez de informações disponíveis sobre os Estudos Culturais Físicos (ECF) em seu estágio inicial, antes de serem formalmente reconhecidos no contexto acadêmico. A metodologia adotada neste estudo consistiu em uma abordagem de pesquisa bibliográfica, conduzida por meio de leituras exploratórias. A partir dessas análises, considera-se que a concepção dos Estudos Culturais Físicos (ECF), advém de diversos acontecimentos históricos e sociais que possibilitaram a criação de uma nova abordagem na produção de conhecimento da Sociologia do Esporte norte- americana e que compreende a subjetividade do corpo/sujeito além da sua capacidade de performance no esporte/cultura física.

This article aims to primarily comprehend the developmental trajectory of Physical Cultural Studies (PCS) prior to its institutionalization within the academic realm. The central issue lies in the scarcity of available information regarding PCS during its nascent stage, before gaining formal recognition within the academic context. The methodology employed in this study involves a bibliographic research approach, conducted through exploratory readings. Based on these analyses, it is considered that the conception of PCS arises from various historical and societal events that facilitated the creation of a novel approach in generating knowledge within American Sociology of Sport. This approach extends beyond the assessment of sporting performance, delving into the realm of the body's and subject's subjectivity, encompassing facets beyond their athletic prowess in sport/physical culture.

Este artículo tiene como objetivo principal comprender la trayectoria de construcción de los Estudios Culturales Físicos (ECF) antes de su institucionalización en el ámbito académico. La problemática central radica en la escasez de información disponible sobre los Estudios Culturales Físicos (ECF) en su etapa inicial, antes de ser reconocidos formalmente en el contexto académico. La metodología adoptada en este estudio consistió en un enfoque de investigación bibliográfica, llevada a cabo mediante lecturas exploratorias. A partir de estos análisis, se considera que la concepción de los Estudios Culturales Físicos (ECF) proviene de diversos acontecimientos históricos y sociales que posibilitaron la creación de un nuevo enfoque en la producción de conocimiento de la Sociología del Deporte estadounidense y que comprende la subjetividad del cuerpo/sujeto más allá de su capacidad de rendimiento en el deporte/cultura física.

Inter-Algorithm Multiobjective Cooperation for Phylogenetic Reconstruction on Amino Acid Data.

Inter-algorithm cooperative approaches are increasingly gaining interest as a way to boost the search capabilities of evolutionary algorithms (EAs). However, the growing complexity of real-world optimization problems demands new cooperative designs that implement performance-driven strategies to improve the solution quality. This article explores multiobjective cooperation to address an important problem in bioinformatics: the reconstruction of phylogenetic histories from amino acid data. The proposed method is built using representative algorithms from the three main multiobjective design trends: 1) nondominated sorting genetic algorithm II; 2) indicator-based evolutionary algorithm; and 3) multiobjective evolutionary algorithm based on decomposition. The cooperation is supervised by an Elite island component that, along with managing migrations, retrieves multitrend performance feedback from each approach to run additional instantiations of the most satisfying algorithm in each stage of the execution. Experimentation on five real-world problem instances shows the benefits of the proposal to handle complex optimization tasks, in comparison to stand-alone algorithms, standard island models, and other state-of-the-art methods.

Computation of induced dipoles in molecular mechanics simulations using graphics processors.

In this work, we present a tentative step toward the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have implemented a GPU accelerated code, based on the Tinker program suite, for the computation of induced dipoles. The largest test system used shows a speedup factor of over 20 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parametrization steps is included. Comparison between different graphic cards and CPU-GPU embedding is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.

A portable and autonomous magnetic detection platform for biosensing.

This paper presents a prototype of a platform for biomolecular recognition detection. The system is based on a magnetoresistive biochip that performs biorecognition assays by detecting magnetically tagged targets. All the electronic circuitry for addressing, driving and reading out signals from spin-valve or magnetic tunnel junctions sensors is implemented using off-the-shelf components. Taking advantage of digital signal processing techniques, the acquired signals are processed in real time and transmitted to a digital analyzer that enables the user to control and follow the experiment through a graphical user interface. The developed platform is portable and capable of operating autonomously for nearly eight hours. Experimental results show that the noise level of the described platform is one order of magnitude lower than the one presented by the previously used measurement set-up. Experimental results also show that this device is able to detect magnetic nanoparticles with a diameter of 250 nm at a concentration of about 40 fM. Finally, the biomolecular recognition detection capabilities of the platform are demonstrated by performing a hybridization assay using complementary and non-complementary probes and a magnetically tagged 20mer single stranded DNA target.