Simulating the behavior of the human brain on GPUS

The simulation of the behavior of the Human Brain is one of the most important challenges in computing today. The main problem consists of finding efficient ways to manipulate and compute the huge volume of data that this kind of simulations need, using the current technology. In this sense, this work is focused on one of the main steps of such simulation, which consists of computing the Voltage on neurons’ morphology. This is carried out using the Hines Algorithm and, although this algorithm is the optimum method in terms of number of operations, it is in need of non-trivial modifications to be efficiently parallelized on GPUs. We proposed several optimizations to accelerate this algorithm on GPU-based architectures, exploring the limitations of both, method and architecture, to be able to solve efficiently a high number of Hines systems (neurons). Each of the optimizations are deeply analyzed and described. Two different approaches are studied, one for mono-morphology simulations (batch of neurons with the same shape) and one for multi-morphology simulations (batch of neurons where every neuron has a different shape). In mono-morphology simulations we obtain a good performance using just a single kernel to compute all the neurons. However this turns out to be inefficient on multi-morphology simulations. Unlike the previous scenario, in multi-morphology simulations a much more complex implementation is necessary to obtain a good performance. In this case, we must execute more than one single GPU kernel. In every execution (kernel call) one specific part of the batch of the neurons is solved. These parts can be seen as multiple and independent tridiagonal systems. Although the present paper is focused on the simulation of the behavior of the Human Brain, some of these techniques, in particular those related to the solving of tridiagonal systems, can be also used for multiple oil and gas simulations. Our studies have proven that the optimizations proposed in the present work can achieve high performance on those computations with a high number of neurons, being our GPU implementations about 4× and 8× faster than the OpenMP multicore implementation (16 cores), using one and two NVIDIA K80 GPUs respectively. Also, it is important to highlight that these optimizations can continue scaling, even when dealing with a very high number of neurons.This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 720270 (HBP SGA1), from the Spanish Ministry of Economy and Competitiveness under the project Computación de Altas Prestaciones VII (TIN2015-65316-P), the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d’Execució Parallels (2014-SGR-1051). We thank the support of NVIDIA through the BSC/UPC NVIDIA GPU Center of Excellence, and the European Union’s Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie Grant Agreement No. 749516.Peer ReviewedPostprint (published version

Proyecto de orientación y mentorización al alumnado de nuevo ingreso en una escuela de ingeniería

En este trabajo se presenta un plan de orientación a alumnos noveles en la ETSI de Telecomunicación de la Universidad de Málaga. El programa, que ha pasado por diversas fases en tres años, utiliza la mentoría de alumnos ve-teranos. Pese a la reducida participación, ha posibilitado el desarrollo de diversas actividades formativas y socializantes (para mentores y mentoriza-dos), así como un mejor conocimiento de los problemas que afectan a los alumnos noveles.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

ETLP: Event-based Three-factor Local Plasticity for online learning with neuromorphic hardware

Neuromorphic perception with event-based sensors, asynchronous hardware and spiking neurons is showing promising results for real-time and energy-efficient inference in embedded systems. The next promise of brain-inspired computing is to enable adaptation to changes at the edge with online learning. However, the parallel and distributed architectures of neuromorphic hardware based on co-localized compute and memory imposes locality constraints to the on-chip learning rules. We propose in this work the Event-based Three-factor Local Plasticity (ETLP) rule that uses (1) the pre-synaptic spike trace, (2) the post-synaptic membrane voltage and (3) a third factor in the form of projected labels with no error calculation, that also serve as update triggers. We apply ETLP with feedforward and recurrent spiking neural networks on visual and auditory event-based pattern recognition, and compare it to Back-Propagation Through Time (BPTT) and eProp. We show a competitive performance in accuracy with a clear advantage in the computational complexity for ETLP. We also show that when using local plasticity, threshold adaptation in spiking neurons and a recurrent topology are necessary to learn spatio-temporal patterns with a rich temporal structure. Finally, we provide a proof of concept hardware implementation of ETLP on FPGA to highlight the simplicity of its computational primitives and how they can be mapped into neuromorphic hardware for online learning with low-energy consumption and real-time interaction

cuHinesBatch: solving multiple hines systems on GPUs Human Brain Project

The simulation of the behavior of the Human Brain is one of the most important challenges today in computing. The main problem consists of finding efficient ways to manipulate and compute the huge volume of data that this kind of simulations need, using the current technology. In this sense, this work is focused on one of the main steps of such simulation, which consists of computing the Voltage on neurons’ morphology. This is carried out using the Hines Algorithm. Although this algorithm is the optimum method in terms of number of operations, it is in need of non-trivial modifications to be efficiently parallelized on NVIDIA GPUs. We proposed several optimizations to accelerate this algorithm on GPU-based architectures, exploring the limitations of both, method and architecture, to be able to solve efficiently a high number of Hines systems (neurons). Each of the optimizations are deeply analyzed and described. To evaluate the impact of the optimizations on real inputs, we have used 6 different morphologies in terms of size and branches. Our studies have proven that the optimizations proposed in the present work can achieve a high performance on those computations with a high number of neurons, being our GPU implementations about 4× and 8× faster than the OpenMP multicore implementation (16 cores), using one and two K80 NVIDIA GPUs respectively. Also, it is important to highlight that these optimizations can continue scaling even when dealing with number of neurons.This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 720270 (HBP SGA1), from the Spanish Ministry of Economy and Competitiveness under the project Computación de Altas Prestaciones VII (TIN2015-65316-P) and the Departament d’Innovació, Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d’Execució Paral·lels (2014-SGR-1051). We thank the support of NVIDIA through the BSC/UPC NVIDIA GPU Center of Excellence. Antonio J. Peña is cofinanced by the Spanish Ministry of Economy and Competitiveness under Juan de la Cierva fellowship number IJCI-2015-23266.Peer ReviewedPostprint (published version

WaLiN-GUI: a graphical and auditory tool for neuron-based encoding

Neuromorphic computing relies on spike-based, energy-efficient communication, inherently implying the need for conversion between real-valued (sensory) data and binary, sparse spiking representation. This is usually accomplished using the real valued data as current input to a spiking neuron model, and tuning the neuron's parameters to match a desired, often biologically inspired behaviour. We developed a tool, the WaLiN-GUI, that supports the investigation of neuron models and parameter combinations to identify suitable configurations for neuron-based encoding of sample-based data into spike trains. Due to the generalized LIF model implemented by default, next to the LIF and Izhikevich neuron models, many spiking behaviors can be investigated out of the box, thus offering the possibility of tuning biologically plausible responses to the input data. The GUI is provided open source and with documentation, being easy to extend with further neuron models and personalize with data analysis functions.Comment: 4 pages, 1 figur

Actividad extracurricular en el ámbito de la Ingeniería para la competencia genérica de comunicación escrita

El objetivo de este trabajo es describir una actividad formativa extracurricular para la competencia de comunicación escrita, que puede ser fácilmente reproducida en otros centros y universidades. Para ello, en este trabajo se indica el marco en el que se pueden desarrollar las competencias genéricas y se analiza brevemente la actividad propuesta a través de sus resultados de aprendizaje, y cómo estos favorecen e influyen en otras competencias genéricas como la capacidad creativa y el aprendizaje para toda la vida.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A brassinosteroid functional analogue increases soybean drought resilience

Drought severely affects soybean productivity, challenging breeding/management strategies to increase crop resilience. Hormone-based biostimulants like brassinosteroids (BRs) modulate growth/defence trade-off, mitigating yield losses; yet, natural molecule's low stability challenges the development of cost-effective and long-lasting analogues. Here, we investigated for the first time the effects of BR functional analogue DI-31 in soybean physiology under drought by assessing changes in growth, photosynthesis, water relations, antioxidant metabolism, nodulation, and nitrogen homeostasis. Moreover, DI-31 application frequencies' effects on crop cycle and commercial cultivar yield stabilisation under drought were assessed. A single foliar application of DI-31 favoured plant drought tolerance, preventing reductions in canopy development and enhancing plant performance and water use since the early stages of stress. The analogue also increased the antioxidant response, favouring nitrogen homeostasis maintenance and attenuating the nodular senescence. Moreover, foliar applications of DI-31 every 21 days enhanced the absolute yield by ~ 9% and reduced drought-induced yield losses by ~ 7% in four commercial cultivars, increasing their drought tolerance efficiency by ~ 12%. These findings demonstrated the practical value of DI-31 as an environmentally friendly alternative for integrative soybean resilience management under drought.Instituto de Fisiología y Recursos Genéticos VegetalesFil: Perez Borroto, Lucia Sandra. Wageningen University and Research. Plant Breeding; Países BajosFil: Guzzo, María Carla. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales; ArgentinaFil: Guzzo, María Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Estudios Agropecuarios (UDEA) ; ArgentinaFil: Posada, Gisella. Instituto Superior Albert Sabin; ArgentinaFil: Peña Malavera, Andrea Natalia. Estación Experimental Agroindustrial Obispo Colombres (EEAOC). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Peña Malavera, Andrea Natalia. Consejo Nacional de Investigaciones Científicas Y Técnicas; ArgentinaFil: Castagnaro, Atilio Pedro. Estación Experimental Agroindustrial Obispo Colombres (EEAOC). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Castagnaro, Atilio Pedro. Consejo Nacional de Investigaciones Científicas Y Técnicas; ArgentinaFil: Gonzalez Olmedo, Justo Lorenzo. Universidad de Ciego de Ávila “Máximo Gómez Báez”. Centro de Bioplantas; CubaFil: Coll García, Yamilet. Universidad de La Habana. Facultad de Química. Centro de Estudios de Productos Naturales; CubaFil: Pardo, Esteban Mariano. Estación Experimental Agroindustrial Obispo Colombres (EEAOC). Instituto de Tecnología Agroindustrial del Noroeste Argentino; ArgentinaFil: Pardo, Esteban Mariano. Consejo Nacional de Investigaciones Científicas Y Técnicas; Argentin

Sostenibilidad de la caza de mamíferos en tres territorios indígenas de la cuenca alta del Putumayo, Nororiente de la Amazonía peruana

Los pueblos indígenas secoyas y kichwas de la cuenca alta del Putumayo cazan mayormente Cuniculus paca “majás”, Pecari tajacu “sajino” y Tayassu pecari “huangana”, debido a su sabor agradable, mayor biomasa y precio en el mercado. Es por ello que la evaluación de la sostenibilidad de la caza es muy importante para que las comunidades nativas aseguren su alimentación y beneficios económicos. Con ese propósito y la de obtener registros cuantificables, entre el 2017 y 2019 se realizaron evaluaciones de fauna silvestre usando métodos de transectos en banda, registros de huella y de cámaras trampa. La densidad poblacional de pecaríes se obtuvo de la división del número de individuos registrados en el área de estudio. Para el cálculo de la densidad de C. paca, se utilizó el conteo de madrigueras. La presión de caza se estimó obteniendo información sobre el número de animales aprovechados en la zona de caza, recopilados mediante registros de caza y entrevistas a cazadores. Se usaron el modelo de cosecha y consenso cultural para evaluar la sostenibilidad de la caza. Los resultados de este estudio demuestran que la caza está siendo sostenible en las tres especies mayormente aprovechadas. Cabe indicar que, durante el 2019, la especie T. pecari no fue registrada mediante transectos, cámaras trampa ni huellas en las comunidades de Mashunta y Belén, pero fue aprovechada y evidenciada en los registros de caza. En conclusión, las comunidades de los pueblos indígenas secoyas y kichwas realizan cacería sostenible y en consecuencia pueden implementar planes de manejo con fines comerciales

Tocilizumab in refractory Caucasian Takayasu's arteritis: a multicenter study of 54 patients and literature review

Objective: To assess the efficacy and safety of tocilizumab (TCZ) in Caucasian patients with refractory Takayasu's arteritis (TAK) in clinical practice. Methods: A multicenter study of Caucasian patients with refractory TAK who received TCZ. The outcome variables were remission, glucocorticoid-sparing effect, improvement in imaging techniques, and adverse events. A comparative study between patients who received TCZ as monotherapy (TCZMONO) and combined with conventional disease modifying anti-rheumatic drugs (cDMARDs) (TCZCOMBO) was performed. Results: The study comprised 54 patients (46 women/8 men) with a median [interquartile range (IQR)] age of 42.0 (32.5-50.5) years. TCZ was started after a median (IQR) of 12.0 (3.0-31.5) months since TAK diagnosis. Remission was achieved in 12/54 (22.2%), 19/49 (38.8%), 23/44 (52.3%), and 27/36 (75%) patients at 1, 3, 6, and 12 months, respectively. The prednisone dose was reduced from 30.0 mg/day (12.5-50.0) to 5.0 (0.0-5.6) mg/day at 12 months. An improvement in imaging findings was reported in 28 (73.7%) patients after a median (IQR) of 9.0 (6.0-14.0) months. Twenty-three (42.6%) patients were on TCZMONO and 31 (57.4%) on TCZCOMBO: MTX (n = 28), cyclosporine A (n = 2), azathioprine (n = 1). Patients on TCZCOMBO were younger [38.0 (27.0-46.0) versus 45.0 (38.0-57.0)] years; difference (diff) [95% confidence interval (CI) = -7.0 (-17.9, -0.56] with a trend to longer TAK duration [21.0 (6.0-38.0) versus 6.0 (1.0-23.0)] months; diff 95% CI = 15 (-8.9, 35.5), and higher c-reactive protein [2.4 (0.7-5.6) versus 1.3 (0.3-3.3)] mg/dl; diff 95% CI = 1.1 (-0.26, 2.99). Despite these differences, similar outcomes were observed in both groups (log rank p = 0.862). Relevant adverse events were reported in six (11.1%) patients, but only three developed severe events that required TCZ withdrawal. Conclusion: TCZ in monotherapy, or combined with cDMARDs, is effective and safe in patients with refractory TAK of Caucasian origin.Funding: This work was partially supported by RETICS Programs, RD08/0075 (RIER), RD12/0009/0013 and RD16/0012 from “Instituto de Salud Carlos III” (ISCIII) (Spain)