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Continuous Video to Simple Signals for Swimming Stroke Detection with Convolutional Neural Networks [article]

Brandon Victor, Zhen He, Stuart Morgan, Dino Miniutti
2017 arXiv   pre-print
In many sports, it is useful to analyse video of an athlete in competition for training purposes. In swimming, stroke rate is a common metric used by coaches; requiring a laborious labelling of each individual stroke. We show that using a Convolutional Neural Network (CNN) we can automatically detect discrete events in continuous video (in this case, swimming strokes). We create a CNN that learns a mapping from a window of frames to a point on a smooth 1D target signal, with peaks denoting the
more » ... ocation of a stroke, evaluated as a sliding window. To our knowledge this process of training and utilizing a CNN has not been investigated before; either in sports or fundamental computer vision research. Most research has been focused on action recognition and using it to classify many clips in continuous video for action localisation. In this paper we demonstrate our process works well on the task of detecting swimming strokes in the wild. However, without modifying the model architecture or training method, the process is also shown to work equally well on detecting tennis strokes, implying that this is a general process. The outputs of our system are surprisingly smooth signals that predict an arbitrary event at least as accurately as humans (manually evaluated from a sample of negative results). A number of different architectures are evaluated, pertaining to slightly different problem formulations and signal targets.
arXiv:1705.09894v1 fatcat:usqsdzc7ajbffgjjcf6czuu3be

Bulk manifestation of the spin Hall effect

Brandon Anderson, Tudor D. Stanescu, Victor Galitski
2010 Physical Review B  
We show that a two-dimensional spin-orbit-coupled system in the presence of a charge/spin-density wave with a wave-vector perpendicular to an applied electric field supports bulk manifestations of the direct/inverse spin-Hall effect. We develop a theory of this phenomenon in the framework of the spin diffusion equation formalism and show that, due to the inhomogeneity created by a spin-grating, an anomalous bulk charge-density wave is induced away from sample boundaries. The optimal conditions
more » ... or the observation of the effect are determined. The main experimental manifestation of the bulk spin-Hall effect, the induced charge/spin-density-wave, is characterized by a pi/2-phase shift relative to the initial non-homogeneous spin/charge-polarization profile and has a non-monotonic time-varying amplitude.
doi:10.1103/physrevb.81.121304 fatcat:pyl6c3nihze6rhtl3t566dizaa

Extracting seismic core phases with array interferometry

Fan-Chi Lin, Victor C. Tsai, Brandon Schmandt, Zacharie Duputel, Zhongwen Zhan
2013 Geophysical Research Letters  
1] Seismic body waves that sample Earth's core are indispensable for studying the most remote regions of the planet. Traditional core phase studies rely on well-defined earthquake signals, which are spatially and temporally limited. We show that, by stacking ambient-noise cross-correlations between USArray seismometers, body wave phases reflected off the outer core (ScS), and twice refracted through the inner core (PKIKP 2 ) can be clearly extracted. Temporal correlation between the amplitude
more » ... these core phases and global seismicity suggests that the signals originate from distant earthquakes and emerge due to array interferometry. Similar results from a seismic array in New Zealand demonstrate that our approach is applicable in other regions and with fewer station pairs. Extraction of core phases by interferometry can significantly improve the spatial sampling of the deep Earth because the technique can be applied anywhere broadband seismic arrays exist.
doi:10.1002/grl.50237 fatcat:7cmtucfgkbbdtpi723xhqibrim

Lexical landscapes as large in silico data for examining advanced properties of fitness landscapes [article]

Victor A. Meszaros, Miles Miller-Dickson, C. Brandon Ogbunugafor
2019 bioRxiv   pre-print
In silico approaches have served a central role in the development of evolutionary theory for generations. This especially applies to the concept of the fitness landscape, one of the most important abstractions in evolutionary genetics, and one which has benefited from the presence of large empirical data sets only in the last decade or so. In this study, we propose a method that allows us to generate enormous data sets that walk the line between in silico and empirical: word usage frequencies
more » ... s catalogued by the Google ngram corpora. These data can be codified or analogized in terms of a multidimensional empirical fitness landscape towards the examination of advanced concepts - adaptive landscape by environment interactions, clonal competition, higher-order epistasis and countless others. We argue that the greater Lexical Landscapes approach can serve as a platform that offers an astronomical number of fitness landscapes for exploration (at least) or theoretical formalism (potentially) in evolutionary biology
doi:10.1101/640151 fatcat:qxjtrjy4ybfp7nfloibxq2lgz4

DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network [article]

Jing Meng, Brandon Victor, Zhen He, Agus Salim
2019 bioRxiv   pre-print
AbstractMotivationIt is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence,
more » ... are expected to produce divergent outputs.ResultsTo overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially-oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidences. Moreover, DeepSSV incorporates the mapping information of both reference-allele-supporting and variant-allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts, and alleviates the need of post-call filters that heavily depend on prior knowledge. We fitted the model on ground truth somatic mutations, and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1 score.Availability and Implementationhttps://github.com/jingmeng-bioinformatics/DeepSSVContacta.salim@latrobe.edu.auSupplementary informationSupplementary data are available at online.
doi:10.1101/555680 fatcat:uuicjuwlt5hz3fts27vq3g564m

Preparation of a conjugation-ready thiol responsive molecular switch

Brandon Tautges, Victor Or, Joel Garcia, Jared T. Shaw, Angelique Y. Louie
2015 Tetrahedron Letters  
In this work we synthesize molecular switches that are responsive to cysteine, homocysteine, and glutathione; three redox systems that make up the majority of the body's antioxidant defenses. Synthesized spiropyran isomers with conjugation-ready linkages showed good selectivity of response to these major antioxidant thiols over nucleophilic amino acids; however the position of the linking group can affect selectivity and reversibility of the switching response. An isomer with selectivity for cysteine against GSH and Hcy was identified.
doi:10.1016/j.tetlet.2015.10.019 pmid:26594066 pmcid:PMC4649948 fatcat:io4uozycijcdhhpykikilt2o5u

Next Stop "NoOps": Enabling Cross-System Diagnostics Through Graph-based Composition of Logs and Metrics [article]

Michał Zasadziński, Marc Solé, Alvaro Brandon, Victor Muntés-Mulero, David Carrera
2018 arXiv   pre-print
Performing diagnostics in IT systems is an increasingly complicated task, and it is not doable in satisfactory time by even the most skillful operators. Systems and their architecture change very rapidly in response to business and user demand. Many organizations see value in the maintenance and management model of NoOps that stands for No Operations. One of the implementations of this model is a system that is maintained automatically without any human intervention. The path to NoOps involves
more » ... ot only precise and fast diagnostics but also reusing as much knowledge as possible after the system is reconfigured or changed. The biggest challenge is to leverage knowledge on one IT system and reuse this knowledge for diagnostics of another, different system. We propose a framework of weighted graphs which can transfer knowledge, and perform high-quality diagnostics of IT systems. We encode all possible data in a graph representation of a system state and automatically calculate weights of these graphs. Then, thanks to the evaluation of similarity between graphs, we transfer knowledge about failures from one system to another and use it for diagnostics. We successfully evaluate the proposed approach on Spark, Hadoop, Kafka and Cassandra systems.
arXiv:1809.07687v1 fatcat:j3wcirkua5borpnrlk3j6p4dya

The epidemic consequences of virulence and free-living survival relationships in models of emerging outbreaks [article]

Lourdes M. Gomez, Victor A. Meszaros, Wendy C. Turner, C. Brandon Ogbunugafor
2020 bioRxiv   pre-print
The relationship between parasite virulence and transmission is a pillar of evolutionary theory that has specific implications for public health. Part of this canon involves the idea that virulence and free-living survival (a key component of transmission) may have different relationships in different host-parasite systems. Most examinations of the evolution of virulence-transmission relationships (theoretical or empirical in nature) tend to focus on the evolution of virulence, with
more » ... a secondary consideration. In virus evolution, recent studies have examined how the evolution of free-living survival can influence other traits. However, few studies have examined the epidemic-scale consequences of evolution across the different virulence-survival relationships, and specifically, of increased free-living survival. In this study, we utilize a mathematical model motivated by aspects of SARS-CoV-2 natural history to investigate how evolutionary changes in survival traits, and their subsequent relationship to virulence traits, may influence several aspects of disease dynamics. Specifically, we examine how each of two different hypothesized relationships between virulence and survival, one deemed the Curse of the Pharaoh hypothesis and the other more classically referred to as the tradeoff hypothesis. Across virulence-survival frameworks, we found that small changes (5% above and below the nominal value) in survival can have a meaningful effect on certain outbreak features, including the R0, and the size of the infectious peak in the population. These results highlight the importance of properly understanding the relationship between virulence and parasite survival, as they offer considerably different predictions for how the evolution of free-living survival will influence the trajectory of an emerging epidemic.
doi:10.1101/2020.06.08.141366 fatcat:4ivnenktyvdonfz2rkyl5d2mmu

Fluctuations in Evolutionary Integration Allow for Big Brains and Disparate Faces

Kory M. Evans, Brandon T. Waltz, Victor A. Tagliacollo, Brian L. Sidlauskas, James S. Albert
2017 Scientific Reports  
doi:10.1038/srep40431 pmid:28091543 pmcid:PMC5238424 fatcat:4jyzcsmsjzfg5kx47bfm4rqxiu

Developmental Variation in Amygdala Volumes Among Children With Posttraumatic Stress

Carl F. Weems, Brandon G. Scott, Justin D. Russell, Allan L. Reiss, Victor G. Carrión
2013 Developmental Neuropsychology  
This article examined associations between indices of maturation (age and Tanner stage) and amygdala volumes in 24 youth (aged 7-14) with posttraumatic stress disorder symptoms and a matched control group. Fifteen of the youth with exposure to trauma were also re-evaluated one year later. A positive association between maturation and right amygdala volumes was observed in the trauma group but not in controls. Associations with maturation remained when controlling for a number of possible
more » ... tes and over time. Developmentally younger youth (Tanner stage 1 and 2) showed increases and older (Tanner stage 3 and 4) decreases in right amygdala volumes.
doi:10.1080/87565641.2013.820307 pmid:24138217 fatcat:glvnpsd3a5dyxn3lgg6y6itab4

GNC Challenges and Opportunities of CubeSat Science Missions Deployed from the Lunar Gateway [article]

Himangshu Kalita, Miguel Donayre, Victor Padilla, Anthony Riley, Jesse Samitas, Brandon Burnett, Erik Asphaug, Mark Robinson, Jekan Thangavelautham
2019 arXiv   pre-print
The Lunar Gateway is expected to be positioned on-orbit around the Moon or in a Halo orbit at the L2 Lagrange point. The proposed Lunar Gateway is a game-changer for enabling new, high-priority lunar science utilizing Cu-beSats and presents a refreshing new opportunity for utilization of these small spacecraft as explorers. In context, CubeSats are being stretched to their limits as interplanetary explorers. The main technological hurdles include high-bandwidth communications and reliable high
more » ... elta-v propulsion. Advances in deep-space attitude determination and control has been made possible from the recent NASA JPL MarCO missions. Due to these limitations, CubeSats are primarily designed to be dropped-off from a larger mission. The limited mass and volume have required compromises of the onboard science instruments, longer wait times to send back science data to Earth, shorter mission durations or higher accepted risk. With the Lunar Gateway being planned to be closer to the Moon, it will provide significant savings for a propulsion system and provide a primary relay for communication apart from the DSN and enable tele-operated command/control. These three factors can simplify the mission enabling routine deployment of CubeSats into lunar orbit and enable surface missions. In this paper, we present preliminary designs of 2 CubeSat lunar landers that will explore the lunar pits, Mare Tranquilitatis and the remnant magnetic fields Reiner Gamma.
arXiv:1904.00497v1 fatcat:wjpkp2oafzcnzexzjvs32aycau

Decision Confidence, Information Usefulness, and Information Seeking Intention in the Presence of Disconfirming Information

Brandon Phillips, Victor R. Prybutok, Daniel A. Peak
2014 Informing Science  
APPENDIX B: Information Seeking Survey Group Instrument (Non-Visual Group) Biographies Brandon K.  ... 
doi:10.28945/1932 fatcat:bwsls2ik6bhi7lnl43wou6hriy

Facile solvolysis of a surprisingly twisted tertiary amide

Aaron J. Bloomfield, Subhajyoti Chaudhuri, Brandon Q. Mercado, Victor S. Batista, Robert H. Crabtree
2016 New Journal of Chemistry  
A twisted 3° amide is cleaved at the same rate as a methyl ester under alkaline conditions at 22 °C.
doi:10.1039/c5nj02449h fatcat:a3xlgri7rjbwdmcxjv36erwn4m

Synthetic 3D Spin-Orbit Coupling

Brandon M. Anderson, Gediminas Juzeliūnas, Victor M. Galitski, I. B. Spielman
2012 Physical Review Letters  
We describe a method for creating a three-dimensional analogue to Rashba spin-orbit coupling in systems of ultracold atoms. This laser induced coupling uses Raman transitions to link four internal atomic states with a tetrahedral geometry, and gives rise to a Dirac point that is robust against environmental perturbations. We present an exact result showing that such a spin-orbit coupling in a fermionic system always rise to a molecular bound state.
doi:10.1103/physrevlett.108.235301 pmid:23003967 fatcat:kdm5zgwzkjcwrjj7wjc62t6tke

Methanol oxidative dehydrogenation in a catalytic packed-bed membrane reactor: experiments and model

Victor Diakov, Brandon Blackwell, Arvind Varma
2002 Chemical Engineering Science  
Methanol oxidative dehydrogenation to formaldehyde over a Fe-Mo oxide catalyst was studied experimentally in three reactor conÿgurations: the conventional ÿxed-bed reactor (FBR) and the packed-bed membrane reactor (PBMR), with either methanol ( PBMR-M) or oxygen (PBMR-O) as the permeating component. The kinetics of methanol and formaldehyde partial oxidation reactions were determined independently from FBR experiments. A steady state plug-ow PBMR model, utilizing these kinetics and no
more » ... parameters, ÿt the experiments accurately. It is shown experimentally and in accordance with the model that for given overall feed conditions, the reactor performance for methanol conversion and formaldehyde yield is in the order PBMR-M ¡ FBR ¡ PBMR-O. ? 2002 Published by (A. Varma). 0009-2509/02/$ -see front matter ? 2002 Published by Elsevier Science Ltd. PII: S 0 0 0 9 -2 5 0 9 ( 0 2 ) 0 0 0 3 1 -3
doi:10.1016/s0009-2509(02)00031-3 fatcat:jeysytq3zbeq3fntl52ibmtsxe
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