Recent Submissions

  • Positivity-preserving CE/SE schemes for solving the compressible Euler and Navier–Stokes equations on hybrid unstructured meshes

    Shen, Hua; Parsani, Matteo (Elsevier BV, 2018-05-28)
    We construct positivity-preserving space–time conservation element and solution element (CE/SE) schemes for solving the compressible Euler and Navier–Stokes equations on hybrid unstructured meshes consisting of triangular and rectangular elements. The schemes use an a posteriori limiter to prevent negative densities and pressures based on the premise of preserving optimal accuracy. The limiter enforces a constraint for spatial derivatives and does not change the conservative property of CE/SE schemes. Several numerical examples suggest that the proposed schemes preserve accuracy for smooth flows and strictly preserve positivity of densities and pressures for the problems involving near vacuum and very strong discontinuities.
  • In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters

    Othoum, Ghofran K; Bougouffa, Salim; Razali, Rozaimi; Bokhari, Ameerah; Alamoudi, Soha; Antunes, André; Gao, Xin; Hoehndorf, Robert; Arold, Stefan T.; Gojobori, Takashi; Hirt, Heribert; Mijakovic, Ivan; Bajic, Vladimir B.; Lafi, Feras Fawzi; Essack, Magbubah (Springer Nature, 2018-05-22)
    BackgroundThe increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions.ResultsWe report the complete circular and annotated genomes of two Red Sea strains, B. paralicheniformis Bac48 isolated from mangrove mud and B. paralicheniformis Bac84 isolated from microbial mat collected from Rabigh Harbor Lagoon in Saudi Arabia. Comparing the genomes of B. paralicheniformis Bac48 and B. paralicheniformis Bac84 with nine publicly available complete genomes of B. licheniformis and three genomes of B. paralicheniformis, revealed that all of the B. paralicheniformis strains in this study are more enriched in nonribosomal peptides (NRPs). We further report the first computationally identified trans-acyltransferase (trans-AT) nonribosomal peptide synthetase/polyketide synthase (PKS/ NRPS) cluster in strains of this species.ConclusionsB. paralicheniformis species have more genes associated with biosynthesis of antimicrobial bioactive compounds than other previously characterized species of B. licheniformis, which suggests that these species are better potential sources for novel antibiotics. Moreover, the genome of the Red Sea strain B. paralicheniformis Bac48 is more enriched in modular PKS genes compared to B. licheniformis strains and other B. paralicheniformis strains. This may be linked to adaptations that strains surviving in the Red Sea underwent to survive in the relatively hot and saline ecosystems.
  • Ensemble Kalman Filter Inference of Spatially-varying Manning’s n coefficients in the Coastal Ocean

    Siripatana, Adil; Mayo, Talea; Knio, Omar; Dawson, Clint; Maître, Olivier Le; Hoteit, Ibrahim (Elsevier BV, 2018-05-16)
    Ensemble Kalman (EnKF) filtering is an established framework for large scale state estimation problems. EnKFs can also be used for state-parameter estimation, using the so-called “Joint-EnKF” approach. The idea is simply to augment the state vector with the parameters to be estimated and assign invariant dynamics for the time evolution of the parameters. In this contribution, we investigate the efficiency of the Joint-EnKF for estimating spatially-varying Manning’s n coefficients used to define the bottom roughness in the Shallow Water Equations (SWEs) of a coastal ocean model.Observation System Simulation Experiments (OSSEs) are conducted using the ADvanced CIRCulation (ADCIRC) model, which solves a modified form of the Shallow Water Equations. A deterministic EnKF, the Singular Evolutive Interpolated Kalman (SEIK) filter, is used to estimate a vector of Manning’s n coefficients defined at the model nodal points by assimilating synthetic water elevation data. It is found that with reasonable ensemble size (O(10)), the filter’s estimate converges to the reference Manning’s field. To enhance performance, we have further reduced the dimension of the parameter search space through a Karhunen-Loéve (KL) expansion. We have also iterated on the filter update step to better account for the nonlinearity of the parameter estimation problem. We study the sensitivity of the system to the ensemble size, localization scale, dimension of retained KL modes, and number of iterations. The performance of the proposed framework in term of estimation accuracy suggests that a well-tuned Joint-EnKF provides a promising robust approach to infer spatially varying seabed roughness parameters in the context of coastal ocean modeling.
  • X-ray created metamaterials: applications to metal-free structural colors with full chromaticity spectrum and 80 nm spatial resolution

    Bonifazi, Marcella; Mazzone, Valerio; Fratalocchi, Andrea (OSA, 2018-05-07)
    We created new types of metamaterials by hard X-rays possessing high fluency. We discuss applications in structural colors that show full spectrum of Cyan, Yellow, Magenta, Black (CYMK), realized in transparent dielectrics with 80 nm resolution.
  • Metagenome-based diversity analyses suggest a strong locality signal for bacterial communities associated with oyster aquaculture farms in Ofunato Bay

    Kobiyama, Atsushi; Ikeo, Kazuho; Reza, Md. Shaheed; Rashid, Jonaira; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Elsevier BV, 2018-04-30)
    Ofunato Bay, in Japan, is the home of buoy-and-rope-type oyster aquaculture activities. Since the oysters filter suspended materials and excrete organic matter into the seawater, bacterial communities residing in its vicinity may show dynamic changes depending on the oyster culture activities. We employed a shotgun metagenomic technique to study bacterial communities near oyster aquaculture facilities at the center of the bay (KSt. 2) and compared the results with those of two other localities far from the station, one to the northeast (innermost bay, KSt. 1) and the other to the southwest (bay entrance, KSt. 3). Seawater samples were collected every month from January to December 2015 from the surface (1 m) and deeper (8 or 10 m) layers of the three locations, and the sequentially filtered fraction on 0.2-μm membranes was sequenced on an Illumina MiSeq system. The acquired reads were uploaded to MG-RAST for KEGG functional abundance analysis, while taxonomic analyses at the phylum and genus levels were performed using MEGAN after parsing the BLAST output. Discrimination analyses were then performed using the ROC-AUC value of the cross validation, targeting the depth (shallow or deep), locality [(KSt. 1 + KSt. 2) vs. KSt 3; (KSt. 1 + KSt. 3) vs. KSt. 2 or the (KSt. 2 + KSt. 3) vs. KSt. 1] and seasonality (12 months). The matrix discrimination analysis on the adjacent 2 continuous seasons by ROC-AUC, which was based on the datasets that originated from different depths, localities and months, showed the strongest discrimination signal on the taxonomy matrix at the phylum level for the datasets from July to August compared with those from September to June, while the KEGG matrix showed the strongest signal for the datasets from March to June compared with those from July to February. Then, the locality combination was subjected to the same ROC-AUC discrimination analysis, resulting in significant differences between KSt. 2 and KSt. 1 + KSt. 3 on the KEGG matrix. These results suggest that aquaculture activities markedly affect bacterial functions.
  • Seasonal changes in the communities of photosynthetic picoeukaryotes in Ofunato Bay as revealed by shotgun metagenomic sequencing

    Rashid, Jonaira; Kobiyama, Atsushi; Reza, Md. Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Elsevier BV, 2018-04-30)
    Small photosynthetic eukaryotes play important roles in oceanic food webs in coastal regions. We investigated seasonal changes in the communities of photosynthetic picoeukaryotes (PPEs) of the class Mamiellophyceae, including the genera Bathycoccus, Micromonas and Ostreococcus, in Ofunato Bay, which is located in northeastern Japan and faces the Pacific Ocean. The abundances of PPEs were assessed over a period of one year in 2015 at three sampling stations, KSt. 1 (innermost bay area), KSt. 2 (middle bay area) and KSt. 3 (bay entrance area) at depths of 1 m (KSt. 1, KSt. 2 and KSt. 3), 8 m (KSt. 1) or 10 m (KSt. 2 and KSt. 3) by employing MiSeq shotgun metagenomic sequencing. The total abundances of Bathycoccus, Ostreococcus and Micromonas were in the ranges of 42–49%, 35–49% and 13–17%, respectively. Considering all assayed sampling stations and depths, seasonal changes revealed high abundances of PPEs during the winter and summer and low abundances during late winter to early spring and late summer to early autumn. Bathycoccus was most abundant in the winter, and Ostreococcus showed a high abundance during the summer. Another genus, Micromonas, was relatively low in abundance throughout the study period. Taken together with previously suggested blooming periods of phytoplankton, as revealed by chlorophyll a concentrations in Ofunato Bay during spring and late autumn, these results for PPEs suggest that greater phytoplankton blooming has a negative influence on the seasonal occurrences of PPEs in the bay.
  • First-order, stationary mean-field games with congestion

    Evangelista, David; Ferreira, Rita; Gomes, Diogo A.; Nurbekyan, Levon; Voskanyan, Vardan K. (Elsevier BV, 2018-04-30)
    Mean-field games (MFGs) are models for large populations of competing rational agents that seek to optimize a suitable functional. In the case of congestion, this functional takes into account the difficulty of moving in high-density areas. Here, we study stationary MFGs with congestion with quadratic or power-like Hamiltonians. First, using explicit examples, we illustrate two main difficulties: the lack of classical solutions and the existence of areas with vanishing densities. Our main contribution is a new variational formulation for MFGs with congestion. With this formulation, we prove the existence and uniqueness of solutions. Finally, we consider applications to numerical methods.
  • Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay

    Reza, Md. Shaheed; Kobiyama, Atsushi; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Elsevier BV, 2018-04-27)
    The Ofunato Bay in Iwate Prefecture, Japan is a deep coastal bay located at the center of the Sanriku Rias coast and considered an economically and environmentally important asset. Here, we describe the first whole genome sequencing (WGS) study on the microbial community of the bay, where surface water samples were collected from three stations along its length to cover the entire bay; we preliminarily sequenced a 0.2 μm filter fraction among sequentially size-fractionated samples of 20.0, 5.0, 0.8 and 0.2 μm filters, targeting the free-living fraction only. From the 0.27–0.34 Gb WGS library, 0.9 × 106–1.2 × 106 reads from three sampling stations revealed 29 bacterial phyla (~80% of assigned reads), 3 archaeal phyla (~4%) and 59 eukaryotic phyla (~15%). Microbial diversity obtained from the WGS approach was compared with 16S rRNA gene results by mining WGS metagenomes, and we found similar estimates. The most frequently recovered bacterial sequences were Proteobacteria, predominantly comprised of 18.0–19.6% Planktomarina (Family Rhodobacteraceae) and 13.7–17.5% Candidatus Pelagibacter (Family Pelagibacterales). Other dominant bacterial genera, including Polaribacter (3.5–6.1%), Flavobacterium (1.8–2.6%), Sphingobacterium (1.4–1.6%) and Cellulophaga (1.4–2.0%), were members of Bacteroidetes and likely associated with the degradation and turnover of organic matter. The Marine Group I Archaea Nitrosopumilus was also detected. Remarkably, eukaryotic green alga Bathycoccus, Ostreococcus and Micromonas accounted for 8.8–15.2%, 3.6–4.9% and 2.1–3.1% of total read counts, respectively, highlighting their potential roles in the phytoplankton bloom after winter mixing.
  • Seasonal changes in the abundance of bacterial genes related to dimethylsulfoniopropionate catabolism in seawater from Ofunato Bay revealed by metagenomic analysis

    Kudo, Toshiaki; Kobiyama, Atsushi; Rashid, Jonaira; Reza, Shaheed; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Segawa, Satoshi; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Elsevier BV, 2018-04-26)
    Ofunato Bay is located in the northeastern Pacific Ocean area of Japan, and it has the highest biodiversity of marine organisms in the world, primarily due to tidal influences from the cold Oyashio and warm Kuroshio currents. Our previous results from performing shotgun metagenomics indicated that Candidatus Pelagibacter ubique and Planktomarina temperata were the dominant bacteria (Reza et al., 2018a, 2018b). These bacteria are reportedly able to catabolize dimethylsulfoniopropionate (DMSP) produced from phytoplankton into dimethyl sulfide (DMS) or methanethiol (MeSH). This study was focused on seasonal changes in the abundances of bacterial genes (dddP, dmdA) related to DMSP catabolism in the seawater of Ofunato Bay by BLAST+ analysis using shotgun metagenomic datasets. We found seasonal changes among the Candidatus Pelagibacter ubique strains, including those of the HTCC1062 type and the Red Sea type. A good correlation was observed between the chlorophyll a concentrations and the abundances of the catabolic genes, suggesting that the bacteria directly interact with phytoplankton in the marine material cycle system and play important roles in producing DMS and MeSH from DMSP as signaling molecules for the possible formation of the scent of the tidewater or as fish attractants.
  • Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay

    Reza, Md. Shaheed; Kobiyama, Atsushi; Yamada, Yuichiro; Ikeda, Yuri; Ikeda, Daisuke; Mizusawa, Nanami; Ikeo, Kazuho; Sato, Shigeru; Ogata, Takehiko; Jimbo, Mitsuru; Kudo, Toshiaki; Kaga, Shinnosuke; Watanabe, Shiho; Naiki, Kimiaki; Kaga, Yoshimasa; Mineta, Katsuhiko; Bajic, Vladimir B.; Gojobori, Takashi; Watabe, Shugo (Elsevier BV, 2018-04-26)
    The Ofunato Bay in the northeastern Pacific Ocean area of Japan possesses the highest biodiversity of marine organisms in the world and has attracted much attention due to its economic and environmental importance. We report here a shotgun metagenomic analysis of the year-round variation in free-living bacterioplankton collected across the entire length of the bay. Phylogenetic differences among spring, summer, autumn and winter bacterioplankton suggested that members of Proteobacteria tended to decrease at high water temperatures and increase at low temperatures. It was revealed that Candidatus Pelagibacter varied seasonally, reaching as much as 60% of all sequences at the genus level in the surface waters during winter. This increase was more evident in the deeper waters, where they reached up to 75%. The relative abundance of Planktomarina also rose during winter and fell during summer. A significant component of the winter bacterioplankton community was Archaea (mainly represented by Nitrosopumilus), as their relative abundance was very low during spring and summer but high during winter. In contrast, Actinobacteria and Cyanobacteria appeared to be higher in abundance during high-temperature periods. It was also revealed that Bacteroidetes constituted a significant component of the summer bacterioplankton community, being the second largest bacterial phylum detected in the Ofunato Bay. Its members, notably Polaribacter and Flavobacterium, were found to be high in abundance during spring and summer, particularly in the surface waters. Principal component analysis and hierarchal clustering analyses showed that the bacterial communities in the Ofunato Bay changed seasonally, likely caused by the levels of organic matter, which would be deeply mixed with surface runoff in the winter.
  • A Fault-Tolerant HPC Scheduler Extension for Large and Operational Ensemble Data Assimilation:Application to the Red Sea

    Toye, Habib; Kortas, Samuel; Zhan, Peng; Hoteit, Ibrahim (Elsevier BV, 2018-04-26)
    A fully parallel ensemble data assimilation and forecasting system has been developed for the Red Sea based on the MIT general circulation model (MITgcm) to simulate the Red Sea circulation and the Data Assimilation Research Testbed (DART) ensemble assimilation software. An important limitation of operational ensemble assimilation systems is the risk of ensemble members’ collapse. This could happen in those situations when the filter update step imposes large corrections on one, or more, of the forecasted ensemble members that are not fully consistent with the model physics. Increasing the ensemble size is expected to improve the assimilation system performances, but obviously increases the risk of members’ collapse. Hardware failure or slow numerical convergence encountered for some members should also occur more frequently. In this context, the manual steering of the whole process appears as a real challenge and makes the implementation of the ensemble assimilation procedure uneasy and extremely time consuming.This paper presents our efforts to build an efficient and fault-tolerant MITgcm-DART ensemble assimilation system capable of operationally running thousands of members. Built on top of Decimate, a scheduler extension developed to ease the submission, monitoring and dynamic steering of workflow of dependent jobs in a fault-tolerant environment, we describe the assimilation system implementation and discuss in detail its coupling strategies. Within Decimate, only a few additional lines of Python is needed to define flexible convergence criteria and to implement any necessary actions to the forecast ensemble members, as for instance (i) restarting faulty job in case of job failure, (ii) changing the random seed in case of poor convergence or numerical instability, (iii) adjusting (reducing or increasing) the number of parallel forecasts on the fly, (iv) replacing members on the fly to enrich the ensemble with new members, etc.We demonstrate the efficiency of the system with numerical experiments assimilating real satellites sea surface height and temperature observations in the Red Sea.
  • Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean’s Deepest Point

    Zhang, Weipeng; Tian, Ren-Mao; Sun, Jin; Bougouffa, Salim; Ding, Wei; Cai, Lin; Lan, Yi; Tong, Haoya; Li, Yongxin; Jamieson, Alan J.; Bajic, Vladimir B.; Drazen, Jeffrey C.; Bartlett, Douglas; Qian, Pei-Yuan (American Society for Microbiology, 2018-04-25)
    Amphipods are the dominant scavenging metazoan species in the Mariana Trench, the deepest known point in Earth's oceans. Here the gut microbiota of the amphipod Hirondellea gigas collected from the Challenger and Sirena Deeps of the Mariana Trench were investigated. The 11 amphipod individuals included for analyses were dominated by Psychromonas, of which a nearly complete genome was successfully recovered (designated CDP1). Compared with previously reported free-living Psychromonas strains, CDP1 has a highly reduced genome. Genome alignment showed deletion of the trimethylamine N-oxide (TMAO) reducing gene cluster in CDP1, suggesting that the
  • Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages

    Roy, Sugata; Schmeier, Sebastian; Kaczkowski, Bogumil; Arner, Erik; Alam, Tanvir; Ozturk, Mumin; Tamgue, Ousman; Parihar, Suraj P.; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Carninci, Piero; Hayashizaki, Yoshihide; Forrest, Alistair R. R.; Guler, Reto; Bajic, Vladimir B.; Brombacher, Frank; Suzuki, Harukazu (Springer Nature, 2018-04-24)
    Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFNγ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFNγ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.
  • Existence of weak solutions to first-order stationary mean-field games with Dirichlet conditions

    Ferreira, Rita; Gomes, Diogo A.; Tada, Teruo (arXiv, 2018-04-19)
    In this paper, we study first-order stationary monotone mean-field games (MFGs) with Dirichlet boundary conditions. While for Hamilton--Jacobi equations Dirichlet conditions may not be satisfied, here, we establish the existence of solutions of MFGs that satisfy those conditions. To construct these solutions, we introduce a monotone regularized problem. Applying Schaefer's fixed-point theorem and using the monotonicity of the MFG, we verify that there exists a unique weak solution to the regularized problem. Finally, we take the limit of the solutions of the regularized problem and using Minty's method, we show the existence of weak solutions to the original MFG.
  • Optimizations of Unstructured Aerodynamics Computations for Many-core Architectures

    Al Farhan, Mohammed Ahmed; Keyes, David E. (Institute of Electrical and Electronics Engineers (IEEE), 2018-04-13)
    We investigate several state-of-the-practice shared-memory optimization techniques applied to key routines of an unstructured computational aerodynamics application with irregular memory accesses. We illustrate for the Intel KNL processor, as a representative of the processors in contemporary leading supercomputers, identifying and addressing performance challenges without compromising the floating point numerics of the original code. We employ low and high-level architecture-specific code optimizations involving thread and data-level parallelism. Our approach is based upon a multi-level hierarchical distribution of work and data across both the threads and the SIMD units within every hardware core. On a 64-core KNL chip, we achieve nearly 2.9x speedup of the dominant routines relative to the baseline. These exhibit almost linear strong scalability up to 64 threads, and thereafter some improvement with hyperthreading. At substantially fewer Watts, we achieve up to 1.7x speedup relative to the performance of 72 threads of a 36-core Haswell CPU and roughly equivalent performance to 112 threads of a 56-core Skylake scalable processor. These optimizations are expected to be of value for many other unstructured mesh PDE-based scientific applications as multi and many-core architecture evolves.
  • On the efficient simulation of the left-tail of the sum of correlated log-normal variates

    Alouini, Mohamed-Slim; Rached, Nadhir B.; Kammoun, Abla; Tempone, Raul (Walter de Gruyter GmbH, 2018-04-04)
    The sum of log-normal variates is encountered in many challenging applications such as performance analysis of wireless communication systems and financial engineering. Several approximation methods have been reported in the literature. However, these methods are not accurate in the tail regions. These regions are of primordial interest as small probability values have to be evaluated with high precision. Variance reduction techniques are known to yield accurate, yet efficient, estimates of small probability values. Most of the existing approaches have focused on estimating the right-tail of the sum of log-normal random variables (RVs). Here, we instead consider the left-tail of the sum of correlated log-normal variates with Gaussian copula, under a mild assumption on the covariance matrix. We propose an estimator combining an existing mean-shifting importance sampling approach with a control variate technique. This estimator has an asymptotically vanishing relative error, which represents a major finding in the context of the left-tail simulation of the sum of log-normal RVs. Finally, we perform simulations to evaluate the performances of the proposed estimator in comparison with existing ones.
  • Extreme Scale FMM-Accelerated Boundary Integral Equation Solver for Wave Scattering

    AbdulJabbar, Mustafa Abdulmajeed; Al Farhan, Mohammed; Al-Harthi, Noha A.; Chen, Rui; Yokota, Rio; Bagci, Hakan; Keyes, David E. (arXiv, 2018-03-27)
    Algorithmic and architecture-oriented optimizations are essential for achieving performance worthy of anticipated energy-austere exascale systems. In this paper, we present an extreme scale FMM-accelerated boundary integral equation solver for wave scattering, which uses FMM as a matrix-vector multiplication inside the GMRES iterative method. Our FMM Helmholtz kernels treat nontrivial singular and near-field integration points. We implement highly optimized kernels for both shared and distributed memory, targeting emerging Intel extreme performance HPC architectures. We extract the potential thread- and data-level parallelism of the key Helmholtz kernels of FMM. Our application code is well optimized to exploit the AVX-512 SIMD units of Intel Skylake and Knights Landing architectures. We provide different performance models for tuning the task-based tree traversal implementation of FMM, and develop optimal architecture-specific and algorithm aware partitioning, load balancing, and communication reducing mechanisms to scale up to 6,144 compute nodes of a Cray XC40 with 196,608 hardware cores. With shared memory optimizations, we achieve roughly 77% of peak single precision floating point performance of a 56-core Skylake processor, and on average 60% of peak single precision floating point performance of a 72-core KNL. These numbers represent nearly 5.4x and 10x speedup on Skylake and KNL, respectively, compared to the baseline scalar code. With distributed memory optimizations, on the other hand, we report near-optimal efficiency in the weak scalability study with respect to both the logarithmic communication complexity as well as the theoretical scaling complexity of FMM. In addition, we exhibit up to 85% efficiency in strong scaling. We compute in excess of 2 billion DoF on the full-scale of the Cray XC40 supercomputer.
  • A symmetrizable extension of polyconvex thermoelasticity and applications to zero-viscosity limits and weak-strong uniqueness

    Christoforou, Cleopatra; Galanopoulou, Myrto Maria; Tzavaras, Athanasios (Taylor & Francis, 2018-03-21)
    We embed the equations of polyconvex thermoviscoelasticity into an augmented, symmetrizable, hyperbolic system and derive a relative entropy identity in the extended variables. Following the relative entropy formulation, we prove the convergence from thermoviscoelasticity with Newtonian viscosity and Fourier heat conduction to smooth solutions of the system of adiabatic thermoelasticity as both parameters tend to zero. Also, convergence from thermoviscoelasticity to smooth solutions of thermoelasticity in the zero-viscosity limit. Finally, we establish a weak-strong uniqueness result for the equations of adiabatic thermoelasticity in the class of entropy weak solutions.
  • Fastest Rates for Stochastic Mirror Descent Methods

    Hanzely, Filip; Richtarik, Peter (arXiv, 2018-03-20)
    Relative smoothness - a notion introduced by Birnbaum et al. (2011) and rediscovered by Bauschke et al. (2016) and Lu et al. (2016) - generalizes the standard notion of smoothness typically used in the analysis of gradient type methods. In this work we are taking ideas from well studied field of stochastic convex optimization and using them in order to obtain faster algorithms for minimizing relatively smooth functions. We propose and analyze two new algorithms: Relative Randomized Coordinate Descent (relRCD) and Relative Stochastic Gradient Descent (relSGD), both generalizing famous algorithms in the standard smooth setting. The methods we propose can be in fact seen as a particular instances of stochastic mirror descent algorithms. One of them, relRCD corresponds to the first stochastic variant of mirror descent algorithm with linear convergence rate.
  • A novel method for improved accuracy of transcription factor binding site prediction

    Khamis, Abdullah M.; Motwalli, Olaa Amin; Oliva, Romina; Jankovic, Boris R.; Medvedeva, Yulia; Ashoor, Haitham; Essack, Magbubah; Gao, Xin; Bajic, Vladimir B. (Oxford University Press (OUP), 2018-03-20)
    Identifying transcription factor (TF) binding sites (TFBSs) is important in the computational inference of gene regulation. Widely used computational methods of TFBS prediction based on position weight matrices (PWMs) usually have high false positive rates. Moreover, computational studies of transcription regulation in eukaryotes frequently require numerous PWM models of TFBSs due to a large number of TFs involved. To overcome these problems we developed DRAF, a novel method for TFBS prediction that requires only 14 prediction models for 232 human TFs, while at the same time significantly improves prediction accuracy. DRAF models use more features than PWM models, as they combine information from TFBS sequences and physicochemical properties of TF DNA-binding domains into machine learning models. Evaluation of DRAF on 98 human ChIP-seq datasets shows on average 1.54-, 1.96- and 5.19-fold reduction of false positives at the same sensitivities compared to models from HOCOMOCO, TRANSFAC and DeepBind, respectively. This observation suggests that one can efficiently replace the PWM models for TFBS prediction by a small number of DRAF models that significantly improve prediction accuracy. The DRAF method is implemented in a web tool and in a stand-alone software freely available at http://cbrc.kaust.edu.sa/DRAF.

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