Analysis of Computational Science Papers from ICCS 2001-2016 using Topic Modeling and Graph Theory

This paper presents results of topic modeling and network models of topics using the International Conference on Computational Science corpus, which contains domain-specific (computational science) papers over sixteen years (a total of 5695 papers). We discuss topical structures of International Conference on Computational Science, how these topics evolve over time in response to the topicality of various problems, technologies and methods, and how all these topics relate to one another. This analysis illustrates multidisciplinary research and collaborations among scientific communities, by constructing static and dynamic networks from the topic modeling results and the keywords of authors. The results of this study give insights about the past and future trends of core discussion topics in computational science. We used the Non-negative Matrix Factorization topic modeling algorithm to discover topics and labeled and grouped results hierarchically.Comment: Accepted by International Conference on Computational Science (ICCS) 2017 which will be held in Zurich, Switzerland from June 11-June 1

Supplemented Alkaline Phosphatase Supports the Immune Response in Patients Undergoing Cardiac Surgery: Clinical and Computational Evidence

Alkaline phosphatase (AP) is an enzyme that exhibits anti-inflammatory effects by dephosphorylating inflammation triggering moieties (ITMs) like bacterial lipopolysaccharides and extracellular nucleotides. AP administration aims to prevent and treat peri- and post-surgical ischemia reperfusion injury in cardiothoracic surgery patients. Recent studies reported that intravenous bolus administration and continuous infusion of AP in patients undergoing coronary artery bypass grafting with cardiac valve surgery induce an increased release of liver-type “tissue non-specific alkaline phosphatase” (TNAP) into the bloodstream. The release of liver-type TNAP into circulation could be the body's way of strengthening its defense against a massive ischemic insult. However, the underlying mechanism behind the induction of TNAP is still unclear. To obtain a deeper insight into the role of AP during surgery, we developed a mathematical model of systemic inflammation that clarifies the relation between supplemented AP and TNAP and describes a plausible induction mechanism of TNAP in patients undergoing cardiothoracic surgery. The model was validated against clinical data from patients treated with bovine Intestinal AP (bIAP treatment) or without AP (placebo treatment), in addition to standard care procedures. We performed additional in-silico experiments adding a secondary source of ITMs after surgery, as observed in some patients with complications, and predicted the response to different AP treatment regimens. Our results show a strong protective effect of supplemented AP for patients with complications. The model provides evidence of the existence of an induction mechanism of liver-type tissue non-specific alkaline phosphatase, triggered by the supplementation of AP in patients undergoing cardiac surgery. To the best of our knowledge this is the first time that a quantitative and validated numerical model of systemic inflammation under clinical treatment conditions is presented

OpenGraphGym: A Parallel Reinforcement Learning Framework for Graph Optimization Problems

This paper presents an open-source, parallel AI environment (named OpenGraphGym) to facilitate the application of reinforcement learning (RL) algorithms to address combinatorial graph optimization problems. This environment incorporates a basic deep reinforcement learning method, and several graph embeddings to capture graph features, it also allows users to rapidly plug in and test new RL algorithms and graph embeddings for graph optimization problems. This new open-source RL framework is targeted at achieving both high performance and high quality of the computed graph solutions. This RL framework forms the foundation of several ongoing research directions, including 1) benchmark works on different RL algorithms and embedding methods for classic graph problems; 2) advanced parallel strategies for extreme-scale graph computations, as well as 3) performance evaluation on real-world graph solutions

UvA-DARE (Digital Academic Repository) How to Speed up Optimization? Opposite-Center Learning and Its Application to Differential Evolution How to Speed up Optimization? Opposite-Center Learning and Its Application to Differential Evolution

Abstract This paper introduces a new sampling technique called Opposite-Center Learning (OCL) intended for convergence speed-up of meta-heuristic optimization algorithms. It comprises an extension of Opposition-Based Learning (OBL), a simple scheme that manages to boost numerous optimization methods by considering the opposite points of candidate solutions. In contrast to OBL, OCL has a theoretical foundation -the opposite center point is defined as the optimal choice in pair-wise sampling of the search space given a random starting point. A concise analytical background is provided. Computationally the opposite center point is approximated by a lightweight Monte Carlo scheme for arbitrary dimension. Empirical results up to dimension 20 confirm that OCL outperforms OBL and random sampling: the points generated by OCL have shorter expected distances to a uniformly distributed global optimum. To further test its practical performance, OCL is applied to differential evolution (DE). This novel scheme for continuous optimization named Opposite-Center DE (OCDE) employs OCL for population initialization and generation jumping. Numerical experiments on a set of benchmark functions for dimensions 10 and 30 reveal that OCDE on average improves the convergence rates by 38% and 27% compared to the original DE and the Oppositionbased DE (ODE), respectively, while remaining fully robust. Most promising are the observations that the accelerations shown by OCDE and OCL increase with problem dimensionality

Perspectives of the International Conference of Computational Science 2014

Computational Science has enabled a raft of science that was either impossible, dangerous, or extremely expensive. It is arguably one of the most multi-disciplinary research endeavors, and draws on foundational work in mathematics and computer science. Computational Science has applicability in almost all scientific domains, and is now an essential tool in many of these. This special section contains extended papers originally published in proceedings of the 14th International Conference on Computational Science (ICCS 2014), an annual event that promotes leading edge research

Dynamic workload balancing of parallel applications with user-level scheduling on the Grid

This paper suggests a hybrid resource management approach for efficient parallel distributed computing on the Grid. It operates on both application and system levels, combining user-level job scheduling with dynamic workload balancing algorithm that automatically adapts a parallel application to the heterogeneous resources, based on the actual resource parameters and estimated requirements of the application. The hybrid environment and the algorithm for automated load balancing are described, the influence of resource heterogeneity level is measured, and the speedup achieved with this technique is demonstrated for different types of applications and resources

A grid-based virtual reactor : parallel performance and adaptive load balancing

We address the problem of porting parallel distributed applications from static homogeneous cluster environments to dynamic heterogeneous Grid resources. We introduce a generic technique for adaptive load balancing of parallel applications on heterogeneous resources and evaluate it using a case study application: a Virtual Reactor for simulation of plasma chemical vapour deposition. This application has a modular architecture with a number of loosely coupled components suitable for distribution over the Grid. It requires large parameter space exploration that allows using Grid resources for high-throughput computing. The Virtual Reactor contains a number of parallel solvers originally designed for homogeneous computer clusters that needed adaptation to the heterogeneity of the Grid. In this paper we study the performance of one of the parallel solvers, apply the technique developed for adaptive load balancing, evaluate the efficiency of this approach and outline an automated procedure for optimal utilization of heterogeneous Grid resources for high-performance parallel computing

Crack Detection in Earth Dam and Levee Passive Seismic Data Using Support Vector Machines

AbstractWe investigate techniques for earth dam and levee health monitoring and automatic detection of anomalous events in passive seismic data. We have developed a novel data-driven workflow that uses machine learning and geophysical data collected from sensors located on the surface of the levee to identify internal erosion events. In this paper, we describe our research experiments with binary and one-class Support Vector Machines (SVMs). We used experimental data from a laboratory earth embankment (80% normal and 20% anomalies) and extracted nine spectral features from decomposed segments of the time series data. The two-class SVM with 10-fold cross validation achieved over 97% accuracy. Experiments with the one-class SVM use the top two features selected by the ReliefF algorithm and our results show that we can successfully separate normal from anomalous data observations with over 83% accuracy

Grid-based simulation of industrial thin-film production

In this article, the authors introduce a Grid-based virtual reactor, a High Level Architecture (HLA)- supported problem-solving environment that allows for detailed numerical study of industrial thin-film production in plasma-enhanced chemical vapor deposition (PECVD) reactors. They briefly describe the physics and chemistry underpinning the deposition process, the numerical approach to simulate these processes on advanced computer architectures, and the associated software environment supporting computational experiments. The authors built an efficient problem-solving environment for scientists studying PECVD processes and end users working in the chemical industry and validated the resulting virtual reactor against real experiments