Integration of continuous-time dynamics in a spiking neural network simulator

Contemporary modeling approaches to the dynamics of neural networks consider two main classes of models: biologically grounded spiking neurons and functionally inspired rate-based units. The unified simulation framework presented here supports the combination of the two for multi-scale modeling approaches, the quantitative validation of mean-field approaches by spiking network simulations, and an increase in reliability by usage of the same simulation code and the same network model specifications for both model classes. While most efficient spiking simulations rely on the communication of discrete events, rate models require time-continuous interactions between neurons. Exploiting the conceptual similarity to the inclusion of gap junctions in spiking network simulations, we arrive at a reference implementation of instantaneous and delayed interactions between rate-based models in a spiking network simulator. The separation of rate dynamics from the general connection and communication infrastructure ensures flexibility of the framework. We further demonstrate the broad applicability of the framework by considering various examples from the literature ranging from random networks to neural field models. The study provides the prerequisite for interactions between rate-based and spiking models in a joint simulation

SimFusion: A Unified Similarity Measurement Algorithm for Multi-Type Interrelated Web Objects

In this paper, we use a Unified Relationship Matrix (URM) to represent a set of heterogeneous web objects (e.g., web pages, queries) and their interrelationships (e.g., hyperlink, user click-through relationships). We claim that iterative computations over the URM can help overcome the data sparseness problem (a common situation in the Web) and detect latent relationships among heterogeneous web objects, thus, can improve the quality of various information applications that require the combination of information from heterogeneous sources. To support our claim, we further propose a unified similarity-calculating algorithm, the SimFusion algorithm. By iteratively computing over the URM, the SimFusion algorithm can effectively integrate relationships from heterogeneous sources when measuring the similarity of two web objects. Experiments based on a real search engine query log and a large real web page collection demonstrate that the SimFusion algorithm can significantly improve similarity measurement of web objects over both traditional content based similarity-calculating algorithms and the cutting edge SimRank algorithm

Multi-agent knowledge integration mechanism using particle swarm optimization

This is the post-print version of the final paper published in Technological Forecasting and Social Change. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2011 Elsevier B.V.Unstructured group decision-making is burdened with several central difficulties: unifying the knowledge of multiple experts in an unbiased manner and computational inefficiencies. In addition, a proper means of storing such unified knowledge for later use has not yet been established. Storage difficulties stem from of the integration of the logic underlying multiple experts' decision-making processes and the structured quantification of the impact of each opinion on the final product. To address these difficulties, this paper proposes a novel approach called the multiple agent-based knowledge integration mechanism (MAKIM), in which a fuzzy cognitive map (FCM) is used as a knowledge representation and storage vehicle. In this approach, we use particle swarm optimization (PSO) to adjust causal relationships and causality coefficients from the perspective of global optimization. Once an optimized FCM is constructed an agent based model (ABM) is applied to the inference of the FCM to solve real world problem. The final aggregate knowledge is stored in FCM form and is used to produce proper inference results for other target problems. To test the validity of our approach, we applied MAKIM to a real-world group decision-making problem, an IT project risk assessment, and found MAKIM to be statistically robust.Ministry of Education, Science and Technology (Korea

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing