Optimizing communication by compression for Multi-GPU Scalable Breadth-First Searches

Debido al creciente aumento del tamaño de los datos en muchos de los actuales sistemas de información, muchos de los algoritmos de recorrido de estas estructuras pierden rendimento para realizar búsquedas en estos. Debido a que la representacion de estos datos en muchos casos se realiza mediante estructuras nodo-vertice (Grafos), en el año 2009 se creó el reto Graph500. Con anterioridad, otros retos como Top500 servían para medir el rendimiento en base a la capacidad de cálculo de los sistemas, mediante tests LINPACK. En caso de Graph500 la medicion se realiza mediante la ejecución de un algoritmo de recorrido en anchura de grafos (BFS en inglés) aplicada a Grafos. El algoritmo BFS es uno de los pilares de otros muchos algoritmos utilizados en grafos como SSSP, shortest path o Betweeness centrality. Una mejora en este ayudaría a la mejora de los otros que lo utilizan. Analisis del Problema El algoritmos BFS utilizado en los sistemas de computación de alto rendimiento (HPC en ingles) es usualmente una version para sistemas distribuidos del algoritmo secuencial original. En esta versión distribuida se inicia la ejecución realizando un particionado del grafo y posteriormente cada uno de los procesadores distribuidos computará una parte y distribuirá sus resultados a los demás sistemas. Debido a que la diferencia de velocidad entre el procesamiento en cada uno de estos nodos y la transfencia de datos por la red de interconexión es muy alta (estando en desventaja la red de interconexion) han sido bastantes las aproximaciones tomadas para reducir la perdida de rendimiento al realizar transferencias. Respecto al particionado inicial del grafo, el enfoque tradicional (llamado 1D-partitioned graph en ingles) consiste en asignar a cada nodo unos vertices fijos que él procesará. Para disminuir el tráfico de datos se propuso otro particionado (2D) en el cual la distribución se haciá en base a las aristas del grafo, en vez de a los vertices. Este particionado reducía el trafico en la red en una proporcion O(NxM) a O(log(N)). Si bien han habido otros enfoques para reducir la transferecnia como: reordemaniento inicial de los vertices para añadir localidad en los nodos, o particionados dinámicos, el enfoque que se va a proponer en este trabajo va a consistir en aplicar técnicas recientes de compression de grandes sistemas de datos como Bases de datos de alto volume o motores de búsqueda en internet para comprimir los datos de las transferencias entre nodos.---ABSTRACT---The Breadth First Search (BFS) algorithm is the foundation and building block of many higher graph-based operations such as spanning trees, shortest paths and betweenness centrality. The importance of this algorithm increases each day due to it is a key requirement for many data structures which are becoming popular nowadays. These data structures turn out to be internally graph structures. When the BFS algorithm is parallelized and the data is distributed into several processors, some research shows a performance limitation introduced by the interconnection network [31]. Hence, improvements on the area of communications may benefit the global performance in this key algorithm. In this work it is presented an alternative compression mechanism. It differs with current existing methods in that it is aware of characteristics of the data which may benefit the compression. Apart from this, we will perform a other test to see how this algorithm (in a dis- tributed scenario) benefits from traditional instruction-based optimizations. Last, we will review the current supercomputing techniques and the related work being done in the area.

Constellations and the unsupervised learning of graphs

In this paper, we propose a novel method for the unsupervised clustering of graphs in the context of the constellation approach to object recognition. Such method is an EM central clustering algorithm which builds prototypical graphs on the basis of fast matching with graph transformations. Our experiments, both with random graphs and in realistic situations (visual localization), show that our prototypes improve the set median graphs and also the prototypes derived from our previous incremental method. We also discuss how the method scales with a growing number of images.

Una nueva técnica de construcción de grafos semánticos para la desambiguación bilingüe del sentido de las palabras

En este trabajo presentamos unos resultados preliminares obtenidos mediante la aplicación de una nueva técnica de construcción de grafos semánticos a la tarea de desambiguación del sentido de las palabras en un entorno multilingüe. Gracias al uso de esta técnica no supervisada, inducimos los sentidos asociados a las traducciones de la palabra ambigua considerada en la lengua destino. Utilizamos las traducciones de las palabras del contexto de la palabra ambigua en la lengua origen para seleccionar el sentido más probable de la traducción. El sistema ha sido evaluado sobre la colección de datos de una tarea de desambiguación multilingüe que se propuso en la competición SemEval-2010, consiguiendo superar los resultados de todos los sistemas no supervisados que participaron en aquella tarea.

Time-series Luminance Distribution Maps: implementation of annual daylight simulation methods for occupant visual comfort analysis

Thesis (Master's)--University of Washington, 2016-06

Communities and emerging semantics in semantic link network:discovery and learning

The World Wide Web provides plentiful contents for Web-based learning, but its hyperlink-based architecture connects Web resources for browsing freely rather than for effective learning. To support effective learning, an e-learning system should be able to discover and make use of the semantic communities and the emerging semantic relations in a dynamic complex network of learning resources. Previous graph-based community discovery approaches are limited in ability to discover semantic communities. This paper first suggests the Semantic Link Network (SLN), a loosely coupled semantic data model that can semantically link resources and derive out implicit semantic links according to a set of relational reasoning rules. By studying the intrinsic relationship between semantic communities and the semantic space of SLN, approaches to discovering reasoning-constraint, rule-constraint, and classification-constraint semantic communities are proposed. Further, the approaches, principles, and strategies for discovering emerging semantics in dynamic SLNs are studied. The basic laws of the semantic link network motion are revealed for the first time. An e-learning environment incorporating the proposed approaches, principles, and strategies to support effective discovery and learning is suggested.

Semantic linking through spaces for cyber-physical-socio intelligence:a methodology

Humans consciously and subconsciously establish various links, emerge semantic images and reason in mind, learn linking effect and rules, select linked individuals to interact, and form closed loops through links while co-experiencing in multiple spaces in lifetime. Machines are limited in these abilities although various graph-based models have been used to link resources in the cyber space. The following are fundamental limitations of machine intelligence: (1) machines know few links and rules in the physical space, physiological space, psychological space, socio space and mental space, so it is not realistic to expect machines to discover laws and solve problems in these spaces; and, (2) machines can only process pre-designed algorithms and data structures in the cyber space. They are limited in ability to go beyond the cyber space, to learn linking rules, to know the effect of linking, and to explain computing results according to physical, physiological, psychological and socio laws. Linking various spaces will create a complex space — the Cyber-Physical-Physiological-Psychological-Socio-Mental Environment CP3SME. Diverse spaces will emerge, evolve, compete and cooperate with each other to extend machine intelligence and human intelligence. From multi-disciplinary perspective, this paper reviews previous ideas on various links, introduces the concept of cyber-physical society, proposes the ideal of the CP3SME including its definition, characteristics, and multi-disciplinary revolution, and explores the methodology of linking through spaces for cyber-physical-socio intelligence. The methodology includes new models, principles, mechanisms, scientific issues, and philosophical explanation. The CP3SME aims at an ideal environment for humans to live and work. Exploration will go beyond previous ideals on intelligence and computing.

On some Properties of Boolean Functions and Their Binary Decision Diagrams

Иво Й. Дамянов - Манипулирането на булеви функции е основнo за теоретичната информатика, в това число логическата оптимизация, валидирането и синтеза на схеми. В тази статия се разглеждат някои първоначални резултати относно връзката между граф-базираното представяне на булевите функции и свойствата на техните променливи.

A continuous-time quantum walk kernel for unattributed graphs

Kernel methods provide a way to apply a wide range of learning techniques to complex and structured data by shifting the representational problem from one of finding an embedding of the data to that of defining a positive semidefinite kernel. In this paper, we propose a novel kernel on unattributed graphs where the structure is characterized through the evolution of a continuous-time quantum walk. More precisely, given a pair of graphs, we create a derived structure whose degree of symmetry is maximum when the original graphs are isomorphic. With this new graph to hand, we compute the density operators of the quantum systems representing the evolutions of two suitably defined quantum walks. Finally, we define the kernel between the two original graphs as the quantum Jensen-Shannon divergence between these two density operators. The experimental evaluation shows the effectiveness of the proposed approach. © 2013 Springer-Verlag.

Visualisation and browsing of image databases

In this chapter we provide a comprehensive overview of the emerging field of visualising and browsing image databases. We start with a brief introduction to content-based image retrieval and the traditional query-by-example search paradigm that many retrieval systems employ. We specify the problems associated with this type of interface, such as users not being able to formulate a query due to not having a target image or concept in mind. The idea of browsing systems is then introduced as a means to combat these issues, harnessing the cognitive power of the human mind in order to speed up image retrieval.We detail common methods in which the often high-dimensional feature data extracted from images can be used to visualise image databases in an intuitive way. Systems using dimensionality reduction techniques, such as multi-dimensional scaling, are reviewed along with those that cluster images using either divisive or agglomerative techniques as well as graph-based visualisations. While visualisation of an image collection is useful for providing an overview of the contained images, it forms only part of an image database navigation system. We therefore also present various methods provided by these systems to allow for interactive browsing of these datasets. A further area we explore are user studies of systems and visualisations where we look at the different evaluations undertaken in order to test usability and compare systems, and highlight the key findings from these studies. We conclude the chapter with several recommendations for future work in this area. © 2011 Springer-Verlag Berlin Heidelberg.

Exploiting heterogeneous scientific literature networks to combat ranking bias:evidence from the computational linguistics area

It is important to help researchers find valuable papers from a large literature collection. To this end, many graph-based ranking algorithms have been proposed. However, most of these algorithms suffer from the problem of ranking bias. Ranking bias hurts the usefulness of a ranking algorithm because it returns a ranking list with an undesirable time distribution. This paper is a focused study on how to alleviate ranking bias by leveraging the heterogeneous network structure of the literature collection. We propose a new graph-based ranking algorithm, MutualRank, that integrates mutual reinforcement relationships among networks of papers, researchers, and venues to achieve a more synthetic, accurate, and less-biased ranking than previous methods. MutualRank provides a unified model that involves both intra- and inter-network information for ranking papers, researchers, and venues simultaneously. We use the ACL Anthology Network as the benchmark data set and construct the gold standard from computer linguistics course websites of well-known universities and two well-known textbooks. The experimental results show that MutualRank greatly outperforms the state-of-the-art competitors, including PageRank, HITS, CoRank, Future Rank, and P-Rank, in ranking papers in both improving ranking effectiveness and alleviating ranking bias. Rankings of researchers and venues by MutualRank are also quite reasonable.

Benchmarking of distributed computing engines spark and GraphLab for big data analytics

In this paper we evaluate and compare two representativeand popular distributed processing engines for large scalebig data analytics, Spark and graph based engine GraphLab. Wedesign a benchmark suite including representative algorithmsand datasets to compare the performances of the computingengines, from performance aspects of running time, memory andCPU usage, network and I/O overhead. The benchmark suite istested on both local computer cluster and virtual machines oncloud. By varying the number of computers and memory weexamine the scalability of the computing engines with increasingcomputing resources (such as CPU and memory). We also runcross-evaluation of generic and graph based analytic algorithmsover graph processing and generic platforms to identify thepotential performance degradation if only one processing engineis available. It is observed that both computing engines showgood scalability with increase of computing resources. WhileGraphLab largely outperforms Spark for graph algorithms, ithas close running time performance as Spark for non-graphalgorithms. Additionally the running time with Spark for graphalgorithms over cloud virtual machines is observed to increaseby almost 100% compared to over local computer clusters.

Fire and grazing in a mesic tallgrass prairie: impacts on plant species and functional traits

Fire is a globally distributed disturbance that impacts terrestrial ecosystems and has been proposed to be a global “herbivore.” Fire, like herbivory, is a top-down driver that converts organic materials into inorganic products, alters community structure, and acts as an evolutionary agent. Though grazing and fire may have some comparable effects in grasslands, they do not have similar impacts on species composition and community structure. However, the concept of fire as a global herbivore implies that fire and herbivory may have similar effects on plant functional traits. Using 22 years of data from a mesic, native tallgrass prairie with a long evolutionary history of fire and grazing, we tested if trait composition between grazed and burned grassland communities would converge, and if the degree of convergence depended on fire frequency. Additionally, we tested if eliminating fire from frequently burned grasslands would result in a state similar to unburned grasslands, and if adding fire into a previously unburned grassland would cause composition to become more similar to that of frequently burned grasslands. We found that grazing and burning once every four years showed the most convergence in traits, suggesting that these communities operate under similar deterministic assembly rules and that fire and herbivory are similar disturbances to grasslands at the trait-group level of organization. Three years after reversal of the fire treatment we found that fire reversal had different effects depending on treatment. The formerly unburned community that was then burned annually became more similar to the annually burned community in trait composition suggesting that function may be rapidly restored if fire is reintroduced. Conversely, after fire was removed from the annually burned community trait composition developed along a unique trajectory indicating hysteresis, or a time lag for structure and function to return following a change in this disturbance regime. We conclude that functional traits and species-based metrics should be considered when determining and evaluating goals for fire management in mesic grassland ecosystems.

Next generation of recommender systems: Algorithms and applications

Personalized recommender systems aim to assist users in retrieving and accessing interesting items by automatically acquiring user preferences from the historical data and matching items with the preferences. In the last decade, recommendation services have gained great attention due to the problem of information overload. However, despite recent advances of personalization techniques, several critical issues in modern recommender systems have not been well studied. These issues include: (1) understanding the accessing patterns of users (i.e., how to effectively model users' accessing behaviors); (2) understanding the relations between users and other objects (i.e., how to comprehensively assess the complex correlations between users and entities in recommender systems); and (3) understanding the interest change of users (i.e., how to adaptively capture users' preference drift over time). To meet the needs of users in modern recommender systems, it is imperative to provide solutions to address the aforementioned issues and apply the solutions to real-world applications. ^ The major goal of this dissertation is to provide integrated recommendation approaches to tackle the challenges of the current generation of recommender systems. In particular, three user-oriented aspects of recommendation techniques were studied, including understanding accessing patterns, understanding complex relations and understanding temporal dynamics. To this end, we made three research contributions. First, we presented various personalized user profiling algorithms to capture click behaviors of users from both coarse- and fine-grained granularities; second, we proposed graph-based recommendation models to describe the complex correlations in a recommender system; third, we studied temporal recommendation approaches in order to capture the preference changes of users, by considering both long-term and short-term user profiles. In addition, a versatile recommendation framework was proposed, in which the proposed recommendation techniques were seamlessly integrated. Different evaluation criteria were implemented in this framework for evaluating recommendation techniques in real-world recommendation applications. ^ In summary, the frequent changes of user interests and item repository lead to a series of user-centric challenges that are not well addressed in the current generation of recommender systems. My work proposed reasonable solutions to these challenges and provided insights on how to address these challenges using a simple yet effective recommendation framework.^

Parallel Problem Solving from Nature – PPSN XIV:14th International Conference, Edinburgh, UK, September 17-21, 2016, Proceedings

This book constitutes the refereed proceedings of the 14th International Conference on Parallel Problem Solving from Nature, PPSN 2016, held in Edinburgh, UK, in September 2016. The total of 93 revised full papers were carefully reviewed and selected from 224 submissions. The meeting began with four workshops which offered an ideal opportunity to explore specific topics in intelligent transportation Workshop, landscape-aware heuristic search, natural computing in scheduling and timetabling, and advances in multi-modal optimization. PPSN XIV also included sixteen free tutorials to give us all the opportunity to learn about new aspects: gray box optimization in theory; theory of evolutionary computation; graph-based and cartesian genetic programming; theory of parallel evolutionary algorithms; promoting diversity in evolutionary optimization: why and how; evolutionary multi-objective optimization; intelligent systems for smart cities; advances on multi-modal optimization; evolutionary computation in cryptography; evolutionary robotics - a practical guide to experiment with real hardware; evolutionary algorithms and hyper-heuristics; a bridge between optimization over manifolds and evolutionary computation; implementing evolutionary algorithms in the cloud; the attainment function approach to performance evaluation in EMO; runtime analysis of evolutionary algorithms: basic introduction; meta-model assisted (evolutionary) optimization. The papers are organized in topical sections on adaption, self-adaption and parameter tuning; differential evolution and swarm intelligence; dynamic, uncertain and constrained environments; genetic programming; multi-objective, many-objective and multi-level optimization; parallel algorithms and hardware issues; real-word applications and modeling; theory; diversity and landscape analysis.

Contextual text mining

With the dramatic growth of text information, there is an increasing need for powerful text mining systems that can automatically discover useful knowledge from text. Text is generally associated with all kinds of contextual information. Those contexts can be explicit, such as the time and the location where a blog article is written, and the author(s) of a biomedical publication, or implicit, such as the positive or negative sentiment that an author had when she wrote a product review; there may also be complex context such as the social network of the authors. Many applications require analysis of topic patterns over different contexts. For instance, analysis of search logs in the context of the user can reveal how we can improve the quality of a search engine by optimizing the search results according to particular users; analysis of customer reviews in the context of positive and negative sentiments can help the user summarize public opinions about a product; analysis of blogs or scientific publications in the context of a social network can facilitate discovery of more meaningful topical communities. Since context information significantly affects the choices of topics and language made by authors, in general, it is very important to incorporate it into analyzing and mining text data. In general, modeling the context in text, discovering contextual patterns of language units and topics from text, a general task which we refer to as Contextual Text Mining, has widespread applications in text mining. In this thesis, we provide a novel and systematic study of contextual text mining, which is a new paradigm of text mining treating context information as the ``first-class citizen.'' We formally define the problem of contextual text mining and its basic tasks, and propose a general framework for contextual text mining based on generative modeling of text. This conceptual framework provides general guidance on text mining problems with context information and can be instantiated into many real tasks, including the general problem of contextual topic analysis. We formally present a functional framework for contextual topic analysis, with a general contextual topic model and its various versions, which can effectively solve the text mining problems in a lot of real world applications. We further introduce general components of contextual topic analysis, by adding priors to contextual topic models to incorporate prior knowledge, regularizing contextual topic models with dependency structure of context, and postprocessing contextual patterns to extract refined patterns. The refinements on the general contextual topic model naturally lead to a variety of probabilistic models which incorporate different types of context and various assumptions and constraints. These special versions of the contextual topic model are proved effective in a variety of real applications involving topics and explicit contexts, implicit contexts, and complex contexts. We then introduce a postprocessing procedure for contextual patterns, by generating meaningful labels for multinomial context models. This method provides a general way to interpret text mining results for real users. By applying contextual text mining in the ``context'' of other text information management tasks, including ad hoc text retrieval and web search, we further prove the effectiveness of contextual text mining techniques in a quantitative way with large scale datasets. The framework of contextual text mining not only unifies many explorations of text analysis with context information, but also opens up many new possibilities for future research directions in text mining.