The network representation of the interactions between proteins and genes allows for a holistic perspective of the complex machinery underlying the living cell. However, the large number of interacting entities within the cell makes network construction a daunting and arduous task, prone to errors and missing information. Fortunately, the structure of biological networks is not different from that of other complex systems, such as social networks, the world-wide web or power grids, for which growth models have been proposed to better understand their structure and function. This means that we can design tools based on these models in order to exploit the topology of biological interactomes with the aim to construct more complete and reliable maps of the cell. In this work, we propose three novel and powerful approaches for the prediction of interactions in biological networks and conclude that it is possible to mine the topology of these complex system representations and produce reliable and biologically meaningful information that enriches the datasets to which we have access today.

As the Internet is becoming information-centric, network services increasingly demand scalable and efficient communication of information between a multitude of information producers and large groups of interested information consumers. Such information-centric services are growing rapidly in use and deployment. Examples of deployed services that are information-centric include: IPTV, MMORPG, VoD, video conferencing, file sharing, software updates, RSS dissemination, online markets, and grid computing. To effectively support future information-centric services, the network infrastructure for multi-point communication has to address a number of significant challenges: (i) how to understand massive information-centric groups in a scalable manner, (ii) how to analyze and predict the evolution of those groups in an accurate and efficient way, and (iii) how to disseminate content from information producers to a vast number of groups with potentially long-lived membership and highly diverse, dynamic group activity levels? This dissertation proposes novel architecture and protocols that effectively address the above challenges in supporting multi-point communication for future information-centric network services. In doing so, we make the following three major contributions: (1) We develop a novel technique called Proximity Embedding (PE) that can approximate a family of path-ensembled based proximity measures for information-centric groups. We develop Clustered Spectral Graph Embedding (SCGE) that captures the essential structure of large graphs in a highly efficient and scalable manner. Our techniques help to explain the proximity (closeness) of users in information-centric groups, and can be applied to a variety of analysis tasks of complex network structures. (2) Based on SCGE, we develop new supervision based link prediction techniques called Clustered Spectral Learning and Clustered Polynomial Learning that enable us to predict the evolution of massive and complex network structures in an accurate and efficient way. By exploiting supervised information from past snapshots of network structures, our methods yield up to 20% improvement in link prediction accuracy when compared to existing state-of-the-art methods. (3) Finally, we develop a novel multicast infrastructure called Multicast with Adaptive Dual-state (MAD). MAD supports large number of group and group membership, and efficient content dissemination in a presence of dynamic group activity. We demonstrate the effectiveness of our approach in extensive simulation, analysis, and emulation through the real system implementation. / text

Predicting connections among objects, based either on a noisy observation or on a sequence of observations, is a problem of interest for numerous applications such as recommender systems for e-commerce and social networks, and also in system biology, for inferring interaction patterns among proteins. This work presents formulations of the graph prediction problem, in both dynamic and static scenarios, as regularization problems. In the static scenario we encode the mixture of two different kinds of structural assumptions in a convex penalty involving the L1 and the trace norm. In the dynamic setting we assume that certain graph features, such as the node degree, follow a vector autoregressive model and we propose to use this information to improve the accuracy of prediction. The solutions of the optimization problems are studied both from an algorithmic and statistical point of view. Empirical evidences on synthetic and real data are presented showing the benefit of using the suggested methods.

abstract: With the rise of social media, hundreds of millions of people spend countless hours all over the globe on social media to connect, interact, share, and create user-generated data. This rich environment provides tremendous opportunities for many different players to easily and effectively reach out to people, interact with them, influence them, or get their opinions. There are two pieces of information that attract most attention on social media sites, including user preferences and interactions. Businesses and organizations use this information to better understand and therefore provide customized services to social media users. This data can be used for different purposes such as, targeted advertisement, product recommendation, or even opinion mining. Social media sites use this information to better serve their users. Despite the importance of personal information, in many cases people do not reveal this information to the public. Predicting the hidden or missing information is a common response to this challenge. In this thesis, we address the problem of predicting user attributes and future or missing links using an egocentric approach. The current research proposes novel concepts and approaches to better understand social media users in twofold including, a) their attributes, preferences, and interests, and b) their future or missing connections and interactions. More specifically, the contributions of this dissertation are (1) proposing a framework to study social media users through their attributes and link information, (2) proposing a scalable algorithm to predict user preferences; and (3) proposing a novel approach to predict attributes and links with limited information. The proposed algorithms use an egocentric approach to improve the state of the art algorithms in two directions. First by improving the prediction accuracy, and second, by increasing the scalability of the algorithms. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2014

Diferentes sistemas do mundo real podem ser representados por redes. As redes são estruturas nas quais seus vértices (nós) representam entidades e links representam relações entre essas entidades. Além disso, as redes caracterizam-se por ser estruturas dinâmicas, o que implica na rápida aparição e desaparição de entidades e seus relacionamentos. Nesse cenário, um dos problemas importantes a serem enfrentados no contexto das redes, é da predição de links, isto é, prever a ocorrência futura de um link ainda não existente entre dois vértices com base nas informações já existentes. A importância da predição de links deve-se ao fato de ter aplicações na recuperação de informação, identificação de interações espúrias e, ainda, na avaliação de mecanismos de evolução das redes. Para enfrentar o problema da predição de links, a maioria dos métodos utiliza informações da vizinhança topológica das redes para atribuir um valor que represente a probabilidade de conexão futura entre um par de vértices analisados. No entanto, recentemente têm aparecido métodos híbridos, caracterizados por usar outras informações além da vizinhança topológica, sendo as informações das comunidades as normalmente usadas, isso, devido ao fato que, ao serem grupos de vértices densamente ligados entre si e esparsamente ligados com vértices de outros grupos, fornecem informações que podem ser úteis para determinar o comportamento futuro das redes. Assim, neste trabalho são apresentadas duas propostas na linha dos métodos baseados nas informações das comunidades para predição de links. A primeira proposta consiste em um novo índice de similaridade que usa as informações dos vértices pertencentes a mesma comunidade na vizinhança de um par de vértices analisados, bem como as informações dos vértices pertencentes a diferentes comunidades nessa mesma vizinhança. A segunda proposta consiste de um conjunto de índices obtidos a partir da reformulação de algumas propostas já existentes, porém, inserindo neles informações dos vértices pertencentes unicamente à mesma comunidade na vizinhança topológica de um par de vértices analisados. Experimentos realizados em dez redes complexas de diferentes domínios demonstraram que, em geral, os índices propostos obtiveram desempenho superior às abordagens usuais / Different real-world systems can be represented as networks. Networks are structures in which vertices (nodes) represent entities and links represent relationships between these entities. Moreover, networks are dynamic structures, which implies rapid appearance and disappearance of entities and their relationships. In this scenario, the link prediction problem attempts to predict the future existence of a link between a pair of vertices considering existing information. The link prediction importance is due to the fact of having different applications in areas such as information retrieval, identification of spurious interactions, as well as for understanding mechanisms of network evolution. To address the link prediction problem, many proposals use topological information to assign a value that represents the likelihood of a future connection between a pair of vertices. However, hybrid methods have appeared recently. These methods use additional information such as community information. Communities are groups of vertices densely connected among them and sparsely connected to vertices from other groups, providing useful information to determinate the future behavior of networks. So, this research presents two proposals for link prediction based on communities information. The first proposal consists of a new similarity index that uses information about the communities that the vertices in the neighborhood of a analyzed pair of vertices belong. The second proposal is a set of indices obtained from the reformulation of various existing proposals, however, using only the information from vertices belonging to the same community in the neighborhood of a pair of vertices analyzed. Experiments conducted in ten complex networks of different fields show the proposals outperform traditional approaches

Computational drug repurposing aims at finding new medical uses for existing drugs. The identification of novel drug-target interactions (DTIs) can be a useful part of such a task. Computational determination of DTIs is a convenient strategy for systematic screening of a large number of drugs in the attempt to identify new DTIs at low cost and with reasonable accuracy. This necessitates development of accurate computational methods that can help focus on the follow-up experimental validation on a smaller number of highly likely targets for a drug. Although many methods have been proposed for computational DTI prediction, they suffer the high false positive prediction rate or they do not predict the effect that drugs exert on targets in DTIs. In this report, first, we present a comprehensive review of the recent progress in the field of DTI prediction from data-centric and algorithm-centric perspectives. The aim is to provide a comprehensive review of computational methods for identifying DTIs, which could help in constructing more reliable methods. Then, we present DDR, an efficient method to predict the existence of DTIs. DDR achieves significantly more accurate results compared to the other state-of-theart methods. As supported by independent evidences, we verified as correct 22 out of the top 25 DDR DTIs predictions. This validation proves the practical utility of DDR, suggesting that DDR can be used as an efficient method to identify 5 correct DTIs. Finally, we present DDR-FE method that predicts the effect types of a drug on its target. On different representative datasets, under various test setups, and using different performance measures, we show that DDR-FE achieves extremely good performance. Using blind test data, we verified as correct 2,300 out of 3,076 DTIs effects predicted by DDR-FE. This suggests that DDR-FE can be used as an efficient method to identify correct effects of a drug on its target.

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Networks are sets of objects that are connected in some way and appear abundantly in nature, sociology, and technology. For many centuries, network theory focused on static networks, which are networks that do not change. However, since all networks transform over time, static networks have limited applications. By comparison, dynamic networks model how connections between objects change over time. In this work, we will explore how connections in dynamic networks change and how we can leverage these changes to make predictions about future iterations of networks. We will do this by first considering the link prediction problem, using either Katz distance or effective resistance to predict future connections, and relate these two metrics. Then we will look at using bipartite network connections to predict group transitions in professional sports teams. Lastly, we will investigate how to use network connections to identify and predict roles in social networks.

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