Link prediction in very large directed graphs: Exploiting hierarchical properties in parallel

Link prediction is a link mining task that tries to find new edges within a given graph. Among the targets of link prediction there is large directed graphs, which are frequent structures nowadays. The typical sparsity of large graphs demands of high precision predictions in order to obtain usable results. However, the size of those graphs only permits the execution of scalable algorithms. As a trade-off between those two problems we recently proposed a link prediction algorithm for directed graphs that exploits hierarchical properties. The algorithm can be classified as a local score, which entails scalability. Unlike the rest of local scores, our proposal assumes the existence of an underlying model for the data which allows it to produce predictions with a higher precision. We test the validity of its hierarchical assumptions on two clearly hierarchical data sets, one of them based on RDF. Then we test it on a non-hierarchical data set based on Wikipedia to demonstrate its broad applicability. Given the computational complexity of link prediction in very large graphs we also introduce some general recommendations useful to make of link prediction an efficiently parallelized problem.Peer ReviewedPostprint (published version

Parallel implementation of the TRANSIMS micro-simulation

This paper describes the parallel implementation of the TRANSIMS traffic micro-simulation. The parallelization method is domain decomposition, which means that each CPU of the parallel computer is responsible for a different geographical area of the simulated region. We describe how information between domains is exchanged, and how the transportation network graph is partitioned. An adaptive scheme is used to optimize load balancing. We then demonstrate how computing speeds of our parallel micro-simulations can be systematically predicted once the scenario and the computer architecture are known. This makes it possible, for example, to decide if a certain study is feasible with a certain computing budget, and how to invest that budget. The main ingredients of the prediction are knowledge about the parallel implementation of the micro-simulation, knowledge about the characteristics of the partitioning of the transportation network graph, and knowledge about the interaction of these quantities with the computer system. In particular, we investigate the differences between switched and non-switched topologies, and the effects of 10 Mbit, 100 Mbit, and Gbit Ethernet. keywords: Traffic simulation, parallel computing, transportation planning, TRANSIM

ProtNN: Fast and Accurate Nearest Neighbor Protein Function Prediction based on Graph Embedding in Structural and Topological Space

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the determination of protein functions in living cells. In this paper, we propose ProtNN, a novel approach for protein function prediction. Given an unannotated protein structure and a set of annotated proteins, ProtNN finds the nearest neighbor annotated structures based on protein-graph pairwise similarities. Given a query protein, ProtNN finds the nearest neighbor reference proteins based on a graph representation model and a pairwise similarity between vector embedding of both query and reference protein-graphs in structural and topological spaces. ProtNN assigns to the query protein the function with the highest number of votes across the set of k nearest neighbor reference proteins, where k is a user-defined parameter. Experimental evaluation demonstrates that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude of runtime compared to state-of-the-art approaches

Forecasting of commercial sales with large scale Gaussian Processes

This paper argues that there has not been enough discussion in the field of applications of Gaussian Process for the fast moving consumer goods industry. Yet, this technique can be important as it e.g., can provide automatic feature relevance determination and the posterior mean can unlock insights on the data. Significant challenges are the large size and high dimensionality of commercial data at a point of sale. The study reviews approaches in the Gaussian Processes modeling for large data sets, evaluates their performance on commercial sales and shows value of this type of models as a decision-making tool for management.Comment: 1o pages, 5 figure

Community Detection in Networks with Node Attributes

Community detection algorithms are fundamental tools that allow us to uncover organizational principles in networks. When detecting communities, there are two possible sources of information one can use: the network structure, and the features and attributes of nodes. Even though communities form around nodes that have common edges and common attributes, typically, algorithms have only focused on one of these two data modalities: community detection algorithms traditionally focus only on the network structure, while clustering algorithms mostly consider only node attributes. In this paper, we develop Communities from Edge Structure and Node Attributes (CESNA), an accurate and scalable algorithm for detecting overlapping communities in networks with node attributes. CESNA statistically models the interaction between the network structure and the node attributes, which leads to more accurate community detection as well as improved robustness in the presence of noise in the network structure. CESNA has a linear runtime in the network size and is able to process networks an order of magnitude larger than comparable approaches. Last, CESNA also helps with the interpretation of detected communities by finding relevant node attributes for each community.Comment: Published in the proceedings of IEEE ICDM '1