The Gray-code filter kernels

Abstract In this paper we introduce a family of filter kernels -the Gray-Code Kernels (GCK) and demonstrate their use in image analysis. Filtering an image with a sequence of Gray-Code Kernels is highly efficient and requires only 2 operations per pixel for each filter kernel, independent of the size or dimension of the kernel. We show that the family of kernels is large and includes the Walsh-Hadamard kernels amongst others. The GCK can be used to approximate any desired kernel and as such forms a complete representation. The efficiency of computation using a sequence of GCK filters can be exploited for various real-time applications, such as, pattern detection, feature extraction, texture analysis, texture synthesis, and more

DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning.

Drug-target interaction (DTI) prediction is a crucial step in drug discovery and repositioning as it reduces experimental validation costs if done right. Thus, developing in-silico methods to predict potential DTI has become a competitive research niche, with one of its main focuses being improving the prediction accuracy. Using machine learning (ML) models for this task, specifically network-based approaches, is effective and has shown great advantages over the other computational methods. However, ML model development involves upstream hand-crafted feature extraction and other processes that impact prediction accuracy. Thus, network-based representation learning techniques that provide automated feature extraction combined with traditional ML classifiers dealing with downstream link prediction tasks may be better-suited paradigms. Here, we present such a method, DTi2Vec, which identifies DTIs using network representation learning and ensemble learning techniques. DTi2Vec constructs the heterogeneous network, and then it automatically generates features for each drug and target using the nodes embedding technique. DTi2Vec demonstrated its ability in drug-target link prediction compared to several state-of-the-art network-based methods, using four benchmark datasets and large-scale data compiled from DrugBank. DTi2Vec showed a statistically significant increase in the prediction performances in terms of AUPR. We verified the novel predicted DTIs using several databases and scientific literature. DTi2Vec is a simple yet effective method that provides high DTI prediction performance while being scalable and efficient in computation, translating into a powerful drug repositioning tool

Coding Theory and Algebraic Combinatorics

This chapter introduces and elaborates on the fruitful interplay of coding theory and algebraic combinatorics, with most of the focus on the interaction of codes with combinatorial designs, finite geometries, simple groups, sphere packings, kissing numbers, lattices, and association schemes. In particular, special interest is devoted to the relationship between codes and combinatorial designs. We describe and recapitulate important results in the development of the state of the art. In addition, we give illustrative examples and constructions, and highlight recent advances. Finally, we provide a collection of significant open problems and challenges concerning future research.Comment: 33 pages; handbook chapter, to appear in: "Selected Topics in Information and Coding Theory", ed. by I. Woungang et al., World Scientific, Singapore, 201

Unsupervised Structural Embedding Methods for Efficient Collective Network Mining

How can we align accounts of the same user across social networks? Can we identify the professional role of an email user from their patterns of communication? Can we predict the medical effects of chemical compounds from their atomic network structure? Many problems in graph data mining, including all of the above, are defined on multiple networks. The central element to all of these problems is cross-network comparison, whether at the level of individual nodes or entities in the network or at the level of entire networks themselves. To perform this comparison meaningfully, we must describe the entities in each network expressively in terms of patterns that generalize across the networks. Moreover, because the networks in question are often very large, our techniques must be computationally efficient. In this thesis, we propose scalable unsupervised methods that embed nodes in vector space by mapping nodes with similar structural roles in their respective networks, even if they come from different networks, to similar parts of the embedding space. We perform network alignment by matching nodes across two or more networks based on the similarity of their embeddings, and refine this process by reinforcing the consistency of each node’s alignment with those of its neighbors. By characterizing the distribution of node embeddings in a graph, we develop graph-level feature vectors that are highly effective for graph classification. With principled sparsification and randomized approximation techniques, we make all our methods computationally efficient and able to scale to graphs with millions of nodes or edges. We demonstrate the effectiveness of structural node embeddings on industry-scale applications, and propose an extensive set of embedding evaluation techniques that lay the groundwork for further methodological development and application.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162895/1/mheimann_1.pd