Learning kernels from biological networks by maximizing entropy
Koji Tsuda,William Stafford Noble +1 more
- Vol. 20, Iss: 1, pp 326-333
Reads0
Chats0
TLDR
It is shown that computing the diffusion kernel is equivalent to maximizing the von Neumann entropy, subject to a global constraint on the sum of the Euclidean distances between nodes, and that the resulting kernel allows for more accurate support vector machine prediction of protein functional classifications from metabolic and protein-protein interaction networks.Abstract:
Motivation: The diffusion kernel is a general method for computing pairwise distances among all nodes in a graph, based on the sum of weighted paths between each pair of nodes. This technique has been used successfully, in conjunction with kernel-based learning methods, to draw inferences from several types of biological networks.
Results: We show that computing the diffusion kernel is equivalent to maximizing the von Neumann entropy, subject to a global constraint on the sum of the Euclidean distances between nodes. This global constraint allows for high variance in the pairwise distances. Accordingly, we propose an alternative, locally constrained diffusion kernel, and we demonstrate that the resulting kernel allows for more accurate support vector machine prediction of protein functional classifications from metabolic and protein--protein interaction networks.
Availability: Supplementary results and data are available at noble.gs.washington.edu/proj/maxentread more
Citations
More filters
BookDOI
Semi-Supervised Learning
TL;DR: Semi-supervised learning (SSL) as discussed by the authors is the middle ground between supervised learning (in which all training examples are labeled) and unsupervised training (where no label data are given).
Proceedings ArticleDOI
Relational learning via latent social dimensions
TL;DR: This work proposes to extract latent social dimensions based on network information, and then utilize them as features for discriminative learning, and outperforms representative relational learning methods based on collective inference, especially when few labeled data are available.
BookDOI
Managing and Mining Graph Data
Charu C. Aggarwal,Haixun Wang +1 more
TL;DR: This is the first comprehensive survey book in the emerging topic of graph data processing and contains extensive surveys on important graph topics such as graph languages, indexing, clustering, data generation, pattern mining, classification, keyword search, pattern matching, and privacy.
Book ChapterDOI
Link prediction via matrix factorization
TL;DR: The model learns latent features from the topological structure of a (possibly directed) graph, and is shown to make better predictions than popular unsupervised scores, and may be combined with optional explicit features for nodes or edges, which yields better performance.
Journal ArticleDOI
Network propagation: a universal amplifier of genetic associations
TL;DR: All these approaches to genetic analysis using networks are variations of a unifying mathematical machinery — network propagation — suggesting that it is a powerful data transformation method of broad utility in genetic research.
References
More filters
Book
Quantum Computation and Quantum Information
TL;DR: In this article, the quantum Fourier transform and its application in quantum information theory is discussed, and distance measures for quantum information are defined. And quantum error-correction and entropy and information are discussed.
Quantum Computation and Quantum Information
TL;DR: This chapter discusses quantum information theory, public-key cryptography and the RSA cryptosystem, and the proof of Lieb's theorem.
Journal ArticleDOI
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
Journal ArticleDOI
Transcriptional Regulatory Networks in Saccharomyces cerevisiae
Tong Ihn Lee,Nicola J. Rinaldi,François Robert,Duncan T. Odom,Ziv Bar-Joseph,Georg K. Gerber,Nancy M. Hannett,Christopher T. Harbison,Craig M. Thompson,Itamar Simon,Julia Zeitlinger,Ezra G. Jennings,Heather L. Murray,D. Benjamin Gordon,Bing Ren,John J. Wyrick,Jean-Bosco Tagne,Thomas L. Volkert,Ernest Fraenkel,David K. Gifford,Richard A. Young +20 more
TL;DR: This work determines how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells, and identifies network motifs, the simplest units of network architecture, and demonstrates that an automated process can use motifs to assemble a transcriptional regulatory network structure.