3,703 research outputs found
Diffusion Component Analysis: Unraveling Functional Topology in Biological Networks
Complex biological systems have been successfully modeled by biochemical and
genetic interaction networks, typically gathered from high-throughput (HTP)
data. These networks can be used to infer functional relationships between
genes or proteins. Using the intuition that the topological role of a gene in a
network relates to its biological function, local or diffusion based
"guilt-by-association" and graph-theoretic methods have had success in
inferring gene functions. Here we seek to improve function prediction by
integrating diffusion-based methods with a novel dimensionality reduction
technique to overcome the incomplete and noisy nature of network data. In this
paper, we introduce diffusion component analysis (DCA), a framework that plugs
in a diffusion model and learns a low-dimensional vector representation of each
node to encode the topological properties of a network. As a proof of concept,
we demonstrate DCA's substantial improvement over state-of-the-art
diffusion-based approaches in predicting protein function from molecular
interaction networks. Moreover, our DCA framework can integrate multiple
networks from heterogeneous sources, consisting of genomic information,
biochemical experiments and other resources, to even further improve function
prediction. Yet another layer of performance gain is achieved by integrating
the DCA framework with support vector machines that take our node vector
representations as features. Overall, our DCA framework provides a novel
representation of nodes in a network that can be used as a plug-in architecture
to other machine learning algorithms to decipher topological properties of and
obtain novel insights into interactomes.Comment: RECOMB 201
Similarity-Based Classification in Partially Labeled Networks
We propose a similarity-based method, using the similarity between nodes, to
address the problem of classification in partially labeled networks. The basic
assumption is that two nodes are more likely to be categorized into the same
class if they are more similar. In this paper, we introduce ten similarity
indices, including five local ones and five global ones. Empirical results on
the co-purchase network of political books show that the similarity-based
method can give high accurate classification even when the labeled nodes are
sparse which is one of the difficulties in classification. Furthermore, we find
that when the target network has many labeled nodes, the local indices can
perform as good as those global indices do, while when the data is sparce the
global indices perform better. Besides, the similarity-based method can to some
extent overcome the unconsistency problem which is another difficulty in
classification.Comment: 13 pages,3 figures,1 tabl
DeepInf: Social Influence Prediction with Deep Learning
Social and information networking activities such as on Facebook, Twitter,
WeChat, and Weibo have become an indispensable part of our everyday life, where
we can easily access friends' behaviors and are in turn influenced by them.
Consequently, an effective social influence prediction for each user is
critical for a variety of applications such as online recommendation and
advertising.
Conventional social influence prediction approaches typically design various
hand-crafted rules to extract user- and network-specific features. However,
their effectiveness heavily relies on the knowledge of domain experts. As a
result, it is usually difficult to generalize them into different domains.
Inspired by the recent success of deep neural networks in a wide range of
computing applications, we design an end-to-end framework, DeepInf, to learn
users' latent feature representation for predicting social influence. In
general, DeepInf takes a user's local network as the input to a graph neural
network for learning her latent social representation. We design strategies to
incorporate both network structures and user-specific features into
convolutional neural and attention networks. Extensive experiments on Open
Academic Graph, Twitter, Weibo, and Digg, representing different types of
social and information networks, demonstrate that the proposed end-to-end
model, DeepInf, significantly outperforms traditional feature engineering-based
approaches, suggesting the effectiveness of representation learning for social
applications.Comment: 10 pages, 5 figures, to appear in KDD 2018 proceeding
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