Graph embedding

Abstract: This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

Abstract: Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However, learning the structure of complex trajectories with multiple branches remains a challenging computational problem. We present Monocle 2, an algorithm that uses reversed graph embedding to describe multiple fate decisions in a fully unsupervised manner. We applied Monocle 2 to two studies of blood development and found that mutations in the genes encoding key lineage transcription factors divert cells to alternative fates.

Abstract: A large family of algorithms - supervised or unsupervised; stemming from statistics or geometry theory - has been designed to provide different solutions to the problem of dimensionality reduction. Despite the different motivations of these algorithms, we present in this paper a general formulation known as graph embedding to unify them within a common framework. In graph embedding, each algorithm can be considered as the direct graph embedding or its linear/kernel/tensor extension of a specific intrinsic graph that describes certain desired statistical or geometric properties of a data set, with constraints from scale normalization or a penalty graph that characterizes a statistical or geometric property that should be avoided. Furthermore, the graph embedding framework can be used as a general platform for developing new dimensionality reduction algorithms. By utilizing this framework as a tool, we propose a new supervised dimensionality reduction algorithm called marginal Fisher analysis in which the intrinsic graph characterizes the intraclass compactness and connects each data point with its neighboring points of the same class, while the penalty graph connects the marginal points and characterizes the interclass separability. We show that MFA effectively overcomes the limitations of the traditional linear discriminant analysis algorithm due to data distribution assumptions and available projection directions. Real face recognition experiments show the superiority of our proposed MFA in comparison to LDA, also for corresponding kernel and tensor extensions

Abstract: A large family of algorithms - supervised or unsupervised; stemming from statistics or geometry theory - has been designed to provide different solutions to the problem of dimensionality reduction Despite the different motivations of these algorithms, we present in this paper a general formulation known as graph embedding to unify them within a common framework In graph embedding, each algorithm can be considered as the direct graph embedding or its linear/kernel/tensor extension of a specific intrinsic graph that describes certain desired statistical or geometric properties of a data set, with constraints from scale normalization or a penalty graph that characterizes a statistical or geometric property that should be avoided Furthermore, the graph embedding framework can be used as a general platform for developing new dimensionality reduction algorithms By utilizing this framework as a tool, we propose a new supervised dimensionality reduction algorithm called marginal Fisher analysis in which the intrinsic graph characterizes the intraclass compactness and connects each data point with its neighboring points of the same class, while the penalty graph connects the marginal points and characterizes the interclass separability We show that MFA effectively overcomes the limitations of the traditional linear discriminant analysis algorithm due to data distribution assumptions and available projection directions Real face recognition experiments show the superiority of our proposed MFA in comparison to LDA, also for corresponding kernel and tensor extensions