Fusion and community detection in multi-layer graphs

Relational data arising in many domains can be represented by networks (or graphs) with nodes capturing entities and edges representing relationships between these entities. Community detection in networks has become one of the most important problems having a broad range of applications. Until recently, the vast majority of papers have focused on discovering community structures in a single network. However, with the emergence of multi-view network data in many real-world applications and consequently with the advent of multilayer graph representation, community detection in multi-layer graphs has become a new challenge. Multi-layer graphs provide complementary views of connectivity patterns of the same set of vertices. Fusion of the network layers is expected to achieve better clustering performance. In this paper, we propose two novel methods, coined as WSSNMTF (Weighted Simultaneous Symmetric Non-Negative Matrix Tri-Factorization) and NG-WSSNMTF (Natural Gradient WSSNMTF), for fusion and clustering of multi-layer graphs. Both methods are robust with respect to missing edges and noise. We compare the performance of the proposed methods with two baseline methods, as well as with three state-of-the-art methods on synthetic and three real-world datasets. The experimental results indicate superior performance of the proposed methods

Fusion and community detection in multi-layer graphs

Relational data arising in many domains can be represented by networks (or graphs) with nodes capturing entities and edges representing relationships between these entities. Community detection in networks has become one of the most important problems having a broad range of applications. Until recently, the vast majority of papers have focused on discovering community structures in a single network. However, with the emergence of multi-view network data in many real-world applications and consequently with the advent of multilayer graph representation, community detection in multi-layer graphs has become a new challenge. Multi-layer graphs provide complementary views of connectivity patterns of the same set of vertices. Fusion of the network layers is expected to achieve better clustering performance. In this paper, we propose two novel methods, coined as WSSNMTF (Weighted Simultaneous Symmetric Non-Negative Matrix Tri-Factorization) and NG-WSSNMTF (Natural Gradient WSSNMTF), for fusion and clustering of multi-layer graphs. Both methods are robust with respect to missing edges and noise. We compare the performance of the proposed methods with two baseline methods, as well as with three state-of-the-art methods on synthetic and three real-world datasets. The experimental results indicate superior performance of the proposed methods

Towards a data-integrated cell

We are increasingly accumulating molecular data about a cell. The challenge is how to integrate them within a unified conceptual and computational framework enabling new discoveries. Hence, we propose a novel, data-driven concept of an integrated cell, iCell. Also, we introduce a computational prototype of an iCell, which integrates three omics, tissue-specific molecular interaction network types. We construct iCells of four cancers and the corresponding tissue controls and identify the most rewired genes in cancer. Many of them are of unknown function and cannot be identified as different in cancer in any specific molecular network. We biologically validate that they have a role in cancer by knockdown experiments followed by cell viability assays. We find additional support through Kaplan-Meier survival curves of thousands of patients. Finally, we extend this analysis to uncover pan-cancer genes. Our methodology is universal and enables integrative comparisons of diverse omics data over cells and tissues

Data-Driven Representation Learning in Multimodal Feature Fusion

abstract: Modern machine learning systems leverage data and features from multiple modalities to gain more predictive power. In most scenarios, the modalities are vastly different and the acquired data are heterogeneous in nature. Consequently, building highly effective fusion algorithms is at the core to achieve improved model robustness and inferencing performance. This dissertation focuses on the representation learning approaches as the fusion strategy. Specifically, the objective is to learn the shared latent representation which jointly exploit the structural information encoded in all modalities, such that a straightforward learning model can be adopted to obtain the prediction. We first consider sensor fusion, a typical multimodal fusion problem critical to building a pervasive computing platform. A systematic fusion technique is described to support both multiple sensors and descriptors for activity recognition. Targeted to learn the optimal combination of kernels, Multiple Kernel Learning (MKL) algorithms have been successfully applied to numerous fusion problems in computer vision etc. Utilizing the MKL formulation, next we describe an auto-context algorithm for learning image context via the fusion with low-level descriptors. Furthermore, a principled fusion algorithm using deep learning to optimize kernel machines is developed. By bridging deep architectures with kernel optimization, this approach leverages the benefits of both paradigms and is applied to a wide variety of fusion problems. In many real-world applications, the modalities exhibit highly specific data structures, such as time sequences and graphs, and consequently, special design of the learning architecture is needed. In order to improve the temporal modeling for multivariate sequences, we developed two architectures centered around attention models. A novel clinical time series analysis model is proposed for several critical problems in healthcare. Another model coupled with triplet ranking loss as metric learning framework is described to better solve speaker diarization. Compared to state-of-the-art recurrent networks, these attention-based multivariate analysis tools achieve improved performance while having a lower computational complexity. Finally, in order to perform community detection on multilayer graphs, a fusion algorithm is described to derive node embedding from word embedding techniques and also exploit the complementary relational information contained in each layer of the graph.Dissertation/ThesisDoctoral Dissertation Electrical Engineering 201