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  1. Multi-omics data analysis has the potential to discover hidden molecular interactions, revealing potential regulatory and/or signal transduction pathways for cellular processes of interest when studying life and disease systems. One of critical challenges when dealing with real-world multi-omics data is that they may manifest heterogeneous structures and data quality as often existing data may be collected from different subjects under different conditions for each type of omics data. We propose a novel deep Bayesian generative model to efficiently infer a multi-partite graph encoding molecular interactions across such heterogeneous views, using a fused Gromov-Wasserstein (FGW) regularization between latent representations of corresponding views for integrative analysis. With such an optimal transport regularization in the deep Bayesian generative model, it not only allows incorporating view-specific side information, either with graph-structured or unstructured data in different views, but also increases the model flexibility with the distribution-based regularization. This allows efficient alignment of heterogeneous latent variable distributions to derive reliable interaction predictions compared to the existing point-based graph embedding methods. Our experiments on several real-world datasets demonstrate enhanced performance of MoReL in inferring meaningful interactions compared to existing baselines. 
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  2. Temporal networks representing a stream of timestamped edges are seemingly ubiquitous in the real world. However, the massive size and continuous nature of these networks make them fundamentally challenging to analyze and leverage for descriptive and predictive modeling tasks. In this work, we propose a general framework for temporal network sampling with unbiased estimation. We develop online, single-pass sampling algorithms, and unbiased estimators for temporal network sampling. The proposed algorithms enable fast, accurate, and memory-efficient statistical estimation of temporal network patterns and properties. In addition, we propose a temporally decaying sampling algorithm with unbiased estimators for studying networks that evolve in continuous time, where the strength of links is a function of time, and the motif patterns are temporally weighted. In contrast to the prior notion of a △ t -temporal motif, the proposed formulation and algorithms for counting temporally weighted motifs are useful for forecasting tasks in networks such as predicting future links, or a future time-series variable of nodes and links. Finally, extensive experiments on a variety of temporal networks from different domains demonstrate the effectiveness of the proposed algorithms. A detailed ablation study is provided to understand the impact of the various components of the proposed framework. 
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  3. null (Ed.)
    High-throughput molecular profiling technologies have produced high-dimensional multi-omics data, enabling systematic understanding of living systems at the genome scale. Studying molecular interactions across different data types helps reveal signal transduction mechanisms across different classes of molecules. In this paper, we develop a novel Bayesian representation learning method that infers the relational interactions across multi-omics data types. Our method, Bayesian Relational Learning (BayReL) for multi-omics data integration, takes advantage of a priori known relationships among the same class of molecules, modeled as a graph at each corresponding view, to learn view-specific latent variables as well as a multi-partite graph that encodes the interactions across views. Our experiments on several real-world datasets demonstrate enhanced performance of BayReL in inferring meaningful interactions compared to existing baselines. 
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  4. null (Ed.)
    Networks are a natural representation of complex systems across the sciences, and higher-order dependencies are central to the understanding and modeling of these systems. However, in many practical applications such as online social networks, networks are massive, dynamic, and naturally streaming, where pairwise interactions among vertices become available one at a time in some arbitrary order. The massive size and streaming nature of these networks allow only partial observation, since it is infeasible to analyze the entire network. Under such scenarios, it is challenging to study the higher-order structural and connectivity patterns of streaming networks. In this work, we consider the fundamental problem of estimating the higher-order dependencies using adaptive sampling. We propose a novel adaptive, single-pass sampling framework and unbiased estimators for higher-order network analysis of large streaming networks. Our algorithms exploit adaptive techniques to identify edges that are highly informative for efficiently estimating the higher-order structure of streaming networks from small sample data. We also introduce a novel James-Stein shrinkage estimator to reduce the estimation error. Our approach is fully analytic, computationally efficient, and can be incrementally updated in a streaming setting. Numerical experiments on large networks show that our approach is superior to baseline methods. 
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  5. Stochastic recurrent neural networks with latent random variables of complex dependency structures have shown to be more successful in modeling sequential data than deterministic deep models. However, the majority of existing methods have limited expressive power due to the Gaussian assumption of latent variables. In this paper, we advocate learning implicit latent representations using semi-implicit variational inference to further increase model flexibility. Semi-implicit stochastic recurrent neural network (SIS-RNN) is developed to enrich inferred model posteriors that may have no analytic density functions, as long as independent random samples can be generated via reparameterization. Extensive experiments in different tasks on real-world datasets show that SIS-RNN outperforms the existing methods. 
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  6. null (Ed.)
    Abstract—The emergence of remote sensing technologies cou- pled with local monitoring workstations enables us the un- precedented ability to monitor the environment in large scale. Information mining from multi-channel geo-spatiotemporal data however poses great challenges to many computational sustainability applications. Most existing approaches adopt various dimensionality reduction techniques without fully taking advantage of the spatiotemporal nature of the data. In addition, the lack of labeled training data raises another challenge for modeling such data. In this work, we propose a novel semi-supervised attention-based deep representation model that learns context-aware spatiotemporal representations for prediction tasks. A combination of convolutional neural networks with a hybrid attention mechanism is adopted to extract spatial and temporal variations in the geo-spatiotemporal data. Recognizing the importance of capturing more complete temporal dependencies, we propose the hybrid attention mechanism which integrates a learnable global query into the classic self-attention mechanism. To overcome the data scarcity issue, sampled spatial and temporal context that naturally reside in the largely-available unlabeled geo-spatiotemporal data are exploited to aid meaningful representation learning. We conduct experiments on a large-scale real-world crop yield prediction task. The results show that our methods significantly outperforms existing state-of-the-art yield prediction methods, especially under the stress of training data scarcity. 
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    We propose a unified framework for adap- tive connection sampling in graph neural net- works (GNNs) that generalizes existing stochas- tic regularization methods for training GNNs. The proposed framework not only alleviates over- smoothing and over-fitting tendencies of deep GNNs, but also enables learning with uncertainty in graph analytic tasks with GNNs. Instead of using fixed sampling rates or hand-tuning them as model hyperparameters as in existing stochas- tic regularization methods, our adaptive connec- tion sampling can be trained jointly with GNN model parameters in both global and local fash- ions. GNN training with adaptive connection sampling is shown to be mathematically equiv- alent to an efficient approximation of training Bayesian GNNs. Experimental results with abla- tion studies on benchmark datasets validate that adaptively learning the sampling rate given graph training data is the key to boosting the perfor- mance of GNNs in semi-supervised node classifi- cation, making them less prone to over-smoothing and over-fitting with more robust prediction. 
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  8. Recently, considerable research attention has been paid to graph embedding, a popular approach to construct representations of vertices in latent space. Due to the curse of dimensionality and sparsity in graphical datasets, this approach has become indispensable for machine learning tasks over large networks. The majority of the existing literature has considered this technique under the assumption that the network is static. However, networks in many applications, including social networks, collaboration networks, and recommender systems, nodes, and edges accrue to a growing network as streaming. A small number of very recent results have addressed the problem of embedding for dynamic networks. However, they either rely on knowledge of vertex attributes, su er high-time complexity or need to be re-trained without closed-form expression. Thus the approach of adapting the existing methods designed for static networks or dynamic networks to the streaming environment faces non-trivial technical challenges. These challenges motivate developing new approaches to the problems of streaming graph embedding. In this paper, we propose a new framework that is able to generate latent representations for new vertices with high e ciency and low complexity under speci ed iteration rounds. We formulate a constrained optimiza- tion problem for the modi cation of the representation resulting from a stream arrival. We show this problem has no closed-form solution and instead develop an online approximation solution. Our solution follows three steps: (1) identify vertices a ected by newly arrived ones, (2) generating latent features for new vertices, and (3) updating the latent features of the most a ected vertices. The new representations are guaranteed to be feasible in the original constrained optimization problem. Meanwhile, the solution only brings about a small change to existing representations and only slightly changes the value of the objective function. Multi-class clas- si cation and clustering on ve real-world networks demonstrate that our model can e ciently update vertex representations and simultaneously achieve comparable or even better performance compared with model retraining. 
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  9. Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction. 
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