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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. In many real-world reinforcement learning (RL) problems, in addition to maximizing the objective, the learning agent has to maintain some necessary safety constraints. We formulate the problem of learning a safe policy as an infinite-horizon discounted Constrained Markov Decision Process (CMDP) with an unknown transition probability matrix, where the safety requirements are modeled as constraints on expected cumulative costs. We propose two model-based constrained reinforcement learning (CRL) algorithms for learning a safe policy, namely, (i) GM-CRL algorithm, where the algorithm has access to a generative model, and (ii) UC-CRL algorithm, where the algorithm learns the model using an upper confidence style online exploration method. We characterize the sample complexity of these algorithms, i.e., the the number of samples needed to ensure a desired level of accuracy with high probability, both with respect to objective maximization and constraint satisfaction.

     
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  3. Many physical systems have underlying safety considerations that require that the policy employed ensures the satisfaction of a set of constraints. The analytical formulation usually takes the form of a Constrained Markov Decision Process (CMDP). We focus on the case where the CMDP is unknown, and RL algorithms obtain samples to discover the model and compute an optimal constrained policy. Our goal is to characterize the relationship between safety constraints and the number of samples needed to ensure a desired level of accuracy---both objective maximization and constraint satisfaction---in a PAC sense. We explore two classes of RL algorithms, namely, (i) a generative model based approach, wherein samples are taken initially to estimate a model, and (ii) an online approach, wherein the model is updated as samples are obtained. Our main finding is that compared to the best known bounds of the unconstrained regime, the sample complexity of constrained RL algorithms are increased by a factor that is logarithmic in the number of constraints, which suggests that the approach may be easily utilized in real systems. 
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  4. Many physical systems have underlying safety considerations that require that the policy employed ensures the satisfaction of a set of constraints. The analytical formulation usually takes the form of a Constrained Markov Decision Process (CMDP).We focus on the case where the CMDP is unknown, and RL algorithms obtain samples to discover the model and compute an optimal constrained policy. Our goal is to characterize the relationship between safety constraints and the number of samples needed to ensure a desired level of accuracy— both objective maximization and constraint satisfaction—in a PAC sense. We explore two classes of RL algorithms, namely, (i) a generative model based approach, wherein samples are taken initially to estimate a model, and (ii) an online approach, wherein the model is updated as samples are obtained. Our main finding is that compared to the best known bounds of the unconstrained regime, the sample complexity of constrained RL algorithms are increased by a factor that is logarithmic in the number of constraints, which suggests that the approach may be easily utilized in real systems 
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  5. 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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  6. 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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  7. 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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  8. null (Ed.)
    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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  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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