Reaction networks are often used to model interacting species in fields such as biochemistry and ecology. When the counts of the species are sufficiently large, the dynamics of their concentrations are typically modeled via a system of differential equations. However, when the counts of some species are small, the dynamics of the counts are typically modeled stochastically via a discrete state, continuous time Markov chain. A key quantity of interest for such models is the probability mass function of the process at some fixed time. Since paths of such models are relatively straightforward to simulate, we can estimate the probabilities by constructing an empirical distribution. However, the support of the distribution is often diffuse across a high-dimensional state space, where the dimension is equal to the number of species. Therefore generating an accurate empirical distribution can come with a large computational cost. We present a new Monte Carlo estimator that fundamentally improves on the "classical" Monte Carlo estimator described above. It also preserves much of classical Monte Carlo's simplicity. The idea is basically one of conditional Monte Carlo. Our conditional Monte Carlo estimator has two parameters, and their choice critically affects the performance of the algorithm. Hence, a key contribution of the present work is that we demonstrate how to approximate optimal values for these parameters in an efficient manner. Moreover, we provide a central limit theorem for our estimator, which leads to approximate confidence intervals for its error.
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Graph Convolutional Networks (GCNs) are one of the most popular architectures that are used to solve classification problems accompanied by graphical information. We present a rigorous theoretical understanding of the effects of graph convolutions in multi-layer networks. We study these effects through the node classification problem of a non-linearly separable Gaussian mixture model coupled with a stochastic block model. First, we show that a single graph convolution expands the regime of the distance between the means where multi-layer networks can classify the data by a factor of at least $1/\sqrt[4]{\mathbb{E}{\rm deg}}$, where $\mathbb{E}{\rm deg}$ denotes the expected degree of a node. Second, we show that with a slightly stronger graph density, two graph convolutions improve this factor to at least $1/\sqrt[4]{n}$, where $n$ is the number of nodes in the graph. Finally, we provide both theoretical and empirical insights into the performance of graph convolutions placed in different combinations among the layers of a network, concluding that the performance is mutually similar for all combinations of the placement. We present extensive experiments on both synthetic and real-world data that illustrate our results.
Many areas of science make extensive use of computer simulators that implicitly encode likelihood functions of complex systems. Classical statistical methods are poorly suited for these so-called likelihood-free inference (LFI) settings, particularly outside asymptotic and low-dimensional regimes. Although new machine learning methods, such as normalizing flows, have revolutionized the sample efficiency and capacity of LFI methods, it remains an open question whether they produce confidence sets with correct conditional coverage for small sample sizes. This paper unifies classical statistics with modern machine learning to present (i) a practical procedure for the Neyman construction of confidence sets with finite-sample guarantees of nominal coverage, and (ii) diagnostics that estimate conditional coverage over the entire parameter space. We refer to our framework as likelihood-free frequentist inference (LF2I). Any method that defines a test statistic, like the likelihood ratio, can leverage the LF2I machinery to create valid confidence sets and diagnostics without costly Monte Carlo samples at fixed parameter settings. We study the power of two test statistics (ACORE and BFF), which, respectively, maximize versus integrate an odds function over the parameter space. Our paper discusses the benefits and challenges of LF2I, with a breakdown of the sources of errors in LF2I confidence sets.
We give a fast algorithm for sampling uniform solutions of general constraint satisfaction problems (CSPs) in a local lemma regime. The expected running time of our algorithm is near-linear in $n$ and a fixed polynomial in $\Delta$, where $n$ is the number of variables and $\Delta$ is the max degree of constraints. Previously, up to similar conditions, sampling algorithms with running time polynomial in both $n$ and $\Delta$, only existed for the almost atomic case, where each constraint is violated by a small number of forbidden local configurations. Our sampling approach departs from all previous fast algorithms for sampling LLL, which were based on Markov chains. A crucial step of our algorithm is a recursive marginal sampler that is of independent interests. Within a local lemma regime, this marginal sampler can draw a random value for a variable according to its marginal distribution, at a local cost independent of the size of the CSP.
This paper is concerned with numerical algorithms for Biot model. By introducing an intermediate variable, the classical 2-field Biot model is written into a 3-field formulation. Based on such a 3-field formulation, we propose a coupled algorithm, some time-extrapolation based decoupled algorithms, and an iterative decoupled algorithm. Our focus is the analysis of the iterative decoupled algorithm. It is shown that the convergence of the iterative decoupled algorithm requires no extra assumptions on physical parameters or stabilization parameters. Numerical experiments are provided to demonstrate the accuracy and efficiency of the proposed method.
Given the prevalence of large-scale graphs in real-world applications, the storage and time for training neural models have raised increasing concerns. To alleviate the concerns, we propose and study the problem of graph condensation for graph neural networks (GNNs). Specifically, we aim to condense the large, original graph into a small, synthetic and highly-informative graph, such that GNNs trained on the small graph and large graph have comparable performance. We approach the condensation problem by imitating the GNN training trajectory on the original graph through the optimization of a gradient matching loss and design a strategy to condense node futures and structural information simultaneously. Extensive experiments have demonstrated the effectiveness of the proposed framework in condensing different graph datasets into informative smaller graphs. In particular, we are able to approximate the original test accuracy by 95.3% on Reddit, 99.8% on Flickr and 99.0% on Citeseer, while reducing their graph size by more than 99.9%, and the condensed graphs can be used to train various GNN architectures.Code is released at //github.com/ChandlerBang/GCond.
Bayesian model selection provides a powerful framework for objectively comparing models directly from observed data, without reference to ground truth data. However, Bayesian model selection requires the computation of the marginal likelihood (model evidence), which is computationally challenging, prohibiting its use in many high-dimensional Bayesian inverse problems. With Bayesian imaging applications in mind, in this work we present the proximal nested sampling methodology to objectively compare alternative Bayesian imaging models for applications that use images to inform decisions under uncertainty. The methodology is based on nested sampling, a Monte Carlo approach specialised for model comparison, and exploits proximal Markov chain Monte Carlo techniques to scale efficiently to large problems and to tackle models that are log-concave and not necessarily smooth (e.g., involving l_1 or total-variation priors). The proposed approach can be applied computationally to problems of dimension O(10^6) and beyond, making it suitable for high-dimensional inverse imaging problems. It is validated on large Gaussian models, for which the likelihood is available analytically, and subsequently illustrated on a range of imaging problems where it is used to analyse different choices of dictionary and measurement model.
The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Generative Adversarial Networks (GANs) can produce images of surprising complexity and realism, but are generally modeled to sample from a single latent source ignoring the explicit spatial interaction between multiple entities that could be present in a scene. Capturing such complex interactions between different objects in the world, including their relative scaling, spatial layout, occlusion, or viewpoint transformation is a challenging problem. In this work, we propose to model object composition in a GAN framework as a self-consistent composition-decomposition network. Our model is conditioned on the object images from their marginal distributions to generate a realistic image from their joint distribution by explicitly learning the possible interactions. We evaluate our model through qualitative experiments and user evaluations in both the scenarios when either paired or unpaired examples for the individual object images and the joint scenes are given during training. Our results reveal that the learned model captures potential interactions between the two object domains given as input to output new instances of composed scene at test time in a reasonable fashion.
Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.
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