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In this work, we delve into the nonparametric empirical Bayes theory and approximate the classical Bayes estimator by a truncation of the generalized Laguerre series and then estimate its coefficients by minimizing the prior risk of the estimator. The minimization process yields a system of linear equations the size of which is equal to the truncation level. We focus on the empirical Bayes estimation problem when the mixing distribution, and therefore the prior distribution, has a support on the positive real half-line or a subinterval of it. By investigating several common mixing distributions, we develop a strategy on how to select the parameter of the generalized Laguerre function basis so that our estimator {possesses a finite} variance. We show that our generalized Laguerre empirical Bayes approach is asymptotically optimal in the minimax sense. Finally, our convergence rate is compared and contrasted with {several} results from the literature.

Neural autoregressive sequence models smear the probability among many possible sequences including degenerate ones, such as empty or repetitive sequences. In this work, we tackle one specific case where the model assigns a high probability to unreasonably short sequences. We define the oversmoothing rate to quantify this issue. After confirming the high degree of oversmoothing in neural machine translation, we propose to explicitly minimize the oversmoothing rate during training. We conduct a set of experiments to study the effect of the proposed regularization on both model distribution and decoding performance. We use a neural machine translation task as the testbed and consider three different datasets of varying size. Our experiments reveal three major findings. First, we can control the oversmoothing rate of the model by tuning the strength of the regularization. Second, by enhancing the oversmoothing loss contribution, the probability and the rank of <eos> token decrease heavily at positions where it is not supposed to be. Third, the proposed regularization impacts the outcome of beam search especially when a large beam is used. The degradation of translation quality (measured in BLEU) with a large beam significantly lessens with lower oversmoothing rate, but the degradation compared to smaller beam sizes remains to exist. From these observations, we conclude that the high degree of oversmoothing is the main reason behind the degenerate case of overly probable short sequences in a neural autoregressive model.

We propose a family of estimators based on kernel ridge regression for nonparametric structural functions (also called dose response curves) and semiparametric treatment effects. Treatment and covariates may be discrete or continuous, and low, high, or infinite dimensional. We reduce causal estimation and inference to combinations of kernel ridge regressions, which have closed form solutions and are easily computed by matrix operations, unlike other machine learning paradigms. This computational simplicity allows us to extend the framework in two directions: from means to increments and distributions of counterfactual outcomes; and from parameters of the full population to those of subpopulations and alternative populations. For structural functions, we prove uniform consistency with finite sample rates. For treatment effects, we prove $\sqrt{n}$ consistency, Gaussian approximation, and semiparametric efficiency with a new double spectral robustness property. We conduct simulations and estimate average, heterogeneous, and incremental structural functions of the US Jobs Corps training program.

We propose a generalised framework for Bayesian Structural Equation Modelling (SEM) that can be applied to a variety of data types. The introduced framework focuses on the approximate zero approach, according to which parameters that would before set to zero (e.g. factor loadings) are now formulated to be approximate zero. It extends previously suggested models by \citeA{MA12} and can handle continuous, binary, and ordinal data. Moreover, we propose a novel model assessment paradigm aiming to address shortcomings of posterior predictive $p-$values, which provide the default metric of fit for Bayesian SEM. The introduced model assessment procedure monitors the out-of-sample predictive performance of the fitted model, and together with a list of guidelines we provide, one can investigate whether the hypothesised model is supported by the data. We incorporate scoring rules and cross-validation to supplement existing model assessment metrics for Bayesian SEM. We study the performance of the proposed methodology via simulations. The model for continuous and binary data is fitted to data on the `Big-5' personality scale and the Fagerstrom test for nicotine dependence respectively.

Attention-based neural networks have achieved state-of-the-art results on a wide range of tasks. Most such models use deterministic attention while stochastic attention is less explored due to the optimization difficulties or complicated model design. This paper introduces Bayesian attention belief networks, which construct a decoder network by modeling unnormalized attention weights with a hierarchy of gamma distributions, and an encoder network by stacking Weibull distributions with a deterministic-upward-stochastic-downward structure to approximate the posterior. The resulting auto-encoding networks can be optimized in a differentiable way with a variational lower bound. It is simple to convert any models with deterministic attention, including pretrained ones, to the proposed Bayesian attention belief networks. On a variety of language understanding tasks, we show that our method outperforms deterministic attention and state-of-the-art stochastic attention in accuracy, uncertainty estimation, generalization across domains, and robustness to adversarial attacks. We further demonstrate the general applicability of our method on neural machine translation and visual question answering, showing great potential of incorporating our method into various attention-related tasks.

In many important graph data processing applications the acquired information includes both node features and observations of the graph topology. Graph neural networks (GNNs) are designed to exploit both sources of evidence but they do not optimally trade-off their utility and integrate them in a manner that is also universal. Here, universality refers to independence on homophily or heterophily graph assumptions. We address these issues by introducing a new Generalized PageRank (GPR) GNN architecture that adaptively learns the GPR weights so as to jointly optimize node feature and topological information extraction, regardless of the extent to which the node labels are homophilic or heterophilic. Learned GPR weights automatically adjust to the node label pattern, irrelevant on the type of initialization, and thereby guarantee excellent learning performance for label patterns that are usually hard to handle. Furthermore, they allow one to avoid feature over-smoothing, a process which renders feature information nondiscriminative, without requiring the network to be shallow. Our accompanying theoretical analysis of the GPR-GNN method is facilitated by novel synthetic benchmark datasets generated by the so-called contextual stochastic block model. We also compare the performance of our GNN architecture with that of several state-of-the-art GNNs on the problem of node-classification, using well-known benchmark homophilic and heterophilic datasets. The results demonstrate that GPR-GNN offers significant performance improvement compared to existing techniques on both synthetic and benchmark data.

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68% chemically valid molecules even without chemical knowledge rules and 100% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.

Network embedding has become a hot research topic recently which can provide low-dimensional feature representations for many machine learning applications. Current work focuses on either (1) whether the embedding is designed as an unsupervised learning task by explicitly preserving the structural connectivity in the network, or (2) whether the embedding is a by-product during the supervised learning of a specific discriminative task in a deep neural network. In this paper, we focus on bridging the gap of the two lines of the research. We propose to adapt the Generative Adversarial model to perform network embedding, in which the generator is trying to generate vertex pairs, while the discriminator tries to distinguish the generated vertex pairs from real connections (edges) in the network. Wasserstein-1 distance is adopted to train the generator to gain better stability. We develop three variations of models, including GANE which applies cosine similarity, GANE-O1 which preserves the first-order proximity, and GANE-O2 which tries to preserves the second-order proximity of the network in the low-dimensional embedded vector space. We later prove that GANE-O2 has the same objective function as GANE-O1 when negative sampling is applied to simplify the training process in GANE-O2. Experiments with real-world network datasets demonstrate that our models constantly outperform state-of-the-art solutions with significant improvements on precision in link prediction, as well as on visualizations and accuracy in clustering tasks.

Recently introduced generative adversarial network (GAN) has been shown numerous promising results to generate realistic samples. The essential task of GAN is to control the features of samples generated from a random distribution. While the current GAN structures, such as conditional GAN, successfully generate samples with desired major features, they often fail to produce detailed features that bring specific differences among samples. To overcome this limitation, here we propose a controllable GAN (ControlGAN) structure. By separating a feature classifier from a discriminator, the generator of ControlGAN is designed to learn generating synthetic samples with the specific detailed features. Evaluated with multiple image datasets, ControlGAN shows a power to generate improved samples with well-controlled features. Furthermore, we demonstrate that ControlGAN can generate intermediate features and opposite features for interpolated and extrapolated input labels that are not used in the training process. It implies that ControlGAN can significantly contribute to the variety of generated samples.

Generative models (GMs) such as Generative Adversary Network (GAN) and Variational Auto-Encoder (VAE) have thrived these years and achieved high quality results in generating new samples. Especially in Computer Vision, GMs have been used in image inpainting, denoising and completion, which can be treated as the inference from observed pixels to corrupted pixels. However, images are hierarchically structured which are quite different from many real-world inference scenarios with non-hierarchical features. These inference scenarios contain heterogeneous stochastic variables and irregular mutual dependences. Traditionally they are modeled by Bayesian Network (BN). However, the learning and inference of BN model are NP-hard thus the number of stochastic variables in BN is highly constrained. In this paper, we adapt typical GMs to enable heterogeneous learning and inference in polynomial time.We also propose an extended autoregressive (EAR) model and an EAR with adversary loss (EARA) model and give theoretical results on their effectiveness. Experiments on several BN datasets show that our proposed EAR model achieves the best performance in most cases compared to other GMs. Except for black box analysis, we've also done a serial of experiments on Markov border inference of GMs for white box analysis and give theoretical results.