We develop \textit{parallel predictive entropy search} (PPES), a novel algorithm for Bayesian optimization of expensive black-box objective functions. At each iteration, PPES aims to select a \textit{batch} of points which will maximize the information gain about the global maximizer of the objective. Well known strategies exist for suggesting a single evaluation point based on previous observations, while far fewer are known for selecting batches of points to evaluate in parallel. The few batch selection schemes that have been studied all resort to greedy methods to compute an optimal batch. To the best of our knowledge, PPES is the first non-greedy batch Bayesian optimization strategy. We demonstrate the benefit of this approach in optimization performance on both synthetic and real world applications, including problems in machine learning, rocket science and robotics.

Efforts to automate the reconstruction of neural circuits from 3D electron microscopic (EM) brain images are critical for the field of connectomics. An important computation for reconstruction is the detection of neuronal boundaries. Images acquired by serial section EM, a leading 3D EM technique, are highly anisotropic, with inferior quality along the third dimension. For such images, the 2D max-pooling convolutional network has set the standard for performance at boundary detection. Here we achieve a substantial gain in accuracy through three innovations. Following the trend towards deeper networks for object recognition, we use a much deeper network than previously employed for boundary detection. Second, we incorporate 3D as well as 2D filters, to enable computations that use 3D context. Finally, we adopt a recursively trained architecture in which a first network generates a preliminary boundary map that is provided as input along with the original image to a second network that generates a final boundary map. Backpropagation training is accelerated by ZNN, a new implementation of 3D convolutional networks that uses multicore CPU parallelism for speed. Our hybrid 2D-3D architecture could be more generally applicable to other types of anisotropic 3D images, including video, and our recursive framework for any image labeling problem.

We introduce the Gaussian Process Convolution Model (GPCM), a two-stage nonparametric generative procedure to model stationary signals as the convolution between a continuous-time white-noise process and a continuous-time linear filter drawn from Gaussian process. The GPCM is a continuous-time nonparametric-window moving average process and, conditionally, is itself a Gaussian process with a nonparametric kernel defined in a probabilistic fashion. The generative model can be equivalently considered in the frequency domain, where the power spectral density of the signal is specified using a Gaussian process. One of the main contributions of the paper is to develop a novel variational free-energy approach based on inter-domain inducing variables that efficiently learns the continuous-time linear filter and infers the driving white-noise process. In turn, this scheme provides closed-form probabilistic estimates of the covariance kernel and the noise-free signal both in denoising and prediction scenarios. Additionally, the variational inference procedure provides closed-form expressions for the approximate posterior of the spectral density given the observed data, leading to new Bayesian nonparametric approaches to spectrum estimation. The proposed GPCM is validated using synthetic and real-world signals.

Supervised deep learning has been successfully applied for many recognition problems in machine learning and computer vision. Although it can approximate a complex many-to-one function very well when large number of training data is provided, the lack of probabilistic inference of the current supervised deep learning methods makes it difficult to model a complex structured output representations. In this work, we develop a scalable deep conditional generative model for structured output variables using Gaussian latent variables. The model is trained efficiently in the framework of stochastic gradient variational Bayes, and allows a fast prediction using stochastic feed-forward inference. In addition, we provide novel strategies to build a robust structured prediction algorithms, such as recurrent prediction network architecture, input noise-injection and multi-scale prediction training methods. In experiments, we demonstrate the effectiveness of our proposed algorithm in comparison to the deterministic deep neural network counterparts in generating diverse but realistic output representations using stochastic inference. Furthermore, the proposed schemes in training methods and architecture design were complimentary, which leads to achieve strong pixel-level object segmentation and semantic labeling performance on Caltech-UCSD Birds 200 and the subset of Labeled Faces in the Wild dataset.

Consider estimating an unknown, but structured (e.g. sparse, low-rank, etc.), signal $x_0\in R^n$ from a vector $y\in R^m$ of measurements of the form $y_i=g_i(a_i^Tx_0)$, where the $a_i$'s are the rows of a known measurement matrix $A$, and, $g$ is a (potentially unknown) nonlinear and random link-function. Such measurement functions could arise in applications where the measurement device has nonlinearities and uncertainties. It could also arise by design, e.g., $g_i(x)=sign(x+z_i)$, corresponds to noisy 1-bit quantized measurements. Motivated by the classical work of Brillinger, and more recent work of Plan and Vershynin, we estimate $x_0$ via solving the Generalized-LASSO, i.e., $\hat x=\arg\min_{x}\|y-Ax_0\|_2+\lambda f(x)$ for some regularization parameter $\lambda >0$ and some (typically non-smooth) convex regularizer $f$ that promotes the structure of $x_0$, e.g. $\ell_1$-norm, nuclear-norm. While this approach seems to naively ignore the nonlinear function $g$, both Brillinger and Plan and Vershynin have shown that, when the entries of $A$ are iid standard normal, this is a good estimator of $x_0$ up to a constant of proportionality $\mu$, which only depends on $g$. In this work, we considerably strengthen these results by obtaining explicit expressions for $\|\hat x-\mu x_0\|_2$, for the regularized Generalized-LASSO, that are asymptotically precise when $m$ and $n$ grow large. A main result is that the estimation performance of the Generalized LASSO with non-linear measurements is asymptotically the same as one whose measurements are linear $y_i=\mu a_i^Tx_0+\sigma z_i$, with $\mu=E[\gamma g(\gamma)]$ and $\sigma^2=E[(g(\gamma)-\mu\gamma)^2]$, and, $\gamma$ standard normal. The derived expressions on the estimation performance are the first-known precise results in this context. One interesting consequence of our result is that the optimal quantizer of the measurements that minimizes the estimation error of the LASSO is the celebrated Lloyd-Max quantizer.

Determinantal point processes (DPPs) are point process models thatnaturally encode diversity between the points of agiven realization, through a positive definite kernel $K$. DPPs possess desirable properties, such as exactsampling or analyticity of the moments, but learning the parameters ofkernel $K$ through likelihood-based inference is notstraightforward. First, the kernel that appears in thelikelihood is not $K$, but another kernel $L$ related to $K$ throughan often intractable spectral decomposition. This issue is typically bypassed in machine learning bydirectly parametrizing the kernel $L$, at the price of someinterpretability of the model parameters. We follow this approachhere. Second, the likelihood has an intractable normalizingconstant, which takes the form of large determinant in the case of aDPP over a finite set of objects, and the form of a Fredholm determinant in thecase of a DPP over a continuous domain. Our main contribution is to derive bounds on the likelihood ofa DPP, both for finite and continuous domains. Unlike previous work, our bounds arecheap to evaluate since they do not rely on approximating the spectrumof a large matrix or an operator. Through usual arguments, these bounds thus yield cheap variationalinference and moderately expensive exact Markov chain Monte Carlo inference methods for DPPs.

We propose a novel distribution that generalizes the Multinomial distribution to enable dependencies between dimensions. Our novel distribution is based on the parametric form of the Poisson MRF model [Yang et al., 2012] but is fundamentally different because of the domain restriction to a fixed-length vector like in a Multinomial where the number of trials is fixed or known. Thus, we propose the Fixed-Length Poisson MRF (LPMRF) distribution. We develop methods to estimate the likelihood and log partition function (i.e. the log normalizing constant), which was not developed for the Poisson MRF model. In addition, we propose novel mixture and topic models that use LPMRF as a base distribution and discuss the similarities and differences with previous topic models such as the recently proposed Admixture of Poisson MRFs [Inouye et al., 2014]. We show the effectiveness of our LPMRF distribution over Multinomial models by evaluating the test set perplexity on a dataset of abstracts and Wikipedia. Qualitatively, we show that the positive dependencies discovered by LPMRF are interesting and intuitive. Finally, we show that our algorithms are fast and have good scaling (code available online).

We show that there is a largely unexplored class of functions (positive polymatroids) that can define proper discrete metrics over pairs of binary vectors and that are fairly tractable to optimize over. By exploiting submodularity, we are able to give hardness results and approximation algorithms for optimizing over such metrics. Additionally, we demonstrate empirically the effectiveness of these metrics and associated algorithms on both a metric minimization task (a form of clustering) and also a metric maximization task (generating diverse k-best lists).

Gibbs sampling on factor graphs is a widely used inference technique, which often produces good empirical results. Theoretical guarantees for its performance are weak: even for tree structured graphs, the mixing time of Gibbs may be exponential in the number of variables. To help understand the behavior of Gibbs sampling, we introduce a new (hyper)graph property, called hierarchy width. We show that under suitable conditions on the weights, bounded hierarchy width ensures polynomial mixing time. Our study of hierarchy width is in part motivated by a class of factor graph templates, hierarchical templates, which have bounded hierarchy width—regardless of the data used to instantiate them. We demonstrate a rich application from natural language processing in which Gibbs sampling provably mixes rapidly and achieves accuracy that exceeds human volunteers.

We present two approaches to use unlabeled data to improve Sequence Learning with recurrent networks. The first approach is to predict what comes next in a sequence, which is a language model in NLP. The second approach is to use a sequence autoencoder, which reads the input sequence into a vector and predicts the input sequence again. These two algorithms can be used as a "pretraining" algorithm for a later supervised sequence learning algorithm. In other words, the parameters obtained from the pretraining step can then be used as a starting point for other supervised training models. In our experiments, we find that long short term memory recurrent networks after pretrained with the two approaches become morestable to train and generalize better. With pretraining, we were able to achieve strong performance in many classification tasks, such as text classification with IMDB, DBpedia or image recognition in CIFAR-10.