An explosion of high-throughput DNA sequencing in the past decade has led to a surge of interest in population-scale inference with whole-genome data. Recent work in population genetics has centered on designing inference methods for relatively simple model classes, and few scalable general-purpose inference techniques exist for more realistic, complex models. To achieve this, two inferential challenges need to be addressed: (1) population data are exchangeable, calling for methods that efficiently exploit the symmetries of the data, and (2) computing likelihoods is intractable as it requires integrating over a set of correlated, extremely high-dimensional latent variables. These challenges are traditionally tackled by likelihood-free methods that use scientific simulators to generate datasets and reduce them to hand-designed, permutation-invariant summary statistics, often leading to inaccurate inference. In this work, we develop an exchangeable neural network that performs summary statistic-free, likelihood-free inference. Our framework can be applied in a black-box fashion across a variety of simulation-based tasks, both within and outside biology. We demonstrate the power of our approach on the recombination hotspot testing problem, outperforming the state-of-the-art.

Recent attempts to achieve fairness in predictive models focus on the balance between fairness and accuracy. In sensitive applications such as healthcare or criminal justice, this trade-off is often undesirable as any increase in prediction error could have devastating consequences. In this work, we argue that the fairness of predictions should be evaluated in context of the data, and that unfairness induced by inadequate samples sizes or unmeasured predictive variables should be addressed through data collection, rather than by constraining the model. We decompose cost-based metrics of discrimination into bias, variance, and noise, and propose actions aimed at estimating and reducing each term. Finally, we perform case-studies on prediction of income, mortality, and review ratings, confirming the value of this analysis. We find that data collection is often a means to reduce discrimination without sacrificing accuracy.

Distributed implementations of mini-batch stochastic gradient descent (SGD) suffer from communication overheads, attributed to the high frequency of gradient updates inherent in small-batch training. Training with large batches can reduce these overheads; however it besets the convergence of the algorithm and the generalization performance. In this work, we take a first step towards analyzing how the structure (width and depth) of a neural network affects the performance of large-batch training. We present new theoretical results which suggest that--for a fixed number of parameters--wider networks are more amenable to fast large-batch training compared to deeper ones. We provide extensive experiments on residual and fully-connected neural networks which suggest that wider networks can be trained using larger batches without incurring a convergence slow-down, unlike their deeper variants.

Variational Auto-Encoders (VAE) have become very popular techniques to perform inference and learning in latent variable models as they allow us to leverage the rich representational power of neural networks to obtain flexible approximations of the posterior of latent variables as well as tight evidence lower bounds (ELBO). Com- bined with stochastic variational inference, this provides a methodology scaling to large datasets. However, for this methodology to be practically efficient, it is neces- sary to obtain low-variance unbiased estimators of the ELBO and its gradients with respect to the parameters of interest. While the use of Markov chain Monte Carlo (MCMC) techniques such as Hamiltonian Monte Carlo (HMC) has been previously suggested to achieve this [23, 26], the proposed methods require specifying reverse kernels which have a large impact on performance. Additionally, the resulting unbiased estimator of the ELBO for most MCMC kernels is typically not amenable to the reparameterization trick. We show here how to optimally select reverse kernels in this setting and, by building upon Hamiltonian Importance Sampling (HIS) [17], we obtain a scheme that provides low-variance unbiased estimators of the ELBO and its gradients using the reparameterization trick. This allows us to develop a Hamiltonian Variational Auto-Encoder (HVAE). This method can be re-interpreted as a target-informed normalizing flow [20] which, within our context, only requires a few evaluations of the gradient of the sampled likelihood and trivial Jacobian calculations at each iteration.

In theory, importance sampling speeds up stochastic gradient algorithms for supervised learning by prioritizing training examples. In practice, the cost of computing importances greatly limits the impact of importance sampling. We propose a robust, approximate importance sampling procedure (RAIS) for stochastic gradient de- scent. By approximating the ideal sampling distribution using robust optimization, RAIS provides much of the benefit of exact importance sampling with drastically reduced overhead. Empirically, we find RAIS-SGD and standard SGD follow similar learning curves, but RAIS moves faster through these paths, achieving speed-ups of at least 20% and sometimes much more.

Stochastic gradient descent (SGD) remains the method of choice for deep learning, despite the limitations arising for ill-behaved objective functions. In cases where it could be estimated, the natural gradient has proven very effective at mitigating the catastrophic effects of pathological curvature in the objective function, but little is known theoretically about its convergence properties, and it has yet to find a practical implementation that would scale to very deep and large networks. Here, we derive an exact expression for the natural gradient in deep linear networks, which exhibit pathological curvature similar to the nonlinear case. We provide for the first time an analytical solution for its convergence rate, showing that the loss decreases exponentially to the global minimum in parameter space. Our expression for the natural gradient is surprisingly simple, computationally tractable, and explains why some approximations proposed previously work well in practice. This opens new avenues for approximating the natural gradient in the nonlinear case, and we show in preliminary experiments that our online natural gradient descent outperforms SGD on MNIST autoencoding while sharing its computational simplicity.

Although the recent progress is substantial, deep learning methods can be vulnerable to the maliciously generated adversarial examples. In this paper, we present a novel training procedure and a thresholding test strategy, towards robust detection of adversarial examples. In training, we propose to minimize the reverse cross-entropy (RCE), which encourages a deep network to learn latent representations that better distinguish adversarial examples from normal ones. In testing, we propose to use a thresholding strategy as the detector to filter out adversarial examples for reliable predictions. Our method is simple to implement using standard algorithms, with little extra training cost compared to the common cross-entropy minimization. We apply our method to defend various attacking methods on the widely used MNIST and CIFAR-10 datasets, and achieve significant improvements on robust predictions under all the threat models in the adversarial setting.

We consider the semi-supervised clustering problem where crowdsourcing provides noisy information about the pairwise comparisons on a small subset of data, i.e., whether a sample pair is in the same cluster. We propose a new approach that includes a deep generative model (DGM) to characterize low-level features of the data, and a statistical relational model for noisy pairwise annotations on its subset. The two parts share the latent variables. To make the model automatically trade-off between its complexity and fitting data, we also develop its fully Bayesian variant. The challenge of inference is addressed by fast (natural-gradient) stochastic variational inference algorithms, where we effectively combine variational message passing for the relational part and amortized learning of the DGM under a unified framework. Empirical results on synthetic and real-world datasets show that our model outperforms previous crowdsourced clustering methods.

Learning to classify new categories based on just one or a few examples is a long-standing challenge in modern computer vision. In this work, we propose a simple yet effective method for few-shot (and one-shot) object recognition. Our approach is based on a modified auto-encoder, denoted delta-encoder, that learns to synthesize new samples for an unseen category just by seeing few examples from it. The synthesized samples are then used to train a classifier. The proposed approach learns to both extract transferable intra-class deformations, or "deltas", between same-class pairs of training examples, and to apply those deltas to the few provided examples of a novel class (unseen during training) in order to efficiently synthesize samples from that new class. The proposed method improves the state-of-the-art of one-shot object-recognition and performs comparably in the few-shot case.

We consider a high dimensional linear regression problem where the goal is to efficiently recover an unknown vector \beta^* from n noisy linear observations Y=X \beta^*+W in R^n, for known X in R^{n \times p} and unknown W in R^n. Unlike most of the literature on this model we make no sparsity assumption on \beta^*. Instead we adopt a regularization based on assuming that the underlying vectors \beta^* have rational entries with the same denominator Q. We call this Q-rationality assumption. We propose a new polynomial-time algorithm for this task which is based on the seminal Lenstra-Lenstra-Lovasz (LLL) lattice basis reduction algorithm. We establish that under the Q-rationality assumption, our algorithm recovers exactly the vector \beta^* for a large class of distributions for the iid entries of X and non-zero noise W. We prove that it is successful under small noise, even when the learner has access to only one observation (n=1). Furthermore, we prove that in the case of the Gaussian white noise for W, n=o(p/\log p) and Q sufficiently large, our algorithm tolerates a nearly optimal information-theoretic level of the noise.