Deep generative models have emerged as a powerful class of priors for signals in various inverse problems such as compressed sensing, phase retrieval and super-resolution. Here, we assume an unknown signal to lie in the range of some pre-trained generative model. A popular approach for signal recovery is via gradient descent in the low-dimensional latent space. While gradient descent has achieved good empirical performance, its theoretical behavior is not well understood. In this paper, we introduce the use of stochastic gradient Langevin dynamics (SGLD) for compressed sensing with a generative prior. Under mild assumptions on the generative model, we prove the convergence of SGLD to the true signal. We also demonstrate competitive empirical performance to standard gradient descent.

Purpose: We propose a general framework for quantifying predictive uncertainties of dose-related quantities and leveraging this information in a dose mimicking problem in the context of automated radiation therapy treatment planning. Methods: A three-step pipeline, comprising feature extraction, dose statistic prediction and dose mimicking, is employed. In particular, the features are produced by a convolutional variational autoencoder and used as inputs in a previously developed nonparametric Bayesian statistical method, estimating the multivariate predictive distribution of a collection of predefined dose statistics. Specially developed objective functions are then used to construct a dose mimicking problem based on the produced distributions, creating deliverable treatment plans. Results: The numerical experiments are performed using a dataset of 94 retrospective treatment plans of prostate cancer patients. We show that the features extracted by the variational autoencoder captures geometric information of substantial relevance to the dose statistic prediction problem, that the estimated predictive distributions are reasonable and outperforms a benchmark method, and that the deliverable plans agree well with their clinical counterparts. Conclusions: We demonstrate that prediction of dose-related quantities may be extended to include uncertainty estimation and that such probabilistic information may be leveraged in a dose mimicking problem. The treatment plans produced by the proposed pipeline resemble their original counterparts well, illustrating the merits of a holistic approach to automated planning based on probabilistic modeling.

Due to spurious correlations, machine learning systems often fail to generalize to environments whose distributions differ from the ones used at training time. Prior work addressing this, either explicitly or implicitly, attempted to find a data representation that has an invariant causal relationship with the target. This is done by leveraging a diverse set of training environments to reduce the effect of spurious features and build an invariant predictor. However, these methods have generalization guarantees only when both data representation and classifiers come from a linear model class. We propose Invariant Causal Representation Learning (ICRL), a learning paradigm that enables out-of-distribution (OOD) generalization in the nonlinear setting (i.e., nonlinear representations and nonlinear classifiers). It builds upon a practical and general assumption: the prior over the data representation factorizes when conditioning on the target and the environment. Based on this, we show identifiability of the data representation up to very simple transformations. We also prove that all direct causes of the target can be fully discovered, which further enables us to obtain generalization guarantees in the nonlinear setting. Extensive experiments on both synthetic and real-world datasets show that our approach significantly outperforms a variety of baseline methods. Finally, in the concluding discussion, we further explore the aforementioned assumption and propose a general view, called the Agnostic Hypothesis: there exist a set of hidden causal factors affecting both inputs and outcomes. The Agnostic Hypothesis can provide a unifying view of machine learning in terms of representation learning. More importantly, it can inspire a new direction to explore the general theory for identifying hidden causal factors, which is key to enabling the OOD generalization guarantees in machine learning.

We propose a similarity measure for sparsely sampled time course data in the form of a log-likelihood ratio of Gaussian processes (GP). The proposed GP similarity is similar to a Bayes factor and provides enhanced robustness to noise in sparse time series, such as those found in various biological settings, e.g., gene transcriptomics. We show that the GP measure is equivalent to the Euclidean distance when the noise variance in the GP is negligible compared to the noise variance of the signal. Our numerical experiments on both synthetic and real data show improved performance of the GP similarity when used in conjunction with two distance-based clustering methods.

Multi-class classification problem is among the most popular and well-studied statistical frameworks. Modern multi-class datasets can be extremely ambiguous and single-output predictions fail to deliver satisfactory performance. By allowing predictors to predict a set of label candidates, set-valued classification offers a natural way to deal with this ambiguity. Several formulations of set-valued classification are available in the literature and each of them leads to different prediction strategies. The present survey aims to review popular formulations using a unified statistical framework. The proposed framework encompasses previously considered and leads to new formulations as well as it allows to understand underlying trade-offs of each formulation. We provide infinite sample optimal set-valued classification strategies and review a general plug-in principle to construct data-driven algorithms. The exposition is supported by examples and pointers to both theoretical and practical contributions. Finally, we provide experiments on real-world datasets comparing these approaches in practice and providing general practical guidelines.

We introduce Density sketches (DS): a succinct online summary of the data distribution. DS can accurately estimate point wise probability density. Interestingly, DS also provides a capability to sample unseen novel data from the underlying data distribution. Thus, analogous to popular generative models, DS allows us to succinctly replace the real-data in almost all machine learning pipelines with synthetic examples drawn from the same distribution as the original data. However, unlike generative models, which do not have any statistical guarantees, DS leads to theoretically sound asymptotically converging consistent estimators of the underlying density function. Density sketches also have many appealing properties making them ideal for large-scale distributed applications. DS construction is an online algorithm. The sketches are additive, i.e., the sum of two sketches is the sketch of the combined data. These properties allow data to be collected from distributed sources, compressed into a density sketch, efficiently transmitted in the sketch form to a central server, merged, and re-sampled into a synthetic database for modeling applications. Thus, density sketches can potentially revolutionize how we store, communicate, and distribute data.

This work considers variational Bayesian inference as an inexpensive and scalable alternative to a fully Bayesian approach in the context of sparsity-promoting priors. In particular, the priors considered arise from scale mixtures of Normal distributions with a generalized inverse Gaussian mixing distribution. This includes the variational Bayesian LASSO as an inexpensive and scalable alternative to the Bayesian LASSO introduced in [56]. It also includes priors which more strongly promote sparsity. For linear models the method requires only the iterative solution of deterministic least squares problems. Furthermore, for $n\rightarrow \infty$ data points and p unknown covariates the method can be implemented exactly online with a cost of O(p$^3$) in computation and O(p$^2$) in memory. For large p an approximation is able to achieve promising results for a cost of O(p) in both computation and memory. Strategies for hyper-parameter tuning are also considered. The method is implemented for real and simulated data. It is shown that the performance in terms of variable selection and uncertainty quantification of the variational Bayesian LASSO can be comparable to the Bayesian LASSO for problems which are tractable with that method, and for a fraction of the cost. The present method comfortably handles n = p = 131,073 on a laptop in minutes, and n = 10$^5$, p = 10$^6$ overnight.

Classification with abstention has gained a lot of attention in recent years as it allows to incorporate human decision-makers in the process. Yet, abstention can potentially amplify disparities and lead to discriminatory predictions. The goal of this work is to build a general purpose classification algorithm, which is able to abstain from prediction, while avoiding disparate impact. We formalize this problem as risk minimization under fairness and abstention constraints for which we derive the form of the optimal classifier. Building on this result, we propose a post-processing classification algorithm, which is able to modify any off-the-shelf score-based classifier using only unlabeled sample. We establish finite sample risk, fairness, and abstention guarantees for the proposed algorithm. In particular, it is shown that fairness and abstention constraints can be achieved independently from the initial classifier as long as sufficiently many unlabeled data is available. The risk guarantee is established in terms of the quality of the initial classifier. Our post-processing scheme reduces to a sparse linear program allowing for an efficient implementation, which we provide. Finally, we validate our method empirically showing that moderate abstention rates allow to bypass the risk-fairness trade-off.

Optimal transport is a notoriously difficult problem to solve numerically, with current approaches often remaining intractable for very large scale applications such as those encountered in machine learning. Wasserstein barycenters -- the problem of finding measures in-between given input measures in the optimal transport sense -- is even more computationally demanding as it requires to solve an optimization problem involving optimal transport distances. By training a deep convolutional neural network, we improve by a factor of 60 the computational speed of Wasserstein barycenters over the fastest state-of-the-art approach on the GPU, resulting in milliseconds computational times on $512\times512$ regular grids. We show that our network, trained on Wasserstein barycenters of pairs of measures, generalizes well to the problem of finding Wasserstein barycenters of more than two measures. We demonstrate the efficiency of our approach for computing barycenters of sketches and transferring colors between multiple images.

Deep kernel learning and related techniques promise to combine the representational power of neural networks with the reliable uncertainty estimates of Gaussian processes. One crucial aspect of these models is an expectation that, because they are treated as Gaussian process models optimized using the marginal likelihood, they are protected from overfitting. However, we identify pathological behavior, including overfitting, on a simple toy example. We explore this pathology, explaining its origins and considering how it applies to real datasets. Through careful experimentation on UCI datasets, CIFAR-10, and the UTKFace dataset, we find that the overfitting from overparameterized deep kernel learning, in which the model is "somewhat Bayesian", can in certain scenarios be worse than that from not being Bayesian at all. However, we find that a fully Bayesian treatment of deep kernel learning can rectify this overfitting and obtain the desired performance improvements over standard neural networks and Gaussian processes.