Models of disease progression are instrumental forpredictingpatient outcomes and understandingdisease dynamics. Existing models provide the patient with pragmatic (supervised) predictions of risk, but do not provide the clinician with intelligible (unsupervised) representations ofdiseasepathology.

Data hiding with deep neural networks (DNNs) has experienced impressive successes in recent years. A prevailing scheme is to train an autoencoder, consisting of an encoding network to embed (or transform) secret messages in (or into) a carrier, and a decoding network to extract the hidden messages. This scheme may suffer from several limitations regarding practicability, security, and embedding capacity. In this work, we describe a different computational framework to hide images in deep probabilistic models. Specifically, we use a DNN to model the probability density of cover images, and hide a secret image in one particular location of the learned distribution.

Data hiding with deep neural networks (DNNs) has experienced impressive successes in recent years. A prevailing scheme is to train an autoencoder, consisting of an encoding network to embed (or transform) secret messages in (or into) a carrier, and a decoding network to extract the hidden messages. This scheme may suffer from several limitations regarding practicability, security, and embedding capacity. In this work, we describe a different computational framework to hide images in deep probabilistic models. Specifically, we use a DNN to model the probability density of cover images, and hide a secret image in one particular location of the learned distribution.

Motivated by deep neural networks, the deep Gaussian process (DGP) generalizes the standard GP by stacking multiple layers of GPs. Despite the enhanced expressiveness, GP, as an $L_2$ regularization prior, tends to be over-smooth and sub-optimal for inhomogeneous subjects, such as images with edges. Recently, Q-exponential process (Q-EP) has been proposed as an $L_q$ relaxation to GP and demonstrated with more desirable regularization properties through a parameter $q>0$ with $q=2$ corresponding to GP. Sharing the similar tractability of posterior and predictive distributions with GP, Q-EP can also be stacked to improve its modeling flexibility. In this paper, we generalize Q-EP to deep Q-EP to enjoy both proper regularization and improved expressiveness. The generalization is realized by introducing shallow Q-EP as a latent variable model and then building a hierarchy of the shallow Q-EP layers. Sparse approximation by inducing points and scalable variational strategy are applied to facilitate the inference. We demonstrate the numerical advantages of the proposed deep Q-EP model by comparing with multiple state-of-the-art deep probabilistic models.

The process of identifying a compound from its mass spectrum is a critical step in the analysis of complex mixtures. Typical solutions for the mass spectrum to compound (MS2C) problem involve matching the unknown spectrum against a library of known spectrum-molecule pairs, an approach that is limited by incomplete library coverage. Compound to mass spectrum (C2MS) models can improve retrieval rates by augmenting real libraries with predicted spectra. Unfortunately, many existing C2MS models suffer from problems with prediction resolution, scalability, or interpretability. We develop a new probabilistic method for C2MS prediction, FraGNNet, that can efficiently and accurately predict high-resolution spectra. FraGNNet uses a structured latent space to provide insight into the underlying processes that define the spectrum. Our model achieves state-of-the-art performance in terms of prediction error, and surpasses existing C2MS models as a tool for retrieval-based MS2C.

Figure 1: Overview of a local variational layer (left) and an attentive variational layer (right) proposed in this post. Attention blocks in the variational layer are responsible for capturing long-range statistical dependencies in the latent space of the hierarchy. Generative models are a class of machine learning models that are able to generate novel data samples such as fictional celebrity faces, digital artwork, and scenic images. Currently, the most powerful generative models are deep probabilistic models. This class of models uses deep neural networks to express statistical hypotheses about the data generation process, and combine them with latent variable models to augment the set of observed data with latent (unobserved) information in order to better characterize the procedure that generates the data of interest.

Probabilistic deep learning is deep learning that accounts for uncertainty, both model uncertainty and data uncertainty. It is based on the use of probabilistic models and deep neural networks. We distinguish two approaches to probabilistic deep learning: probabilistic neural networks and deep probabilistic models. The former employs deep neural networks that utilize probabilistic layers which can represent and process uncertainty; the latter uses probabilistic models that incorporate deep neural network components which capture complex non-linear stochastic relationships between the random variables. We discuss some major examples of each approach including Bayesian neural networks and mixture density networks (for probabilistic neural networks), and variational autoencoders, deep Gaussian processes and deep mixed effects models (for deep probabilistic models). TensorFlow Probability is a library for probabilistic modeling and inference which can be used for both approaches of probabilistic deep learning. We include its code examples for illustration.

Data poisoning attacks compromise the integrity of machine-learning models by introducing malicious training samples to influence the results during test time. In this work, we investigate backdoor data poisoning attack on deep neural networks (DNNs) by inserting a backdoor pattern in the training images. The resulting attack will misclassify poisoned test samples while maintaining high accuracies for the clean test-set. We present two approaches for detection of such poisoned samples by quantifying the uncertainty estimates associated with the trained models. In the first approach, we model the outputs of the various layers (deep features) with parametric probability distributions learnt from the clean held-out dataset. At inference, the likelihoods of deep features w.r.t these distributions are calculated to derive uncertainty estimates. In the second approach, we use Bayesian deep neural networks trained with mean-field variational inference to estimate model uncertainty associated with the predictions. The uncertainty estimates from these methods are used to discriminate clean from the poisoned samples.

Probabilistic models are a critical part of the modern deep learning toolbox - ranging fromgenerative models (VAEs, GANs), sequence to sequence models used in machine translation and speech processing to models over functional spaces (conditional neuralprocesses, neural processes). Given the size and complexity of these models, safely deploying them in applications requires the development of tools to analyze their behavior rigorously and provide some guarantees that these models are consistent with a list of desirable properties or specifications. For example, a machine translation model should produce semantically equivalent outputs for innocuous changes in the input to the model. A functional regression model that is learning a distribution over monotonic functions should predict a larger value at a larger input. Verification of these properties requires a new framework that goes beyond notions of verification studied in deterministic feedforward networks, since requiring worst-case guarantees in probabilistic models is likely to produce conservative orvacuous results. We propose a novel formulation of verification for deep probabilistic models that take in conditioning inputs and sample latent variables in the course of producing an output: We require that the output of the model satisfies a linear constraint with high probability over the sampling of latent variables and for every choice of conditioning input to the model. We show that rigorous lower bounds on the probability that the constraint is satisfied can be obtained efficiently. Experiments with neural processes show that several properties of interest while modeling functional spaces can be modeled within this framework (monotonicity, convexity) and verified efficiently using our algorithms.

Deep probabilistic programming combines deep neural networks (for automatic hierarchical representation learning) with probabilistic models (for principled handling of uncertainty). Unfortunately, it is difficult to write deep probabilistic models, because existing programming frameworks lack concise, high-level, and clean ways to express them. To ease this task, we extend Stan, a popular high-level probabilistic programming language, to use deep neural networks written in PyTorch. Training deep probabilistic models works best with variational inference, so we also extend Stan for that. We implement these extensions by translating Stan programs to Pyro. Our translation clarifies the relationship between different families of probabilistic programming languages. Overall, our paper is a step towards making deep probabilistic programming easier.