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Deep Learning (DL) methods have dramatically increased in popularity in recent years. While its initial success was demonstrated in the classification and manipulation of image data, there has been significant growth in the application of DL methods to problems in the biomedical sciences. However, the greater prevalence and complexity of missing data in biomedical datasets present significant challenges for DL methods. Here, we provide a formal treatment of missing data in the context of Variational Autoencoders (VAEs), a popular unsupervised DL architecture commonly used for dimension reduction, imputation, and learning latent representations of complex data. We propose a new VAE architecture, NIMIWAE, that is one of the first to flexibly account for both ignorable and non-ignorable patterns of missingness in input features at training time. Following training, samples can be drawn from the approximate posterior distribution of the missing data can be used for multiple imputation, facilitating downstream analyses on high dimensional incomplete datasets. We demonstrate through statistical simulation that our method outperforms existing approaches for unsupervised learning tasks and imputation accuracy. We conclude with a case study of an EHR dataset pertaining to 12,000 ICU patients containing a large number of diagnostic measurements and clinical outcomes, where many features are only partially observed. 

Voice conversion (VC) aims at altering a person's voice to make it sound similar to the voice of another person while preserving linguistic content. Existing methods suffer from a dilemma between content intelligibility and speaker similarity; i.e., methods with higher intelligibility usually have a lower speaker similarity, while methods with higher speaker similarity usually require plenty of target speaker voice data to achieve high intelligibility. In this work, we propose a novel method Phoneme Hallucinator that achieves the best of both worlds. Phoneme Hallucinator is a one-shot VC model; it adopts a novel model to hallucinate diversified and high-fidelity target speaker phonemes based just on a short target speaker voice (e.g. 3 seconds). The hallucinated phonemes are then exploited to perform neighbor-based voice conversion. Our model is a text-free, any-to-any VC model that requires no text annotations and supports conversion to any unseen speaker. Quantitative and qualitative evaluations show that Phoneme Hallucinator outperforms existing VC methods for both intelligibility and speaker similarity. 

Modeling distributions of covariates, or density estimation, is a core challenge in unsupervised learning. However, the majority of work only considers the joint distribution, which has limited utility in practical situations. A more general and useful problem is arbitrary conditional density estimation, which aims to model any possible conditional distribution over a set of covariates, reflecting the more realistic setting of inference based on prior knowledge. We propose a novel method, Arbitrary Conditioning with Energy (ACE), that can simultaneously estimate the distribution p(x_u | x_o) for all possible subsets of unobserved features x_u and observed features x_o. ACE is designed to avoid unnecessary bias and complexity — we specify densities with a highly expressive energy function and reduce the problem to only learning one-dimensional conditionals (from which more complex distributions can be recovered during inference). This results in an approach that is both simpler and higher-performing than prior methods. We show that ACE achieves state-of-the-art for arbitrary conditional likelihood estimation and data imputation on standard benchmarks. 

Neural networks have enabled learning over examples that contain thousands of dimensions. However, most of these models are limited to training and evaluating on a finite collection of points and do not consider the hypervolume in which the data resides. Any analysis of the model’s local or global behavior is therefore limited to very expensive or imprecise estimators. We propose to formulate neural networks as a composition of a bijective (flow) network followed by a learnable, separable network. This construction allows for learning (or assessing) over full hypervolumes with precise estimators at tractable computational cost via integration over the input space. We develop the necessary machinery, propose several practical integrals to use during training, and demonstrate their utility.