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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. 

We develop novel methodology for active feature acquisition (AFA), the study of sequentially acquiring a dynamic subset of features that minimizes acquisition costs whilst still yielding accurate inference. The AFA framework can be useful in a myriad of domains, including health care applications where the cost of acquiring additional features for a patient (in terms of time, money, risk, etc.) can be weighed against the expected improvement to diagnostic performance. Previous approaches for AFA have employed either: deep learning RL techniques, which have difficulty training policies due to a complicated state and action space; deep learning surrogate generative models, which require modeling complicated multidimensional conditional distributions; or greedy policies, which cannot account for jointly informative feature acquisitions. We show that we can bypass many of these challenges with a novel, nonparametric oracle based approach, which we coin the acquisition conditioned oracle (ACO). Extensive experiments show the superiority of the ACO to state-of-the-art AFA methods when acquiring features for both predictions and general decision-making. 

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. 

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.