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Register a new userMultiple Imputation for Biomedical Data using Monte Carlo Dropout Autoencoders
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Due to complex experimental settings, missing values are common in biomedical data. To handle this issue, many methods have been proposed, from ignoring incomplete instances to various data imputation approaches. With the recent rise of deep neural networks, the field of missing data imputation has oriented towards modelling of the data distribution. This paper presents an approach based on Monte Carlo dropout within (Variational) Autoencoders which offers not only very good adaptation to the distribution of the data but also allows generation of new data, adapted to each specific instance. The evaluation shows that the imputation error and predictive similarity can be improved with the proposed approach.
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Missing values exist in nearly all clinical studies because data for a variable or question are not collected or not available. Inadequate handling of missing values can lead to biased results and loss of statistical power in analysis. Existing models usually do not consider privacy concerns or do not utilise the inherent correlations across multiple features to impute the missing values. In healthcare applications, we are usually confronted with high dimensional and sometimes small sample size datasets that need more effective augmentation or imputation techniques. Besides, imputation and augmentation processes are traditionally conducted individually. However, imputing missing values and augmenting data can significantly improve generalisation and avoid bias in machine learning models. A Bayesian approach to impute missing values and creating augmented samples in high dimensional healthcare data is proposed in this work. We propose folded Hamiltonian Monte Carlo (F-HMC) with Bayesian inference as a more practical approach to process the cross-dimensional relations by applying a random walk and Hamiltonian dynamics to adapt posterior distribution and generate large-scale samples. The proposed method is applied to a cancer symptom assessment dataset and confirmed to enrich the quality of data in precision, accuracy, recall, F1 score, and propensity metric.
For many analytical problems the challenge is to handle huge amounts of available data. However, there are data science application areas where collecting information is difficult and costly, e.g., in the study of geological phenomena, rare diseases, faults in complex systems, insurance frauds, etc. In many such cases, generators of synthetic data with the same statistical and predictive properties as the actual data allow efficient simulations and development of tools and applications. In this work, we propose the incorporation of Monte Carlo Dropout method within Autoencoder (MCD-AE) and Variational Autoencoder (MCD-VAE) as efficient generators of synthetic data sets. As the Variational Autoencoder (VAE) is one of the most popular generator techniques, we explore its similarities and differences to the proposed methods. We compare the generated data sets with the original data based on statistical properties, structural similarity, and predictive similarity. The results obtained show a strong similarity between the results of VAE, MCD-VAE and MCD-AE; however, the proposed methods are faster and can generate values similar to specific selected initial instances.
We consider the topic of data imputation, a foundational task in machine learning that addresses issues with missing data. To that end, we propose MCFlow, a deep framework for imputation that leverages normalizing flow generative models and Monte Carlo sampling. We address the causality dilemma that arises when training models with incomplete data by introducing an iterative learning scheme which alternately updates the density estimate and the values of the missing entries in the training data. We provide extensive empirical validation of the effectiveness of the proposed method on standard multivariate and image datasets, and benchmark its performance against state-of-the-art alternatives. We demonstrate that MCFlow is superior to competing methods in terms of the quality of the imputed data, as well as with regards to its ability to preserve the semantic structure of the data.
The problem of missing values in multivariable time series is a key challenge in many applications such as clinical data mining. Although many imputation methods show their effectiveness in many applications, few of them are designed to accommodate clinical multivariable time series. In this work, we propose a multiple imputation model that capture both cross-sectional information and temporal correlations. We integrate Gaussian processes with mixture models and introduce individualized mixing weights to handle the variance of predictive confidence of Gaussian process models. The proposed model is compared with several state-of-the-art imputation algorithms on both real-world and synthetic datasets. Experiments show that our best model can provide more accurate imputation than the benchmarks on all of our datasets.
Monte Carlo (MC) dropout is one of the state-of-the-art approaches for uncertainty estimation in neural networks (NNs). It has been interpreted as approximately performing Bayesian inference. Based on previous work on the approximation of Gaussian processes by wide and deep neural networks with random weights, we study the limiting distribution of wide untrained NNs under dropout more rigorously and prove that they as well converge to Gaussian processes for fixed sets of weights and biases. We sketch an argument that this property might also hold for infinitely wide feed-forward networks that are trained with (full-batch) gradient descent. The theory is contrasted by an empirical analysis in which we find correlations and non-Gaussian behaviour for the pre-activations of finite width NNs. We therefore investigate how (strongly) correlated pre-activations can induce non-Gaussian behavior in NNs with strongly correlated weights.
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