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Register a new userA Hamiltonian Monte Carlo Model for Imputation and Augmentation of Healthcare Data
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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.
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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.
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.
Today, there are two major understandings for graph convolutional networks, i.e., in the spectral and spatial domain. But both lack transparency. In this work, we introduce a new understanding for it -- data augmentation, which is more transparent than the previous understandings. Inspired by it, we propose a new graph learning paradigm -- Monte Carlo Graph Learning (MCGL). The core idea of MCGL contains: (1) Data augmentation: propagate the labels of the training set through the graph structure and expand the training set; (2) Model training: use the expanded training set to train traditional classifiers. We use synthetic datasets to compare the strengths of MCGL and graph convolutional operation on clean graphs. In addition, we show that MCGLs tolerance to graph structure noise is weaker than GCN on noisy graphs (four real-world datasets). Moreover, inspired by MCGL, we re-analyze the reasons why the performance of GCN becomes worse when deepened too much: rather than the mainstream view of over-smoothing, we argue that the main reason is the graph structure noise, and experimentally verify our view. The code is available at https://github.com/DongHande/MCGL.
The Hamiltonian Monte Carlo (HMC) sampling algorithm exploits Hamiltonian dynamics to construct efficient Markov Chain Monte Carlo (MCMC), which has become increasingly popular in machine learning and statistics. Since HMC uses the gradient information of the target distribution, it can explore the state space much more efficiently than the random-walk proposals. However, probabilistic inference involving multi-modal distributions is very difficult for standard HMC method, especially when the modes are far away from each other. Sampling algorithms are then often incapable of traveling across the places of low probability. In this paper, we propose a novel MCMC algorithm which aims to sample from multi-modal distributions effectively. The method improves Hamiltonian dynamics to reduce the autocorrelation of the samples and uses a variational distribution to explore the phase space and find new modes. A formal proof is provided which shows that the proposed method can converge to target distributions. Both synthetic and real datasets are used to evaluate its properties and performance. The experimental results verify the theory and show superior performance in multi-modal sampling.
Probabilistic programming uses programs to express generative models whose posterior probability is then computed by built-in inference engines. A challenging goal is to develop general purpose inference algorithms that work out-of-the-box for arbitrary programs in a universal probabilistic programming language (PPL). The densities defined by such programs, which may use stochastic branching and recursion, are (in general) nonparametric, in the sense that they correspond to models on an infinite-dimensional parameter space. However standard inference algorithms, such as the Hamiltonian Monte Carlo (HMC) algorithm, target distributions with a fixed number of parameters. This paper introduces the Nonparametric Hamiltonian Monte Carlo (NP-HMC) algorithm which generalises HMC to nonparametric models. Inputs to NP-HMC are a new class of measurable functions called tree representable, which serve as a language-independent representation of the density functions of probabilistic programs in a universal PPL. We provide a correctness proof of NP-HMC, and empirically demonstrate significant performance improvements over existing approaches on several nonparametric examples.
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