Longitudinal data, which is widely used in many disciplines to study cause and effect, poses significant computational challenges to both modeling and analysis. Longitudinal data is composed of readings on the same variable collected over time and is often high-dimensional with correlated features. The combinatorial search approach for identifying the optimal features is unrealistic for most applications. The alternative approaches, such as heuristics, greedy searches, and regularization techniques, including LASSO, can result in models that suffer from both low accuracy and unclear feature attribution. In this paper, we propose a binary transformation on the data before applying LASSO for feature learning. As demonstrated in the paper, the binary transformation enhances signal in the data, resulting in highly accurate feature attribution, including associated time lags. It avoids the typical shortcomings of the LASSO algorithm, including saturation of the feature space and arbitrary or inconsistent sparse feature selection. Both synthetic data and real-world data sets were used to demonstrate the value of the proposed transformation and in all cases substantial improvements in feature learning were seen. In addition, the scalable parallelism of the solution is superior to that of the standard LASSO since transformation itself occurs in linear time and computing the LASSO solution using the transformed data results in a speedup of almost double.

In an era when big data are becoming the norm, there is less concern with the quantity but more with the quality and completeness of the data. In many disciplines, data are collected from heterogeneous sources, resulting in multi-view or multi-modal datasets. The missing data problem has been challenging to address in multi-view data analysis. Especially, when certain samples miss an entire view of data, it creates the missing view problem. Classic multiple imputations or matrix completion methods are hardly effective here when no information can be based on in the specific view to impute data for such samples. The commonly-used simple method of removing samples with a missing view can dramatically reduce sample size, thus diminishing the statistical power of a subsequent analysis. In this paper, we propose a novel approach for view imputation via generative adversarial networks (GANs), which we name by VIGAN. This approach first treats each view as a separate domain and identifies domain-to-domain mappings via a GAN using randomly-sampled data from each view, and then employs a multi-modal denoising autoencoder (DAE) to reconstruct the missing view from the GAN outputs based on paired data across the views. Then, by optimizing the GAN and DAE jointly, our model enables the knowledge integration for domain mappings and view correspondences to effectively recover the missing view. Empirical results on benchmark datasets validate the VIGAN approach by comparing against the state of the art. The evaluation of VIGAN in a genetic study of substance use disorders further proves the effectiveness and usability of this approach in life science.

Longitudinal analysis is important in many disciplines, such as the study of behavioral transitions in social science. Only very recently, feature selection has drawn adequate attention in the context of longitudinal modeling. Standard techniques, such as generalized estimating equations, have been modified to select features by imposing sparsity-inducing regularizers. However, they do not explicitly model how a dependent variable relies on features measured at proximal time points. Recent graphical Granger modeling can select features in lagged time points but ignores the temporal correlations within an individual's repeated measurements. We propose an approach to automatically and simultaneously determine both the relevant features and the relevant temporal points that impact the current outcome of the dependent variable. Meanwhile, the proposed model takes into account the non-i.i.d nature of the data by estimating the within-individual correlations. This approach decomposes model parameters into a summation of two components and imposes separate block-wise LASSO penalties to each component when building a linear model in terms of the past τ measurements of features. One component is used to select features whereas the other is used to select temporal contingent points. An accelerated gradient descent algorithm is developed to efficiently solve the related optimization problem with detailed convergence analysis and asymptotic analysis. Computational results on both synthetic and real world problems demonstrate the superior performance of the proposed approach over existing techniques.

Identifying genetic variation underlying a complex disease is important. Many complex diseases have heterogeneous phenotypes and are products of a variety of genetic and environmental factors acting in concert. Deriving highly heritable quantitative traits of a complex disease can improve the identification of genetic risk of the disease. The most sophisticated methods so far perform unsupervised cluster analysis on phenotypic features; and then a quantitative trait is derived based on each resultant cluster. Heritability is estimated to assess the validity of the derived quantitative traits. However, none of these methods explicitly maximize the heritability of the derived traits. We propose a quadratic optimization approach that directly utilizes heritability as an objective during the derivation of quantitative traits of a disease. This method maximizes an objective function that is formulated by decomposing the traditional maximum likelihood method for estimating heritability of a quantitative trait. We demonstrate the effectiveness of the proposed method on both synthetic data and real-world problems. We apply our algorithm to identify highly heritable traits of complex human-behavior disorders including opioid and cocaine use disorders, and highly heritable traits of dairy cattle that are economically important. Our approach outperforms standard cluster analysis and several previous methods.

Alcohol misuse is one of the most serious public health problems facing adolescents and young adults in the United States. National statistics shows that nearly 90% of alcohol consumed by youth under 21 years of age involves binge drinking and 44% of college students engage in high-risk drinking activities. Conventional alcohol intervention programs, which aim at installing either an alcohol reduction norm or prohibition against underage drinking, have yielded little progress in controlling college binge drinking over the years. Existing alcohol studies are deductive where data are collected to investigate a psychological/behavioral hypothesis, and statistical analysis is applied to the data to confirm the hypothesis. Due to this confirmatory manner of analysis, the resulting statistical models are cohort-specific and typically fail to replicate on a different sample. This article presents two machine learning approaches for a secondary analysis of longitudinal data collected in college alcohol studies sponsored by the National Institute on Alcohol Abuse and Alcoholism. Our approach aims to discover knowledge, from multiwave cohort-sequential daily data, which may or may not align with the original hypothesis but quantifies predictive models with higher likelihood to generalize to new samples. We first propose a so-called temporally-correlated support vector machine to construct a classifier as a function of daily moods, stress, and drinking expectancies to distinguish days with nighttime binge drinking from days without for individual students. We then propose a combination of cluster analysis and feature selection, where cluster analysis is used to identify drinking patterns based on averaged daily drinking behavior and feature selection is used to identify risk factors associated with each pattern. We evaluate our methods on two cohorts of 530 total college students recruited during the Spring and Fall semesters, respectively. Cross validation on these two cohorts and further on 100 random partitions of the total students demonstrate that our methods improve the model generalizability in comparison with traditional multilevel logistic regression. The discovered risk factors and the interaction of these factors delineated in our models can set a potential basis and offer insights to a new design of more effective college alcohol interventions.