MOTIVATION: The human microbiome, which is linked to various diseases by growing evidence, has a profound impact on human health. Since changes in the composition of the microbiome across time are associated with disease and clinical outcomes, microbiome analysis should be performed in a longitudinal study. However, due to limited sample sizes and differing numbers of timepoints for different subjects, a significant amount of data cannot be utilized, directly affecting the quality of analysis results. Deep generative models have been proposed to address this lack of data issue. Specifically, a generative adversarial network (GAN) has been successfully utilized for data augmentation to improve prediction tasks. Recent studies have also shown improved performance of GAN-based models for missing value imputation in a multivariate time series dataset compared with traditional imputation methods. RESULTS: This work proposes DeepMicroGen, a bidirectional recurrent neural network-based GAN model, trained on the temporal relationship between the observations, to impute the missing microbiome samples in longitudinal studies. DeepMicroGen outperforms standard baseline imputation methods, showing the lowest mean absolute error for both simulated and real datasets. Finally, the proposed model improved the predicted clinical outcome for allergies, by providing imputation for an incomplete longitudinal dataset used to train the classifier. AVAILABILITY AND IMPLEMENTATION: DeepMicroGen is publicly available at https://github.com/joungmin-choi/DeepMicroGen.

Ying Liab, Fangzhou Youc, Ming Jiab* & Xuqun Youab*a School of Psychology, Shaanxi Normal University, Xi’an, Chinab Shaanxi Provincial Key Laboratory of Behavior and Cognitive Neuroscience, Shannxi Normal University, Xi’an, Chinac Design School, Loughborough University, Loughborough, UKYing Li received her M.S. degrees in Applied Psychology from Shaanxi Normal University, Xi’an. She is studying for Ph. D. degree in Aviation Psychology from Shaanxi Normal University. She has worked in the areas of human factors and ergonomics, human errors, safety operation behavior, and safety culture.Fangzhou You received her M.S. degrees in Interactive Design from Tongji University, Shanghai. She is studying for Ph. D. degree in Design School from Loughborough University, United Kingdom. She has worked in the areas of human factors and ergonomics, design, and safety culture.Ming Ji is an associate professor at Shaanxi Normal University, a member of the Engineering Psychology Branch of the Chinese Psychological Association. He has published more than 20 academic papers of aviation safety and pilots’ human errors and discussed the mechanism of pilots’ human errors.Xuqun You is currently a professor at Shaanxi Normal University, responsible for the first-level discipline of psychology, the head of the national teaching team, and the head of the national-level specialty. He has presided more than 20 research projects and he has published more than 100 academic papers.CONTACT Ming Ji [email protected] You [email protected] Chang ’an South Road, Yanta District, Xi’an, Shaanxi, China.ABSTRACTText input on smartphones plays an increasingly important role in people’s daily lives. This study aims to explore the impact of posture and environment on the user experience of smartphone input methods. A combination of performance, subjective, and physiological measures is used to assess the user experience of 32 subjects (12 male, 20 female; 18–26 years old) using QWERTY and T9 input methods in walking and sitting postures in indoor and outdoor environments. The results showed that T9 was more effective for indoors and when sitting than QWERTY, while QWERTY was more effective than T9 for outdoors and when walking. In our tests, using T9 indoors while sitting showed a significantly higher performance than QWERTY, while using QWERTY outdoors while walking elicited significantly lower emotional arousal than T9. The findings allow us to propose both the optimal contexts in which to use particular input methods, and to highlight new approaches for improving the user experience of these devices.

We describe an efficient gradient computation for solving inverse problems arising in magnetic resonance elastography (MRE). The algorithm can be considered as a generalized 'adjoint method' based on a Lagrangian formulation. One requirement for the classic adjoint method is assurance of the self-adjoint property of the stiffness matrix in the elasticity problem. In this paper, we show this property is no longer a necessary condition in our algorithm, but the computational performance can be as efficient as the classic method, which involves only two forward solutions and is independent of the number of parameters to be estimated. The algorithm is developed and implemented in material property reconstructions using poroelastic and viscoelastic modeling. Various gradient- and Hessian-based optimization techniques have been tested on simulation, phantom and in vivo brain data. The numerical results show the feasibility and the efficiency of the proposed scheme for gradient calculation.

In typical studies of node grouping detection, the grouping is presumed to have a certain type of correlation with the network structure (e.g., densely connected groups of nodes that are loosely connected in between). People have defined different fitness measures (modularity, conductance, etc.) to quantify such correlation, and group the nodes by optimizing a certain fitness measure. However, a particular grouping with desired semantics, as the target of the detection, is not promised to be detectable by each measure. We study a fundamental problem in the process of node grouping discovery: Given a particular grouping in a network, whether and to what extent it can be discovered with a given fitness measure. We propose two approaches of testing the detectability, namely ranking-based and correlation-based randomization tests. Our methods are evaluated on both synthetic and real datasets, which shows the proposed methods can effectively predict the detectability of groupings of various types, and support explorative process of node grouping discovery.

Recently, ranking data with respect to the intrinsic geometric structure (manifold ranking) has received considerable attentions, with encouraging performance in many applications in pattern recognition, information retrieval and recommendation systems. Most of the existing manifold ranking methods focus on learning a ranking function that varies smoothly along the data manifold. However, beyond smoothness, a desirable ranking function should vary monotonically along the geodesics of the data manifold, such that the ranking order along the geodesics is preserved. In this article, we aim to learn a ranking function that varies linearly and therefore monotonically along the geodesics of the data manifold. Recent theoretical work shows that the gradient field of a linear function on the manifold has to be a parallel vector field. Therefore, we propose a novel ranking algorithm on the data manifolds, called Parallel Field Ranking. Specifically, we try to learn a ranking function and a vector field simultaneously. We require the vector field to be close to the gradient field of the ranking function, and the vector field to be as parallel as possible. Moreover, we require the value of the ranking function at the query point to be the highest, and then decrease linearly along the manifold. Experimental results on both synthetic data and real data demonstrate the effectiveness of our proposed algorithm.

Recently, ranking data with respect to the intrinsic geometric structure (manifold ranking) has received considerable attentions, with encouraging performance in many applications in pattern recognition, information retrieval and recommendation systems. Most of the existing manifold ranking methods focus on learning a ranking function that varies smoothly along the data manifold. However, beyond smoothness, a desirable ranking function should vary monotonically along the geodesics of the data manifold, such that the ranking order along the geodesics is preserved. In this paper, we aim to learn a ranking function that varies linearly and therefore monotonically along the geodesics of the data manifold. Recent theoretical work shows that the gradient field of a linear function on the manifold has to be a parallel vector field. Therefore, we propose a novel ranking algorithm on the data manifolds, called Parallel Field Ranking. Specifically, we try to learn a ranking function and a vector field simultaneously. We require the vector field to be close to the gradient field of the ranking function, and the vector field to be as parallel as possible. Moreover, we require the value of the ranking function at the query point to be the highest, and then decrease linearly along the manifold. Experimental results on both synthetic data and real data demonstrate the effectiveness of our proposed algorithm.

It has been recently recognized that heterogeneous information networks composed of multiple types of nodes and links are prevalent in the real world. Both classification and ranking of the nodes (or data objects) in such networks are essential for network analysis. However, so far these approaches have generally been performed separately. In this paper, we combine ranking and classification in order to perform more accurate analysis of a heterogeneous information network. Our intuition is that highly ranked objects within a class should play more important roles in classification. On the other hand, class membership information is important for determining a quality ranking over a dataset. We believe it is therefore beneficial to integrate classification and ranking in a simultaneous, mutually enhancing process, and to this end, propose a novel ranking-based iterative classification framework, called RankClass. Specifically, we build a graph-based ranking model to iteratively compute the ranking distribution of the objects within each class. At each iteration, according to the current ranking results, the graph structure used in the ranking algorithm is adjusted so that the sub-network corresponding to the specific class is emphasized, while the rest of the network is weakened. As our experiments show, integrating ranking with classification not only generates more accurate classes than the state-of-art classification methods on networked data, but also provides meaningful ranking of objects within each class, serving as a more informative view of the data than traditional classification.

As the Internet grows explosively, search engines play a more and more important role for users in effectively accessing online information. Recently, it has been recognized that a query is often triggered by a search task that the user wants to accomplish. Similarly, many web pages are specifically designed to help accomplish a certain task. Therefore, learning hidden tasks behind queries and web pages can help search engines return the most useful web pages to users by task matching. For instance, the search task that triggers query "thinkpad T410 broken" is to maintain a computer, and it is desirable for a search engine to return the Lenovo troubleshooting page on the top of the list. However, existing search engine technologies mainly focus on topic detection or relevance ranking, which are not able to predict the task that triggers a query and the task a web page can accomplish.

In many information processing tasks, one is often confronted with very high-dimensional data. Feature selection techniques are designed to find the meaningful feature subset of the original features which can facilitate clustering, classification, and retrieval. In this paper, we consider the feature selection problem in unsupervised learning scenarios, which is particularly difficult due to the absence of class labels that would guide the search for relevant information. Based on Laplacian regularized least squares, which finds a smooth function on the data manifold and minimizes the empirical loss, we propose two novel feature selection algorithms which aim to minimize the expected prediction error of the regularized regression model. Specifically, we select those features such that the size of the parameter covariance matrix of the regularized regression model is minimized. Motivated from experimental design, we use trace and determinant operators to measure the size of the covariance matrix. Efficient computational schemes are also introduced to solve the corresponding optimization problems. Extensive experimental results over various real-life data sets have demonstrated the superiority of the proposed algorithms.

With the maturity and wide availability of GPS, wireless, telecommunication, and Web technologies, massive amounts of object movement data have been collected from various moving object targets, such as animals, mobile devices, vehicles, and climate radars. Analyzing such data has deep implications in many applications, such as, ecological study, traffic control, mobile communication management, and climatological forecast. In this article, we focus our study on animal movement data analysis and examine advanced data mining methods for discovery of various animal movement patterns. In particular, we introduce a moving object data mining system, MoveMine, which integrates multiple data mining functions, including sophisticated pattern mining and trajectory analysis. In this system, two interesting moving object pattern mining functions are newly developed: (1) periodic behavior mining and (2) swarm pattern mining . For mining periodic behaviors, a reference location-based method is developed, which first detects the reference locations, discovers the periods in complex movements, and then finds periodic patterns by hierarchical clustering. For mining swarm patterns, an efficient method is developed to uncover flexible moving object clusters by relaxing the popularly-enforced collective movement constraints. In the MoveMine system, a set of commonly used moving object mining functions are built and a user-friendly interface is provided to facilitate interactive exploration of moving object data mining and flexible tuning of the mining constraints and parameters. MoveMine has been tested on multiple kinds of real datasets, especially for MoveBank applications and other moving object data analysis. The system will benefit scientists and other users to carry out versatile analysis tasks to analyze object movement regularities and anomalies. Moreover, it will benefit researchers to realize the importance and limitations of current techniques and promote future studies on moving object data mining. As expected, a mastery of animal movement patterns and trends will improve our understanding of the interactions between and the changes of the animal world and the ecosystem and therefore help ensure the sustainability of our ecosystem.

With the maturity of GPS, wireless, and Web technologies, increasing amounts of movement data collected from various moving objects, such as animals, vehicles, mobile devices, and climate radars, have become widely available. Analyzing such data has broad applications, e.g., in ecological study, vehicle control, mobile communication management, and climatological forecast. However, few data mining tools are available for flexible and scalable analysis of massive-scale moving object data. Our system, MoveMine, is designed for sophisticated moving object data mining by integrating several attractive functions including moving object pattern mining and trajectory mining. We explore the state-of-the-art and novel techniques at implementation of the selected functions. A user-friendly interface is provided to facilitate interactive exploration of mining results and flexible tuning of the underlying methods. Since MoveMine is tested on multiple kinds of real data sets, it will benefit users to carry out versatile analysis on these kinds of data. At the same time, it will benefit researchers to realize the importance and limitations of current techniques as well as the potential future studies in moving object data mining.

We consider the problem of lossy image compression from machine learning perspective. Typical image compression algorithms first transform the image from its spatial domain representation to frequency domain representation using some transform technique, such as discrete cosine transform and discrete wavelet transform, and then code the transformed values. Recently, instead of performing a frequency transformation, machine learning based approach has been proposed which uses the color information from a few representative pixels to learn a model which predicts color on the rest of the pixels. Selecting the most representative pixels is essentially an active learning problem, while colorization is a semi-supervised learning problem. In this paper, we propose a novel active learning algorithm, called graph regularized experimental design (GRED), which shares the same principle of the semi-supervised learning algorithm used for colorization. This way, active and semi-supervised learning is unified into a single framework for pixel selection and colorization. Our experimental results suggest that the proposed approach achieves higher compression ratio and image quality, while the compression time is significantly reduced.

This paper studies a variation of a simple step-stress life testing in which the stress change time is random, and the test is subject to type II censoring. We assume that only two order statistics from the test are observed. The first observed order statistic is the stress change time from a low level stress to a high level stress during the testing, and the second observed order statistic is the final failure time when the test is censored. We first present the joint probability distribution of the two order statistics observed from the simple step-stress accelerated life test. Maximum likelihood estimates, and the method of moment estimates for model parameters based on the joint distribution are considered. We also present the exact confidence interval estimates for the model parameters based on various pivotal quantities, and demonstrate the estimation procedure by a simulated example.

Current digital rights management systems employ proprietary methods to protect contents. Hence, they are incapable of interoperation with each other. This causes great inconvenience for users who want to subscribe to contents from different providers. We introduce a new, intellectual property management & protection method (IPMP extension), which enables users to enjoy content services delivered from different providers which are based on individual content protection mechanisms. The method is proposed to ISO/IEC JTC1/SC29/WG11 (MPEG) and the standardization is in the final stage. IPMP is also proposed to DVB-CPT (digital video broadcasting-copy protection technologies). TV Anytime Forum ISMA (Internet Streaming Media Alliance) have adopted IPMP in the ISMA1.0 Encryption & Authentication specification.

This paper studies statistical analysis of grouped and censored data obtained from a step-stress accelerated life test. We assume that the stress change times in the step-stress life test are fixed and the lifetimes observed are type I censored. Maximum likelihood estimates and asymptotic confidence intervals for model parameters are obtained. We provide an asymptotic statistical test for the cumulative exposure model based on the grouped and type I censored data. We also present the optimum test plan for a simple step-stress test when the lifetime under constant stress is assumed exponential. Finally we give an application of our methods by applying our analysis process to a real life data set. The proposed statistical methodology is especially useful when intermittent inspection is the only feasible way of checking the status of test units during a step-stress test.