MildInt: Deep Learning-Based Multimodal Longitudinal Data Integration Framework

As large amounts of heterogeneous biomedical data become available, numerous methods for integrating such datasets have been developed to extract complementary knowledge from multiple domains of sources. Recently, a deep learning approach has shown promising results in a variety of research areas. However, applying the deep learning approach requires expertise for constructing a deep architecture that can take multimodal longitudinal data. Thus, in this paper, a deep learning-based python package for data integration is developed. The python package deep learning-based multimodal longitudinal data integration framework (MildInt) provides the preconstructed deep learning architecture for a classification task. MildInt contains two learning phases: learning feature representation from each modality of data and training a classifier for the final decision. Adopting deep architecture in the first phase leads to learning more task-relevant feature representation than a linear model. In the second phase, linear regression classifier is used for detecting and investigating biomarkers from multimodal data. Thus, by combining the linear model and the deep learning model, higher accuracy and better interpretability can be achieved. We validated the performance of our package using simulation data and real data. For the real data, as a pilot study, we used clinical and multimodal neuroimaging datasets in Alzheimer's disease to predict the disease progression. MildInt is capable of integrating multiple forms of numerical data including time series and non-time series data for extracting complementary features from the multimodal dataset

Predicting Alzheimer’s disease progression using multi-modal deep learning approach

Alzheimer’s disease (AD) is a progressive neurodegenerative condition marked by a decline in cognitive functions with no validated disease modifying treatment. It is critical for timely treatment to detect AD in its earlier stage before clinical manifestation. Mild cognitive impairment (MCI) is an intermediate stage between cognitively normal older adults and AD. To predict conversion from MCI to probable AD, we applied a deep learning approach, multimodal recurrent neural network. We developed an integrative framework that combines not only cross-sectional neuroimaging biomarkers at baseline but also longitudinal cerebrospinal fluid (CSF) and cognitive performance biomarkers obtained from the Alzheimer’s Disease Neuroimaging Initiative cohort (ADNI). The proposed framework integrated longitudinal multi-domain data. Our results showed that 1) our prediction model for MCI conversion to AD yielded up to 75% accuracy (area under the curve (AUC) = 0.83) when using only single modality of data separately; and 2) our prediction model achieved the best performance with 81% accuracy (AUC = 0.86) when incorporating longitudinal multi-domain data. A multi-modal deep learning approach has potential to identify persons at risk of developing AD who might benefit most from a clinical trial or as a stratification approach within clinical trials

Biological Brain Age Prediction Using Cortical Thickness Data: A Large Scale Cohort Study

Brain age estimation from anatomical features has been attracting more attention in recent years. This interest in brain age estimation is motivated by the importance of biological age prediction in health informatics, with an application to early prediction of neurocognitive disorders. It is well-known that normal brain aging follows a specific pattern, which enables researchers and practitioners to predict the age of a human's brain from its degeneration. In this paper, we model brain age predicted by cortical thickness data gathered from large cohort brain images. We collected 2,911 cognitively normal subjects (age 45–91 years) at a single medical center and acquired their brain magnetic resonance (MR) images. All images were acquired using the same scanner with the same protocol. We propose to first apply Sparse Group Lasso (SGL) for feature selection by utilizing the brain's anatomical grouping. Once the features are selected, a non-parametric non-linear regression using the Gaussian Process Regression (GPR) algorithm is applied to fit the final age prediction model. Experimental results demonstrate that the proposed method achieves the mean absolute error of 4.05 years, which is comparable with or superior to several recent methods. Our method can also be a critical tool for clinicians to differentiate patients with neurodegenerative brain disease by extracting a cortical thinning pattern associated with normal aging

In Defense of Pure 16-bit Floating-Point Neural Networks

Reducing the number of bits needed to encode the weights and activations of neural networks is highly desirable as it speeds up their training and inference time while reducing memory consumption. For these reasons, research in this area has attracted significant attention toward developing neural networks that leverage lower-precision computing, such as mixed-precision training. Interestingly, none of the existing approaches has investigated pure 16-bit floating-point settings. In this paper, we shed light on the overlooked efficiency of pure 16-bit floating-point neural networks. As such, we provide a comprehensive theoretical analysis to investigate the factors contributing to the differences observed between 16-bit and 32-bit models. We formalize the concepts of floating-point error and tolerance, enabling us to quantitatively explain the conditions under which a 16-bit model can closely approximate the results of its 32-bit counterpart. This theoretical exploration offers perspective that is distinct from the literature which attributes the success of low-precision neural networks to its regularization effect. This in-depth analysis is supported by an extensive series of experiments. Our findings demonstrate that pure 16-bit floating-point neural networks can achieve similar or even better performance than their mixed-precision and 32-bit counterparts. We believe the results presented in this paper will have significant implications for machine learning practitioners, offering an opportunity to reconsider using pure 16-bit networks in various applications

Integrative web cloud computing and analytics using MiPair for design-based comparative analysis with paired microbiome data

Abstract Pairing (or blocking) is a design technique that is widely used in comparative microbiome studies to efficiently control for the effects of potential confounders (e.g., genetic, environmental, or behavioral factors). Some typical paired (block) designs for human microbiome studies are repeated measures designs that profile each subject’s microbiome twice (or more than twice) (1) for pre and post treatments to see the effects of a treatment on microbiome, or (2) for different organs of the body (e.g., gut, mouth, skin) to see the disparity in microbiome between (or across) body sites. Researchers have developed a sheer number of web-based tools for user-friendly microbiome data processing and analytics, though there is no web-based tool currently available for such paired microbiome studies. In this paper, we thus introduce an integrative web-based tool, named MiPair, for design-based comparative analysis with paired microbiome data. MiPair is a user-friendly web cloud service that is built with step-by-step data processing and analytic procedures for comparative analysis between (or across) groups or between baseline and other groups. MiPair employs parametric and non-parametric tests for complete or incomplete block designs to perform comparative analyses with respect to microbial ecology (alpha- and beta-diversity) and taxonomy (e.g., phylum, class, order, family, genus, species). We demonstrate its usage through an example clinical trial on the effects of antibiotics on gut microbiome. MiPair is an open-source software that can be run on our web server ( http://mipair.micloud.kr ) or on user’s computer ( https://github.com/yj7599/mipairgit )

Development of Mobile App to Enable Local Update on Mapping API: Construction Sites Monitoring through Digital Twin

Unmanned ground vehicles (UGVs) have emerged as a promising solution for reconnaissance missions, overcoming labor cost, frequency, and subjectivity issues associated with manual procedures. However, for dynamic environments such as construction sites, the constantly changing conditions hinder a manager from planning the UGV’s paths. For an autonomous monitoring mission, the path planning should be dealt with by having a map with the site’s most recent scene. In this study, we develop a mobile app capable of local map updates by overlaying an image on a mapping API (e.g., Google Maps) hence working as a digital twin capable of creating a dynamic representation of the updated terrain over the mapping API. UGV operators can draw a path on such an updated construction scene using a tablet PC or smartphone. Discrete GPS information (e.g., latitudinal, and longitudinal) is executed for the UGV’s controller. In the overlaying procedure, the homographic relation between the image and map is automatically computed and then projected. We successfully demonstrated the capabilities of the technique with two construction sites and a soccer field using images from the ground and satellite, respectively. The error generation is quantitatively measured and analyzed