Distance Correlation Based Brain Functional Connectivity Estimation and Non-Convex Multi-Task Learning for Developmental fMRI Studies

Resting-state functional magnetic resonance imaging (rs-fMRI)-derived functional connectivity patterns have been extensively utilized to delineate global functional organization of the human brain in health, development, and neuropsychiatric disorders. In this paper, we investigate how functional connectivity in males and females differs in an age prediction framework. We first estimate functional connectivity between regions-of-interest (ROIs) using distance correlation instead of Pearson's correlation. Distance correlation, as a multivariate statistical method, explores spatial relations of voxel-wise time courses within individual ROIs and measures both linear and nonlinear dependence, capturing more complex information of between-ROI interactions. Then, a novel non-convex multi-task learning (NC-MTL) model is proposed to study age-related gender differences in functional connectivity, where age prediction for each gender group is viewed as one task. Specifically, in the proposed NC-MTL model, we introduce a composite regularizer with a combination of non-convex $\ell_{2,1-2}$ and $\ell_{1-2}$ regularization terms for selecting both common and task-specific features. Finally, we validate the proposed NC-MTL model along with distance correlation based functional connectivity on rs-fMRI of the Philadelphia Neurodevelopmental Cohort for predicting ages of both genders. The experimental results demonstrate that the proposed NC-MTL model outperforms other competing MTL models in age prediction, as well as characterizing developmental gender differences in functional connectivity patterns.

Causal inference of brain connectivity from fMRI with $ψ$-Learning Incorporated Linear non-Gaussian Acyclic Model ($ψ$-LiNGAM)

Functional connectivity (FC) has become a primary means of understanding brain functions by identifying brain network interactions and, ultimately, how those interactions produce cognitions. A popular definition of FC is by statistical associations between measured brain regions. However, this could be problematic since the associations can only provide spatial connections but not causal interactions among regions of interests. Hence, it is necessary to study their causal relationship. Directed acyclic graph (DAG) models have been applied in recent FC studies but often encountered problems such as limited sample sizes and large number of variables (namely high-dimensional problems), which lead to both computational difficulty and convergence issues. As a result, the use of DAG models is problematic, where the identification of DAG models in general is nondeterministic polynomial time hard (NP-hard). To this end, we propose a $\psi$-learning incorporated linear non-Gaussian acyclic model ($\psi$-LiNGAM). We use the association model ($\psi$-learning) to facilitate causal inferences and the model works well especially for high-dimensional cases. Our simulation results demonstrate that the proposed method is more robust and accurate than several existing ones in detecting graph structure and direction. We then applied it to the resting state fMRI (rsfMRI) data obtained from the publicly available Philadelphia Neurodevelopmental Cohort (PNC) to study the cognitive variance, which includes 855 individuals aged 8-22 years. Therein, we have identified three types of hub structure: the in-hub, out-hub and sum-hub, which correspond to the centers of receiving, sending and relaying information, respectively. We also detected 16 most important pairs of causal flows. Several of the results have been verified to be biologically significant.

A Bayesian incorporated linear non-Gaussian acyclic model for multiple directed graph estimation to study brain emotion circuit development in adolescence

Emotion perception is essential to affective and cognitive development which involves distributed brain circuits. The ability of emotion identification begins in infancy and continues to develop throughout childhood and adolescence. Understanding the development of brain's emotion circuitry may help us explain the emotional changes observed during adolescence. Our previous study delineated the trajectory of brain functional connectivity (FC) from late childhood to early adulthood during emotion identification tasks. In this work, we endeavour to deepen our understanding from association to causation. We proposed a Bayesian incorporated linear non-Gaussian acyclic model (BiLiNGAM), which incorporated our previous association model into the prior estimation pipeline. In particular, it can jointly estimate multiple directed acyclic graphs (DAGs) for multiple age groups at different developmental stages. Simulation results indicated more stable and accurate performance over various settings, especially when the sample size was small (high-dimensional cases). We then applied to the analysis of real data from the Philadelphia Neurodevelopmental Cohort (PNC). This included 855 individuals aged 8-22 years who were divided into five different adolescent stages. Our network analysis revealed the development of emotion-related intra- and inter- modular connectivity and pinpointed several emotion-related hubs. We further categorized the hubs into two types: in-hubs and out-hubs, as the center of receiving and distributing information. Several unique developmental hub structures and group-specific patterns were also discovered. Our findings help provide a causal understanding of emotion development in the human brain.

Interpretable multimodal fusion networks reveal mechanisms of brain cognition

Multimodal fusion benefits disease diagnosis by providing a more comprehensive perspective. Developing algorithms is challenging due to data heterogeneity and the complex within- and between-modality associations. Deep-network-based data-fusion models have been developed to capture the complex associations and the performance in diagnosis has been improved accordingly. Moving beyond diagnosis prediction, evaluation of disease mechanisms is critically important for biomedical research. Deep-network-based data-fusion models, however, are difficult to interpret, bringing about difficulties for studying biological mechanisms. In this work, we develop an interpretable multimodal fusion model, namely gCAM-CCL, which can perform automated diagnosis and result interpretation simultaneously. The gCAM-CCL model can generate interpretable activation maps, which quantify pixel-level contributions of the input features. This is achieved by combining intermediate feature maps using gradient-based weights. Moreover, the estimated activation maps are class-specific, and the captured cross-data associations are interest/label related, which further facilitates class-specific analysis and biological mechanism analysis. We validate the gCAM-CCL model on a brain imaging-genetic study, and show gCAM-CCL's performed well for both classification and mechanism analysis. Mechanism analysis suggests that during task-fMRI scans, several object recognition related regions of interests (ROIs) are first activated and then several downstream encoding ROIs get involved. Results also suggest that the higher cognition performing group may have stronger neurotransmission signaling while the lower cognition performing group may have problem in brain/neuron development, resulting from genetic variations.

A generalized kernel machine approach to identify higher-order composite effects in multi-view datasets

In recent years, a comprehensive study of multi-view datasets (e.g., multi-omics and imaging scans) has been a focus and forefront in biomedical research. State-of-the-art biomedical technologies are enabling us to collect multi-view biomedical datasets for the study of complex diseases. While all the views of data tend to explore complementary information of a disease, multi-view data analysis with complex interactions is challenging for a deeper and holistic understanding of biological systems. In this paper, we propose a novel generalized kernel machine approach to identify higher-order composite effects in multi-view biomedical datasets. This generalized semi-parametric (a mixed-effect linear model) approach includes the marginal and joint Hadamard product of features from different views of data. The proposed kernel machine approach considers multi-view data as predictor variables to allow more thorough and comprehensive modeling of a complex trait. The proposed method can be applied to the study of any disease model, where multi-view datasets are available. We applied our approach to both synthesized datasets and real multi-view datasets from adolescence brain development and osteoporosis study, including an imaging scan dataset and five omics datasets. Our experiments demonstrate that the proposed method can effectively identify higher-order composite effects and suggest that corresponding features (genes, region of interests, and chemical taxonomies) function in a concerted effort. We show that the proposed method is more generalizable than existing ones.

OptSample: A Resilient Buffer Management Policy for Robotic Systems based on Optimal Message Sampling

Modern robotic systems have become an alternative to humans to perform risky or exhausting tasks. In such application scenarios, communications between robots and the control center have become one of the major problems. Buffering is a commonly used solution to relieve temporary network disruption. But the assumption that newer messages are more valuable than older ones is not true for many application scenarios such as explorations, rescue operations, and surveillance. In this paper, we proposed a novel resilient buffer management policy named OptSample. It can uniformly sampling messages and dynamically adjust the sample rate based on run-time network situation. We define an evaluation function to estimate the profit of a message sequence. Based on the function, our analysis and simulation shows that the OptSample policy can effectively prevent losing long segment of continuous messages and improve the overall profit of the received messages. We implement the proposed policy in ROS. The implementation is transparent to user and no user code need to be changed. Experimental results on several application scenarios show that the OptSample policy can help robotic systems be more resilient against network disruption.

Multimodal Sparse Classifier for Adolescent Brain Age Prediction

The study of healthy brain development helps to better understand the brain transformation and brain connectivity patterns which happen during childhood to adulthood. This study presents a sparse machine learning solution across whole-brain functional connectivity (FC) measures of three sets of data, derived from resting state functional magnetic resonance imaging (rs-fMRI) and task fMRI data, including a working memory n-back task (nb-fMRI) and an emotion identification task (em-fMRI). These multi-modal image data are collected on a sample of adolescents from the Philadelphia Neurodevelopmental Cohort (PNC) for the prediction of brain ages. Due to extremely large variable-to-instance ratio of PNC data, a high dimensional matrix with several irrelevant and highly correlated features is generated and hence a pattern learning approach is necessary to extract significant features. We propose a sparse learner based on the residual errors along the estimation of an inverse problem for the extreme learning machine (ELM) neural network. The purpose of the approach is to overcome the overlearning problem through pruning of several redundant features and their corresponding output weights. The proposed multimodal sparse ELM classifier based on residual errors (RES-ELM) is highly competitive in terms of the classification accuracy compared to its counterparts such as conventional ELM, and sparse Bayesian learning ELM.

TZC: Efficient Inter-Process Communication for Robotics Middleware with Partial Serialization

Inter-process communication (IPC) is one of the core functions of modern robotics middleware. We propose an efficient IPC technique called TZC (Towards Zero-Copy). As a core component of TZC, we design a novel algorithm called partial serialization. Our formulation can generate messages that can be divided into two parts. During message transmission, one part is transmitted through a socket and the other part uses shared memory. The part within shared memory is never copied or serialized during its lifetime. We have integrated TZC with ROS and ROS2 and find that TZC can be easily combined with current open-source platforms. By using TZC, the overhead of IPC remains constant when the message size grows. In particular, when the message size is 4MB (less than the size of a full HD image), TZC can reduce the overhead of ROS IPC from tens of milliseconds to hundreds of microseconds and can reduce the overhead of ROS2 IPC from hundreds of milliseconds to less than 1 millisecond. We also demonstrate the benefits of TZC by integrating with TurtleBot2 that are used in autonomous driving scenarios. We show that by using TZC, the braking distance can be shortened by 16% than ROS.