Algorithms in nature: the convergence of systems biology and computational thinking

Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. This Perspectives discusses the recent convergence of these two ways of thinking

Visual Attention in Dynamic Environments and its Application to Playing Online Games

Abstract In this thesis we present a prototype of Cognitive Programs (CPs) - an executive controller built on top of Selective Tuning (ST) model of attention. CPs enable top-down control of visual system and interaction between the low-level vision and higher-level task demands. Abstract We implement a subset of CPs for playing online video games in real time using only visual input. Two commercial closed-source games - Canabalt and Robot Unicorn Attack - are used for evaluation. Their simple gameplay and minimal controls put the emphasis on reaction speed and attention over planning. Abstract Our implementation of Cognitive Programs plays both games at human expert level, which experimentally proves the validity of the concept. Additionally we resolved multiple theoretical and engineering issues, e.g. extending the CPs to dynamic environments, finding suitable data structures for describing the task and information flow within the network and determining the correct timing for each process

A Systematic Survey of Control Techniques and Applications: From Autonomous Vehicles to Connected and Automated Vehicles

Vehicle control is one of the most critical challenges in autonomous vehicles (AVs) and connected and automated vehicles (CAVs), and it is paramount in vehicle safety, passenger comfort, transportation efficiency, and energy saving. This survey attempts to provide a comprehensive and thorough overview of the current state of vehicle control technology, focusing on the evolution from vehicle state estimation and trajectory tracking control in AVs at the microscopic level to collaborative control in CAVs at the macroscopic level. First, this review starts with vehicle key state estimation, specifically vehicle sideslip angle, which is the most pivotal state for vehicle trajectory control, to discuss representative approaches. Then, we present symbolic vehicle trajectory tracking control approaches for AVs. On top of that, we further review the collaborative control frameworks for CAVs and corresponding applications. Finally, this survey concludes with a discussion of future research directions and the challenges. This survey aims to provide a contextualized and in-depth look at state of the art in vehicle control for AVs and CAVs, identifying critical areas of focus and pointing out the potential areas for further exploration

Structured Sparse Methods for Imaging Genetics

abstract: Imaging genetics is an emerging and promising technique that investigates how genetic variations affect brain development, structure, and function. By exploiting disorder-related neuroimaging phenotypes, this class of studies provides a novel direction to reveal and understand the complex genetic mechanisms. Oftentimes, imaging genetics studies are challenging due to the relatively small number of subjects but extremely high-dimensionality of both imaging data and genomic data. In this dissertation, I carry on my research on imaging genetics with particular focuses on two tasks---building predictive models between neuroimaging data and genomic data, and identifying disorder-related genetic risk factors through image-based biomarkers. To this end, I consider a suite of structured sparse methods---that can produce interpretable models and are robust to overfitting---for imaging genetics. With carefully-designed sparse-inducing regularizers, different biological priors are incorporated into learning models. More specifically, in the Allen brain image--gene expression study, I adopt an advanced sparse coding approach for image feature extraction and employ a multi-task learning approach for multi-class annotation. Moreover, I propose a label structured-based two-stage learning framework, which utilizes the hierarchical structure among labels, for multi-label annotation. In the Alzheimer's disease neuroimaging initiative (ADNI) imaging genetics study, I employ Lasso together with EDPP (enhanced dual polytope projections) screening rules to fast identify Alzheimer's disease risk SNPs. I also adopt the tree-structured group Lasso with MLFre (multi-layer feature reduction) screening rules to incorporate linkage disequilibrium information into modeling. Moreover, I propose a novel absolute fused Lasso model for ADNI imaging genetics. This method utilizes SNP spatial structure and is robust to the choice of reference alleles of genotype coding. In addition, I propose a two-level structured sparse model that incorporates gene-level networks through a graph penalty into SNP-level model construction. Lastly, I explore a convolutional neural network approach for accurate predicting Alzheimer's disease related imaging phenotypes. Experimental results on real-world imaging genetics applications demonstrate the efficiency and effectiveness of the proposed structured sparse methods.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Regenerative Patterning in Swarm Robots: Mutual Benefits of Research in Robotics and Stem Cell Biology

This paper presents a novel perspective of Robotic Stem Cells (RSCs), defined as the basic non-biological elements with stem cell like properties that can self-reorganize to repair damage to their swarming organization. Self here means that the elements can autonomously decide and execute their actions without requiring any preset triggers, commands, or help from external sources. We develop this concept for two purposes. One is to develop a new theory for self-organization and self-assembly of multi-robots systems that can detect and recover from unforeseen errors or attacks. This self-healing and self-regeneration is used to minimize the compromise of overall function for the robot team. The other is to decipher the basic algorithms of regenerative behaviors in multi-cellular animal models, so that we can understand the fundamental principles used in the regeneration of biological systems. RSCs are envisioned to be basic building elements for future systems that are capable of self-organization, self-assembly, self-healing and self-regeneration. We first discuss the essential features of biological stem cells for such a purpose, and then propose the functional requirements of robotic stem cells with properties equivalent to gene controller, program selector and executor. We show that RSCs are a novel robotic model for scalable self-organization and self-healing in computer simulations and physical implementation. As our understanding of stem cells advances, we expect that future robots will be more versatile, resilient and complex, and such new robotic systems may also demand and inspire new knowledge from stem cell biology and related fields, such as artificial intelligence and tissue engineering