Reconstructing dynamical networks via feature ranking

Empirical data on real complex systems are becoming increasingly available. Parallel to this is the need for new methods of reconstructing (inferring) the topology of networks from time-resolved observations of their node-dynamics. The methods based on physical insights often rely on strong assumptions about the properties and dynamics of the scrutinized network. Here, we use the insights from machine learning to design a new method of network reconstruction that essentially makes no such assumptions. Specifically, we interpret the available trajectories (data) as features, and use two independent feature ranking approaches -- Random forest and RReliefF -- to rank the importance of each node for predicting the value of each other node, which yields the reconstructed adjacency matrix. We show that our method is fairly robust to coupling strength, system size, trajectory length and noise. We also find that the reconstruction quality strongly depends on the dynamical regime

Robust subspace learning for static and dynamic affect and behaviour modelling

Machine analysis of human affect and behavior in naturalistic contexts has witnessed a growing attention in the last decade from various disciplines ranging from social and cognitive sciences to machine learning and computer vision. Endowing machines with the ability to seamlessly detect, analyze, model, predict as well as simulate and synthesize manifestations of internal emotional and behavioral states in real-world data is deemed essential for the deployment of next-generation, emotionally- and socially-competent human-centered interfaces. In this thesis, we are primarily motivated by the problem of modeling, recognizing and predicting spontaneous expressions of non-verbal human affect and behavior manifested through either low-level facial attributes in static images or high-level semantic events in image sequences. Both visual data and annotations of naturalistic affect and behavior naturally contain noisy measurements of unbounded magnitude at random locations, commonly referred to as ‘outliers’. We present here machine learning methods that are robust to such gross, sparse noise. First, we deal with static analysis of face images, viewing the latter as a superposition of mutually-incoherent, low-complexity components corresponding to facial attributes, such as facial identity, expressions and activation of atomic facial muscle actions. We develop a robust, discriminant dictionary learning framework to extract these components from grossly corrupted training data and combine it with sparse representation to recognize the associated attributes. We demonstrate that our framework can jointly address interrelated classification tasks such as face and facial expression recognition. Inspired by the well-documented importance of the temporal aspect in perceiving affect and behavior, we direct the bulk of our research efforts into continuous-time modeling of dimensional affect and social behavior. Having identified a gap in the literature which is the lack of data containing annotations of social attitudes in continuous time and scale, we first curate a new audio-visual database of multi-party conversations from political debates annotated frame-by-frame in terms of real-valued conflict intensity and use it to conduct the first study on continuous-time conflict intensity estimation. Our experimental findings corroborate previous evidence indicating the inability of existing classifiers in capturing the hidden temporal structures of affective and behavioral displays. We present here a novel dynamic behavior analysis framework which models temporal dynamics in an explicit way, based on the natural assumption that continuous- time annotations of smoothly-varying affect or behavior can be viewed as outputs of a low-complexity linear dynamical system when behavioral cues (features) act as system inputs. A novel robust structured rank minimization framework is proposed to estimate the system parameters in the presence of gross corruptions and partially missing data. Experiments on prediction of dimensional conflict and affect as well as multi-object tracking from detection validate the effectiveness of our predictive framework and demonstrate that for the first time that complex human behavior and affect can be learned and predicted based on small training sets of person(s)-specific observations.Open Acces

Recent Advances in Robust Control

Robust control has been a topic of active research in the last three decades culminating in H_2/H_\infty and \mu design methods followed by research on parametric robustness, initially motivated by Kharitonov's theorem, the extension to non-linear time delay systems, and other more recent methods. The two volumes of Recent Advances in Robust Control give a selective overview of recent theoretical developments and present selected application examples. The volumes comprise 39 contributions covering various theoretical aspects as well as different application areas. The first volume covers selected problems in the theory of robust control and its application to robotic and electromechanical systems. The second volume is dedicated to special topics in robust control and problem specific solutions. Recent Advances in Robust Control will be a valuable reference for those interested in the recent theoretical advances and for researchers working in the broad field of robotics and mechatronics

Resolving Biological Trajectories in Single-cell Data using Feature Selection and Multi-modal Integration

Single-cell technologies can readily measure the expression of thousands of molecular features from individual cells undergoing dynamic biological processes, such as cellular differentiation, immune response, and disease progression. While computational trajectory inference methods and RNA velocity approaches have been developed to study how subtle changes in gene or protein expression impact cell fate decision-making, identifying characteristic features that drive continuous biological processes remains difficult to detect due to the inherent biological or technical challenges associated with single-cell data. Here, we developed two data representation-based approaches for improving inference of cellular dynamics. First, we present DELVE, an unsupervised feature selection method for identifying a representative subset of dynamically-expressed molecular features that resolve cellular trajectories in noisy data. In contrast to previous work, DELVE uses a bottom-up approach to mitigate the effect of unwanted sources of variation confounding inference and models cell states from dynamic feature modules that constitute core regulatory complexes. Using simulations, single-cell RNA sequencing data, and iterative immunofluorescence imaging data in the context of cell cycle and cellular differentiation, we demonstrate that DELVE selects genes or proteins that more accurately characterize cell populations and improve the recovery of cell type transitions. Next, we present the first task-oriented benchmarking study that investigates integration of temporal gene expression modalities for dynamic cell state prediction. We benchmark ten multi-modal integration approaches on ten datasets spanning different biological contexts, sequencing technologies, and species. This study illustrates how temporal gene expression modalities can be optimally combined to improve inference of cellular trajectories and more accurately predict sample-associated perturbation and disease phenotypes. Lastly, we illustrate an application of these approaches and perform an integrative analysis of gene expression and RNA velocity data to study the crosstalk between signaling pathways that govern the mesendoderm fate decision during directed definitive endoderm differentiation. Results of this study suggest that lineage-specific, temporally expressed genes within the primitive streak may serve as a potential target for increasing definitive endoderm efficiency. Collectively, this work uses scalable data-driven approaches to effectively manage the inherent biological or technical challenges associated with single-cell data in order to improve inference of cellular dynamics.Doctor of Philosoph

Hierarchical feature extraction from spatiotemporal data for cyber-physical system analytics

With the advent of ubiquitous sensing, robust communication and advanced computation, data-driven modeling is increasingly becoming popular for many engineering problems. Eliminating difficulties of physics-based modeling, avoiding simplifying assumptions and ad hoc empirical models are significant among many advantages of data-driven approaches, especially for large-scale complex systems. While classical statistics and signal processing algorithms have been widely used by the engineering community, advanced machine learning techniques have not been sufficiently explored in this regard. This study summarizes various categories of machine learning tools that have been applied or may be a candidate for addressing engineering problems. While there are increasing number of machine learning algorithms, the main steps involved in applying such techniques to the problems consist in: data collection and pre-processing, feature extraction, model training and inference for decision-making. To support decision-making processes in many applications, hierarchical feature extraction is key. Among various feature extraction principles, recent studies emphasize hierarchical approaches of extracting salient features that is carried out at multiple abstraction levels from data. In this context, the focus of the dissertation is towards developing hierarchical feature extraction algorithms within the framework of machine learning in order to solve challenging cyber-physical problems in various domains such as electromechanical systems and agricultural systems. Furthermore, the feature extraction techniques are described using the spatial, temporal and spatiotemporal data types collected from the systems. The wide applicability of such features in solving some selected real-life domain problems are demonstrated throughout this study

Deep Learning for Decision Making and Autonomous Complex Systems

Deep learning consists of various machine learning algorithms that aim to learn multiple levels of abstraction from data in a hierarchical manner. It is a tool to construct models using the data that mimics a real world process without an exceedingly tedious modelling of the actual process. We show that deep learning is a viable solution to decision making in mechanical engineering problems and complex physical systems. In this work, we demonstrated the application of this data-driven method in the design of microfluidic devices to serve as a map between the user-defined cross-sectional shape of the flow and the corresponding arrangement of micropillars in the flow channel that contributed to the flow deformation. We also present how deep learning can be used in the early detection of combustion instability for prognostics and health monitoring of a combustion engine, such that appropriate measures can be taken to prevent detrimental effects as a result of unstable combustion. One of the applications in complex systems concerns robotic path planning via the systematic learning of policies and associated rewards. In this context, a deep architecture is implemented to infer the expected value of information gained by performing an action based on the states of the environment. We also applied deep learning-based methods to enhance natural low-light images in the context of a surveillance framework and autonomous robots. Further, we looked at how machine learning methods can be used to perform root-cause analysis in cyber-physical systems subjected to a wide variety of operation anomalies. In all studies, the proposed frameworks have been shown to demonstrate promising feasibility and provided credible results for large-scale implementation in the industry

ICASE

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in the areas of (1) applied and numerical mathematics, including numerical analysis and algorithm development; (2) theoretical and computational research in fluid mechanics in selected areas of interest, including acoustics and combustion; (3) experimental research in transition and turbulence and aerodynamics involving Langley facilities and scientists; and (4) computer science

Measurements, Models, Systems and Design

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