Algorithms, applications and systems towards interpretable pattern mining from multi-aspect data

How do humans move around in the urban space and how do they differ when the city undergoes terrorist attacks? How do users behave in Massive Open Online courses~(MOOCs) and how do they differ if some of them achieve certificates while some of them not? What areas in the court elite players, such as Stephen Curry, LeBron James, like to make their shots in the course of the game? How can we uncover the hidden habits that govern our online purchases? Are there unspoken agendas in how different states pass legislation of certain kinds? At the heart of these seemingly unconnected puzzles is this same mystery of multi-aspect mining, i.g., how can we mine and interpret the hidden pattern from a dataset that simultaneously reveals the associations, or changes of the associations, among various aspects of the data (e.g., a shot could be described with three aspects, player, time of the game, and area in the court)? Solving this problem could open gates to a deep understanding of underlying mechanisms for many real-world phenomena. While much of the research in multi-aspect mining contribute broad scope of innovations in the mining part, interpretation of patterns from the perspective of users (or domain experts) is often overlooked. Questions like what do they require for patterns, how good are the patterns, or how to read them, have barely been addressed. Without efficient and effective ways of involving users in the process of multi-aspect mining, the results are likely to lead to something difficult for them to comprehend. This dissertation proposes the M^3 framework, which consists of multiplex pattern discovery, multifaceted pattern evaluation, and multipurpose pattern presentation, to tackle the challenges of multi-aspect pattern discovery. Based on this framework, we develop algorithms, applications, and analytic systems to enable interpretable pattern discovery from multi-aspect data. Following the concept of meaningful multiplex pattern discovery, we propose PairFac to close the gap between human information needs and naive mining optimization. We demonstrate its effectiveness in the context of impact discovery in the aftermath of urban disasters. We develop iDisc to target the crossing of multiplex pattern discovery with multifaceted pattern evaluation. iDisc meets the specific information need in understanding multi-level, contrastive behavior patterns. As an example, we use iDisc to predict student performance outcomes in Massive Open Online Courses given users' latent behaviors. FacIt is an interactive visual analytic system that sits at the intersection of all three components and enables for interpretable, fine-tunable, and scrutinizable pattern discovery from multi-aspect data. We demonstrate each work's significance and implications in its respective problem context. As a whole, this series of studies is an effort to instantiate the M^3 framework and push the field of multi-aspect mining towards a more human-centric process in real-world applications

Dynamic mode decomposition in vector-valued reproducing kernel Hilbert spaces for extracting dynamical structure among observables

Understanding nonlinear dynamical systems (NLDSs) is challenging in a variety of engineering and scientific fields. Dynamic mode decomposition (DMD), which is a numerical algorithm for the spectral analysis of Koopman operators, has been attracting attention as a way of obtaining global modal descriptions of NLDSs without requiring explicit prior knowledge. However, since existing DMD algorithms are in principle formulated based on the concatenation of scalar observables, it is not directly applicable to data with dependent structures among observables, which take, for example, the form of a sequence of graphs. In this paper, we formulate Koopman spectral analysis for NLDSs with structures among observables and propose an estimation algorithm for this problem. This method can extract and visualize the underlying low-dimensional global dynamics of NLDSs with structures among observables from data, which can be useful in understanding the underlying dynamics of such NLDSs. To this end, we first formulate the problem of estimating spectra of the Koopman operator defined in vector-valued reproducing kernel Hilbert spaces, and then develop an estimation procedure for this problem by reformulating tensor-based DMD. As a special case of our method, we propose the method named as Graph DMD, which is a numerical algorithm for Koopman spectral analysis of graph dynamical systems, using a sequence of adjacency matrices. We investigate the empirical performance of our method by using synthetic and real-world data.Comment: 34 pages with 4 figures, Published in Neural Networks, 201

Bayesian multi-view models for data-driven drug response analysis

A central challenge faced by biological and medical research is to understand the impact of chemical entities on living cells. Identifying the relationships between the chemical structures and their cellular responses is valuable for improving drug design and targeted therapies. The chemical structures and their detailed molecular responses need to be combined through a systematic analysis to learn the complex dependencies, which can then assist in improving understanding of the molecular mechanisms of drugs as well as predictions on the effects of unknown molecules. Moreover, with emerging drug-response data sets being profiled over several disease types and phenotypic details, it is pertinent to develop advanced computational methods that can be used to study multiple sets of data together. In this thesis, a novel multi-disciplinary challenge is undertaken for computationally analyzing interactions between multiple biological responses and chemical properties of drugs, while simultaneously advancing the computational methods to better learn these interactions. Specifically, multi-view dependency modeling of paired data sets is formulated as a means of systematically studying the drug-response relationships. First, the systematic analysis of drug structures and their genome-wide responses is presented as a multi-set dependency modeling problem and established methods are adopted to test the novel hypothesis. Several novel extensions of the drug-response analysis are then presented that explore responses measured over multiple disease types and multiple levels of phenotypic detail, uncovering novel biological insights of potential impact. These analyses are made possible by novel advancements in multi-view methods. Specifically, the first Bayesian tensor canonical correlation analysis and its extensions are introduced to capture the underlying multi-way structure and applied in analyzing novel toxicogenomic interactions. The results illustrate that modeling the precise multi-view and multi-way formulation of the data is valuable for discovering interpretable latent components as well as for the prediction of unseen responses of drugs. Therefore, the original contribution to knowledge in this dissertation is two-fold: first, the data-driven identification of relationships between structural properties of drugs and their genome-wide responses in cells and, second, novel advancements of multi-view methods that find dependencies between paired data sets. Open source implementations of the new methods have been released to facilitate further research

Blending generative models with deep learning for multidimensional phenotypic prediction from brain connectivity data

Network science as a discipline has provided us with foundational machinery to study complex relational entities such as social networks, genomics, econometrics etc. The human brain is a complex network that has recently garnered immense interest within the data science community. Connectomics or the study of the underlying connectivity patterns in the brain has become an important field of study for the characterization of various neurological disorders such as Autism, Schizophrenia etc. Such connectomic studies have provided several fundamental insights into its intrinsic organisation and implications on our behavior and health. This thesis proposes a collection of mathematical models that are capable of fusing information from functional and structural connectivity with phenotypic information. Here, functional connectivity is measured by resting state functional MRI (rs-fMRI), while anatomical connectivity is captured using Diffusion Tensor Imaging (DTI). The phenotypic information of interest could refer to continuous measures of behavior or cognition, or may capture levels of impairment in the case of neuropsychiatric disorders. We first develop a joint network optimization framework to predict clinical severity from rs-fMRI connectivity matrices. This model couples two key terms into a unified optimization framework: a generative matrix factorization and a discriminative linear regression model. We demonstrate that the proposed joint inference strategy is successful in generalizing to prediction of impairments in Autism Spectrum Disorder (ASD) when compared with several machine learning, graph theoretic and statistical baselines. At the same time, the model is capable of extracting functional brain biomarkers that are informative of individual measures of clinical severity. We then present two modeling extensions to non-parametric and neural network regression models that are coupled with the same generative framework. Building on these general principles, we extend our framework to incorporate multimodal information from Diffusion Tensor Imaging (DTI) and dynamic functional connectivity. At a high level, our generative matrix factorization now estimates a time-varying functional decomposition. At the same time, it is guided by anatomical connectivity priors in a graph-based regularization setup. This connectivity model is coupled with a deep network that predicts multidimensional clinical characterizations and models the temporal dynamics of the functional scan. This framework allows us to simultaneously explain multiple impairments, isolate stable multi-modal connectivity signatures, and study the evolution of various brain states at rest. Lastly, we shift our focus to end-to-end geometric frameworks. These are designed to characterize the complementarity between functional and structural connectivity data spaces, while using clinical information as a secondary guide. As an alternative to the previous generative framework for functional connectivity, our representation learning scheme of choice is a matrix autoencoder that is crafted to reflect the underlying data geometry. This is coupled with a manifold alignment model that maps from function to structure and a deep network that maps to phenotypic information. We demonstrate that the model reliably recovers structural connectivity patterns across individuals, while robustly extracting predictive yet interpretable brain biomarkers. Finally, we also present a preliminary analytical and experimental exposition on the theoretical aspects of the matrix autoencoder representation

Analyzing Granger causality in climate data with time series classification methods

Attribution studies in climate science aim for scientifically ascertaining the influence of climatic variations on natural or anthropogenic factors. Many of those studies adopt the concept of Granger causality to infer statistical cause-effect relationships, while utilizing traditional autoregressive models. In this article, we investigate the potential of state-of-the-art time series classification techniques to enhance causal inference in climate science. We conduct a comparative experimental study of different types of algorithms on a large test suite that comprises a unique collection of datasets from the area of climate-vegetation dynamics. The results indicate that specialized time series classification methods are able to improve existing inference procedures. Substantial differences are observed among the methods that were tested

Non-convex Optimization for Machine Learning

A vast majority of machine learning algorithms train their models and perform inference by solving optimization problems. In order to capture the learning and prediction problems accurately, structural constraints such as sparsity or low rank are frequently imposed or else the objective itself is designed to be a non-convex function. This is especially true of algorithms that operate in high-dimensional spaces or that train non-linear models such as tensor models and deep networks. The freedom to express the learning problem as a non-convex optimization problem gives immense modeling power to the algorithm designer, but often such problems are NP-hard to solve. A popular workaround to this has been to relax non-convex problems to convex ones and use traditional methods to solve the (convex) relaxed optimization problems. However this approach may be lossy and nevertheless presents significant challenges for large scale optimization. On the other hand, direct approaches to non-convex optimization have met with resounding success in several domains and remain the methods of choice for the practitioner, as they frequently outperform relaxation-based techniques - popular heuristics include projected gradient descent and alternating minimization. However, these are often poorly understood in terms of their convergence and other properties. This monograph presents a selection of recent advances that bridge a long-standing gap in our understanding of these heuristics. The monograph will lead the reader through several widely used non-convex optimization techniques, as well as applications thereof. The goal of this monograph is to both, introduce the rich literature in this area, as well as equip the reader with the tools and techniques needed to analyze these simple procedures for non-convex problems.Comment: The official publication is available from now publishers via http://dx.doi.org/10.1561/220000005

Computational Methods for Cognitive and Cooperative Robotics

In the last decades design methods in control engineering made substantial progress in the areas of robotics and computer animation. Nowadays these methods incorporate the newest developments in machine learning and artificial intelligence. But the problems of flexible and online-adaptive combinations of motor behaviors remain challenging for human-like animations and for humanoid robotics. In this context, biologically-motivated methods for the analysis and re-synthesis of human motor programs provide new insights in and models for the anticipatory motion synthesis. This thesis presents the author’s achievements in the areas of cognitive and developmental robotics, cooperative and humanoid robotics and intelligent and machine learning methods in computer graphics. The first part of the thesis in the chapter “Goal-directed Imitation for Robots” considers imitation learning in cognitive and developmental robotics. The work presented here details the author’s progress in the development of hierarchical motion recognition and planning inspired by recent discoveries of the functions of mirror-neuron cortical circuits in primates. The overall architecture is capable of ‘learning for imitation’ and ‘learning by imitation’. The complete system includes a low-level real-time capable path planning subsystem for obstacle avoidance during arm reaching. The learning-based path planning subsystem is universal for all types of anthropomorphic robot arms, and is capable of knowledge transfer at the level of individual motor acts. Next, the problems of learning and synthesis of motor synergies, the spatial and spatio-temporal combinations of motor features in sequential multi-action behavior, and the problems of task-related action transitions are considered in the second part of the thesis “Kinematic Motion Synthesis for Computer Graphics and Robotics”. In this part, a new approach of modeling complex full-body human actions by mixtures of time-shift invariant motor primitives in presented. The online-capable full-body motion generation architecture based on dynamic movement primitives driving the time-shift invariant motor synergies was implemented as an online-reactive adaptive motion synthesis for computer graphics and robotics applications. The last chapter of the thesis entitled “Contraction Theory and Self-organized Scenarios in Computer Graphics and Robotics” is dedicated to optimal control strategies in multi-agent scenarios of large crowds of agents expressing highly nonlinear behaviors. This last part presents new mathematical tools for stability analysis and synthesis of multi-agent cooperative scenarios.In den letzten Jahrzehnten hat die Forschung in den Bereichen der Steuerung und Regelung komplexer Systeme erhebliche Fortschritte gemacht, insbesondere in den Bereichen Robotik und Computeranimation. Die Entwicklung solcher Systeme verwendet heutzutage neueste Methoden und Entwicklungen im Bereich des maschinellen Lernens und der künstlichen Intelligenz. Die flexible und echtzeitfähige Kombination von motorischen Verhaltensweisen ist eine wesentliche Herausforderung für die Generierung menschenähnlicher Animationen und in der humanoiden Robotik. In diesem Zusammenhang liefern biologisch motivierte Methoden zur Analyse und Resynthese menschlicher motorischer Programme neue Erkenntnisse und Modelle für die antizipatorische Bewegungssynthese. Diese Dissertation präsentiert die Ergebnisse der Arbeiten des Autors im Gebiet der kognitiven und Entwicklungsrobotik, kooperativer und humanoider Robotersysteme sowie intelligenter und maschineller Lernmethoden in der Computergrafik. Der erste Teil der Dissertation im Kapitel “Zielgerichtete Nachahmung für Roboter” behandelt das Imitationslernen in der kognitiven und Entwicklungsrobotik. Die vorgestellten Arbeiten beschreiben neue Methoden für die hierarchische Bewegungserkennung und -planung, die durch Erkenntnisse zur Funktion der kortikalen Spiegelneuronen-Schaltkreise bei Primaten inspiriert wurden. Die entwickelte Architektur ist in der Lage, ‘durch Imitation zu lernen’ und ‘zu lernen zu imitieren’. Das komplette entwickelte System enthält ein echtzeitfähiges Pfadplanungssubsystem zur Hindernisvermeidung während der Durchführung von Armbewegungen. Das lernbasierte Pfadplanungssubsystem ist universell und für alle Arten von anthropomorphen Roboterarmen in der Lage, Wissen auf der Ebene einzelner motorischer Handlungen zu übertragen. Im zweiten Teil der Arbeit “Kinematische Bewegungssynthese für Computergrafik und Robotik” werden die Probleme des Lernens und der Synthese motorischer Synergien, d.h. von räumlichen und räumlich-zeitlichen Kombinationen motorischer Bewegungselemente bei Bewegungssequenzen und bei aufgabenbezogenen Handlungs übergängen behandelt. Es wird ein neuer Ansatz zur Modellierung komplexer menschlicher Ganzkörperaktionen durch Mischungen von zeitverschiebungsinvarianten Motorprimitiven vorgestellt. Zudem wurde ein online-fähiger Synthesealgorithmus für Ganzköperbewegungen entwickelt, der auf dynamischen Bewegungsprimitiven basiert, die wiederum auf der Basis der gelernten verschiebungsinvarianten Primitive konstruiert werden. Dieser Algorithmus wurde für verschiedene Probleme der Bewegungssynthese für die Computergrafik- und Roboteranwendungen implementiert. Das letzte Kapitel der Dissertation mit dem Titel “Kontraktionstheorie und selbstorganisierte Szenarien in der Computergrafik und Robotik” widmet sich optimalen Kontrollstrategien in Multi-Agenten-Szenarien, wobei die Agenten durch eine hochgradig nichtlineare Kinematik gekennzeichnet sind. Dieser letzte Teil präsentiert neue mathematische Werkzeuge für die Stabilitätsanalyse und Synthese von kooperativen Multi-Agenten-Szenarien