Approximate Bayesian Computation in State Space Models

A new approach to inference in state space models is proposed, based on approximate Bayesian computation (ABC). ABC avoids evaluation of the likelihood function by matching observed summary statistics with statistics computed from data simulated from the true process; exact inference being feasible only if the statistics are sufficient. With finite sample sufficiency unattainable in the state space setting, we seek asymptotic sufficiency via the maximum likelihood estimator (MLE) of the parameters of an auxiliary model. We prove that this auxiliary model-based approach achieves Bayesian consistency, and that - in a precise limiting sense - the proximity to (asymptotic) sufficiency yielded by the MLE is replicated by the score. In multiple parameter settings a separate treatment of scalar parameters, based on integrated likelihood techniques, is advocated as a way of avoiding the curse of dimensionality. Some attention is given to a structure in which the state variable is driven by a continuous time process, with exact inference typically infeasible in this case as a result of intractable transitions. The ABC method is demonstrated using the unscented Kalman filter as a fast and simple way of producing an approximation in this setting, with a stochastic volatility model for financial returns used for illustration

Study of the track reconstruction in the FOOT experiment for Hadrontherapy

In adroterapia vengono utilizzati fasci di ioni (protoni e ioni carbonio) per il trattamento di tumori profondi; queste particelle possiedono molti vantaggi rispetto ai fotoni utilizzati nella radioterapia convenzionale. Il profilo dose-profondità di questi ioni è caratterizzato da una bassa dose nel canale di entrata e da un massimo molto pronunciato situato alla fine del loro range, chiamato picco di Bragg, la cui profondità dipende dall'energia del fascio. Inoltre gli ioni più pesanti del protone, come il carbonio o l'ossigeno, mostrano un'efficacia biologica maggiore nella regione del picco di Bragg, aprendo così alla possibilità di trattare anche tumori ipossici. Tuttavia il problema più grande nell'utilizzo di questi ioni è la loro frammentazione nucleare che causa una dose non nulla oltre il picco di Bragg. Nei trattamenti con fasci di protoni invece, è la frammentazione del bersaglio ad essere un problema: una conoscenza corretta e approfondita di questo fenomeno sarebbe davvero importante per valutare la reale efficacia biologica dei protoni. L'esperimento FOOT (FragmentatiOn Of Target) è stato proposto proprio per fare luce su questi aspetti: il suo obiettivo finale è quello di misurare la sezione d'urto dei frammenti pesanti, con Z>2, con un'incertezza massima del 5% e il loro spettro energetico con una risoluzione dell'ordine di 1-2 MeV/u, così da ottenere una migliore caratterizzazione radiobiologica dei protoni. In questa tesi si intende studiare come si determinano i momenti dei frammenti ricostruendo le loro tracce in campo magnetico usando il filtro di Kalman. Inoltre vengono sviluppati e discussi due algoritmi che hanno lo scopo di assegnare correttamente le hit con le tracce

Reduced order modelling through system identification using stochastic filtering

This thesis presents a novel approach to model order reduction, through system identification and using stochastic filtering. Order reduction is a particularly relevant application in the automotive context, as the generation of simplified simulation models for the whole vehicle and its subsystems is an increasingly important aspect of vehicle design. First, grey-box parameter identification of vehicle handling dynamics is explored, including identification of a combined-slip tyre model. This introductory study serves as an intermediate step to review three alternative stochastic filters: identifying forms of the unscented Kalman filter, extended Kalman filter and particle filter are here compared for effectiveness, complexity and computational efficiency. Despite being initially merely considered as a stepping stone towards black-box identification, this phase of the PhD generated its own and independent outcomes and might be viewed as a spin-off of the main research topic. All three filters appear suited to system identification and could operate in on-line model predictive controllers or estimators, with varying levels of practicability at different sampling rates. Work on black-box system identification then starts through a non-linear Kalman filter, extended to identify all the parameters of a canonical linear state-space structure. In spite of all model parameters being unknown at the start, the filter is able to evolve parameter estimates to achieve 100$\%$ accuracy in noise-free test cases, and is also proven to be robust to noise in the measurements. The canonical form ensures that a minimal number of parameters need to be identified and produces additional information in terms of eigenvalues and dominant modes. After extensive testing in the linear domain, state-space is extended into a non-linear framework, with each parameter becoming a non-linear function of system inputs or states. Parameter variation is first constrained by cubic spline polynomials, to provide continuity and maintain relatively small extended state-parameter vectors. This early approach is later simplified, with each element of state-space generated through unconstrained, generic non-linear functions and defined through a number of equally spaced, fixed nodes. Conditioning and convergence are maintained through the definition of additional system outputs, based on specific functions of the non-linear node ordinates. Unlike other methods published in the literature, this new approach does not focus on a specific non-linear structure, but consists in the prescription of a generic and yet simple non-linear state-space model structure, that allows various non-linearities to be identified and approximated solely based on inputs and outputs. The method is illustrated in practice through simple non-linear examples and test cases, which include the identification of a full vehicle model, a highly non-linear brake model and CFD data. These applications show that it is possible to easily expand the order of the system and the complexity of the non-linearities, to achieve higher accuracy while ensuring good parameter conditioning. The approach is completely black-box and requires no physical understanding of the process for successful identification, making it an ideally suited mechanism for order reduction of high order simulation models. In addition to high order simulation data, the developed approach can be used as a tool for conventional system identification and applied to experimental test data as well.</div

Optimal experimental design for parameter identification and model selection

Magdeburg, Univ., Fak. für Elektrotechnik und Informationstechnik, Diss., 2014René Schenkendor

Design of false data injection attack on distributed process estimation

Herein, design of false data injection attack on a distributed cyber-physical system is considered. A stochastic process with linear dynamics and Gaussian noise is measured by multiple agent nodes, each equipped with multiple sensors. The agent nodes form a multi-hop network among themselves. Each agent node computes an estimate of the process by using its sensor observation and messages obtained from neighboring nodes, via Kalman-consensus filtering. An external attacker, capable of arbitrarily manipulating the sensor observations of some or all agent nodes, injects errors into those sensor observations. The goal of the attacker is to steer the estimates at the agent nodes as close as possible to a pre-specified value, while respecting a constraint on the attack detection probability. To this end, a constrained optimization problem is formulated to find the optimal parameter values of a certain class of linear attacks. The parameters of linear attack are learnt on-line via a combination of stochastic approximation based update of a Lagrange multiplier, and an optimization technique involving either the Karush-Kuhn-Tucker (KKT) conditions or online stochastic gradient descent. The problem turns out to be convex for some special cases. Desired convergence of the proposed algorithms are proved by exploiting the convexity and properties of stochastic approximation algorithms. Finally, numerical results demonstrate the efficacy of the attack

Extraction and Detection of Fetal Electrocardiograms from Abdominal Recordings

The non-invasive fetal ECG (NIFECG), derived from abdominal surface electrodes, offers novel diagnostic possibilities for prenatal medicine. Despite its straightforward applicability, NIFECG signals are usually corrupted by many interfering sources. Most significantly, by the maternal ECG (MECG), whose amplitude usually exceeds that of the fetal ECG (FECG) by multiple times. The presence of additional noise sources (e.g. muscular/uterine noise, electrode motion, etc.) further affects the signal-to-noise ratio (SNR) of the FECG. These interfering sources, which typically show a strong non-stationary behavior, render the FECG extraction and fetal QRS (FQRS) detection demanding signal processing tasks. In this thesis, several of the challenges regarding NIFECG signal analysis were addressed. In order to improve NIFECG extraction, the dynamic model of a Kalman filter approach was extended, thus, providing a more adequate representation of the mixture of FECG, MECG, and noise. In addition, aiming at the FECG signal quality assessment, novel metrics were proposed and evaluated. Further, these quality metrics were applied in improving FQRS detection and fetal heart rate estimation based on an innovative evolutionary algorithm and Kalman filtering signal fusion, respectively. The elaborated methods were characterized in depth using both simulated and clinical data, produced throughout this thesis. To stress-test extraction algorithms under ideal circumstances, a comprehensive benchmark protocol was created and contributed to an extensively improved NIFECG simulation toolbox. The developed toolbox and a large simulated dataset were released under an open-source license, allowing researchers to compare results in a reproducible manner. Furthermore, to validate the developed approaches under more realistic and challenging situations, a clinical trial was performed in collaboration with the University Hospital of Leipzig. Aside from serving as a test set for the developed algorithms, the clinical trial enabled an exploratory research. This enables a better understanding about the pathophysiological variables and measurement setup configurations that lead to changes in the abdominal signal's SNR. With such broad scope, this dissertation addresses many of the current aspects of NIFECG analysis and provides future suggestions to establish NIFECG in clinical settings.:Abstract Acknowledgment Contents List of Figures List of Tables List of Abbreviations List of Symbols (1)Introduction 1.1)Background and Motivation 1.2)Aim of this Work 1.3)Dissertation Outline 1.4)Collaborators and Conflicts of Interest (2)Clinical Background 2.1)Physiology 2.1.1)Changes in the maternal circulatory system 2.1.2)Intrauterine structures and feto-maternal connection 2.1.3)Fetal growth and presentation 2.1.4)Fetal circulatory system 2.1.5)Fetal autonomic nervous system 2.1.6)Fetal heart activity and underlying factors 2.2)Pathology 2.2.1)Premature rupture of membrane 2.2.2)Intrauterine growth restriction 2.2.3)Fetal anemia 2.3)Interpretation of Fetal Heart Activity 2.3.1)Summary of clinical studies on FHR/FHRV 2.3.2)Summary of studies on heart conduction 2.4)Chapter Summary (3)Technical State of the Art 3.1)Prenatal Diagnostic and Measuring Technique 3.1.1)Fetal heart monitoring 3.1.2)Related metrics 3.2)Non-Invasive Fetal ECG Acquisition 3.2.1)Overview 3.2.2)Commercial equipment 3.2.3)Electrode configurations 3.2.4)Available NIFECG databases 3.2.5)Validity and usability of the non-invasive fetal ECG 3.3)Non-Invasive Fetal ECG Extraction Methods 3.3.1)Overview on the non-invasive fetal ECG extraction methods 3.3.2)Kalman filtering basics 3.3.3)Nonlinear Kalman filtering 3.3.4)Extended Kalman filter for FECG estimation 3.4)Fetal QRS Detection 3.4.1)Merging multichannel fetal QRS detections 3.4.2)Detection performance 3.5)Fetal Heart Rate Estimation 3.5.1)Preprocessing the fetal heart rate 3.5.2)Fetal heart rate statistics 3.6)Fetal ECG Morphological Analysis 3.7)Problem Description 3.8)Chapter Summary (4)Novel Approaches for Fetal ECG Analysis 4.1)Preliminary Considerations 4.2)Fetal ECG Extraction by means of Kalman Filtering 4.2.1)Optimized Gaussian approximation 4.2.2)Time-varying covariance matrices 4.2.3)Extended Kalman filter with unknown inputs 4.2.4)Filter calibration 4.3)Accurate Fetal QRS and Heart Rate Detection 4.3.1)Multichannel evolutionary QRS correction 4.3.2)Multichannel fetal heart rate estimation using Kalman filters 4.4)Chapter Summary (5)Data Material 5.1)Simulated Data 5.1.1)The FECG Synthetic Generator (FECGSYN) 5.1.2)The FECG Synthetic Database (FECGSYNDB) 5.2)Clinical Data 5.2.1)Clinical NIFECG recording 5.2.2)Scope and limitations of this study 5.2.3)Data annotation: signal quality and fetal amplitude 5.2.4)Data annotation: fetal QRS annotation 5.3)Chapter Summary (6)Results for Data Analysis 6.1)Simulated Data 6.1.1)Fetal QRS detection 6.1.2)Morphological analysis 6.2)Own Clinical Data 6.2.1)FQRS correction using the evolutionary algorithm 6.2.2)FHR correction by means of Kalman filtering (7)Discussion and Prospective 7.1)Data Availability 7.1.1)New measurement protocol 7.2)Signal Quality 7.3)Extraction Methods 7.4)FQRS and FHR Correction Algorithms (8)Conclusion References (A)Appendix A - Signal Quality Annotation (B)Appendix B - Fetal QRS Annotation (C)Appendix C - Data Recording GU

Phenotype Extraction: Estimation and Biometrical Genetic Analysis of Individual Dynamics

Within-person data can exhibit a virtually limitless variety of statistical patterns, but it can be difficult to distinguish meaningful features from statistical artifacts. Studies of complex traits have previously used genetic signals like twin-based heritability to distinguish between the two. This dissertation is a collection of studies applying state-space modeling to conceptualize and estimate novel phenotypic constructs for use in psychiatric research and further biometrical genetic analysis. The aims are to: (1) relate control theoretic concepts to health-related phenotypes; (2) design statistical models that formally define those phenotypes; (3) estimate individual phenotypic values from time series data; (4) consider hierarchical methods for biometrical genetic analysis of individual phenotypic variation