Data-assisted modeling of complex chemical and biological systems

Complex systems are abundant in chemistry and biology; they can be multiscale, possibly high-dimensional or stochastic, with nonlinear dynamics and interacting components. It is often nontrivial (and sometimes impossible), to determine and study the macroscopic quantities of interest and the equations they obey. One can only (judiciously or randomly) probe the system, gather observations and study trends. In this thesis, Machine Learning is used as a complement to traditional modeling and numerical methods to enable data-assisted (or data-driven) dynamical systems. As case studies, three complex systems are sourced from diverse fields: The first one is a high-dimensional computational neuroscience model of the Suprachiasmatic Nucleus of the human brain, where bifurcation analysis is performed by simply probing the system. Then, manifold learning is employed to discover a latent space of neuronal heterogeneity. Second, Machine Learning surrogate models are used to optimize dynamically operated catalytic reactors. An algorithmic pipeline is presented through which it is possible to program catalysts with active learning. Third, Machine Learning is employed to extract laws of Partial Differential Equations describing bacterial Chemotaxis. It is demonstrated how Machine Learning manages to capture the rules of bacterial motility in the macroscopic level, starting from diverse data sources (including real-world experimental data). More importantly, a framework is constructed though which already existing, partial knowledge of the system can be exploited. These applications showcase how Machine Learning can be used synergistically with traditional simulations in different scenarios: (i) Equations are available but the overall system is so high-dimensional that efficiency and explainability suffer, (ii) Equations are available but lead to highly nonlinear black-box responses, (iii) Only data are available (of varying source and quality) and equations need to be discovered. For such data-assisted dynamical systems, we can perform fundamental tasks, such as integration, steady-state location, continuation and optimization. This work aims to unify traditional scientific computing and Machine Learning, in an efficient, data-economical, generalizable way, where both the physical system and the algorithm matter

Nonlinear Dynamics

This volume covers a diverse collection of topics dealing with some of the fundamental concepts and applications embodied in the study of nonlinear dynamics. Each of the 15 chapters contained in this compendium generally fit into one of five topical areas: physics applications, nonlinear oscillators, electrical and mechanical systems, biological and behavioral applications or random processes. The authors of these chapters have contributed a stimulating cross section of new results, which provide a fertile spectrum of ideas that will inspire both seasoned researches and students

Modeling complex cell regulation in the zebrafish circadian clock

The interdisciplinary "systems biology" approach of combining traditional biological investigations with tools from the mathematical and computer sciences has enabled novel insights into many highly complex and dynamic biological systems. The use of models has, for instance, revealed much about the intricate feedback mechanisms and acute importance of gene regulatory networks, and one such network of special note is our internal time keeper, or circadian clock. The circadian clock plays a pivotal role in modulating critical physiological processes, and has also been implicated, either directly or indirectly, in a whole range of pathological states. This research project investigates how the underlying dynamics of the circadian clock in the zebrafish model organism may be captured by a mathematical model, considering in particular the entrainment effect due to external cues such as light. Simulated data is contrasted with experimental results from different light regime experiments to validate the model and guide its refinement. Furthermore, various statistical methods are implemented to process the raw data and support its analysis. Extending the initial deterministic approach to take into account stochastic effects and additive population level effects emerges as a powerful means of representing the circadian signal decay in prolonged darkness, as well as light initiated re-synchronization as a strong component of entrainment. Consequently, it emerges that stochastic effects may be considered an essential feature of the circadian clock in zebrafish. A further cornerstone of the project is the implementation of an integrated simulation environment, including a Sequential Monte Carlo parameter estimation function, which succeeds in predicting a range of previously determined and also novel suitable parameter values. However, considerable difficulties in obtaining parameter values that satisfy the entire range of important target values simultaneously highlights the inherent complexity of accurately simulating the circadian clock

Modeling diversity by strange attractors with application to temporal pattern recognition

This thesis belongs to the general discipline of establishing black-box models from real-word data, more precisely, from measured time-series. This is an old subject and a large amount of papers and books has been written about it. The main difficulty is to express the diversity of data that has essentially the same origin without creating confusion with data that has a different origin. Normally, the diversity of time-series is modeled by a stochastic process, such as filtered white noise. Often, it is reasonable to assume that the time series is generated by a deterministic dynamical system rather than a stochastic process. In this case, the diversity of the data is expressed by the variability of the parameters of the dynamical system. The parameter variability itself is then, once again, modeled by a stochastic process. In both cases the diversity is generated by some form of exogenous noise. In this thesis a further step has been taken. A single chaotic dynamical system is used to model the data and their diversity. Indeed, a chaotic system produces a whole family of trajectories that are different but nonetheless very similar. It is believed that chaotic dynamics not only are a convenient means to represent diversity but that in many cases the origin of diversity stems actually from chaotic dynamic. Since the approach of this thesis explores completely new grounds the most suitable kind of data is considered, namely approximately periodic signals. In nature such time-series are rather common, in particular the physiological signal of living beings, such as the electrocardiograms (ECG), parts of speech signals, electroencephalograms (EEG), etc. Since there are strong arguments in favor of the chaotic nature of these signals, they appear to be the best candidates for modeling diversity by chaos. It should be stressed however, that the modeling approach pursued in this thesis is thought to be quite general and not limited to signals produced by chaotic dynamics in nature. The intended application of the modeling effort in this thesis is temporal signal classification. The reason for this is twofold. Firstly, classification is one of the basic building block of any cognitive system. Secondly, the recently studied phenomenon of synchronization of chaotic systems suggests a way to test a signal against its chaotic model. The essential content of this work can now be formulated as follows. Thesis: The diversity of approximately periodic signals found in nature can be modeled by means of chaotic dynamics. This kind of modeling technique, together with selective properties of the synchronization of chaotic systems, can be exploited for pattern recognition purposes. This Thesis is advocated by means of the following five points. Models of randomness (Chapter 2) It is argued that the randomness observed in nature is not necessarily the result of exogenous noise, but it could be endogenally generated by deterministic chaotic dynamics. The diversity of real signals is compared with signals produced by the most common chaotic systems. Qualitative resonance (Chapter 3) The behavior of chaotic systems forced by periodic or approximately periodic input signals is studied theoretically and by numerical simulation. It is observed that the chaotic system "locks" approximately to an input signal that is related to its internal chaotic dynamic. In contrast to this, its chaotic behavior is reinforced when the input signal has nothing to do with its internal dynamics. This new phenomenon is called "qualitative resonance". Modeling and recognizing (Chapter 4) In this chapter qualitative resonance is used for pattern recognition. The core of the method is a chaotic dynamical system that is able to reproduce the class of time-series that is to be recognized. This model is excited in a suitable way by an input signal such that qualitative resonance is realized. This means that if the input signal belongs to the modeled class of time-series, the system approximately "locks" into it. If not, the trajectory of the system and the input signal remain unrelated. Automated design of the recognizer (Chapters 5 and 6) For the kind of signals considered in this thesis a systematic design method of the recognizer is presented. The model used is a system of Lur'e type, i.e. a model where the linear dynamic and nonlinear static part are separated. The identification of the model parameters from the given data proceed iteratively, adapting in turn the linear and the nonlinear part. Thus, the difficult nonlinear dynamical system identification task is decomposed into the easier problems of linear dynamical and nonlinear static system identification. The way to apply the approximately periodic input signal in order to realize qualitative resonance is chosen with the help of periodic control theory. Validation (Chapter 7) The pattern recognition method has been validated on the following examples — A synthetic example — Laboratory measurement from Colpitts oscillator — ECG — EEG — Vowels of a speech signals In the first four cases a binary classification and in the last example a classification with five classes was performed. To the best of the knowledge of the author the recognition method is original. Chaotic systems have been already used to produce pseudo-noise and to model signal diversity. Also, parameter identification of chaotic systems has been already carried out. However, the direct establishment of the model from the given data and its subsequent use for classification based on the phenomenon of qualitative resonance is entirely new

Theoretical Approaches in Non-Linear Dynamical Systems

From Preface: The 15th International Conference „Dynamical Systems - Theory and Applications” (DSTA 2019, 2-5 December, 2019, Lodz, Poland) gathered a numerous group of outstanding scientists and engineers who deal with widely understood problems of theoretical and applied dynamics. Organization of the conference would not have been possible without great effort of the staff of the Department of Automation, Biomechanics and Mechatronics of the Lodz University of Technology. The patronage over the conference has been taken by the Committee of Mechanics of the Polish Academy of Sciences and Ministry of Science and Higher Education of Poland. It is a great pleasure that our event was attended by over 180 researchers from 35 countries all over the world, who decided to share the results of their research and experience in different fields related to dynamical systems. This year, the DSTA Conference Proceedings were split into two volumes entitled „Theoretical Approaches in Non-Linear Dynamical Systems” and „Applicable Solutions in Non-Linear Dynamical Systems”. In addition, DSTA 2019 resulted in three volumes of Springer Proceedings in Mathematics and Statistics entitled „Control and Stability of Dynamical Systems”, „Mathematical and Numerical Approaches in Dynamical Systems” and „Dynamical Systems in Mechatronics and Life Sciences”. Also, many outstanding papers will be recommended to special issues of renowned scientific journals.Cover design: Kaźmierczak, MarekTechnical editor: Kaźmierczak, Mare