Publications by Eduardo D. Sontag in year 2022 |
Articles in journal or book chapters |
Metastasis can occur after malignant cells transition from the epithelial phenotype to the mesenchymal phenotype. This transformation allows cells to migrate via the circulatory system and subsequently settle in distant organs after undergoing the reverse transition. The core gene regulatory network controlling these transitions consists of a system made up of coupled SNAIL/miRNA-34 and ZEB1/miRNA-200 subsystems. In this work, we formulate a mathematical model and analyze its long-term behavior. We start by developing a detailed reaction network with 24 state variables. Assuming fast promoter and mRNA kinetics, we then show how to reduce our model to a monotone four-dimensional system. For the reduced system, monotone dynamical systems theory can be used to prove generic convergence to the set of equilibria for all bounded trajectories. The theory does not apply to the full model, which is not monotone, but we briefly discuss results for singularly-perturbed monotone systems that provide a tool to extend convergence results from reduced to full systems, under appropriate time separation assumptions. |
In order to control highly-contagious and prolonged outbreaks, public health authorities intervene to institute social distancing, lock-down policies, and other Non-Pharmaceutical Interventions (NPIs). Given the high social, educational, psychological, and economic costs of NPIs, authorities tune them, alternatively tightening up or relaxing rules, with the result that, in effect, a relatively flat infection rate results. For example, during the summer of 2020 in parts of the United States, daily COVID-19 infection numbers dropped to a plateau. This paper approaches NPI tuning as a control-theoretic problem, starting from a simple dynamic model for social distancing based on the classical SIR epidemics model. Using a singular-perturbation approach, the plateau becomes a Quasi-Steady-State (QSS) of a reduced two-dimensional SIR model regulated by adaptive dynamic feedback. It is shown that the QSS can be assigned and it is globally asymptotically stable. Interestingly, the dynamic model for social distancing can be interpreted as a nonlinear integral controller. Problems of data fitting and parameter identifiability are also studied for this model. This letter also discusses how this simple model allows for a meaningful study of the effect of population size, vaccinations, and the emergence of second waves. |
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as Gene Regulatory Networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators in addition to local transcription factors, and show the counter-intuitive consequences of such interactions. We apply our approach to recent experimental findings on the Epithelial-Mesenchymal Transition (EMT). We show that it can explain the puzzling experimental data as well provide new verifiable predictions. |
Internal models are nowadays customarily used in different domains of science and engineering to describe how living organisms or artificial computational units embed their acquired knowledge about recurring events taking place in the surrounding environment. This article reviews the internal model principle in control theory, bioengineering, and neuroscience, illustrating the fundamental concepts and theoretical developments of the last few decades of research. |
Recent work on data-driven control and reinforcement learning has renewed interest in a relatively old field in control theory: model-free optimal control approaches which work directly with a cost function and do not rely upon perfect knowledge of a system model. Instead, an "oracle" returns an estimate of the cost associated to, for example, a proposed linear feedback law to solve a linear-quadratic regulator problem. This estimate, and an estimate of the gradient of the cost, might be obtained by performing experiments on the physical system being controlled. This motivates in turn the analysis of steepest descent algorithms and their associated gradient differential equations. This paper studies the effect of errors in the estimation of the gradient, framed in the language of input to state stability, where the input represents a perturbation from the true gradient. Since one needs to study systems evolving on proper open subsets of Euclidean space, a self-contained review of input to state stability definitions and theorems for systems that evolve on such sets is included. The results are then applied to the study of noisy gradient systems, as well as the associated steepest descent algorithms. |
Differentiation within multicellular organisms is a complex process that helps to establish spatial patterning and tissue formation within the body. Often, the differentiation of cells is governed by morphogens and intercellular signaling molecules that guide the fate of each cell, frequently using toggle-like regulatory components. Synthetic biologists have long sought to recapitulate patterned differentiation with engineered cellular communities and various methods for differentiating bacteria have been invented. Here, we couple a synthetic co-repressive toggle switch with intercellular signaling pathways to create a "quorum-sensing toggle." We show that this circuit not only exhibits population-wide bistability in a well-mixed liquid environment, but also generates patterns of differentiation in colonies grown on agar containing an externally supplied morphogen. |
Conference articles |
Due to the usage of social distancing as a means to control the spread of the novel coronavirus disease COVID-19, there has been a large amount of research into the dynamics of epidemiological models with time-varying transmission rates. Such studies attempt to capture population responses to differing levels of social distancing, and are used for designing policies which both inhibit disease spread but also allow for limited economic activity. One common criterion utilized for the recent pandemic is the peak of the infected population, a measure of the strain placed upon the health care system; protocols which reduce this peak are commonly said to "flatten the curve". In this work, we consider a very specialized distancing mandate, which consists of one period of fixed length of distancing, and addresses the question of optimal initiation time. We prove rigorously that this time is characterized by an equal peaks phenomenon: the optimal protocol will experience a rebound in the infected peak after distancing is relaxed, which is equal in size to the peak when distancing is commenced. In the case of a non-perfect lockdown (i.e. disease transmission is not completely suppressed), explicit formulas for the initiation time cannot be computed, but implicit relations are provided which can be pre-computed given the current state of the epidemic. Expected extensions to more general distancing policies are also hypothesized, which suggest designs for the optimal timing of non-overlapping lockdowns. |
Systems theory can play an important in unveiling fundamental limitations of learning algorithms and architectures when used to control a dynamical system, and in suggesting strategies for overcoming these limitations. As an example, a feedforward neural network cannot stabilize a double integrator using output feedback. Similarly, a recurrent NN with differentiable activation functions that stabilizes a non-strongly stabilizable system must be itself open loop unstable, a fact that has profound implications for training with noisy, finite data. A potential solution to this problem, motivated by results on stabilization with periodic control, is the use of neural nets with periodic resets, showing that indeed systems theoretic analysis is instrumental in developing architectures capable of controlling certain classes of unstable systems. This short conference paper also argues that when the goal is to learn control oriented models, the loss function should reflect closed loop, rather than open loop model performance, a fact that can be accomplished by using gap-metric motivated loss functions. |
In this paper, we investigate the problem of finding a sparse sensor and actuator (S/A) schedule that minimizes the approximation error between the input-output behavior of a fully sensed/actuated bilinear system and the system with the scheduling. The quality of this approximation is measuredby an H2-like metric, which is defined for a bilinear (time-varying) system with S/A scheduling based on the discrete Laplace transform of its Volterra kernels. First, we discuss the difficulties of designing S/A schedules for bilinear systems, which prevented us from finding a polynomial time algorithmfor solving the problem. We then propose a polynomial-time S/A scheduling heuristic that selects a fraction of sensors and node actuators at each time step while maintaining a small approximation error between the input-output behavior of thefully sensed/actuated system and the one with S/A scheduling in this H2-based sense. Numerical experiments illustrate the good approximation quality of our proposed methods. |
Internal reports |
For a general class of translationally invariant systems with a specific category of nonlinearity in the output, this paper presents necessary and sufficient conditions for global observability. Critically, this class of systems cannot be stabilized to an isolated equilibrium point by dynamic output feedback. These analyses may help explain the active sensing movements made by animals when they perform certain motor behaviors, despite the fact that these active sensing movements appear to run counter to the primary motor goals. The findings presented here establish that active sensing underlies the maintenance of observability for such biological systems, which are inherently nonlinear due to the presence of the high-pass sensor dynamics. |
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