From Cardiac Cells to Genetic Regulatory Networks

Characterizing behavioural differentiation in gene regulatory networks with representation graphs

We introduce the formal notion of representation graphs, encapsulating the state space structure of gene regulatory network models in a compact and concise form that highlights the most significant features of stable states and differentiation processes leading to distinct stability regions. The concept has been developed in the context of a hybrid system-based gene network modelling framework; however, we anticipate that it can also be adapted to other approaches of modelling gene networks in discrete terms. We describe a practical algorithm for representation graph computation as well as two case studies demonstrating their real-world application and utility. The first case study presents models for three phage viruses. It shows that the process of differentiation into lytic and lysogenic behavioural states for all these models is described by the same representation graph despite the distinctive underlying mechanisms for differentiation. The second case study shows the advantages of our approach for modelling the process of myeloid cell differentiation from a common progenitor into different cell types. Both case studies also demonstrate the potential of the representation graph approach for deriving and validating hypotheses about regulatory interactions that must be satisfied for biologically viable behaviours.

Modeling and Analysis of Cardiac Hybrid Cellular Automata via GPU-Accelerated Monte Carlo Simulation

The heart consists of a complex network of billions of cells. Under physiological conditions, cardiac cells propagate electrical signals in space, generating the heartbeat in a synchronous and coordinated manner. When such a synchronization fails, life-threatening events can arise. The inherent complexity of the underlying nonlinear dynamics and the large number of biological components involved make the modeling and the analysis of electrophysiological properties in cardiac tissue still an open challenge. We consider here a Hybrid Cellular Automata (HCA) approach modeling the cardiac cell-cell membrane resistance with a free variable. We show that the modeling approach can reproduce important and complex spatiotemporal properties paving the ground for promising future applications. We show how GPU-based technology can considerably accelerate the simulation and the analysis. Furthermore, we study the cardiac behavior within a unidimensional domain considering inhomogeneous resistance and we perform a Monte Carlo analysis to evaluate our approach.

Reachability Analysis Using Message Passing over Tree Decompositions

In this paper, we study efficient approaches to reachability analysis for discrete-time nonlinear dynamical systems when the dependencies among the variables of the system have low treewidth. Reachability analysis over nonlinear dynamical systems asks if a given set of target states can be reached, starting from an initial set of states. This is solved by computing conservative over approximations of the reachable set using abstract domains to represent these approximations. However, most approaches must tradeoff the level of conservatism against the cost of performing analysis, especially when the number of system variables increases. This makes reachability analysis challenging for nonlinear systems with a large number of state variables. Our approach works by constructing a dependency graph among the variables of the system. The tree decomposition of this graph builds a tree wherein each node of the tree is labeled with subsets of the state variables of the system. Furthermore, the tree decomposition satisfies important structural properties. Using the tree decomposition, our approach abstracts a set of states of the high dimensional system into a tree of sets of lower dimensional projections of this state. We derive various properties of this abstract domain, including conditions under which the original high dimensional set can be fully recovered from its low dimensional projections. Next, we use ideas from message passing developed originally for belief propagation over Bayesian networks to perform reachability analysis over the full state space in an efficient manner. We illustrate our approach on some interesting nonlinear systems with low treewidth to demonstrate the advantages of our approach.

Cardiac Electrical Modeling for Closed-Loop Validation of Implantable Devices

OBJECTIVE

Evaluating and testing cardiac electrical devices in a closed-physiologic-loop can help design safety, but this is rarely practical or comprehensive. Furthermore, in silico closed-loop testing with biophysical computer models cannot meet the requirements of time-critical cardiac device systems, while simplified models meeting time-critical requirements may not have the necessary dynamic features. We propose a new high-level (abstracted) physiologically-based computational heart model that is time-critical and dynamic.

METHODS

The model comprises cardiac regional cellular-electrophysiology types connected by a path model along a conduction network. The regional electrophysiology and paths are modeled with hybrid automata that capture non-linear dynamics, such as action potential and conduction velocity restitution and overdrive suppression. The hierarchy of pacemaker functions is incorporated to generate sinus rhythms, while abnormal automaticity can be introduced to form a variety of arrhythmias such as escape ectopic rhythms. Model parameters are calibrated using experimental data and prior model simulations.

CONCLUSION

Regional electrophysiology and paths in the model match human action potentials, dynamic behavior, and cardiac activation sequences. Connected in closed loop with a pacing device in DDD mode, the model generates complex arrhythmia such as atrioventricular nodal reentry tachycardia. Such device-induced outcomes have been observed clinically and we can establish the key physiological features of the heart model that influence the device operation.

SIGNIFICANCE

These findings demonstrate how an abstract heart model can be used for device validation and to design personalized treatment.

Closed-Loop Quantitative Verification of Rate-Adaptive Pacemakers

Rate-adaptive pacemakers are cardiac devices able to automatically adjust the pacing rate in patients with chronotropic incompetence, i.e., whose heart is unable to provide an adequate rate at increasing levels of physical, mental, or emotional activity. These devices work by processing data from physiological sensors in order to detect the patient’s activity and update the pacing rate accordingly. Rate adaptation parameters depend on many patient-specific factors, and effective personalization of such treatments can only be achieved through extensive exercise testing, which is normally intolerable for a cardiac patient. In this work, we introduce a data-driven and model-based approach for the automated verification of rate-adaptive pacemakers and formal analysis of personalized treatments. To this purpose, we develop a novel dual-sensor pacemaker model where the adaptive rate is computed by blending information from an accelerometer, and a metabolic sensor based on the QT interval. Our approach enables personalization through the estimation of heart model parameters from patient data (electrocardiogram), and closed-loop analysis through the online generation of synthetic, model-based QT intervals and acceleration signals. In addition to personalization, we also support the derivation of models able to account for the varied characteristics of a virtual patient population, thus enabling safety verification of the device. To capture the probabilistic and nonlinear dynamics of the heart, we define a probabilistic extension of timed I/O automata with data and employ statistical model checking for quantitative verification of rate modulation. We evaluate our rate-adaptive pacemaker design on three subjects and a pool of virtual patients, demonstrating the potential of our approach to provide rigorous, quantitative insights into the closed-loop behavior of the device under different exercise levels and heart conditions.

Computational Modeling, Formal Analysis, and Tools for Systems Biology

As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.

Systems biology of cancer: a challenging expedition for clinical and quantitative biologists

A systems-biology approach to complex disease (such as cancer) is now complementing traditional experience-based approaches, which have typically been invasive and expensive. The rapid progress in biomedical knowledge is enabling the targeting of disease with therapies that are precise, proactive, preventive, and personalized. In this paper, we summarize and classify models of systems biology and model checking tools, which have been used to great success in computational biology and related fields. We demonstrate how these models and tools have been used to study some of the twelve biochemical pathways implicated in but not unique to pancreatic cancer, and conclude that the resulting mechanistic models will need to be further enhanced by various abstraction techniques to interpret phenomenological models of cancer progression.

Curvature analysis of cardiac excitation wavefronts

We present the Spiral Classification Algorithm (SCA), a fast and accurate algorithm for classifying electrical spiral waves and their associated breakup in cardiac tissues. The classification performed by SCA is an essential component of the detection and analysis of various cardiac arrhythmic disorders, including ventricular tachycardia and fibrillation. Given a digitized frame of a propagating wave, SCA constructs a highly accurate representation of the front and the back of the wave, piecewise interpolates this representation with cubic splines, and subjects the result to an accurate curvature analysis. This analysis is more comprehensive than methods based on spiral-tip tracking, as it considers the entire wave front and back. To increase the smoothness of the resulting symbolic representation, the SCA uses weighted overlapping of adjacent segments which increases the smoothness at join points. SCA has been applied to a number of representative types of spiral waves, and, for each type, a distinct curvature evolution in time (signature) has been identified. Distinct signatures have also been identified for spiral breakup. These results represent a significant first step in automatically determining parameter ranges for which a computational cardiac-cell network accurately reproduces a particular kind of cardiac arrhythmia, such as ventricular fibrillation.