This Title All WIREs
How to cite this WIREs title:
WIREs Syst Biol Med
Impact Factor: 4.192

Calibration of ionic and cellular cardiac electrophysiology models

Full article on Wiley Online Library:   HTML PDF

Can't access this content? Tell your librarian.

Abstract Cardiac electrophysiology models are among the most mature and well‐studied mathematical models of biological systems. This maturity is bringing new challenges as models are being used increasingly to make quantitative rather than qualitative predictions. As such, calibrating the parameters within ion current and action potential (AP) models to experimental data sets is a crucial step in constructing a predictive model. This review highlights some of the fundamental concepts in cardiac model calibration and is intended to be readily understood by computational and mathematical modelers working in other fields of biology. We discuss the classic and latest approaches to calibration in the electrophysiology field, at both the ion channel and cellular AP scales. We end with a discussion of the many challenges that work to date has raised and the need for reproducible descriptions of the calibration process to enable models to be recalibrated to new data sets and built upon for new studies. This article is categorized under: Analytical and Computational Methods > Computational Methods Physiology > Mammalian Physiology in Health and Disease Models of Systems Properties and Processes > Cellular Models
Cardiac electrophysiology models and parameters to calibrate. Left: currents through ion channels or active pumps are modeled using Markov or Hodgkin–Huxley models which contain several reaction rate coefficients. These rates determine the current kinetics, and finding the parameters of these rates is the subject of Section 3. Right: an action potential model contains (among other things) submodels for its ion channels, pumps, and transporters, and the magnitude of each current type depends on a parameter for its maximum conductance or permeability. Section 4 deals with the problem of setting these parameters
[ Normal View | Magnified View ]
Improved optimization with parameter transforms. Left: blue crosses indicate some dose–response data points in arbitrary units. The orange line represents the best fit with smallest root‐mean‐square error (RMSE). The yellow and red lines indicate possible different initial guesses. Middle: untransformed parameter space—a heatmap of RMSE for across a wide range of parameters. Twenty initial guesses (gray crosses) and final optimization locations (orange/purple circles) are shown linked with dashed lines. Only half of the initial guesses reach the global optimum with the others becoming stuck (purple circles) due to the optimizer seeing a “flat” surface. Right: transformed parameter space (ln [IC50])—in this case all 20 initial guesses sampled across this space reach the global minimum
[ Normal View | Magnified View ]
A summary of some of the methods outlined in this review used to calibrate existing models of the action potential (AP). Methods are colored according to whether they represent a generic approach (red), cell‐specific approach (blue), or patient‐specific approach (green). Generic approaches shown include recalibrating ionic current balance using clinical gene mutation data (Mann et al., ), by accounting for co‐regulation of ion‐channel expression (Ballouz et al., ), and based on drug block measurements (Dutta et al., ). Cell‐specific approaches illustrated include adding the membrane resistance, Rm, to the function objective (Kaur, Nygren, & Vigmond, ), using information‐rich voltage and current clamp electrophysiology protocols to identify cell‐specific conductances (Groenendaal et al., ), and using genetic algorithms to adjust ionic conductances based on dynamic clamp experiments (Devenyi et al., ). The patient‐specific approach shown involves using endocardial electrogram clinical mapping data to tailor simplified models of human atrial electrophysiology to individual patients (Corrado et al., , )
[ Normal View | Magnified View ]
The evolving complexity of cardiac AP models. Selected action potential model schematics are presented in chronological order, including the models of Noble () (the first model of the cardiac AP), McAllister et al. () (which added more heart‐specific currents), DiFrancesco and Noble () (which added ion pumps and exchangers), Hilgemann and Noble () (which represented a significant advance in modeling calcium dynamics), Jafri et al. () (which added calcium dynamics to the commonly used Luo & Rudy, model), Saucerman, Brunton, Michailova, and McCulloch () (which modeled β‐adrenergic signaling), and Decker, Heijman, Silva, Hund, and Rudy () (which included Markov formulations of both ICaL and IKs). All cell‐model schematics are available from (https://models.cellml.org/cellml) under a CC‐BY license. AP, action potential
[ Normal View | Magnified View ]
Four ways of fitting a voltage‐dependent ion‐channel model to whole‐cell current experiments, as described in Clerx, Beattie, et al. (). (a) Method 1. Currents are measured using classical voltage‐clamp protocols and analyzed to obtain time constants and steady‐state (in)activation levels for several voltages. Next, curves are fit to the obtained points and inserted directly into the model. (b) Method 2. Applying the same voltage‐clamp protocols in a simulation leads to a simulated set of currents, that can be similarly processed to obtain simulated (in)activation steady states and time constants. Next, an error measure is defined between the simulated and experimental summary data points, and minimized using numerical optimization. (c) Method 3. Like Method 2, but now the error measure is defined directly on the current traces, eliminating the need to perform processing to generate summary curves. (d) Method 4. Like Method 3, but using a single condensed voltage‐clamp protocol instead of a series of classical protocols
[ Normal View | Magnified View ]
(a) An energy barrier model of a channel with two stable states: activated (A) and deactivated (D). This leads naturally to a reaction scheme as shown below, with reaction rates k1 and k2. (b) Adding a second, independent, transition leads to a two “gate” Hodgkin–Huxley model including an inactivated (I) and recovered (R) state. The equivalent Markov model representation is shown to its right. (c) Markov models are a more general class of models which would allow transitions between any different states
[ Normal View | Magnified View ]
Consequences of unidentifiable parameters. Top: two voltage‐clamp protocols—(Left) an action potential clamp and (Right) a “staircase” clamp from Lei, Clerx, Beattie, et al. (). In this example we generate synthetic data under these protocols (shown with a gray jagged line) using the ten Tusscher, Noble, Noble, and Panfilov () IKr model, saying for this example that this model with its published parameters represents the “ground truth.” Twelve kinetic parameters were set as per the original paper values (and conductance was fixed to one for simplicity), then a realistic amount of Gaussian noise () was added to represent a whole‐cell patch‐clamp expression system experiment. Middle: the currents that result from the voltage‐clamp protocols above: (left) in blue we show 45 of the best fits to the action potential clamp that we achieved from different initial guesses, all of these fits are closely overlaid and appear to be excellent. (Right) we use these parameter sets to make predictions of staircase protocol currents, shown in orange. The simulations diverge wildly from the data and often make very bad predictions in this new setting. Bottom: (right) we perform the opposite procedure and fit the 12 kinetic parameters to the staircase protocol current, in this case all 45 fits (blue) are tightly constrained and indeed return almost the same parameter set (close to the one that generated the synthetic data). (Left) predictions from these fits (orange) are all excellent for the action potential clamp. This example is based on one from Fink, Niederer, et al. ()
[ Normal View | Magnified View ]
A simple example illustrating interpolation, extrapolation, and overfitting. (a) The gray line in all plots is , the time it would take a mass to fall a distance y from rest under gravitational acceleration g = 9.81 m/s2 (with no air resistance). The yellow circles denote observations we might make when dropping a mass from different heights up a tower if there were normally distributed error in timing the process with a stopwatch (σ = 0.1 s in this case). (b) If we were taking a purely statistical approach we might fit the red straight line through these data. This line would be reliable for interpolation between the measured yellow data points, but bad for extrapolation outside them (the red line predicts it would take 0.78 s for the mass to fall no distance at all at height = 0). (c) We could fit a polynomial spline to the data, shown in green. This curve goes through all eight data points exactly (in this case the polynomial is of degree 7, with eight parameters), but by doing so we are fitting the noise in the data and this line is less reliable for interpolation, and very bad for extrapolation, even compared to the straight line in (b). (d) The blue dashed line is what we get when fitting g in the (correct) mechanistic model , in this case a best fit (least squares) returns g = 9.84 m/s2 rather than 9.81 m/s2 due to the noise on the data, but this would still provide reliable interpolation and extrapolation for many contexts of use
[ Normal View | Magnified View ]

Browse by Topic

Models of Systems Properties and Processes > Cellular Models
Physiology > Mammalian Physiology in Health and Disease
Analytical and Computational Methods > Computational Methods

Access to this WIREs title is by subscription only.

Recommend to Your
Librarian Now!

The latest WIREs articles in your inbox

Sign Up for Article Alerts