Comments for Mathematical Matters of the Heart
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Mirams' Modelling Musings. A place to put interesting observations, problems, and other musings that aren't big enough for whole journal articles!Fri, 28 Feb 2020 15:06:54 +0000
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Comment on Numerical errors from ODE solvers can mess up optimisation and inference very easily by Our new review on fitting cardiac models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/10/17/ode-errors-and-optimisation/#comment-626
Fri, 28 Feb 2020 15:06:54 +0000http://mirams.wordpress.com/?p=1307#comment-626[…] Numerical convergence – with respect to parameter changes as discussed on the blog before. […]
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Comment on Three potassium channel modelling papers by Our new review on fitting cardiac models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2019/09/08/three-herg-papers/#comment-625
Fri, 28 Feb 2020 15:06:52 +0000http://mirams.wordpress.com/?p=1365#comment-625[…] – mainly discussed in the “sinusoidal wave” paper and “4 ways to fit“, it can be very sensible to constrain parameters with either a transform or a prior to only […]
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Comment on Short and rich voltage-clamp protocols by Our new review on fitting cardiac models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/05/02/sine-wave/#comment-624
Fri, 28 Feb 2020 15:06:50 +0000http://mirams.wordpress.com/?p=950#comment-624[…] – mainly discussed in the “sinusoidal wave” paper and “4 ways to fit“, it can be very sensible to constrain parameters with […]
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Comment on Triangles and Conductances by Our new review on fitting cardiac models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2015/06/08/triangles/#comment-623
Fri, 28 Feb 2020 15:06:48 +0000http://mirams.wordpress.com/?p=317#comment-623[…] Parameter Transforms – make a surprising amount of difference to even simple optimisation problems, as seen in Figure 8 which uses a simple dose-response curve as the example. We included suggested transforms for ion channel rate parameters, as seen in Fig 3 of Michael Clerx’s “Four Ways to Fit An Ion Channel Model” paper, and there is much more on the relative performance of an optimiser with different transforms in the supplement of that paper. We’ve also included some that we found useful when fitting conductances in action potential models. […]
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Comment on Model Complexity by Our new review on fitting cardiac models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2015/10/20/model-complexity/#comment-622
Fri, 28 Feb 2020 15:06:41 +0000http://mirams.wordpress.com/?p=485#comment-622[…] Overfitting, training and validation, as I’ve talked about on this blog before. […]
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Comment on Three potassium channel modelling papers by Job Available: Statistical inference for mechanistic models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2019/09/08/three-herg-papers/#comment-604
Fri, 04 Oct 2019 13:25:17 +0000http://mirams.wordpress.com/?p=1365#comment-604[…] our research, which we’ve been working on recently in these papers – sinusoidal protocols, high-throughput model building. Open challenges on how to do model selection as well as parameterisation, whilst accounting for […]
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Comment on Short and rich voltage-clamp protocols by Job Available: Statistical inference for mechanistic models | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/05/02/sine-wave/#comment-603
Fri, 04 Oct 2019 13:25:15 +0000http://mirams.wordpress.com/?p=950#comment-603[…] big pre-requisite for our research, which we’ve been working on recently in these papers – sinusoidal protocols, high-throughput model building. Open challenges on how to do model selection as well as […]
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Comment on Short and rich voltage-clamp protocols by Hodgkin-Huxley models and Markov equivalents | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/05/02/sine-wave/#comment-602
Mon, 30 Sep 2019 10:48:07 +0000http://mirams.wordpress.com/?p=950#comment-602[…] Hodgkin & Huxley did some incredible work in the 1930s-50s on ion currents flowing through biological membranes. Despite not knowing what an ion channel was, they managed to work out an incredibly accurate predictive mathematical model for the currents that flow through them, and solved the differential equations numerically on a hand calculator. These models are still fundamental to a lot of electrophysiology work – we are still publishing Hodgkin-Huxley style models of particular currents (we just tried to parameterise them better)! […]
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Comment on Numerical errors from ODE solvers can mess up optimisation and inference very easily by Three potassium channel modelling papers | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/10/17/ode-errors-and-optimisation/#comment-583
Sun, 08 Sep 2019 11:08:18 +0000http://mirams.wordpress.com/?p=1307#comment-583[…] of parameter transforms, sensible bounds for voltage-dependent ion channel rate parameters, and the solver tolerance issue discussed on this blog […]
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Comment on Short and rich voltage-clamp protocols by Three potassium channel modelling papers | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/05/02/sine-wave/#comment-582
Sun, 08 Sep 2019 11:08:14 +0000http://mirams.wordpress.com/?p=950#comment-582[…] are sensible to use for doing this. In a lot of ways this paper is the partner for Kylie’s sinusoidal clamp paper that we published last year, which explains how people have typically done it, and then goes on to […]
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