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, 04 Oct 2019 13:25:17 +0000
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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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Comment on Postdoctoral Research Positions Available by SMB Digest Volume 18 Issue 53
https://mirams.wordpress.com/2018/12/15/positions-available/#comment-498
Mon, 24 Dec 2018 15:31:45 +0000http://mirams.wordpress.com/?p=1340#comment-498[…] Applications open now and will close on 16th January. Please see Postdoctoral Research Positions Available […]
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Comment on Short and rich voltage-clamp protocols by Postdoctoral Research Positions Available | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/05/02/sine-wave/#comment-493
Sat, 15 Dec 2018 10:40:14 +0000http://mirams.wordpress.com/?p=950#comment-493[…] Deciding appropriate baseline models for the ion currents (see my recent talk in Banff on this topic), and parameterising these models effectively is a big pre-requisite for this, which we’ve been working on recently. […]
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Comment on A report on the Toronto CiPA in-silico modelling workshop by Postdoctoral Research Positions Available | Mathematical Matters of the Heart
https://mirams.wordpress.com/2018/07/16/cipa-workshop/#comment-492
Sat, 15 Dec 2018 10:40:09 +0000http://mirams.wordpress.com/?p=1258#comment-492[…] for drug safety studies”. As you’ll see from some of the previous blog articles, and associated work on the CiPA project, we’ve been working on ways to understand and predict how certain pharmaceutical drugs are […]
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Comment on Numerical errors from ODE solvers can mess up optimisation and inference very easily by Gary Mirams
https://mirams.wordpress.com/2018/10/17/ode-errors-and-optimisation/#comment-481
Wed, 24 Oct 2018 11:21:39 +0000http://mirams.wordpress.com/?p=1307#comment-481Some interesting comments from Chris Rackauckas who develops the Julia ODE solvers on a twitter thread above this tweet: https://twitter.com/ChrisRackauckas/status/1053018882972106752
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Comment on Numerical errors from ODE solvers can mess up optimisation and inference very easily by Gary Mirams
https://mirams.wordpress.com/2018/10/17/ode-errors-and-optimisation/#comment-480
Tue, 23 Oct 2018 15:48:02 +0000http://mirams.wordpress.com/?p=1307#comment-480Interesting Raf thanks – I’ve seen Gaussian Processes (through time) used to describe this sort of ‘model discrepancy’ term (Kennedy & O’Hagan style). Or are you considering a single scalar additive random variable (that describes error in the overall likelihood?) drawn from a distribution whose properties are a function of parameters?
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