Understanding Epidemiology Models(arstechnica.com)
arstechnica.com
Understanding Epidemiology Models
https://arstechnica.com/science/2020/06/understanding-epidemiology-models/
18 comments
That's a very interesting approach -- I really enjoyed reading your transcript, and your implementation of the system as a circuit is really quite unique!
I think you're onto something with your motivation: most epidemiological models basically consider the infection/mortality/recovery rate to be fixed, or at most modifiable over many years by national investments in health. It seems that, before COVID-19, nobody had really thought that the trajectory of an ongoing pandemic could be changed, so I haven't seen any models which incorporate that.
But I think it's unfair to use scare-quotes around "models". The truth is, there is a tremendous amount of insight to be gained from those "models" (SIS, SIR, SEIR, etc.). I mean, your own proposed model is even just a small variation of one of the classical models, and you don't even show that it makes better long-term predictions, which is what you criticise in the other models.
Sorry, that was a long-winded way of basically saying: Great work, but don't discount the classic models entirely!
I think you're onto something with your motivation: most epidemiological models basically consider the infection/mortality/recovery rate to be fixed, or at most modifiable over many years by national investments in health. It seems that, before COVID-19, nobody had really thought that the trajectory of an ongoing pandemic could be changed, so I haven't seen any models which incorporate that.
But I think it's unfair to use scare-quotes around "models". The truth is, there is a tremendous amount of insight to be gained from those "models" (SIS, SIR, SEIR, etc.). I mean, your own proposed model is even just a small variation of one of the classical models, and you don't even show that it makes better long-term predictions, which is what you criticise in the other models.
Sorry, that was a long-winded way of basically saying: Great work, but don't discount the classic models entirely!
Thank you! Oh I absolutely agree -- the core of my model is a 100%-standard compartmental SIR model. https://en.wikipedia.org/wiki/Compartmental_models_in_epidem...
But, the differential equation models shown on the Wikipedia page have no policy/response variables, and basically assume an unintelligent, static null response. That was what was feared initially (early March), but of course fear drives behavior, so there's a closed-loop system here. That's my small variation and I think it's probably an important one.
But, the differential equation models shown on the Wikipedia page have no policy/response variables, and basically assume an unintelligent, static null response. That was what was feared initially (early March), but of course fear drives behavior, so there's a closed-loop system here. That's my small variation and I think it's probably an important one.
This is the same reason why such models are no longer popular in social sciences since the 1970s: responses to policy change are complex and one usually tries (with more or less success, which is another topic) to model the micro behavior, so the incentives of actors, rather than find fixed systemic parameters.
Cf. Lucas critique
Ironically, models without such complexities are often referred to as engineering or physics inspired - from the observation that human behavior is more complex and interdependent than the objects under consideration in physical systems. Natural scientists and engineers delving into social systems frequently fall prey to these issues.
Ironically, models without such complexities are often referred to as engineering or physics inspired - from the observation that human behavior is more complex and interdependent than the objects under consideration in physical systems. Natural scientists and engineers delving into social systems frequently fall prey to these issues.
Have you had any luck in informing your local authorities of your results so to try to advise them towards better policy decisions?
I just published this last week and haven't contacted any local authorities. I have been able to get responses from a few national/global policymakers (so far: World Bank and a Washington D.C. defense think-tank).
There are a lot of parameters.
Assuming the models are good, the inputs makes all the difference and the input numbers have been largely off at least till recently.
I would be interested to see how the values change with a specific parameter movement.
It would be also good to see a montecarlo simulation after defining a realistic distribution of the parameters to find how the numbers of infected and death change.
I toyed with a simple (probably semplistic model) early on, I was finding that because of the exponential nature of the relations, small changes were producing huge changes in the output. That was telling me that unless we could get more realistic data we could go from having a number of death smaller than the actual number given for the flu to numbers more than 1-2 orders of magnitude larger...
Assuming the models are good, the inputs makes all the difference and the input numbers have been largely off at least till recently.
I would be interested to see how the values change with a specific parameter movement.
It would be also good to see a montecarlo simulation after defining a realistic distribution of the parameters to find how the numbers of infected and death change.
I toyed with a simple (probably semplistic model) early on, I was finding that because of the exponential nature of the relations, small changes were producing huge changes in the output. That was telling me that unless we could get more realistic data we could go from having a number of death smaller than the actual number given for the flu to numbers more than 1-2 orders of magnitude larger...
I know I'm being cynical, but I'm not sure anyone understands these things. If the top scientists from well-funded teams came up with estimates that were so wildly off, I'm not sure why we have any hope of getting these things right.
We need a better philosophical explanation. If you ask me, the biggest issue is that they assume that it just spreads kind of randomly. That doesn't seem to be what happened with COVID-19. It flourished in some parts and limped along in others. We have theories about subways or air pollution but none are very well correlated.
And then there's Farr's law which doesn't match these models very well.
We need a better philosophical explanation. If you ask me, the biggest issue is that they assume that it just spreads kind of randomly. That doesn't seem to be what happened with COVID-19. It flourished in some parts and limped along in others. We have theories about subways or air pollution but none are very well correlated.
And then there's Farr's law which doesn't match these models very well.
> If the top scientists from well-funded teams came up with estimates that were so wildly off, I'm not sure why we have any hope of getting these things right.
I think there's a lot of confusion from the general public about how to evaluate models. A modeling being "correct" is sometimes not possible, and useful, sometimes a model has to be used instead to reduce uncertainty, not to exactly predict X amount of cases in Y amount of time. There's just so much randomness in systems that prevent accuracy in predictions.
I think there's a lot of confusion from the general public about how to evaluate models. A modeling being "correct" is sometimes not possible, and useful, sometimes a model has to be used instead to reduce uncertainty, not to exactly predict X amount of cases in Y amount of time. There's just so much randomness in systems that prevent accuracy in predictions.
> If the top scientists from well-funded teams came up with estimates that were so wildly off, I'm not sure why we have any hope of getting these things right.
A "top" scientist produces a ton of publications and brings in a lot of grant money. You don't need to be right to be a "top" scientist. Change the incentives and you'll change the outcomes.
The failure of blind predictions (i.e., without the opportunity to calibrate the model to the data) says more about the culture than whether this is possible. Weather forecasting does a fairly good job:
https://journals.ametsoc.org/doi/full/10.1175/2011MWR3525.1
It's instructive to figure out why. I'd say it's because weather forecasters have a ton of data, forecasts can quickly be proven right or wrong (so they get a lot of feedback), and they have a culture emphasizing accuracy. It also helps that they're modeling physics, though various submodels (turbulence, etc.) may not be any more credible than the models in epidemiology.
Blind predictions have been tried in a variety of domains. I'm most familiar with computational fluid dynamics, e.g.:
https://www.sciencedirect.com/science/article/abs/pii/S03797...
https://ntrs.nasa.gov/search.jsp?R=19970027380
(There are many more examples.)
As I recall, it's not uncommon for different groups even using the same software to come up with radically different predictions. I'd say scientists and engineers need much more practice making blind predictions. Blind prediction exercises should occur regularly.
There's a yearly competition to predict the heat release rate of a Christmas tree: https://fpe.umd.edu/events/christmas-fire-safety-demo
I entered one year. Rather than using a fancy computer model, I merely smoothed last year's data and scaled it by the ratio of the mass of this year's tree to the mass of last year's tree. As I recall, I did better than most!
A "top" scientist produces a ton of publications and brings in a lot of grant money. You don't need to be right to be a "top" scientist. Change the incentives and you'll change the outcomes.
The failure of blind predictions (i.e., without the opportunity to calibrate the model to the data) says more about the culture than whether this is possible. Weather forecasting does a fairly good job:
https://journals.ametsoc.org/doi/full/10.1175/2011MWR3525.1
It's instructive to figure out why. I'd say it's because weather forecasters have a ton of data, forecasts can quickly be proven right or wrong (so they get a lot of feedback), and they have a culture emphasizing accuracy. It also helps that they're modeling physics, though various submodels (turbulence, etc.) may not be any more credible than the models in epidemiology.
Blind predictions have been tried in a variety of domains. I'm most familiar with computational fluid dynamics, e.g.:
https://www.sciencedirect.com/science/article/abs/pii/S03797...
https://ntrs.nasa.gov/search.jsp?R=19970027380
(There are many more examples.)
As I recall, it's not uncommon for different groups even using the same software to come up with radically different predictions. I'd say scientists and engineers need much more practice making blind predictions. Blind prediction exercises should occur regularly.
There's a yearly competition to predict the heat release rate of a Christmas tree: https://fpe.umd.edu/events/christmas-fire-safety-demo
I entered one year. Rather than using a fancy computer model, I merely smoothed last year's data and scaled it by the ratio of the mass of this year's tree to the mass of last year's tree. As I recall, I did better than most!
The models are insufficiently multidisciplinary and some of the needed expertise is almost entirely outside of academia and scientific circles whence expertise is drawn to create the models. This is really evident when you look at the epidemiological models that were actually used.
What you find in practice is that the quality of the myriad sub-models that make up the models is extremely uneven, and reflect the expertise of the people building the model, both good and bad. Some key elements of the models are expertly designed, but other critical elements are so naively designed for lack of domain expertise that it completely destroys any signal one might hope to find from the expertly designed parts. This is unfortunately endemic, I've seen this in every model I've been asked to look at.
As for why multidisciplinary expertise is not used to build these models, in my experience there is a lot of gatekeeping against non-academics, even though critical state-of-the-art modeling research and know-how on things like population-scale behavioral dynamics is done almost completely outside academia.
What you find in practice is that the quality of the myriad sub-models that make up the models is extremely uneven, and reflect the expertise of the people building the model, both good and bad. Some key elements of the models are expertly designed, but other critical elements are so naively designed for lack of domain expertise that it completely destroys any signal one might hope to find from the expertly designed parts. This is unfortunately endemic, I've seen this in every model I've been asked to look at.
As for why multidisciplinary expertise is not used to build these models, in my experience there is a lot of gatekeeping against non-academics, even though critical state-of-the-art modeling research and know-how on things like population-scale behavioral dynamics is done almost completely outside academia.
A discussion about modeling:
https://www.youtube.com/watch?v=gxAaO2rsdIs
https://www.youtube.com/watch?v=gxAaO2rsdIs
Amy open source models worth looking into?
I pulled an epidemiology textbook from the 1970s, from a reputable author.. the math is very dense, but basically an extension of calculus-type curves from the 1950s or so.. The overall effect seems overbearing and self-referential (to my untrained eye). The serious gravity of the subject, with so many lives affected in an event, leads to a combination of erudition and also solemn, unapproachable pronouncements, it seems. Maybe there are useful aspects to this curve approach, in hindsight.. but, as mentioned in other posts here, data-driven feedback is now a thing, where it just was not a thing then..
lessons learned -- Question Authority!? use good tools .. look for data and use it well.. ask the right questions..
lessons learned -- Question Authority!? use good tools .. look for data and use it well.. ask the right questions..
you picked up a source from 50 years ago in a field you (seemingly) know little about and your takeaway was 'question authority'?
Some reflection on your own epistemic commitments and beliefs may be in order...
Honestly the ongoing discussion of COVID treatment and modeling in HN scares the pants off me given how uninformed but self-assured it is.
Some reflection on your own epistemic commitments and beliefs may be in order...
Honestly the ongoing discussion of COVID treatment and modeling in HN scares the pants off me given how uninformed but self-assured it is.
I took some time to review something that was "authoritative" from 50 years ago, and yes, the carry-over to the modern times is not great. Does it make me weak to question it ?
I am purposefully not "self-assured" but rather, looking into the topic. As a learner, why would I not question the contents I found?
The textbook leaves no room for alternative -- in fact, the tone and presentation of the textbook is that the topic is settled, and the math is "best".
I am purposefully not "self-assured" but rather, looking into the topic. As a learner, why would I not question the contents I found?
The textbook leaves no room for alternative -- in fact, the tone and presentation of the textbook is that the topic is settled, and the math is "best".
That's the nature of a textbook though, not the field.
Most textbooks present a pretty definitive take on a topic, if only for pedagogical reasons. You might get a few well-defined controversies, like various theories of matter in chemistry, or frequentist vs. Bayesians in a stats book. Even there though, that debate is often resolved, one way or the other, by the end of the first chapter.
The actual back-and-forth in most fields happens in journal articles and conference presentations instead.
Most textbooks present a pretty definitive take on a topic, if only for pedagogical reasons. You might get a few well-defined controversies, like various theories of matter in chemistry, or frequentist vs. Bayesians in a stats book. Even there though, that debate is often resolved, one way or the other, by the end of the first chapter.
The actual back-and-forth in most fields happens in journal articles and conference presentations instead.
Having formerly been a medical scientist, i don't entirely trust medical scientists to get this stuff right. But currently being a computer programmer, i really, really don't trust computer programmers to get this stuff right.
In contrast, I've recently modeled the pandemic response as a feedback control system, where policy/public behavior affects infection rate, which affects policy. This is a classic feedback engineering problem. I'm able to vary suppression vs. mitigation along a continuous curve and look at the long-term course of the pandemic. Counterintuitively, the policy frontier (economic vs human damage) is concave and non-monotonic, and has three distinct regions. https://www.circuitlab.com/blog/2020/05/28/surprising-covid-...
We need engineering-driven long-term thinking, so that we can agree on an optimal strategy, before we choose individual tactics to implement that strategy.