A Virus Testing Probability Puzzle

Here is a topical puzzle for you.

A test is designed to show whether or not a person is carrying a particular virus.

The test has only two possible outcomes, positive or negative.

If the person is carrying the virus the test has a 95% probability of giving a positive result.

If the person is not carrying the virus the test has a 95% probability of giving a negative result.

A given individual, selected at random, is tested and obtains a positive result. What is the probability that they are carrying the virus?

Update 1: the comments so far have correctly established that the answer is not what you might naively think (ie 95%) and that it depends on the fraction of people in the population actually carrying the virus. Suppose this is f. Now what is the answer?

Update 2: OK so we now have the probability for a fixed value of f. Suppose we know nothing about f in advance. Can we still answer the question?

Answers and/or comments through the comments box please.

54 Responses to “A Virus Testing Probability Puzzle”

  1. David Henley Says:

    Surely there is insufficient information, since we do not know the prior probability that the patient has the virus (i.e., we don’t know how common the virus is in the general population).

    • Yes, it’s a nice illustration. Suppose the true prevalence of the virus is 1% of the population, then 95% of that 1% get a correct positive result (so about 1%), but about 5% of the 99% not infected also get a (false) positive result, so about 5%. The result would be 6% testing positive….

      So in this case the probability that any one of the positive-testing subjects is actually infected, is about 1 in 6.

    • telescoper Says:

      We do at least know that f is between 0 and 1. Using this and no other information I think we can give an answer that doesn’t depend on f…

  2. Tom Shanks Says:

    Depends on fraction with virus? If everyone has virus then your requested probability is 1. If no-one has virus then your probability=0.

    Regretting writing this already!

  3. Well, yes, as Tom says, a Baysian problem depends on your prior.

  4. Simon Kemp Says:

    Isn’t the answer just f? This is the total of 0.95f (from the 95% of positives that would be detected by the test) and 0.05f (from the 5% of negative tests that are really positive).

  5. (apologies if this is a duplicate)

  6. David Henley Says:

    Let + indicate a positive test, and v indicate having the virus (and !v indicates not having the virus). We therefore want

    P(v|+) = P(+|v) * f / (P(+|v) * f + P(+|!v) * (1-f))
    = 0.95*f / (0.95*f + 0.05*(1-f))
    = 0.95*f / (0.05 + 0.9*f)

    For f = 0.1%, P(v|+) is only 1.9%
    f = 1%, P(v|+) = 16.1%
    f = 10%, P(v|+) = 67.9%

    (Unless I’ve made an arithmetical error somewhere along the way.)

    • David Henley Says:

      …the point being that even though the test looks good at first glance, the probability that a positive test is correct about the patient having the virus is quite small if only a small fraction of the tested population is expected to have the virus.

  7. telescoper Says:

    I think you mean 0.05 on the second term in the denominator.

    The answer is equal to 0.95 if and only if f=0.5.

  8. telescoper Says:

    I still think you can give a sensible, Bayesian, answer to the original question that doesn’t depend on f.

    • telescoper Says:

      “Our weapon is our knowledge. But remember, it may be a knowledge we may not know that we possess.”

      Agatha Christie, The A.B.C. Murders

    • telescoper Says:

      I think you need to show your working!

    • telescoper Says:

      Well you need p(v|+) so you start with p(v|+, f) and use a uniform prior p(f) to create p(v, f|+) then marginalise over f to give p(v|+).

  9. Tom Shanks Says:

    OK I actually got the D Henley solution before I posted last night – honest! But I didn’t get the last Bayesian step.

    Am still wondering whether anyone else should take that last step either. At the end any prior is a subjective guess including in this case a flat prior. So how do we judge if 88% is reasonable if prior not based on any repeat trials? So this example is also nice because it brings out the fundamental problem with Bayesian statistics!

    There – I’ve walked into trap – now waiting tutorials on Bayesian evidence etc!

    • telescoper Says:

      It’s not a problem with Bayesian reasoning, it’s a strength!

      (And it’s reasonable precisely because it’s Bayesian!)

      Of course if you have more information about f (say from samples) you can feed that into the prior. That’s actually difficult to do with Covid-19 because the testing is done in a complicated way: it’s certainly not a random subset of the population that is tested.

      • Tom Shanks Says:

        “(And it’s reasonable precisely because it’s Bayesian!)”

        Seems to depend on a strong prior that Bayesian approach is reasonable!

        I rest my case!

      • telescoper Says:

        What I meant is that Bayesian inference is *proven* to be the unique way of dealing with these problems in a logically consistent manner. If the result depends strongly on the prior then that tells you that you need more data.

      • Tom Shanks Says:

        “(And it’s reasonable precisely because it’s Bayesian!)”

        Seems to depend on a strong prior that Bayesian approach is reasonable!

        I rest my case!

    • telescoper Says:

      It reminds of a problem of tossing a coin.

      Suppose you know nothing about the coin. What is the probability that if toss it you will get Heads?

      Surely you would say 0.5.

      Now you toss it 10 times and get Heads every time. What is the probability that you would get Heads on the 11th toss?

      I think you shouldn’t say 0.5 because the previous throws give you information that suggests it might not be a fair coin…

      • Tom Shanks Says:

        I recall ruining a holiday in Rio arguing remotely with Anton Garrett on your blog about this topic so may I refer you to that!

        Meanwhile best wishes to you and Philip!

      • Anton Garrett Says:

        What you want in any problem involving uncertainty is a number representing how strongly the things you think you know (ie, binary propositions which you take to be true) imply the truth of the binary proposition you are interested in. Let’s call this quantity the implicability, and it has two arguments: the proposition you are interested in, and the ‘conditioning’ proposition that you take to be true.

        Of course these may be compound propositions, and you can also break down continuous spaces into propositions such as “the physical quantity measured lies in the range (x,x+dx)”.

        Since implicability has binary propositions as its arguments, the calculus of binary propositions, ie Boolean logic, implies a calculus for implicabilities.

        This calculus turns out to be the sum and product rules. The pioneer derivation of them in this way was by RT Cox in 1946, and it has since been improved by myself and then Kevin Knuth.

        As implicability obeys the “laws of probability”, and as it is what you want in any problem involving uncertainty, I reckon it deserves to be called “probability”. But if anybody takes exception to this definition, I am not going to fight. I am just going to say “you define what you want; I’ll calculate my implicability and solve the problem”.

        All of this has nothing to do with the question of priors. Priors enter when we get data with which we wish to update our implicability by incorporating that data in the conditioning information as a logical product together with our prior information. This is unavoidable – and a strength of Bayesian analysis, not a weakness. Suppose you are certain before doing a noisy experiment what the value of a parameter is, and you are doing the experiment only because your boss has commanded you to. Then your prior is a delta-function at the value you know and zero elsewhere. Bayes’ theorem, which follows from the sum and product rule, tells you that the posterior is equal to a normalised product of the prior and likelihood. So the posterior is a delta-function at that value: exactly as intuition demands. Use sampling-theoretical methods beloved of frequentists, though, and you get answers strewing probability where you know it can’t be! Never use a method in a complex problem that fails in a simple one.

        So the use of prior information is a strength, not a weakness. If you find you need it, that is a flag. As to what prior to assign in any problem, this should be viewed as a matter for research rather than for denigrating Bayesianism (although I will concede that even of the word ‘Bayesianism’ there are too many meanings…)

        Don’t wreck any holiday for this stuff, especially in Rio!

      • telescoper Says:

        If the answer depends strongly on the choice of prior that’s not in itself a problem: it just means that you need more data. Sometimes it’s good to be shown how little you know given the information available.

      • Tom Shanks Says:

        Hi Anton, in Durham not Rio this time!

        So at risk of devaluing the debate, do you agree with Peter that the correct answer to the above problem is 0.883?

      • Anton Garrett Says:

        I would write the answer in terms of the prior for f, as Peter didn’t specify what “the probability” was to be conditioned upon. Give me some prior info re f and I’ll do my best to translate it into a prior and then marginalise over f to get the posterior.

      • Anton Garrett Says:

        Let me add some more about the prior. “Complete ignorance” would mean that we didn’t even understand the phrase “have a virus” and that viruses are contagious – complete ignorance would mean assigning each individual 50:50 of “having the virus” or not. (I don’t go with a log prior on f because the prior for complete ignorance should be invariant under f –> 1-f.) Once you know that viruses are contagious, you have to average over *how* contagious – unless you know how contagious, and then you need stats for the distribution of household sizes. And so it goes…

  10. Garret Cotter Says:

    How do you know the false positive and false negative accuracies without knowing something about f? It’s a bootstrapping problem, isn’t it? Agree with Philip’s comment above about flat prior.

    • telescoper Says:

      In this simplified problem you know because I told you! They might be determined in a controlled laboratory setting without reference to an infected population. But I agree that in a real situation, like the one we find ourselves in now, you could not justify using a flat prior.

    • Tom Shanks Says:

      Anton, I agree that you have to specify the prior for f. But if we assume no knowledge about f do we gain anything meaningful by then assuming a flat prior as is often done in these “no knowledge” situations?

      • Anton Garrett Says:

        What do you mean by “no knowledge”, please? Even knowing the meaning of a variable is knowledge, as I suggested in one post.

      • Tom Shanks Says:

        Anton, To quote Peter “Update 2: OK so we now have the probability for a fixed value of f. Suppose we know nothing about f in advance. Can we still answer the question?”

        Would you answer “yes” or “no”?

      • Anton Garrett Says:

        I’d like to ask Peter what *he* means by “no knowledge”, because even knowing that it is a virus conveyed from person to person is significant relevant prior information; but if you absolutely demand a Yes or No then I’d assign 50% probability to any individual having it and then treat it as an urn problem, which does mean that you can derive a unique numerical answer.

      • telescoper Says:

        What I meant was just to make it entirely abstract, with + and – being two outcomes of a test and ‘v’ and ‘not v’ just being two mutually exclusive states of the thing being tested.

  11. John Peacock Says:

    (19/324)(18-ln19) = 0.883, as Philip said. This is for a flat prior on the population infected fraction, f. A more committed Bayesian than me would probably say that a number known to lie between 0 and 1 should take a double Jeffreys prior p(f) propto 1 / [ f(1-f) ], but then all integrals of interest diverge and you have to cut the range to between a and 1-b where a and b are small. Then you can get any answer you like depending on how you take the limits of a and b tending to zero. But I don’t think this prior is reasonable here: it amounts to saying that f is either almost exactly 0 or 1, and it’s clear we wouldn’t be worrying about this problem if that was the case. So this is almost the anthropic principle applied to prior choice….

    • Tom Shanks Says:

      Can’t resist! So who agrees with Peter that the correct answer to the original problem is 0.883?

    • I am a bit late to this discussion, due to to all the on-line meetings. I can see the reason behind a flat prior but it seems a bit of a cop-out. As we know that a disease advances exponentially, wouldn’t a log distribution not make more sense? A flat distribution is ok for large f but here it is unlikely that f exceeds 0.1 (not impossible, but not likely) because that phase doesn’t last very long. Is there a way to assign an uncertainty to Tom’s preferred answer of 0.883?

      • Tom Shanks Says:

        As Philip says, there’s no doubt that the
        number 0.883 is correct. More onto Bayesian philosophy now. Peter framed problem that additional benefit accrues from last Bayesian step when a flat prior on the fraction of popn with virus was applied. But does it?

      • To put it bluntly: if you can’t assign an uncertainty, then your number has little validity. In that case the answer is no, you can’t get the answer without knowing something about f.

        (And the rate of false positives may also be poorly known if you don’t know f.)

        When in doubt, get better data.

      • telescoper Says:

        The rate of false positives is given in the question.

      • telescoper Says:

        OK. I toss a coin that looks fair. What’s the probability of it being Heads?

        I think the answer is 1/2.

        What’s the uncertainty on that answer?

      • Indeed, the rate of false positives is given. But if it is known, it has been measured and it is hard to realistically measure it if you don’t know f. Although I expect you have a Bayesan answer to that! As for the flat prior in f, if this is an infectious disease, it should progress as a logistic function, and it should have a finite recovery time. You didn’t specify that this was about an infectious disease, but in that case your solution is not well applicable to the current epidemic.

      • telescoper Says:

        As I said in the thread above, the test outcomes could in principle be quantified using controlled experiments in a laboratory rather than by sampling a population.

      • telescoper Says:

        I didn’t say it was!

  12. telescoper Says:

    All I wanted from this was to draw attention to the fact that the answer wasn’t simply 0.95!

    The arguments about Bayes have been an unexpected bonus!

    • Tom Shanks Says:

      It’s beginning to feel like Rio! Is that a song?

    • Tom Shanks Says:

      To conclude(!), one can assume a flat prior but that is no less subjective than any other prior with our level of knowledge in this example. So looking for extra information on the probability of having virus if testing positive from this Bayesian route is fruitless.

      But the problem does bring out the main issue with Bayesian inference – the potential subjectivity of even a flat prior.

  13. Alan Heavens Says:

    If I calculated correctly, the Jeffreys prior in this case is constant, where the aim is to choose the least-informative prior, so the inference comes as far as possible from the data rather than the prior. To an Objective Bayesian, this would justify the choice of a uniform prior. But it’s late…

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