# Choosing the "Correct" Seed for Reproducible Research/Results

I have created this post to spark a discussion around an idea I had regarding the choice of the seed number used to replicate the results of a statistical model. Here is some background on how I came up with this idea and how it may be applied.

I have a data set, called data, which has 506 observations, 13 predictor variables, and 1 continuous response variable. I split the data into a training and test set by randomly sampling 380 indexes without replacement, storing the observations in the rows equal to the 380 indexes from the data dataframe into a dataframe called train, and storing the remaining 126 observations into a dataframe called test.

Once I created the training and test sets, I built a linear model using the glm function, predicted the outcomes of the test set using the predict function, and computed the MSE between the test set's predicted values and its actual values. In this instance, I obtained an MSE of 16.65786. I left the code here for the night as it was time to go home.

The R code for this is:

library(MASS)
data <- Boston

index <- sample(x = 1:nrow(data), size = round(nrow(data)*0.75), replace = FALSE)
train <- data[index, ]
test <- data[-index, ]

lm1.fit <- glm(medv ~ ., data = train)

pr.lm1 <- predict(lm1.fit, test)
(MSE.lm1 <- sum((pr.lm1 - test$medv)^2) / nrow(test))  The following day, I realized that I should have set a seed so that the random sample of indexes (rows) used to create the training and test sets are the same each time the code is run. So I chose a seed of 1 and reran the code above. This time I received an MSE of 28.72933, a huge difference from the MSE I obtained the night before. This sparked the question of what if the seed I chose was one that lead to an outlier case or that the unseeded result that I obtained was an outlier case. Maybe both results were outlier cases! So I did some investigating. I used a for loop 10,000 times, each time getting a new random sample of indices, created a new training and test set, built a linear model, predicted outcomes for the test set, and calculated the MSE. I stored each of the 10,000 MSEs in a dataframe and computed the mean and median MSE. I also looked at the distribution of the MSEs which appeared to be approximately normal. I reran the forloop again just to make sure that the mean and median of the MSEs did not change much, they didn't. The first 10,000 MSEs had a mean of 24.13 and a median of 23.51. The second 10,000 MSEs had a mean of 24.01 and a median of 23.48. The R code for this is: error <- data.frame(err = rep(0, 10000)) for(i in 1:10000) { index <- sample(x = 1:nrow(data), size = round(nrow(data)*0.75), replace = FALSE) train <- data[index, ] test <- data[-index, ] #Linear Model 1 - No Data Cleaning lm1.fit <- glm(medv ~ ., data = train) summary(lm1.fit) pr.lm1 <- predict(lm1.fit, test) error[i, 1] <- sum((pr.lm1 - test$medv)^2) / nrow(test)
}
summary(error[, 1])


The last thing I did was loop through this same model building process until I found a seed that lead to an MSE in between the mean and the median of the 20,000 MSEs.

The R code for this is:

for(i in 1:10000)
{
set.seed(i)
index <- sample(x = 1:nrow(data), size = round(nrow(data)*0.75),
replace = FALSE)
train <- data[index, ]
test <- data[-index, ]

#Linear Model 1 - No Data Cleaning
lm1.fit <- glm(medv ~ ., data = train)
summary(lm1.fit)

pr.lm1 <- predict(lm1.fit, test)
error <- sum((pr.lm1 - test$medv)^2) / nrow(test) if(error > 23 & error < 24){print(i)} }  I chose to use a seed of 47 which lead to an MSE of 23.63085. I believe that this method for obtaining a seed more accurately depicts a model's ability to accurately predict versus just randomly picking a seed or finding a seed which gives the best results (which I view as "cheating"). My question to all you statisticians out there is does this seem like a reasonable ideology / approach? Is there a more appropriate method out there? Is there a downside to picking a seed this way? Thank you everyone in advance for your input! [Scortchi] Thanks - I was trying to be pithy & conflated two points: (1) Specifically the OP's re-inventing Monte-Carlo cross-validation; & (2) the sensitivity of the out-of-sample MSE estimate to the seed used shows that they should be using some form of re-sampling validation rather than a train/test split. – Scortchi [Brandon] @Scortchi So what you're saying is I should simply use the following code instead: library(MASS) data <- Boston lm1.fit <- glm(medv ~ ., data = data) library(boot) set.seed(1) cvResult <- cv.glm(data = data, glmfit = lm1.fit, K = 10) cvResult$delta


Which leads to a cv prediction error of 23.38074, very close to the prediction error obtained using my long method above. Am I correct?

• Two objections come immediately to mind. First, when you select the seed based on the results, the simulation no longer is random. The approach appears to be self-defeating. Second, why keep only the 1/10000 part of the simulation results? What a waste of effort! Use them all. For another take on setting seeds see stats.stackexchange.com/questions/80407.
– whuber
Mar 21, 2018 at 19:50
• @MichaelChernick: Good pseudo-random number generator with "convenient seeds" give "convenient results". The OP here is for example using the Mersenne Twister which is an excellent RNG for general-purpose Statistics. The quality of the RNG is not the issue here. Mar 21, 2018 at 20:47
• I've known people to choose random seeds by rolling a 10-sided die six (or whatever) times, recording the digits sequentially, and using that at the seed. One might argue that because this procedure is uniform over all such die outcomes, it's preferable.
– Sycorax
Mar 21, 2018 at 21:12
• The moral ought to be not to use sample splitting on such small data-sets: use cross-validation - which you're close to re-inventing! Mar 21, 2018 at 22:04
• @Scortchi: cross-validation is great, but there's plenty of cases in which the expected difference between CV error is on the same scale as the standard deviation of CV error. In those cases "seed optimization" is still very viable, although giving your script with the seed declared at the top kinda kills that. Mar 22, 2018 at 0:12

The seed choice should not affect the ultimate result, otherwise you have an issue. Then why do we need a seed at all? The reason is mainly for debugging and trouble shooting.

What do I call an ultimate result? Suppose that you're analyzing a drug efficacy, and using Monte Carlo simulation to come up with some kind of a critical value. The seed shouldn't matter to your conclusion about whether the drug is efficient or not.

Consider this: what if you're using R and I'm suing Excel, how would I use your seed? I should be able to reproduce the ultimate result regardless of the differences in our software packages and platforms.

Of course, the seed will impact the exact value obtained for the critical value, e.g. 3.1278765876 instead of 3.128765987 with another seed, but this is not the ultimate result of your study. Suppose the test statistic is 20.5, then the difference in critical values between two seeds is not material. Actually, you should not even report the critical value beyond the third digit, just show 3.13, unless it's for debugging purposes.

However, if somehow the difference in fourth significant digit makes it or breaks it for this drug, then we have an issue. It means that we can't use this critical value, OR that we need to increase the number of simulations to nail the fourth digit and reduce the variation between seeds to a much smaller number.

Therefore, you need to set other parameters of simulation in such a way that seed wouldn't matter for the conclusion of your study. Do not "optimize" the seed in any way.

In my practice I had funny projects, where the client would insist on reporting all the calculated digits, e.g. \$31,456,890.01. The simulations would yield maybe 1% precision, hence the number would be changing in second or third digit between different seeds. Moreover, the model itself had accuracy around 10% at best, so to a physicist I would have reported 3e7. However, accountants would complain that the number looks "rounded" which drives auditors nuts: it looks to them as if someone's "cooking the books." We ended up reporting the numbers to the cents, and storing the seeds so that the numbers would be reproducible upon audit requests.

• "The seed choice should not affect the ultimate result, otherwise you have an issue." For something like MCMC, this should be a reasonable assumption. For looking at something like cross-validated MSE for competing state-of-art prediction algorithms, probably not. Mar 21, 2018 at 23:39
• @CliffAB, so will you choose different algorithms at different seeds? Mar 21, 2018 at 23:42
• @CliffAB, if it's true, it's horrible. Mar 21, 2018 at 23:59
• @user1993951: I think there's some major wires getting crossed at this point. I'm not saying you should use seed optimization or anything like that. What I'm saying is that occasionally, decisions will be made with something like cross-validation, choosing between several estimators with very similar predictive power. Then it's very possible that your final outcome will be different based on what seed you used. If this completely changes your predictions, that's should be of concern... Mar 23, 2018 at 21:38
• ...but if the predictions themselves are very similar, then it's really not a big deal that some part of the process was completely different even though a different seed was used. Mar 23, 2018 at 21:39

You certainly can use "seed optimization" to be deceptive about performance. For example, suppose I'm comparing two estimators that just give back pure noise. Fifty percent of my seeds will say estimator A is better than B when using cross validation, so all I need to do is make sure I pick a good seed and then go publish my paper!

Does that mean the use of saved seeds is bad? Not really. The whole point of the seeds is that you've got a script that someone can use to completely reproduce the exact results you got. If you claim the cross validated MSE was 1.2, and a researcher says "hmm, I don't believe that...", just rerun the script right in front of them and they will see it's what you got.

Now, could you have seed optimized to get that 1.2 MSE? Absolutely. But in the exact same manner, they can take your same script, change the seed a few times, and make sure the results almost replicate! So you can use a seed to replicate exactly the results you saw...and then test how reliable that is by randomly using other seeds on the exact same script.