Why I'm bailing on Julia for machine learning

Posted on Fri 04 November 2016 in programming

I'm bailing on Julia for machine learning — just for my one class, that is. Don't worry ~too much~!

I'm taking graduate machine learning (6.867) this semester at MIT. There are three homework assignments in the course that are structured as mini-projects, in which students implement canonical algorithms from scratch and then use them to analyze datasets or explore the effects of hyperparameters. "Official support" — in the sense of skeleton code, plotting routines, and TA assistance — is provided for MATLAB and Python only. Working in Julia (or another language) is allowed, but the going is solo.

After sticking with Julia for the first two assignments, I'm bailing for the rest of the semester. Although Julia is great-looking, fun to write, and performant as ever, there were a lot of challenges I ran into in using existing functionality within my assignments. Specifically, I found the stats/ML packages pale in comparison to sklearn in terms of functionality and ease of use. While it was great to use Julia to implement my own algorithms, it turned out to be a real hassle to tie in with existing functionality.

As one of several small issues, here's the trouble I went through just to use pre-existing functionality to fit a logistic regression model.

Logistic regression case study

What's the quickest way to fit a logistic regression model for classification? A quick search brings up the JuliaStats page (as my first result, at least) with a variety of packages listed. From the descriptions, it seems like our candidates for logistic regression solvers are GLM.jl and RegERMs.jl. The next search results are for Regression.jl and a couple DIY logistic regression examples.

Let's assess our options:

  • GLM.jl: Has most of the goods, but as we'll see, it didn't have all the features I needed for my assignment.
  • RegERMs.jl: Doesn't even load on Julia 0.5, last commit over a year ago.
julia> Pkg.add("RegERMs")
ERROR: unsatisfiable package requirements detected: no feasible version could be found
for package: Optim
  • Regression.jl: Doesn't even load on Julia 0.5, last commit over a year ago.
julia> using Regression
ERROR: LoadError: LoadError: LoadError: UndefVarError: FloatingPoint not defined

So GLM.jl is our only option. And at this, a new Julia user might be lucky to even find it. It's not immediate from the JuliaStats blurb that GLM.jl can be used for logistic regression, and there's no mention of "logistic" neither in the documentation nor in the repo itself besides a comment in a test case. (An astute user, of course, may note that LogitLink is relevant, and will likely be aware of the features of the popular R package.)

But it's not too bad to fit a logistic regression model using GLM.jl:

using GLM, DataFrames
df = DataFrame(x = rand(10,1), y = rand([0,1], 10))
model = fit(GeneralizedLinearModel, y ~ x, df, Binomial(), LogitLink())

Note as well that the DIY logistic regression attempts that rank highly in search results (like here and here) are not super helpful for the purposes of quickly fitting a model, but are typical of the content that comes up in results for Julia queries.

Adding L1/L2 regularization

In one of the 6.867 assignments, we are asked to apply logistic regression with L1/L2 regularization. GLM.jl doesn't provide this functionality and the other seeming possibilities were non-functional RegERMs.jl. I was out of luck. I switched to sklearn for the rest of the problem.

import numpy as np
from sklearn.linear_model import LogisticRegression
X = np.random.rand(10,1)
Y = np.random.rand(10).round()
model = LogisticRegression(penalty='l1')
model.fit(X, Y)

After later investigation, I did realize that GLMNet.jl, which wraps the glmnet Fortran library, would have done the job, with sufficient user effort.

The pieces are there, the whole is missing

We were able to fit our logistic regression classifier after a fair amount of digging. But this digging shouldn't be necessary. It should have been easier to find a logistic regression that works from the JuliaStats landing page, given that this is a pretty standard learning algorithm. And inconsistencies within the JuliaStats organization seem to be a fair problem. A user might start by using GLM.jl. But to add regularization to the loss function requires to switch to a different package, with a slightly different API so that the old code can't be dropped in. The "interface" in StatsBase.jl isn't totally implemented in some of these more niche packages (GLMNet.jl, Lasso.jl), or isn't particularly followed at all, especially when the package wraps some underlying library (LIBSVM.jl).

Then, we have the entirely different entity that is JuliaML. Here, we have a design and API that seem to be in direct competition with JuliaStats (StatsBase.jl/MLBase.jl vs LearnBase.jl, Distances.jl vs LossFunctions.jl, RegERMs.jl vs MLRisk.jl, etc.). I wasn't sure how to even start using it, let alone attempt to theoretically combine LossFunctions.jl, StochasticOptimization.jl, and MLMetrics.jl into something resembling an end-to-end model. I can't quite figure out what space JuliaML is trying to fit.

Overall, I think that JuliaStats is doing a very good job and is almost there. Packages like StatsBase.jl, DataFrames.jl, and Distributions.jl are really great to use. Certainly, the obvious response to the difficulties I had above is that more community support is needed. Can't argue with that.


Julia has been perfectly suited for quickly coding up ML algorithms from scratch and really getting my hands dirty. But when I wanted to quickly and easily drop in robust community packages, I found that the functionality wasn't there.

I'll be using the Python ecosystem for the next assignment, in which we implement neural nets/backprop. If I find myself having to bust out sklearn more regularly, I better figure out how to use it fluidly.