Rob's approach to replicability

In my opinion, replicability is a very important factor of any research done (and it should be included in the reviewing process, but that's another discussion). To clarify, I use the following definition of replicability:

replicability: reproduce exact results with access to same code/data+annotations (narrower than reproducability)

As opposed to reproducibility:

reproducibility: reproduce conclusion in a *similar* setup

During my early career, I realized that even after cleaning my code, it is very hard to replicate the exact results reported in my papers for someone else, or even for myself a couple months later. Hence, I came up with a simple system to improve this in future projects. I have now been using more-or-less the same system for 5 years, and since then many colleagues/collaborators have expressed that even though this method does not guarantee getting the exact same scores, it is a nice, easy-to-use approach to replicability that gets you a long way. In my experience it is also an approach that does not cost time (in fact it saved me loads of time instead). It should be noted that this method is not a full solution, and orthogonal measures are encouraged (i.e. sharing the output of models, versions of software used etc.) Below I will explain the two parts of this approach, the scripts folder, and the runAll.sh script.

The scripts folder

In the scripts folder, I include only the scripts necessary to re-run experiments, the key to keeping this folder comprehensible is to divide the scripts into experiments, and numbering them. In practice, I use the number 0 for preparation scripts, that download data and other code that is necessary for the rest of the scripts to run. This script is typically called 0.prep.sh, and looks something like:

# get and clean data
wget https://lindat.mff.cuni.cz/repository/xmlui/bitstream/handle/11234/1-3424/ud-treebanks-v2.7.tgz
tar -zxvf ud-treebanks-v2.7.tgz
python3 scripts/0.resplit.py
python3 mtp/scripts/misc/cleanconl.py newsplits-v2.7/*/*conllu

# get machamp
git clone https://bitbucket.org/ahmetustunn/mtp.git
cd mtp
git reset --hard 7fd68fc105a3308cc1344b37c5ac425c0facd258
pip3 install -r requirements.txt
cd ../

If the preparation is more complicated it can of course be scattered across multiple scripts instead, like here

The rest of the scripts is then divided per experiment, which could for example be one number per model, dataset, or type of analysis. Which division fits best depends on the structure of you paper/experiment. I find it easiest to order them chronologically based on the paper. Besides numbering the experiments, I also usually try to name them, and if there are multiple scripts per experiments, I even make sub-names. The full name of the first experiment-script could for example be 1.mt.train.py, if the first step is to train a machine translation (mt) system. If we then need to also run a prediction step, the next script would be called 1.mt.predict.py.

runAll.sh

For small/simple projects, the above scripts folder will probably be self explanatory. However, for larger projects, it quickly becomes infeasable to remember how all these scripts were invoked exactly. Hence, I always keep a runAll.sh script, which is like a diary for running scripts. Here I put the exact commands that I have ran to get to the results reported in the paper. An example of a runAll.sh script:

./scripts/0.prep.sh

python3 scripts/1.mt.train.py
python3 scripts/1.mt.predict.py

python3 scripts/2.machamp.train.py
python3 scripts/2.machamp.predict.py

python3 scripts/3.analysis.oovs.py
python3 scripts/3.analysis.learningCurve.py
python3 scripts/3.analysis.ablation.py

python3 scripts/4.test.eval.py

Note that I didn't put any comments in the file, as the file names are quite self-explanatory in this case. Furthermore, it should be noted that in practice I almost never run the whole runAll.sh script, I just use it as a reference. In general, I do not need scripts beyond the number 9, so it is not necessary to prefix the numbers. In cases where this does happen its usually because many of them contain a high level of redundancy and they should be merged, or because there are old experiments that are not used in the final paper, I would suggest to save those elsewhere to keep the scripts folder concise.

Other tricks

I often separate the code for running the experiments and the code for generating tables/graphs. Yes, I would also strongly suggest to have code for generating tables, as it saves a lot of time (and boring work), and is less error-prone compared to manually entering the values in the report. For generating the graphs and tables I then make a scripts/genAll.sh script. This genAll.sh script is generally very simple: Example.

In many cases, it would take too long to run all the commands sequentially, so it is highly beneficial to run code parallel to save time. In the example above, this could for example be the case for 1.mt.train.py, where multiple machine translation models are trained. In this case, I tend to write a script that generates the commands necessary to train the models. The relevant part of runAll.sh could then be rewritten to something like:

function run {
    $1 > $2.sh
    parallel -j $3 < $2.sh
}

./scripts/0.prep.sh

run "python3 scripts/1.mt.train.py" "1.mt.train"
python3 scripts/1.mt.predict.py

For SLURM-based environments the following could be used instead:

function run {
    $1 > $2.sh
    python3 scripts/slurm.py $2.sh $2 24
}

./scripts/0.prep.sh

run "python3 scripts/1.mt.train.py" "1.mt.train" 4
python3 scripts/1.mt.predict.py

Note that in this example, the slurm.py script has no number, as it can be useful for multiple experiments. I try to keep the number of unnumbered scripts as small as possible though. This is dependent on the slurm.py script from: https://github.com/machamp-nlp/machamp/blob/master/scripts/misc/slurm.py

For more examples of how this strategy could be used, you can check out most of the code links on my list of papers.