Beyond Computational Reproducibility, let us Aim for Reusability Beyond Computational Reproducibility, let us Aim for Reusability
Scientific progress calls for reproducing results. Due to limited resources, this is difficult even in computational sciences. Yet, reproducibility is only... Beyond Computational Reproducibility, let us Aim for Reusability

Scientific progress calls for reproducing results. Due to limited resources, this is difficult even in computational sciences. Yet, reproducibility is only a means to an end. It is not enough by itself to enable new scientific results. Rather, new discoveries must build on reuse and modification of the state of the art. As time goes, this state of the art must be consolidated in software libraries, just as scientific knowledge as been consolidated on bookshelves of brick-and-mortar libraries.

I am reposting an essay that I wrote on reproducible science and software libraries. The full discussion is in IEEE CIS TC Cognitive and Developmental Systems, but I’ve been told that it is hard to find.

Science is based on the ability to falsify claims. Thus, reproduction or replication of published results is central to the progress of science. Researchers failing to reproduce a result will raise questions: Are these investigators not skilled enough? Did they misunderstand the original scientific endeavor? Or is the scientific claim unfounded? For this reason, the quality of the methods description in a research paper is crucial. Beyond papers, computers —central to science in our digital era— bring the hope of automating reproduction. Indeed, computers excel at doing the same thing several times.

However, there are many challenges to computational reproducibility. To begin with, computers enable reproducibility only if all steps of a scientific study are automated. In this sense, interactive environments —productivity-boosters for many— are detrimental unless they enable easy recording and replay of the actions performed. Similarly, as a computational-science study progresses, it is crucial to keep track of changes to the corresponding data and scripts. With a software-engineering perspective, version control is the solution. It should be in the curriculum of today’s scientists. But it does not suffice. Automating a computational study is difficult. This is because it comes with a large maintenance burden: operations change rapidly, straining limited resources —processing power and storage. Saving intermediate results helps. As does devising light experiments that are easier to automate. These are crucial to the progress of science, as laboratory classes or thought experiments in physics. A software engineer would relate them to unit tests, elementary operations checked repeatedly to ensure the quality of a program.

Archiving computers in thermally-regulated nuclear-proof vaults?

Once a study is automated and published, ensuring reproducibility should be easy; just a matter of archiving the computer used, preferably in a thermally-regulated nuclear-proof vault. Maybe, dear reader, the scientist in you frowns at this solution. Indeed, studies should also be reproduced by new investigators. Hardware and software variations then get in the way. Portability, ie achieving identical results across platforms, is well-known by the software industry as being a difficult problem. It faces great hurdles due to incompatibilities in compilers, libraries, or operating systems. Beyond these issues, portability also faces numerical and statistical stability issues in scientific computing. Hiding instability problems with heavy restrictions on the environment is like rearranging deck chairs on the Titanic. While enough freezing will recover reproducibility, unstable operations cast doubt upon scientific conclusions they might lead to. Computational reproducibility is more than a software engineering challenge; it must build upon solid numerical and statistical methods.

Reproducibility is not enough. It is only a means to an end, scientific progress. Setting in stone a numerical pipeline that produces a figure is of little use to scientific thinking if it is a black box. Researchers need to understand the corresponding set of operations to relate them to modeling assumptions. New scientific discoveries will arise from varying those assumptions, or applying the methodology to new questions or new data. Future studies build upon past studies, standing on the shoulders of giants, as Isaac Newton famously wrote. In this process, published results need to be modified and adapted, not only reproduced. Enabling reuse is an important goal.

Libraries as reusable computational experiments

To a software architect, a reusable computational experiment may sound like a library. Software libraries are not only a good analogy, but also an essential tool. The demanding process of designing a good library involves isolating elementary steps, ensuring their quality, and documenting them. It is akin to the editorial work needed to assemble a textbook from the research literature.

Science should value libraries made of code, and not only bookshelves. But they are expensive to develop, and even more so to maintain. Where to set the cursor? It is clear that in physics not every experimental setup can be stored for later reuse. Costs are less tangible with computational science; but they should not be underestimated. In addition, the race to publish creates legions of studies. As an example, Google scholar lists 28000 publications concerning compressive sensing in 2015. Arguably many are incremental and research could do with less publications. Yet the very nature of research is to explore new ideas, not all of which are to stay.

Identifying and consolidating major results for reuse

Computational research will best create scientific progress by identifying and consolidating the major results. It is a difficult but important task. These studies should be made reusable. Limited resources imply that the remainder will suffer from “code rot”, with results becoming harder and harder to reproduce as their software environment becomes obsolete. Libraries, curated and maintained, are the building blocks that can enable progress.

Original Source
Gael Varoquaux

Gael Varoquaux

Gaël Varoquaux is an INRIA faculty researcher working on data science for brain imaging in the Neurospin brain research institute (Paris, France). His research focuses on modeling and mining brain activity in relation to cognition. Years before the NSA, he was hoping to make bleeding-edge data processing available across new fields, and he has been working on a mastermind plan building easy-to-use open-source software in Python. He is a core developer of scikit-learn, joblib, Mayavi and nilearn, a nominated member of the PSF, and often teaches scientific computing with Python using the scipy lecture notes.