Publishing Identifiable Experiment Code And Configuration Is Important, Good and Easy

04/10/2012 ∙ by Richard Vaughan, et al. ∙ Simon Fraser University 0

We argue for the value of publishing the exact code, configuration and data processing scripts used to produce empirical work in robotics. In particular, we recommend publishing a unique identifier for the code package in the paper itself, as a promise to the reader that this is the relavant code. We review some recent discussion of best practice for reproducibility in various professional organisations and journals, and discuss the current reward structure for publishing code in robotics, along with some ideas for improvement.

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1 Introduction

A few months ago, a graduate student in another country called me (Vaughan) to ask for the source code of one of my multi-robot simulation experiments. The student had an idea for a modification that she thought would improve the system’s performance. By the standards of scientific practice this was a perfectly reasonable request and I felt obliged to give it to her. With our original code, the student could (i) re-run our experiments to verify that we reported the results correctly; (ii) inspect the code to make sure that it actually implements the algorithm described in our paper; (iii) change parameters and initial conditions to make sure our results were not a fluke of the particular experimental setting; (iv) modify the robot controllers and quantitatively compare her new method with our originals. It would cost me nothing to make her a copy of our code, and her methodology would be impeccable. Why then do we read so few papers using this methodology?

It turned out to be impossible to identify exactly which code was used to perform the experiments in our years-old paper. We had not labeled the source code at that moment, and it had subsequently been modified. All the code was under version control, so we could obtain approximately the right code by looking at revision dates. But having only

approximately the right code strictly invalidates the replication of the experiments. The user has no way of knowing what the differences are between the code she has and the code we used. So we were able to offer the requesting student some code that may or may not be that used in the paper. This was better than nothing, but not good enough, and we suspect this is quite typical in our community.

This disappointing episode was a wake-up call for me, and our group has been discussing how we can make sure this doesn’t happen again. We propose to routinely publish the exact code for each experiment that we use to justify any claims at all.

This paper explains why we think complete experiment publication is important and why it is good for the originating researchers as well as subsequent users. The second half of the paper examines current standards of scientific data and code publications, and cites some evidence of its benefits. But first we present our protocol for publishing identifiable code and show how easy it is to do.

2 Publishing code is easy

2.1 What to do

  1. The complete and exact source code, build scripts, configuration files, maps, log analysis scripts, list of critical external dependencies, details of run-time environment and any other instructions and resources necessary for a skilled researcher to replicate the experiment should be packaged and placed in public for free and anonymous download by any reader.

  2. The source package should be labeled with a textual identifier that is specific to the version described in the paper, and the paper should contain the identifier.

2.2 Doing it easily

This can be easily and cheaply achieved as follows. The code is assembled into an archive file (tarball, gzip, etc), and a digital signature is obtained using a cryptographic hash function such as SHA1[24]. The archive is published at some reliable Internet host, and its URI and signature are published in the paper. The archive can also be linked from the authors’ web publication list.

Upon downloading the file, the user can determine that the archive matches the signature in the paper. Use of a good hash identifier makes it very difficult for authors to modify the code by mistake or design, without this being detectable by the user/reader.

Modern software development tools make for an even easier process. Revision control systems like Git111http://git-scm.com/

automatically generate a SHA1 cryptographic hash key for each committed version, such that there is a low probability of any two packages or versions having the same key. The entire revision control database can be easily cloned from an URI, and users can check out the correct version by its signature, while still having access to later versions. The differences between versions are easy to inspect using Git’s tools. We have chosen this approach, and are hosting our Git repositories at the independent host GitHub

222http://github.com. While GitHub’s tools and convenience are currently compelling, the ideal host would be a reliable and long-lived independent institution such as a university, national library or professional organization such as the IEEE.

The idea of identifying a code package with a crypotgraphic hash is not new – on the contrary the standard way to distribute packages on the Internet such that the downloader can trust that they received the “real thing” is for the author to post a web page containing a URI to an archive file along with the SHA1 hash of the same file. Our contribution here is to recommend this practice to our community as a means to achieve the benefits of trustworthy code publication.

3 Publishing code is important

3.1 Falsifiability and shared artifacts

Publishing the actual experiment alongside the paper which describes and interprets it increases the scientific and practical value of the work. It goes a long way to solving a problem our field faces from a philosophy of science point of view: the fact that we are a synthetic science that creates and studies artifacts, rather than a natural science that studies an extant universe common to all scientists. By reproducing and sharing our artifacts we synthesize a common environment.

Scientific claims are required to be falsifiable. If I make a claim in a paper about a system I created, and to which you do not have access, my claim is not falsifiable in practice. My claims are more scientifically valuable if I make them as easy to falsify as possible, which I can achieve by publishing the artifacts.

3.2 Repeatability and quantitative comparison

In the natural sciences experimental results gain credibility after they are independently repeated at least once. In order to be able to repeat an experiment, we often require many details that are not available in the paper. As we are often able to make the exact and entire experiment available for replication at negligible cost, we can achieve the best possible repeatability.

Of course, we can not prove experiments are correct and while simply re-running a program is not a strong validation, even this alone can show up mistakes. A stronger validation is obtained by completely re-implementing the code, or the important parts of it, but by testing the new version using the original setting, as determined by inspecting the original code, we can improve our confidence in the results.

As in all of science, much work in robotics can be considered incremental improvement over the work of another. This usually requires reimplementing the original experiment from natural language and formal mathematical descriptions. This re–implementation step usually allows only qualitative comparison, since the details of parameters and initial conditions, etc, are rarely published. It can also be a source of error and raises question such as “did the new author really find the very best parameter set?”. Experiments made public in an executable form will improve fairness to the original author and will allow quantitative comparison of results.

A second level of repeatability is available to us. Components of experiments can be re-used in different experiments and settings. If the component performs as expected in this new setting, our confidence in it increases. In fact this re-use of code is a cheap way of reproducing experiments.

4 Publishing code is good

4.1 Efficiency

Having access to data sets and software implementations increases the efficiency of the scientific process in several ways. In the case of incremental work, it saves a great deal of re-implementation effort. While the use of middleware like Player[8], ROS333http://www.ros.org, and Microsoft Robotics Developer Studio444http://msdn.microsoft.com/robotics has increased the rate of code reuse in recent years, these systems focus on low-level components and it is still unusual for a robot controller or an implementation of an algorithm to be substantially reused. Making code available by default would encourage reuse, particularly if the code is of good quality.

4.2 Quality

The quality of a research contribution is a function of the soundness and originality of its theoretical foundation, the depth of analysis given and the clarity and thoroughness of its presentation. It is assumed that the software that produces the results is correct. Yet it is all too easy to make implementation mistakes that grossly influence the outcome of an experiment. Even when a paper presents a complete formal algorithm, discrepancies between the description and the implementation that produced the results are possible. Such discrepancies are impossible to detect without access to the source code. We can very easily make code available for peer review, and so we should.

Further, it is often argued that well written and documented software has fewer bugs. Developing software with the expectation that it will be peer reviewed and reused is likely to cause roboticists to write better code, thus increasing the overall quality of the work even before external review. We should write code as we write papers: to be read and understood; to contribute to knowledge.

5 Issues and objections

Achieving code publication requires a number of issues to be addressed. Some of the most significant are:

  1. “I object! All that extra work takes too long….”

    There are three arguments. First, while producing peer-reviewable code may feel like it takes longer, the additional discipline and code review should result in improved code quality. By reducing bug-hunting and re-runs of faulty experiments, the experimenter could actually save time compared to a typical messy code base. Second, starting with others’ published code saves time in the first place. Third, extra work is justified by the methodological advantages: the main role of the “extra” work is to improve the quality and usefulness of the research results, thus it should not be considered overhead.

    Some documentation is usually required for code to be usable. Extensive end-user documentation can be very costly to produce, but often just a few notes can be sufficient to guide a colleague through reproducing and understanding an experiment. Documentation, particularly when written in-line with the code, can also help the author’s confidence in its correctness. This idea is well developed in Knuth’s literate programming model[1].

  2. Offline vs. online For work that does not need to interactively control the robot (e.g. offline SLAM) logs of original sensor data along with the algorithm code allow perfect experiment reproduction. The Radish repository exists to curate such datasets, and some of its maps have become familiar 555http://radish.sourceforge.net. Sharing interactive robot code is more troublesome.

  3. Real world and unique robots: For interactive controller experiments, complete reproduction may be straightforward when experiments are done in simulation only. Yet real-robot experiments are essential. The arguments for experiment source sharing still hold for real robot systems, and the value of the work is maximized if the authors facilitate replication and extension. This can be done by using a well-known robot e.g. Pioneer, Khepera, which can be assumed to be widely available in research labs around the world. Well-known robots also have the advantage that respected simulation models are readily available.

    If a custom robot is essential, we suggest providing either (i) a model for a well-known simulator, or (ii) a dedicated simulator including source code. Also when using custom hardware, using a well-known and open API for controller code, (e.g. Player, ROS) makes porting to another robot or simulator as easy as currently possible. Ideally, in all cases where a simulation can produce similar results to the real robot with a reasonable amount of effort that simulation should be provided.

    Work that uses novel mechatronics will not be reproducible at the very low cost of software-only or common-robot systems, but we suggest that engineering drawings, CAD models, materials and machining details can be published using the same methodology. The goal is to minimize the cost of reproduction. Work that does not require novel mechatronics should use a well known hardware and software platform. Section 8 below discusses a recent major effort to bootstrap a widely-used platform.

  4. Licensing: The free reading, copying, modification and subsequent redistribution of modified code is absolutely required. In most jurisdictions copyright law automatically applies, so the code must be explicitly licensed to allow redistribution. The community already makes extensive use of Free and Open Source Software, so we have experience with suitable licenses. Licences that prohibit commercial uses may be acceptable for traditional academic purposes, but clearly make the code less valuable for some users (the difference in value being what they are willing to pay to use the code under a commercial license).

  5. Trade secrets and competitive advantage: Some authors feel that since their code is precious, by “giving it away” they give away their competitive advantage. If a “competing” lab needs six months to replicate my experiment, I can get further ahead in the meantime. While this position is tempting for the individual, we are seeking advantages in efficiency and quality for the entire community, including our taxpayer-supported funding agencies. Companies are under no obligation to serve the community, but they can get the benefits described above by first protecting their ideas with patents before publication. If groups withhold their code for their own interest and against the interest of the community, their work is manifestly less valuable than it could be, and should be evaluated accordingly. Conversely, releasing high quality code should enhance a group’s reputation and success rates. This provides a feedback mechanism that reinforces code publication.

6 Encouraging Code Publication

How can the publication of source code be made a community norm? Assuming the existence of a few suitable protocols, how can researchers be encouraged to use them? Though we believe the research quality and efficiency benefits should persuade many researchers, achieving such a large cultural change is likely to require activism at various levels in the community.

At the most executive level, organizations such as the IEEE could make paper publication conditional on code publication, perhaps with exceptions in extenuating circumstances. Such a policy seems impossibly heavy-handed at the moment, though it might be possible for individual journals and conferences. Perhaps a new journal or conference could adopt this strategy as a differentiating feature: if the arguments above are true, such a venue could expect to become disproportionately influential. We cite some evidence of this effect from other fields below.

If requiring code publication seems too ambitious, it is straightforward to prefer it. Publishers, editors, program committees and individual reviewers can state that, all else being equal, submissions that provide code are preferred over those that do not. In practice, editors would need to advise reviewers on the weighting of this preference, as with any other major criteria.

One simple concrete proposal is that the major conferences offer a new prize for “best” (in quality, novelty or significance) published code, along with the usual best paper and service prizes. This would be a low cost, high visibility measure that recognizes this as a new and significant way to contribute to the community.

At the most grassroots level, professors can expect their students to back up all written work with published code. Generations of grad students are short, and norms can be quickly established by generational change.

Generational change may happen last to tenure and promotion committees. We hope that academic departments will gradually come to recognize code publication as a valuable academic activity. However, we have argued above (and will provide evidence below) that papers with code have more impact than papers without code. Better quality, higher citation rates and good community visibility leading to stronger referee letters are benefits that are already working under the traditional evaluation criteria.

We have argued above (Sections 4.1, 5 points 1 & 2) that increased code re-use can make work more efficient, so the candidate’s number of papers need not be reduced, but if this is a concern, the following idea could help boost publication rates. When an experiment is substantially re-used and the modifications reported, the original author could be named as a co-author on the new paper. This is not appropriate for middleware and simulation platform code (e.g. Player and Stage), where normal citation is enough, but rather when the code that embodies the idea of a specific experiment is inherited. This is a way of rewarding production of impactful experimental infrastructure, and is analagous to the long author lists seen in for example genomics and astronomy, where infrastructure – much of which is now software – is recognized as extremely valuable.

7 The Trend Toward Experiment Publishing

We have argued that publishing code and experimental data is important for the robotics research community, is good for researchers and easy to do. Yet it is not standard practice in our field. The idea of publishing experimental data and other artifacts beyond finished papers is not new but it seems to be becoming popular. Here we survey some government policies, practice in other scientific disciplines and editorial policies of high impact journals.

7.1 Government and Funding Agency Policies

The US National Science Foundation (NSF)…

…expects investigators to share with other researchers, at no more than incremental cost and within a reasonable time, the data, samples, physical collections and other supporting materials created or gathered in the course of the work. It also encourages awardees to share software and inventions or otherwise act to make the innovations they embody widely useful and usable.[12]

Since October 2003 the US National Institutes of Health (NIH) has required grant applications for $500K per year and above to include a plan for data sharing or a statement why data sharing is not possible [11]. While the form of data sharing is not considered during the proposal assessment, the NIH sends a clear signal to encourage publication of data.

The 2003 Berlin Declaration on Open Access to Knowledge [2] may come to be seen as an important milestone. At the time of writing the declaration has been signed by 264 funding agencies, universities and research organizations, including CERN, the Chinese Academy of Sciences, the Indian National Science Academy, and the German Research Foundation. The declaration states:

A complete version of the work and all supplemental materials […] in an appropriate standard electronic format is deposited (and thus published) in at least one online repository using suitable technical standards (such as the Open Archive definitions) that is supported and maintained by an academic institution, scholarly society, government agency, or other well established organization that seeks to enable open access, unrestricted distribution, inter operability, and long-term archiving. [2]

In a 2004 statement by the Organization for Economic Co-operation and Development (OECD) numerous governments including those of North America and Europe agreed on a declaration on access to research data from public funding. The OECD recognizes that

an optimum international exchange of data, information and knowledge contributes decisively to the advancement of scientific research and innovation. […] Open access to, and unrestricted use of, data promotes scientific progress and facilitates the training of researchers. [20].

In 2007 the US government passed the “America COMPETES Act” [26] requiring federal civilian agencies that conduct scientific research to openly exchange data and results with other agencies, policymakers and the public.

All of these national and international governmental efforts are aimed at improving the quality and efficiency of the science performed at public expense, and each requires or requests that experimental data and artifacts are shared.

7.2 Practice in non-robotics disciplines

According to Nielsen [18] since 1991 physicists have made extensive use of the preprint server arXiv, which makes papers freely available at the same time as they are submitted to a journal for publication. Nielsen views arXiv as an important tool to speed up the transfer of knowledge, but goes further by calling for the next generation of openness in science by “… making more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing.”.

Arguably the life sciences are leading the trend. For example a US National Academy of Sciences document on life science best practice [4] requires authors to be consistent with the principles of publication. This means that anything that is central to a paper is to be made available in a way that enables replication, verification and furtherance of science. When it comes to publishing algorithms, these guidelines are very explicit:

…if the intricacies of the algorithm make it difficult to describe in a publication, the author could provide an outline of it in the paper and make the source code […] available to investigators… [4]

In epidemiology usually more is at stake than in everyday robotics. Epidemiological findings often influence policymakers, thus society requires highly reliable results from this field. Peng et al. [21] acknowledge the sensitive nature of this kind of work, and argue that reproducibility is the minimum standard for epidemiological research. Reproducibility allows independent investigators to subject the original data to their own analysis and interpretation. To enable reproducibility Peng

…calls for data sets and software to be made available for 1) verifying published findings, 2) conducting alternative analyzes of the same data, 3) eliminating uninformed criticisms that do not stand up to existing data, and 4) expediting the interchange of ideas among investigators. [21]

7.3 Journals

While scientists like Leonardo da Vinci, Galileo Galilei and Christiaan Huygens kept their discoveries secret [18], modern science is characterized by publication. Britain’s Royal Society mandated peer-review of published scientific articles in its Philosophical Transactions, first published in 1665. This policy reflected the philosphy of the Royal Society, expressed in their motto Nullius in Verba (nothing in words / take nobody’s word for it), that scientific claims are only valid if reproducible. Since then, peer-reviewed journals have been the most important way to communicate scientific results. Now, as the cost of distributing large amounts of digital data becomes very low - a small fraction of the total cost of an experiment, or of paper publication - many journals require or at least encourage publication of data, samples, code and detailed method descriptions alongside the traditional paper.

7.3.1 Science

In 2004 and 2005 Science published two stem cell papers (Science 303, 1669 (2004) and Science 308, 1777 (2005)) which were later discovered to be fraudulent and retracted by the journal. As a consequence Science enlisted the help of an outside committee to investigate the handling of the two papers and suggest improvements to the editorial process of their journal. The committee concluded that Science had correctly followed their policies and that no procedure could protect against deliberate fraud [9]. Interesting in the context of our paper is the committee’s recommendation for improving the editorial process “Science should have substantially stricter requirements about reporting the primary data”. Today Science requires that

  • large data sets are deposited in approved public databases prior to publication and an accession number is included in the published paper.

  • all data necessary to understand, assess, and extend the conclusions of the paper must be made available to the reader, flowing the policies of [12] and [4].

  • all reasonable requests for sharing materials are to be fulfilled. [3]

7.3.2 Nature

The Nature Publishing Group’s policy on availability of data for all their Nature publications is very similar:

An inherent principle of publication is that others should be able to replicate and build upon the authors’ published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make material, data and associated protocols promptly available to readers without preconditions. [13]

As with Science, Nature requires depositing dataset in publicly accessible databases. Of high interest in relation to our paper is Nature’s policy on sharing biological materials. It reads

For materials such as mutant strains and cell lines, the Nature journals require authors to use established public repositories whenever possible […] and provide accession numbers in the manuscript. [13]

Nature recently highlighted the importance of this issue on the cover of an issue that featured a related editorial and three news/opinion articles. The editorial described “data’s shameful neglect”, calling for funding agencies to boost support for (and pressure on) researchers to make data available [14]. Various reasons why many researchers choose not to share, despite the existence of purpose-built infrastructure, are discussed in the context of the perceived failure of a digital archive project at the University of Rochester[17]. A distinction is made between the issues of pre-publication [16] and post-publication [15] sharing of data and tools. We are advocating simultaneous sharing and publication, which is a special case of post-publication sharing.

7.3.3 Others

Other journals like Nucleic Acids Research [19] and the Public Library of Science journal series [23] have very similar policies on data sharing and access to research material.

A less rigorous procedure is employed by the Annals of Internal Medicine. To foster reproducible research and to enhance trust in scientific results of publications, the journal encourages authors to make their data publicly available and mandates authors to include a statement of whether materials are being made available or not and if under which conditions [10].

7.3.4 Robotics

The journal Autonomous Robots appears to have no stated policy on code and data publication, though it does support the bundling of supplementary material such as videos and data spreadsheets. The IEEE Transactions on Robotics is similar, with no policy recommending data or code sharing. However, it does mention these explicitly in the “multimedia” instructions:

Multimedia can be “playable” files […] or “dataset” files (e.g., raw data with programs to manipulate them). Such material is intended to enhance the contents of a paper, both in clarity and in added value.

7.4 Impact on citation rates

Citation counts are commonly used to assess the impact of an author’s work [5]. A 2007 meta-study of cancer micorarray clinical trials revealed that papers which shared their mircoarray data were cited about 70% more frequently [22] than those that did not. If this effect generalizes to robotics, authors would have an interest in publishing code in order to boost their citation counts. An increase in citations can also be achieved by publishing in open-access journals [6].

7.5 Related efforts

A system for sharing and reproducing computations is proposed by Schwab et al. [25], who use their system, based on GNU make, as the principal means for organizing and transferring scientific computations in their geophysics laboratory. The motivation for ReDoc is essentially the same as that described in this paper. However, perhaps unfortunately, this tool does not appear to have made a large impact in computer science so far. ReDoc is clever and powerful, but requires the user to learn to read special Make macros. The method we advocate in this paper is more simple and does not prescribe a particular build system, and can be thought of as a subset of the ReDoc workflow.

8 Sharing in Robotics

Various free-to-use middleware and simulartion platforms for robotics have been used over the last fifteen years, of which Carmen[7], Player[8] and recently ROS666http://ros.org are probably the most influential in research. Much of the code-sharing that has occurred is facilitated by one of these three platforms, each of which is the result of many hours of work.

ROS is currently the platform for a major effort to bootstrap a community based around common resources. In 2010 Willow Garage777http://willowgarage.com used their unusual resources to provide ten groups with highly capable PR2 mobile manipulator robots running ROS software under the condition that resulting code be made available for later users. While the PR2 is too expensive to be ubiquitous, Willow Garage publishes a family of simulation models of their robot based on well-known and free platforms. ROS goes much further than Carmen and Player in encapsulating algorithms, including recent SLAM, vision and control methods, and making them ready to use as components of a downstream system. While ROS is open source and has maby contributors, Willow Garage curates the project and does significant development.

Willow Garage’s expensive effort is the first to provide state-of-the-art mechatronics and system engineering along with free software tools, and is explicitly intended to accelerate research progress by providing resources shared resources to the community. While there will always be central place for custom robots in research, more resources from components to complete systems will become available in future. We can leverage the large investment in open source software and projects like the PR2 by shifting to code sharing as standard practice.

9 Conclusion

We have shown that meta-government organizations like the OECD see scientific data exchange as an important tool for the efficient advancement of scientific research. We have also argued that code is a form of data that is particularly important for robotics research. Thus making experimental data including code and configurations publicly available is important for the progress of robotics.

Building upon other peoples work is an integral part of the scientific process. Increasing the efficiency of this process increases community productivity. We suggest that making experimental code identifiable will be helpful. We have also argued that the direct and indirect effects of publishing identifiable code are good for the researcher that shares, as well as for the wider community.

Other research fields, especially life sciences, have strong requirements to share data sets and provide free access to supporting materials alongside with traditional paper publications. In the case of Nature a submission of biological material to a public repository may be required. In robotics, while sharing physical robots may be prohibitively expensive, sharing digital resources takes little time or treasure. Freely available infrastructure allows the upload of a complete experiment (software, build scripts, data, analysis scripts etc.) to a public repository in a few seconds with a few button presses. Code sharing in robotics is easy.

The issues discussed here are not new, and a subset of robotics researchers does publish source code implementations of their algorithms, to the benefit of everyone. The main contribution here is to point out the importance of distributing uniquely identifiable versions and not just the latest and “best” version. We have argued that this methodological issue is important, that originators and subsequent users can both benefit, and suggested an easy-to-follow publishing protocol. Our group will follow this protocol and observe its effects.

Acknowledgements

Thanks to Greg Mori, Alex Couture-Beil, Yaroslav Litus, Brian Gerkey, Gaurav Sukhatme, and the organizers and attendees of the RSS’09 Workshop on Methodology in Experimental Robotics for useful discussions on this issue.

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