Posts about reproducible paper (old posts, page 11)

Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail

Replicability and reproducibility of computational models has been somewhat understudied by “the replication movement.” In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and model reproductions in computational neuroscience. We contend that model replicability, or independent researchers' ability to obtain the same output using original code and data, and model reproducibility, or independent researchers' ability to recreate a model without original code, serve different functions and fail for different reasons. This means that measures designed to improve model replicability may not enhance (and, in some cases, may actually damage) model reproducibility. We claim that although both are undesirable, low model reproducibility poses more of a threat to long-term scientific progress than low model replicability. In our opinion, low model reproducibility stems mostly from authors' omitting to provide crucial information in scientific papers and we stress that sharing all computer code and data is not a solution. Reports of computational studies should remain selective and include all and only relevant bits of code.

To Clean or Not to Clean: Document Preprocessing and Reproducibility

Web document collections such as WT10G, GOV2, and ClueWeb are widely used for text retrieval experiments. Documents in these collections contain a fair amount of non-content-related markup in the form of tags, hyperlinks, and so on. Published articles that use these corpora generally do not provide specific details about how this markup information is handled during indexing. However, this question turns out to be important: Through experiments, we find that including or excluding metadata in the index can produce significantly different results with standard IR models. More importantly, the effect varies across models and collections. For example, metadata filtering is found to be generally beneficial when using BM25, or language modeling with Dirichlet smoothing, but can significantly reduce retrieval effectiveness if language modeling is used with Jelinek-Mercer smoothing. We also observe that, in general, the performance differences become more noticeable as the amount of metadata in the test collections increase. Given this variability, we believe that the details of document preprocessing are significant from the point of view of reproducibility. In a second set of experiments, we also study the effect of preprocessing on query expansion using RM3. In this case, once again, we find that it is generally better to remove markup before using documents for query expansion.

Experimental deception: Science, performance, and reproducibility

Experimental deception has not been seriously examined in terms of its impact on reproducible science. I demonstrate, using data from the Open Science Collaboration’s Reproducibility Project (2015), that experiments involving deception have a higher probability of not replicating and have smaller effect sizes compared to experiments that do not have deception procedures. This trend is possibly due to missing information about the context and performance of agents in the studies in which the original effects were generated, leading to either compromised internal validity, or an incomplete specification and control of variables in replication studies. Of special interest are the mechanisms by which deceptions are implemented and how these present challenges for the efficient transmission of critical information from experimenter to participant. I rehearse possible frameworks that might form the basis of a future research program on experimental deception and make some recommendations as to how such a program might be initiated.

Teaching Computational Reproducibility for Neuroimaging

We describe a project-based introduction to reproducible and collaborative neuroimaging analysis. Traditional teaching on neuroimaging usually consists of a series of lectures that emphasize the big picture rather than the foundations on which the techniques are based. The lectures are often paired with practical workshops in which students run imaging analyses using the graphical interface of specific neuroimaging software packages. Our experience suggests that this combination leaves the student with a superficial understanding of the underlying ideas, and an informal, inefficient, and inaccurate approach to analysis. To address these problems, we based our course around a substantial open-ended group project. This allowed us to teach: (a) computational tools to ensure computationally reproducible work, such as the Unix command line, structured code, version control, automated testing, and code review and (b) a clear understanding of the statistical techniques used for a basic analysis of a single run in an MR scanner. The emphasis we put on the group project showed the importance of standard computational tools for accuracy, efficiency, and collaboration. The projects were broadly successful in engaging students in working reproducibly on real scientific questions. We propose that a course on this model should be the foundation for future programs in neuroimaging. We believe it will also serve as a model for teaching efficient and reproducible research in other fields of computational science.

The Rule of Two: A Star Wars Edict or a Method of Reproducibility and Quality?

In recent years, biomedical research has faced increased scrutiny over issues related to reproducibility and quality in scientific findings(1-3). In response to this scrutiny, funding institutions and journals have implemented top-down policies for grant and manuscript review. While a positive step forward, the long-term merit of these policies is questionable given their emphasis on completing a check-list of items instead of a fundamental re-assessment of how scientific investigation is conducted. Moreover, the top-down style of management used to institute these policies can be argued as being ineffective in engaging the scientific workforce to act upon these issues. To meet current and future biomedical needs, new investigative methods that emphasize collective-thinking, teamwork, shared knowledge and cultivate change from the bottom-up are warranted. Here, a perspective on a new approach to biomedical investigation within the individual laboratory that emphasizes collaboration and quality is discussed.

Open Science as Better Gatekeepers for Science and Society: A Perspective from Neurolaw

Results from cognitive neuroscience have been cited as evidence in courtrooms around the world, and their admissibility has been a challenge for the legal system. Unfortunately, the recent reproducibility crisis in cognitive neuroscience, showing that the published studies in cognitive neuroscience may not be as trustworthy as expected, has made the situation worse. Here we analysed how the irreproducible results in cognitive neuroscience literature could compromise the standards for admissibility of scientific evidence, and pointed out how the open science movement may help to alleviate these problems. We conclude that open science not only benefits the scientific community but also the legal system, and society in a broad sense. Therefore, we suggest both scientists and practitioners follow open science recommendations and uphold the best available standards in order to serve as good gatekeepers in their own fields. Moreover, scientists and practitioners should collaborate closely to maintain an effective functioning of the entire gatekeeping system of the law.