Archive for reproducible research

reproducibility

Posted in Books, Statistics with tags , , , , , , , , on December 1, 2015 by xi'an

WariseWhile in Warwick this week, I borrowed a recent issue (Oct. 08, 2015) of Nature from Tom Nichols and read it over diners in a maths house. Its featured topic was reproducibility, with a long initial (or introductory) article about “Fooling ourselves”, starting with an illustration from Andrew himself who had gotten a sign wrong in one of those election studies that are the basis of Red State, Blue State. While this article is not bringing radically new perspectives on the topic, there is nothing shocking about it and it even goes on mentioning Peter Green and his Royal Statistical Society President’s tribune about the Sally Clark case and Eric-Jan Wagenmakers with a collaboration with competing teams that sounded like “putting one’s head on a guillotine”. Which relates to a following “comment” on crowdsourcing research or data analysis.

I however got most interested by another comment by MacCoun and Perlmutter, where they advocate a systematic blinding of data to avoid conscious or unconscious biases. While I deem the idea quite interesting and connected with anonymisation techniques in data privacy, I find the presentation rather naïve in its goals (from a statistical perspective). Indeed, if we consider data produced by a scientific experiment towards the validation or invalidation of a scientific hypothesis, it usually stands on its own, with no other experiment of a similar kind to refer to. Add too much noise and only noise remains. Add too little and the original data remains visible. This means it is quite difficult to calibrate the blinding mechanisms in order for the blinded data to remain realistic enough to be analysed. Or to be different enough from the original data for different conclusions to be drawn. The authors suggest blinding being done by a software, by adding noise, bias, label switching, &tc. But I do not think this blinding can be done blindly, i.e., without a clear idea of what the possible models are, so that the perturbed datasets created out of the original data favour more one of the models under comparison. And are realistic for at least one of those models. Thus, some preliminary analysis of the original or of some pseudo-data from each of the proposed models is somewhat unavoidable to calibrate the blinding machinery towards realistic values. If designing a new model is part of the inferential goals, this may prove impossible… Again, I think having several analyses run in parallel with several perturbed datasets quite a good idea to detect the impact of some prior assumptions. But this requires statistically savvy programmers. And possibly informative prior distributions.

beyond subjective and objective in Statistics

Posted in Books, Statistics, University life with tags , , , , , , , , , , , , , , on August 28, 2015 by xi'an

“At the level of discourse, we would like to move beyond a subjective vs. objective shouting match.” (p.30)

This paper by Andrew Gelman and Christian Hennig calls for the abandonment of the terms objective and subjective in (not solely Bayesian) statistics. And argue that there is more than mere prior information and data to the construction of a statistical analysis. The paper is articulated as the authors’ proposal, followed by four application examples, then a survey of the philosophy of science perspectives on objectivity and subjectivity in statistics and other sciences, next to a study of the subjective and objective aspects of the mainstream statistical streams, concluding with a discussion on the implementation of the proposed move. Continue reading →

can we trust computer simulations? [day #2]

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , , , , , on July 13, 2015 by xi'an

Herrenhausen“Sometimes the models are better than the data.” G. Krinner

Second day at the conference on building trust in computer simulations. Starting with a highly debated issue, climate change projections. Since so many criticisms are addressed to climate models as being not only wrong but also unverifiable. And uncheckable. As explained by Gerhart Krinner, the IPCC has developed methodologies to compare models and evaluate predictions. However, from what I understood, this validation does not say anything about the future, which is the part of the predictions that matters. And that is attacked by critics and feeds climatic-skeptics. Because it is so easy to argue against the homogeneity of the climate evolution and for “what you’ve seen is not what you’ll get“! (Even though climatic-skeptics are the least likely to use this time-heterogeneity argument, being convinced as they are of the lack of human impact over the climate.)  The second talk was by Viktoria Radchuk about validation in ecology. Defined here as a test of predictions against independent data (and designs). And mentioning Simon Wood’s synthetic likelihood as the Bayesian reference for conducting model choice (as a synthetic likelihoods ratio). I had never thought of this use (found in Wood’s original paper) for synthetic likelihood, I feel a bit queasy about using a synthetic likelihood ratio as a genuine likelihood ratio. Which led to a lively discussion at the end of her talk. The next talk was about validation in economics by Matteo Richiardi, who discussed state-space models where the hidden state is observed through a summary statistic, perfect playground for ABC! But Matteo opted instead for a non-parametric approach that seems to increase imprecision and that I have never seen used in state-space models. The last part of the talk was about non-ergodic models, for which checking for validity becomes much more problematic, in my opinion. Unless one manages multiple observations of the non-ergodic path. Nicole Saam concluded this “Validation in…” morning with Validation in Sociology. With a more pessimistic approach to the possibility of finding a falsifying strategy, because of the vague nature of sociology models. For which data can never be fully informative. She illustrated the issue with an EU negotiation analysis. Where most hypotheses could hardly be tested.

“Bayesians persist with poor examples of randomness.” L. Smith

“Bayesians can be extremely reasonable.” L. Smith

The afternoon session was dedicated to methodology, mostly statistics! Andrew Robinson started with a talk on (frequentist) model validation. Called splitters and lumpers. Illustrated by a forest growth model. He went through traditional hypothesis tests like Neyman-Pearson’s that try to split between samples. And (bio)equivalence tests that take difference as the null. Using his equivalence R package. Then Leonard Smith took over [in a literal way!] from a sort-of-Bayesian perspective, in a work joint with Jim Berger and Gary Rosner on pragmatic Bayes which was mostly negative about Bayesian modelling. Introducing (to me) the compelling notion of structural model error as a representation of the inadequacy of the model. With illustrations from weather and climate models. His criticism of the Bayesian approach is that it cannot be holistic while pretending to be [my wording]. And being inadequate to measure model inadequacy, to the point of making prior choice meaningless. Funny enough, he went back to the ball dropping experiment David Higdon discussed at one JSM I attended a while ago, with the unexpected outcome that one ball did not make it to the bottom of the shaft. A more positive side was that posteriors are useful models but should not be interpreted from a probabilistic perspective. Move beyond probability was his final message. (For most of the talk, I misunderstood P(BS), the probability of a big surprise, for something else…) This was certainly the most provocative talk of the conference  and the discussion could have gone on for the rest of day! Somewhat, Lenny was voluntarily provocative in piling the responsibility upon the Bayesian’s head for being overconfident and not accounting for the physicist’ limitations in modelling the phenomenon of interest. Next talk was by Edward Dougherty on methods used in biology. He separated within-model uncertainty from outside-model inadequacy. The within model part is mostly easy to agree upon. Even though difficulties in estimating parameters creates uncertainty classes of models. Especially because of being from a small data discipline. He analysed the impact of machine learning techniques like classification as being useless without prior knowledge. And argued in favour of the Bayesian minimum mean square error estimator. Which can also lead to a classifier. And experimental design. (Using MSE seems rather reductive when facing large dimensional parameters.) Last talk of the day was by Nicolas Becu, a geographer, with a surprising approach to validation via stakeholders. A priori not too enticing a name! The discussion was of a more philosophical nature, going back to (re)define validation against reality and imperfect models. And including social aspects of validation, e.g., reality being socially constructed. This led to the stakeholders, because a model is then a shared representation. Nicolas illustrated the construction by simulation “games” of a collective model in a community of Thai farmers and in a group of water users.

In a rather unique fashion, we also had an evening discussion on points we share and points we disagreed upon. After dinner (and wine), which did not help I fear! Bill Oberkampf mentioned the use of manufactured solutions to check code, which seemed very much related to physics. But then we got mired into the necessity of dividing between verification and validation. Which sounded very and too much engineering-like to me. Maybe because I do not usually integrate coding errors and algorithmic errors into my reasoning (verification)… Although sharing code and making it available makes a big difference. Or maybe because considering all models are wrong is neither part of my methodology (validation). This part ended up in a fairly pessimistic conclusion on the lack of trust in most published articles. At least in the biological sciences.

implementing reproducible research [short book review]

Posted in Books, Kids, pictures, R, Statistics, Travel, University life with tags , , , , , , , , , , , on July 15, 2014 by xi'an

As promised, I got back to this book, Implementing reproducible research (after the pigeons had their say). I looked at it this morning while monitoring my students taking their last-chance R exam (definitely last chance as my undergraduate R course is not reconoduced next year). The book is in fact an edited collection of papers on tools, principles, and platforms around the theme of reproducible research. It obviously links with other themes like open access, open data, and open software. All positive directions that need more active support from the scientific community. In particular the solutions advocated through this volume are mostly Linux-based. Among the tools described in the first chapter, knitr appears as an alternative to sweave. I used the later a while ago and while I like its philosophy. it does not extend to situations where the R code within takes too long to run… (Or maybe I did not invest enough time to grasp the entire spectrum of sweave.) Note that, even though the book is part of the R Series of CRC Press, many chapters are unrelated to R. And even more [unrelated] to statistics.

This limitation is somewhat my difficulty with [adhering to] the global message proposed by the book. It is great to construct such tools that monitor and archive successive versions of code and research, as anyone can trace back the research steps conducting to the published result(s). Using some of the platforms covered by the book establishes for instance a superb documentation principle, going much further than just providing an “easy” verification tool against fraudulent experiments. The notion of a super-wiki where notes and preliminary versions and calculations (and dead ends and failures) would be preserved for open access is just as great. However this type of research processing and discipline takes time and space and human investment, i.e. resources that are sparse and costly. Complex studies may involve enormous amounts of data and, neglecting the notions of confidentiality and privacy, the cost of storing such amounts is significant. Similarly for experiments that require days and weeks of huge clusters. I thus wonder where those resources would be found (journals, universities, high tech companies, …?) for the principle to hold in full generality and how transient they could prove. One cannot expect the research time to garantee availability of those meta-documents for remote time horizons. Just as a biased illustration, checking the available Bayes’ notebooks meant going to a remote part of London at a specific time and with a preliminary appointment. Those notebooks are not available on line for free. But for how long?

“So far, Bob has been using Charlie’s old computer, using Ubuntu 10.04. The next day, he is excited to find the new computer Alice has ordered for him has arrived. He installs Ubuntu 12.04” A. Davison et al.

Putting their principles into practice, the authors of Implementing reproducible research have made all chapters available for free on the Open Science Framework. I thus encourage anyone interesting in those principles (and who would not be?!) to peruse the chapters and see how they can benefit from and contribute to open and reproducible research.

revenge of the pigeons

Posted in Books, Kids, pictures, R, Statistics, Travel, University life with tags , , , , , , on June 24, 2014 by xi'an

pigeonpooWhile I had not had kamikaze pigeons hitting my windows for quite a while…, it may be that one of them decided to move to biological warfare: when I came back from Edinburgh, my office at the University was in a terrible state as a bird had entered through a tiny window opening and wrecked havoc on the room, dropping folders and rocks from my shelves and… leaving a most specific proof of its visit. This bird was particularly attracted by and aggressive against the above book, Implementing Reproducible Research, standing on top of my books to review for CHANCE. Obvious disclaimer: this reflects neither my opinion nor the University opinion about the book contents, but only the bird’s, which is solely responsible for its action!