andrew_gelman_stats andrew_gelman_stats-2013 andrew_gelman_stats-2013-2078 knowledge-graph by maker-knowledge-mining
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Introduction: Mike Zyphur sent along this paper by Corinna Kruse: This article draws attention to communication across professions as an important aspect of forensic evidence. Based on ethnographic fieldwork in the Swedish legal system, it shows how forensic scientists use a particular quantitative approach to evaluating forensic laboratory results, the Bayesian approach, as a means of quantifying uncertainty and communicating it accurately to judges, prosecutors, and defense lawyers, as well as a means of distributing responsibility between the laboratory and the court. This article argues that using the Bayesian approach also brings about a particular type of intersubjectivity; in order to make different types of forensic evidence commensurable and combinable, quantifications must be consistent across forensic specializations, which brings about a transparency based on shared understandings and practices. Forensic scientists strive to keep the black box of forensic evidence – at least partly
sentIndex sentText sentNum sentScore
1 Mike Zyphur sent along this paper by Corinna Kruse: This article draws attention to communication across professions as an important aspect of forensic evidence. [sent-1, score-1.088]
2 Forensic scientists strive to keep the black box of forensic evidence – at least partly – open in order to achieve this transparency. [sent-4, score-1.317]
3 I like the linking of Bayes with transparency; this is related to my shtick about “ institutional decision analysis ” (this also appears in the decision analysis chapter of BDA). [sent-5, score-0.421]
4 In particular, I hate hate hate things like this: To me, the whole point of probabilities is that they can be treated directly as numbers. [sent-7, score-0.558]
5 If 5:1 odds doesn’t count as support for a hypothesis, this suggests to me that the odds are not really being taken at face value. [sent-8, score-0.388]
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same-blog 1 0.99999988 2078 andrew gelman stats-2013-10-26-“The Bayesian approach to forensic evidence”
Introduction: Mike Zyphur sent along this paper by Corinna Kruse: This article draws attention to communication across professions as an important aspect of forensic evidence. Based on ethnographic fieldwork in the Swedish legal system, it shows how forensic scientists use a particular quantitative approach to evaluating forensic laboratory results, the Bayesian approach, as a means of quantifying uncertainty and communicating it accurately to judges, prosecutors, and defense lawyers, as well as a means of distributing responsibility between the laboratory and the court. This article argues that using the Bayesian approach also brings about a particular type of intersubjectivity; in order to make different types of forensic evidence commensurable and combinable, quantifications must be consistent across forensic specializations, which brings about a transparency based on shared understandings and practices. Forensic scientists strive to keep the black box of forensic evidence – at least partly
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Introduction: In light of the recent article about drug-target research and replication (Andrew blogged it here ) and l’affaire Potti , I have mentioned the “Forensic Bioinformatics” paper (Baggerly & Coombes 2009) to several colleagues in passing this week. I have concluded that it has not gotten the attention it deserves, though it has been discussed on this blog before too. Figure 1 from Baggerly & Coombes 2009 The authors try to reproduce published data, and end up “reverse engineering” what the original authors had to have done. Some examples: §2.2: “Training data sensitive/resistant labels are reversed.” §2.4: “Only 84/122 test samples are distinct; some samples are labeled both sensitive and resistant.” §2.7: Almost half of the data is incorrectly labeled resistant. §3.2: “This offset involves a single row shift: for example, … [data from] row 98 were used instead of those from row 97.” §5.4: “Poor documentation led a report on drug A to include a heatmap
3 0.091708735 991 andrew gelman stats-2011-11-04-Insecure researchers aren’t sharing their data
Introduction: Jelte Wicherts writes: I thought you might be interested in reading this paper that is to appear this week in PLoS ONE. In it we [Wicherts, Marjan Bakker, and Dylan Molenaar] show that the willingness to share data from published psychological research is associated both with “the strength of the evidence” (against H0) and the prevalence of errors in the reporting of p-values. The issue of data archiving will likely be put on the agenda of granting bodies and the APA/APS because of what Diederik Stapel did . I hate hate hate hate hate when people don’t share their data. In fact, that’s the subject of my very first column on ethics for Chance magazine. I have a story from 22 years ago, when I contacted some scientists and showed them how I could reanalyze their data more efficiently (based on a preliminary analysis of their published summary statistics). They seemed to feel threatened by the suggestion and refused to send me their raw data. (It was an animal experiment
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Introduction: Following a recent email exchange regarding path sampling and thermodynamic integration (sadly, I’ve gotten rusty and haven’t thought seriously about these challenges for many years), a correspondent referred to the marginal distribution of the data under a model as “the evidence.” I hate that expression! As we discuss in chapter 6 of BDA, for continuous-parametered models, this quantity can be completely sensitive to aspects of the prior that have essentially no impact on the posterior. In the examples I’ve seen, this marginal probability is not “evidence” in any useful sense of the term. When I told this to my correspondent, he replied, I actually don’t find “the evidence” too bothersome. I don’t have BDA at home where I’m working from at the moment, so I’ll read up on chapter 6 later, but I assume you refer to the problem of the marginal likelihood being strongly sensitive to the prior in a way that the posterior typically isn’t, thereby diminishing the value of the margi
5 0.069932289 1095 andrew gelman stats-2012-01-01-Martin and Liu: Probabilistic inference based on consistency of model with data
Introduction: What better way to start then new year than with some hard-core statistical theory? Ryan Martin and Chuanhai Liu send along a new paper on inferential models: Probability is a useful tool for describing uncertainty, so it is natural to strive for a system of statistical inference based on probabilities for or against various hypotheses. But existing probabilistic inference methods struggle to provide a meaningful interpretation of the probabilities across experiments in sufficient generality. In this paper we further develop a promising new approach based on what are called inferential models (IMs). The fundamental idea behind IMs is that there is an unobservable auxiliary variable that itself describes the inherent uncertainty about the parameter of interest, and that posterior probabilistic inference can be accomplished by predicting this unobserved quantity. We describe a simple and intuitive three-step construction of a random set of candidate parameter values, each being co
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Introduction: Mike Zyphur sent along this paper by Corinna Kruse: This article draws attention to communication across professions as an important aspect of forensic evidence. Based on ethnographic fieldwork in the Swedish legal system, it shows how forensic scientists use a particular quantitative approach to evaluating forensic laboratory results, the Bayesian approach, as a means of quantifying uncertainty and communicating it accurately to judges, prosecutors, and defense lawyers, as well as a means of distributing responsibility between the laboratory and the court. This article argues that using the Bayesian approach also brings about a particular type of intersubjectivity; in order to make different types of forensic evidence commensurable and combinable, quantifications must be consistent across forensic specializations, which brings about a transparency based on shared understandings and practices. Forensic scientists strive to keep the black box of forensic evidence – at least partly
Introduction: Ken Rice writes: In the recent discussion on stopping rules I saw a comment that I wanted to chip in on, but thought it might get a bit lost, in the already long thread. Apologies in advance if I misinterpreted what you wrote, or am trying to tell you things you already know. The comment was: “In Bayesian decision making, there is a utility function and you choose the decision with highest expected utility. Making a decision based on statistical significance does not correspond to any utility function.” … which immediately suggests this little 2010 paper; A Decision-Theoretic Formulation of Fisher’s Approach to Testing, The American Statistician, 64(4) 345-349. It contains utilities that lead to decisions that very closely mimic classical Wald tests, and provides a rationale for why this utility is not totally unconnected from how some scientists think. Some (old) slides discussing it are here . A few notes, on things not in the paper: * I know you don’t like squared-
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Introduction: In response to the discussion of X and me of his recent paper , Val Johnson writes: I would like to thank Andrew for forwarding his comments on uniformly most powerful Bayesian tests (UMPBTs) to me and his invitation to respond to them. I think he (and also Christian Robert) raise a number of interesting points concerning this new class of Bayesian tests, but I think that they may have confounded several issues that might more usefully be examined separately. The first issue involves the choice of the Bayesian evidence threshold, gamma, used in rejecting a null hypothesis in favor of an alternative hypothesis. Andrew objects to the higher values of gamma proposed in my recent PNAS article on grounds that too many important scientific effects would be missed if thresholds of 25-50 were routinely used. These evidence thresholds correspond roughly to p-values of 0.005; Andrew suggests that evidence thresholds around 5 should continue to be used (gamma=5 corresponds approximate
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Introduction: Sam Seaver writes: I [Seaver] happened to be reading an ironic article by Karl Friston when I learned something new about frequentist vs bayesian, namely Lindley’s paradox, on page 12. The text is as follows: So why are we worried about trivial effects? They are important because the probability that the true effect size is exactly zero is itself zero and could cause us to reject the null hypothesis inappropriately. This is a fallacy of classical inference and is not unrelated to Lindley’s paradox (Lindley 1957). Lindley’s paradox describes a counterintuitive situation in which Bayesian and frequentist approaches to hypothesis testing give opposite results. It occurs when; (i) a result is significant by a frequentist test, indicating sufficient evidence to reject the null hypothesis d=0 and (ii) priors render the posterior probability of d=0 high, indicating strong evidence that the null hypothesis is true. In his original treatment, Lindley (1957) showed that – under a parti
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Introduction: A recent discussion between commenters Question and Fernando captured one of the recurrent themes here from the past year. Question: The problem is simple, the researchers are disproving always false null hypotheses and taking this disproof as near proof that their theory is correct. Fernando: Whereas it is probably true that researchers misuse NHT, the problem with tabloid science is broader and deeper. It is systemic. Question: I do not see how anything can be deeper than replacing careful description, prediction, falsification, and independent replication with dynamite plots, p-values, affirming the consequent, and peer review. From my own experience I am confident in saying that confusion caused by NHST is at the root of this problem. Fernando: Incentives? Impact factors? Publish or die? “Interesting” and “new” above quality and reliability, or actually answering a research question, and a silly and unbecoming obsession with being quoted in NYT, etc. . . . Giv
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Introduction: Mike Zyphur sent along this paper by Corinna Kruse: This article draws attention to communication across professions as an important aspect of forensic evidence. Based on ethnographic fieldwork in the Swedish legal system, it shows how forensic scientists use a particular quantitative approach to evaluating forensic laboratory results, the Bayesian approach, as a means of quantifying uncertainty and communicating it accurately to judges, prosecutors, and defense lawyers, as well as a means of distributing responsibility between the laboratory and the court. This article argues that using the Bayesian approach also brings about a particular type of intersubjectivity; in order to make different types of forensic evidence commensurable and combinable, quantifications must be consistent across forensic specializations, which brings about a transparency based on shared understandings and practices. Forensic scientists strive to keep the black box of forensic evidence – at least partly
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Introduction: I was trying to make some new graphs using 5-year-old R code and I got all these problems because I was reading in files with variable names such as “co.fipsid” and now R is automatically changing them to “co_fipsid”. Or maybe the names had underbars all along, and the old R had changed them into dots. Whatever. I understand that backward compatibility can be hard to maintain, but this is just annoying.
Introduction: Alexander at GiveWell writes : The Disease Control Priorities in Developing Countries (DCP2), a major report funded by the Gates Foundation . . . provides an estimate of $3.41 per disability-adjusted life-year (DALY) for the cost-effectiveness of soil-transmitted-helminth (STH) treatment, implying that STH treatment is one of the most cost-effective interventions for global health. In investigating this figure, we have corresponded, over a period of months, with six scholars who had been directly or indirectly involved in the production of the estimate. Eventually, we were able to obtain the spreadsheet that was used to generate the $3.41/DALY estimate. That spreadsheet contains five separate errors that, when corrected, shift the estimated cost effectiveness of deworming from $3.41 to $326.43. [I think they mean to say $300 -- ed.] We came to this conclusion a year after learning that the DCP2’s published cost-effectiveness estimate for schistosomiasis treatment – another kind of
4 0.93490809 1470 andrew gelman stats-2012-08-26-Graphs showing regression uncertainty: the code!
Introduction: After our discussion of visual displays of regression uncertainty, I asked Solomon Hsiang and Lucas Leeman to send me their code. Both of them replied. Solomon wrote: The matlab and stata functions I wrote, as well as the script that replicates my figures, are all posted on my website . Also, I just added options to the main matlab function (vwregress.m) to make it display the spaghetti plot (similar to what Lucas did, but a simple bootstrap) and the shaded CI that you suggested (see figs below). They’re good suggestions. Personally, I [Hsiang] like the shaded CI better, since I think that all the visual activity in the spaghetti plot is a little distracting and sometimes adds visual weight in places where I wouldn’t want it. But the option is there in case people like it. Solomon then followed up with: I just thought of this small adjustment to your filled CI idea that seems neat. Cartographers like map projections that conserve area. We can do som
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Introduction: Troels Ring writes: I have measured total phosphorus, TP, on a number of dialysis patients, and also measured conventional phosphate, Pi. Now P is exchanged with the environment as Pi, so in principle a correlation between TP and Pi could perhaps be expected. I’m really most interested in the fraction of TP which is not Pi, that is TP-Pi. I would also expect that to be positively correlated with Pi. However, looking at the data using a mixed model an insignificant negative correlation is obtained. Then I thought, that since TP-Pi is bound to be small if Pi is large a negative correlation is almost dictated by the math even if the biology would have it otherwise in so far as the the TP-Pi, likely organic P, must someday have been Pi. Hence I thought about correcting the slight negative correlation between TP-Pi and Pi for the expected large negative correlation due to the math – to eventually recover what I came from: a positive correlation. People seems to agree that this thinki
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