This document provides advice on habits that make statisticians effective. It discusses the importance of understanding causation, control, comparison and counterfactuals when thinking about effectiveness. It warns against proposing habits as causes without proper evaluation. Seven key habits are identified: read, listen, understand, think, do, calculate, and communicate. The document illustrates these habits through examples of invalid inversion, regression to the mean, and statistical mistakes. It emphasizes understanding concepts fundamentally rather than just mathematically and finding simple ways to communicate ideas.
Talk given at RSS 2016 Manchester
I consider the problems that the ASA faced in getting a P-value statement together, not in terms of the process, but by looking at the expressed opinion of 21 published commentaries of the agreed statement. I then trace the history of the development of P-values. I show that the perceived problem with P-values in not just one of a supposed inadequacy of frequentist statistics but reflects a struggle at the very heart of Bayesian inference. I conclude that replacing P-values by automatic Bayesian approaches is unlikely to abolish controversy. It may be better to try and embrace diversity than to pretend it is not there.
The history of p-values is covered to try and shed light on a mystery: why did Student and Fisher agree numerically but disagree in terms of interpretation.?
Unfortunately, some have interpreted Numbers Needed to Treat as indicating the proportion of patients on whom the treatment has had a causal effect. This interpretation is very rarely, if ever, necessarily correct. It is certainly inappropriate if based on a responder dichotomy. I shall illustrate the problem using simple causal models.
One also sometimes encounters the claim that the extent to which two distributions of outcomes overlap from a clinical trial indicates how many patients benefit. This is also false and can be traced to a similar causal confusion.
How to combine results from randomised clinical trials on the additive scale with real world data to provide predictions on the clinically relevant scale for individual patients
Personalised medicine a sceptical viewStephen Senn
Some grounds for believing that the current enthusiasm about personalised medicine is exaggerated, founded on poor statistics and represents a disappointing loss of ambition.
Talk given at RSS 2016 Manchester
I consider the problems that the ASA faced in getting a P-value statement together, not in terms of the process, but by looking at the expressed opinion of 21 published commentaries of the agreed statement. I then trace the history of the development of P-values. I show that the perceived problem with P-values in not just one of a supposed inadequacy of frequentist statistics but reflects a struggle at the very heart of Bayesian inference. I conclude that replacing P-values by automatic Bayesian approaches is unlikely to abolish controversy. It may be better to try and embrace diversity than to pretend it is not there.
The history of p-values is covered to try and shed light on a mystery: why did Student and Fisher agree numerically but disagree in terms of interpretation.?
Unfortunately, some have interpreted Numbers Needed to Treat as indicating the proportion of patients on whom the treatment has had a causal effect. This interpretation is very rarely, if ever, necessarily correct. It is certainly inappropriate if based on a responder dichotomy. I shall illustrate the problem using simple causal models.
One also sometimes encounters the claim that the extent to which two distributions of outcomes overlap from a clinical trial indicates how many patients benefit. This is also false and can be traced to a similar causal confusion.
How to combine results from randomised clinical trials on the additive scale with real world data to provide predictions on the clinically relevant scale for individual patients
Personalised medicine a sceptical viewStephen Senn
Some grounds for believing that the current enthusiasm about personalised medicine is exaggerated, founded on poor statistics and represents a disappointing loss of ambition.
Developing and validating statistical models for clinical prediction and prog...Evangelos Kritsotakis
Talk on clinical prediction models presented at the Joint Seminar Series in Translational and Clinical Medicine organised by the University of Crete Medical School, the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas (IMBB-FORTH), and the University of Crete Research Center (UCRC), Heraklion [online], Greece, April 7, 2021.
When estimating sample sizes for clinical trials there are several different views that might be taken as to what definition and meaning should be given to the sought-for treatment effect. However, if the concept of a ‘minimally important difference’ (MID) does have relevance to interpreting clinical trials (which can be disputed) then its value cannot be the same as the ‘clinically relevant difference’ (CRD) that would be used for planning them.
A doubly pernicious use of the MID is as a means of classifying patients as responders and non-responders. Not only does such an analysis lead to an increase in the necessary sample size but it misleads trialists into making causal distinctions that the data cannot support and has been responsible for exaggerating the scope for personalised medicine.
In this talk these statistical points will be explained using a minimum of technical detail.
Whatever happened to design based inferenceStephenSenn2
Given as the Sprott lecture, University of Waterloo September 2022
Abstract
What exactly should we think about appropriate analyses for designed experiments and why? If conditional inference trumps marginal inference, why should we care about randomisation? Isn’t everything just modelling? The Rothamsted School held that design matters. Taking an example of applying John Nelder’s general balance approach to a notorious problem, Lord’s paradox, I shall show that there may be some lessons for two fashionable topics: causal analysis and big data. I shall conclude that if we want not only to make good estimates but estimate how good our estimates are, design does matter.
This presentation educates you about T-Test, Key takeways, Assumptions for Performing a t-test, Types of t-tests, One sample t-test, Independent two-sample t-test and Paired sample t-test.
For more topics Stay tuned with Learnbay
Improving predictions: Lasso, Ridge and Stein's paradoxMaarten van Smeden
Slides of masterclass "Improving predictions: Lasso, Ridge and Stein's paradox" at the (Dutch) National Institute for Public Health and the Environment (RIVM)
Methods of randomisation in clinical trialsAmy Mehaboob
Randomization is the process by which allocation of subjects to treatment groups is done by chance, without the ability to predict who is in what group. A randomized clinical trial is a clinical trial in which participants are randomly assigned to separate groups that compare different treatments.
Randomized trials are gold standard of study designs because the potential for bias (selection into treatment groups) is avoided.
This document includes the purpose, types, advantages and disadvantages of each type of randomisation.
A non technical overview of sample size calculation and why it is necessary with some brief examples of how to approach the problem and why it is useful to actually think of these calculations.
Prediction, Big Data, and AI: Steyerberg, Basel Nov 1, 2019Ewout Steyerberg
Title"Clinical prediction models in the age of artificial intelligence and big data", presented at the Basel Biometrics Society seminar Nov 1, 2019, Basel, by Ewout Steyerberg, with substantial inout from Maarten van Smeden and Ben van Calster
Clinical trials are about comparability not generalisability V2.pptxStephenSenn2
Lecture delivered at the September 2022 EFSPI meeting in Basle in which I argued that the patients in a clinical trial should not be viewed as being a representative sample of some target population.
What should we expect from reproducibiliryStephen Senn
Is there really a reproducibility crisis and if so are P-values to blame? Choose any statistic you like and carry out two identical independent studies and report this statistic for each. In advance of collecting any data, you ought to expect that it is just as likely that statistic 1 will be smaller than statistic 2 as vice versa. Once you have seen statistic 1, things are not so simple but if they are not so simple, it is that you have other information in some form. However, it is at least instructive that you need to be careful in jumping to conclusions about what to expect from reproducibility. Furthermore, the forecasts of good Bayesians ought to obey a Martingale property. On average you should be in the future where you are now but, of course, your inferential random walk may lead to some peregrination before it homes in on “the truth”. But you certainly can’t generally expect that a probability will get smaller as you continue. P-values, like other statistics are a position not a movement. Although often claimed, there is no such things as a trend towards significance.
Using these and other philosophical considerations I shall try and establish what it is we want from reproducibility. I shall conclude that we statisticians should probably be paying more attention to checking that standard errors are being calculated appropriately and rather less to inferential framework.
Developing and validating statistical models for clinical prediction and prog...Evangelos Kritsotakis
Talk on clinical prediction models presented at the Joint Seminar Series in Translational and Clinical Medicine organised by the University of Crete Medical School, the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology Hellas (IMBB-FORTH), and the University of Crete Research Center (UCRC), Heraklion [online], Greece, April 7, 2021.
When estimating sample sizes for clinical trials there are several different views that might be taken as to what definition and meaning should be given to the sought-for treatment effect. However, if the concept of a ‘minimally important difference’ (MID) does have relevance to interpreting clinical trials (which can be disputed) then its value cannot be the same as the ‘clinically relevant difference’ (CRD) that would be used for planning them.
A doubly pernicious use of the MID is as a means of classifying patients as responders and non-responders. Not only does such an analysis lead to an increase in the necessary sample size but it misleads trialists into making causal distinctions that the data cannot support and has been responsible for exaggerating the scope for personalised medicine.
In this talk these statistical points will be explained using a minimum of technical detail.
Whatever happened to design based inferenceStephenSenn2
Given as the Sprott lecture, University of Waterloo September 2022
Abstract
What exactly should we think about appropriate analyses for designed experiments and why? If conditional inference trumps marginal inference, why should we care about randomisation? Isn’t everything just modelling? The Rothamsted School held that design matters. Taking an example of applying John Nelder’s general balance approach to a notorious problem, Lord’s paradox, I shall show that there may be some lessons for two fashionable topics: causal analysis and big data. I shall conclude that if we want not only to make good estimates but estimate how good our estimates are, design does matter.
This presentation educates you about T-Test, Key takeways, Assumptions for Performing a t-test, Types of t-tests, One sample t-test, Independent two-sample t-test and Paired sample t-test.
For more topics Stay tuned with Learnbay
Improving predictions: Lasso, Ridge and Stein's paradoxMaarten van Smeden
Slides of masterclass "Improving predictions: Lasso, Ridge and Stein's paradox" at the (Dutch) National Institute for Public Health and the Environment (RIVM)
Methods of randomisation in clinical trialsAmy Mehaboob
Randomization is the process by which allocation of subjects to treatment groups is done by chance, without the ability to predict who is in what group. A randomized clinical trial is a clinical trial in which participants are randomly assigned to separate groups that compare different treatments.
Randomized trials are gold standard of study designs because the potential for bias (selection into treatment groups) is avoided.
This document includes the purpose, types, advantages and disadvantages of each type of randomisation.
A non technical overview of sample size calculation and why it is necessary with some brief examples of how to approach the problem and why it is useful to actually think of these calculations.
Prediction, Big Data, and AI: Steyerberg, Basel Nov 1, 2019Ewout Steyerberg
Title"Clinical prediction models in the age of artificial intelligence and big data", presented at the Basel Biometrics Society seminar Nov 1, 2019, Basel, by Ewout Steyerberg, with substantial inout from Maarten van Smeden and Ben van Calster
Clinical trials are about comparability not generalisability V2.pptxStephenSenn2
Lecture delivered at the September 2022 EFSPI meeting in Basle in which I argued that the patients in a clinical trial should not be viewed as being a representative sample of some target population.
What should we expect from reproducibiliryStephen Senn
Is there really a reproducibility crisis and if so are P-values to blame? Choose any statistic you like and carry out two identical independent studies and report this statistic for each. In advance of collecting any data, you ought to expect that it is just as likely that statistic 1 will be smaller than statistic 2 as vice versa. Once you have seen statistic 1, things are not so simple but if they are not so simple, it is that you have other information in some form. However, it is at least instructive that you need to be careful in jumping to conclusions about what to expect from reproducibility. Furthermore, the forecasts of good Bayesians ought to obey a Martingale property. On average you should be in the future where you are now but, of course, your inferential random walk may lead to some peregrination before it homes in on “the truth”. But you certainly can’t generally expect that a probability will get smaller as you continue. P-values, like other statistics are a position not a movement. Although often claimed, there is no such things as a trend towards significance.
Using these and other philosophical considerations I shall try and establish what it is we want from reproducibility. I shall conclude that we statisticians should probably be paying more attention to checking that standard errors are being calculated appropriately and rather less to inferential framework.
Stephen Senn slides:"‘Repligate’: reproducibility in statistical studies. What does it mean and in what sense does it matter?" presented May 23 at the session on "The Philosophy of Statistics: Bayesianism, Frequentism and the Nature of Inference"," at the 2015 APS Annual Convention in NYC
Sample size determination in clinical trials is considered from various ethical and practical perspectives. It is concluded that cost is a missing dimension and that the value of information is key.
The replication crisis: are P-values the problem and are Bayes factors the so...StephenSenn2
Today’s posterior is tomorrow’s prior. Dennis Lindley1 (P2)
It has been claimed that science is undergoing a replication crisis and that when looking for culprits, the cult of significance is the chief suspect. It has also been claimed that Bayes factors might provide a solution.
In my opinion, these claims are misleading and part of the problem is our understanding of the purpose and nature of replication, which has only recently been subject to formal analysis2. What we are or should be interested in is truth. Replication is a coherence not a correspondence requirement3 and one that has a strong dependence on the size of the replication study4.
Consideration of Bayes factors raises a puzzling question. Should the Bayes factor for a replication study be calculated as if it were the initial study? If the answer is yes, the approach is not fully Bayesian and furthermore the Bayes factors will be subject to exactly the same replication ‘paradox’ as P-values. If the answer is no, then in what sense can an initially found Bayes factor be replicated and what are the implications for how we should view replication of P-values?
A further issue is that little attention has been paid to false negatives and, by extension to true negative values. Yet, as is well known from the theory of diagnostic tests, it is meaningless to consider the performance of a test in terms of false positives alone.
I shall argue that we are in danger of confusing evidence with the conclusions we draw and that any reforms of scientific practice should concentrate on producing evidence that is reliable as it can be qua evidence. There are many basic scientific practices in need of reform. Pseudoreplication5, for example, and the routine destruction of information through dichotomisation6 are far more serious problems than many matters of inferential framing that seem to have excited statisticians.
References
1. Lindley DV. Bayesian statistics: A review. SIAM; 1972.
2. Devezer B, Navarro DJ, Vandekerckhove J, Ozge Buzbas E. The case for formal methodology in scientific reform. R Soc Open Sci. Mar 31 2021;8(3):200805. doi:10.1098/rsos.200805
3. Walker RCS. Theories of Truth. In: Hale B, Wright C, Miller A, eds. A Companion to the Philosophy of Language. John Wiley & Sons,; 2017:532-553:chap 21.
4. Senn SJ. A comment on replication, p-values and evidence by S.N.Goodman, Statistics in Medicine 1992; 11:875-879. Letter. Statistics in Medicine. 2002;21(16):2437-44.
5. Hurlbert SH. Pseudoreplication and the design of ecological field experiments. Ecological monographs. 1984;54(2):187-211.
6. Senn SJ. Being Efficient About Efficacy Estimation. Research. Statistics in Biopharmaceutical Research. 2013;5(3):204-210. doi:10.1080/19466315.2012.754726
The replication crisis: are P-values the problem and are Bayes factors the so...jemille6
Today’s posterior is tomorrow’s prior. Dennis Lindley
It has been claimed that science is undergoing a replication crisis and that when looking for culprits, the cult of significance is the chief suspect. It has also been claimed that Bayes factors might provide a solution.
In my opinion, these claims are misleading and part of the problem is our understanding
of the purpose and nature of replication, which has only recently been subject to formal
analysis.
What we are or should be interested in is truth. Replication is a coherence not a correspondence requirement and one that has a strong dependence on the size
of the replication study
.
Consideration of Bayes factors raises a puzzling question. Should the Bayes factor for a replication study be calculated as if it were the initial study? If the answer is yes, the approach is not fully Bayesian and furthermore the Bayes factors will be subject to
exactly the same replication ‘paradox’ as P-values. If the answer is no, then in what
sense can an initially found Bayes factor be replicated and what are the implications for how we should view replication of P-values?
A further issue is that little attention has been paid to false negatives and, by extension
to true negative values. Yet, as is well known from the theory of diagnostic tests, it is
meaningless to consider the performance of a test in terms of false positives alone.
I shall argue that we are in danger of confusing evidence with the conclusions we draw and that any reforms of scientific practice should concentrate on producing evidence
that is reliable as it can be qua evidence. There are many basic scientific practices in
need of reform. Pseudoreplication, for example, and the routine destruction of
information through dichotomisation are far more serious problems than many matters of inferential framing that seem to have excited statisticians.
Minimisation is an approach to allocating patients to treatment in clinical trials that forces a greater degree of balance than does randomisation. Here I explain why I dislike it.
P Values and Replication: the problem is not what you think
Lecture at MRC Brain Science & Cognition, Cambridge 16 December 2015
Abstract
It has been claimed that there is a crisis of replication in science. Prominent amongst the many factors that have been fingered as being responsible is the humble and ubiquitous P-value. One journal has even gone so far as to ban all inferential statistics. However, it is one thing to banish measures of uncertainty and another to banish uncertainty from your measures. I shall claim that the apparent discrepancy between P-values and posterior probabilities is as much a discrepancy between two approaches to Bayesian inference as it is between frequentist and Bayesian frameworks and that a further problem has been misunderstandings regarding predictive probabilities. I conclude that banning P-values won’t make all published results repeatable and that it is possible undesirable that it should.
Clinical trials are about comparability not generalisability V2.pptxStephenSenn3
It is a fundamental but common mistake to regard clinical trials as being a form of representative inference. The key issue is comparability. Experiments do not involve typical material. In clinical trials; it is concurrent control that is key and randomisation is a device for calculating standard errors appropriately that should reflect the design.
Generalisation beyond the clinical trial always involves theory.
Similar to The Seven Habits of Highly Effective Statisticians (20)
There are many questions one might ask of a clinical trial, ranging from what was the effect in the patients studied to what might the effect be in future patients via what was the effect in individual patients? The extent to which the answer to these questions is similar depends on various assumptions made and in some cases the design used may not permit any meaningful answer to be given at all.
A related issue is confusion between randomisation, random sampling, linear model and true multivariate based modelling. These distinctions don’t matter much for some purposes and under some circumstances but for others they do.
A yet further issue is that causal analysis in epidemiology, which has brought valuable insights in many cases, has tended to stress point estimates and ignore standard errors. This has potentially misleading consequences.
An understanding of components of variation is key. Unfortunately, the development of two particular topics in recent years, evidence synthesis by the evidence based medicine movement and personalised medicine by bench scientists has either paid scant attention to components of variation or to the questions being asked or both resulting in confusion about many issues.
For instance, it is often claimed that numbers needed to treat indicate the proportion of patients for whom treatments work, that inclusion criteria determine the generalisability of results and that heterogeneity means that a random effects meta-analysis is required. None of these is true. The scope for personalised medicine has very plausibly been exaggerated and an important cause of variation in the healthcare system, physicians, is often overlooked.
I shall argue that thinking about questions is important.
The response to the COVID-19 crisis by various vaccine developers has been extraordinary, both in terms of speed of response and the delivered efficacy of the vaccines. It has also raised some fascinating issues of design, analysis and interpretation. I shall consider some of these issues, taking as my example, five vaccines: Pfizer/BioNTech, AstraZeneca/Oxford, Moderna, Novavax, and J&J Janssen but concentrating mainly on the first two. Among matters covered will be concurrent control, efficient design, issues of measurement raised by two-shot vaccines and implications for roll-out, and the surprising effectiveness of simple analyses. Differences between the five development programmes as they affect statistics will be covered but some essential similarities will also be discussed.
The statistical revolution of the 20th century was largely concerned with developing methods for analysing small datasets. Student’s paper of 1908 was the first in the English literature to address the problem of second order uncertainty (uncertainty about the measures of uncertainty) seriously and was hailed by Fisher as heralding a new age of statistics. Much of what Fisher did was concerned with problems of what might be called ‘small data’, not only as regards efficient analysis but also as regards efficient design and in addition paying close attention to what was necessary to measure uncertainty validly.
I shall consider the history of some of these developments, in particular those that are associated with what might be called the Rothamsted School, starting with Fisher and having its apotheosis in John Nelder’s theory of General Balance and see what lessons they hold for the supposed ‘big data’ revolution of the 21st century.
Talk given at ISCB 2016 Birmingham
For indications and treatments where their use is possible, n-of-1 trials represent a promising means of investigating potential treatments for rare diseases. Each patient permits repeated comparison of the treatments being investigated and this both increases the number of observations and reduces their variability compared to conventional parallel group trials.
However, depending on whether the framework for analysis used is randomisation-based or model- based produces puzzling difference in inferences. This can easily be shown by starting on the one hand with the randomisation philosophy associated with the Rothamsted school of inference and building up the analysis through the block + treatment structure approach associated with John Nelder’s theory of general balance (as implemented in GenStat®) or starting on the other hand with a plausible variance component approach through a mixed model. However, it can be shown that these differences are related not so much to modelling approach per se but to the questions one attempts to answer: ranging from testing whether there was a difference between treatments in the patients studied, to predicting the true difference for a future patient, via making inferences about the effect in the average patient.
This in turn yields interesting insight into the long-run debate over the use of fixed or random effect meta-analysis.
Some practical issues of analysis will also be covered in R and SAS®, in which languages some functions and macros to facilitate analysis have been written. It is concluded that n-of-1 hold great promise in investigating chronic rare diseases but that careful consideration of matters of purpose, design and analysis is necessary to make best use of them.
Acknowledgement
This work is partly supported by the European Union’s 7th Framework Programme for research, technological development and demonstration under grant agreement no. 602552. “IDEAL”
Clinical trials: quo vadis in the age of covid?Stephen Senn
A discussion of the role of clinical trials in the age of COVID. My contribution to the phastar 2020 life sciences summit https://phastar.com/phastar-life-science-summit
It is argued that when it comes to nuisance parameters an assumption of ignorance is harmful. On the other hand this raises problems as to how far one should go in searching for further data when combining evidence.
An early and overlooked causal revolution in statistics was the development of the theory of experimental design, initially associated with the "Rothamstead School". An important stage in the evolution of this theory was the experimental calculus developed by John Nelder in the 1960s with its clear distinction between block and treatment factors in designed experiments. This experimental calculus produced appropriate models automatically from more basic formal considerations but was, unfortunately, only ever implemented in Genstat®, a package widely used in agriculture but rarely so in medical research. In consequence its importance has not been appreciated and the approach of many statistical packages to designed experiments is poor. A key feature of the Rothamsted School approach is that identification of the appropriate components of variation for judging treatment effects is simple and automatic.
The impressive more recent causal revolution in epidemiology, associated with Judea Pearl, seems to have no place for components of variation, however. By considering the application of Nelder’s experimental calculus to Lord’s Paradox, I shall show that this reveals that solutions that have been proposed using the more modern causal calculus are problematic. I shall also show that lessons from designed clinical trials have important implications for the use of historical data and big data more generally.
Views of the role of hypothesis falsification in statistical testing do not divide as cleanly between frequentist and Bayesian views as is commonly supposed. This can be shown by considering the two major variants of the Bayesian approach to statistical inference and the two major variants of the frequentist one.
A good case can be made that the Bayesian, de Finetti, just like Popper, was a falsificationist. A thumbnail view, which is not just a caricature, of de Finetti’s theory of learning, is that your subjective probabilities are modified through experience by noticing which of your predictions are wrong, striking out the sequences that involved them and renormalising.
On the other hand, in the formal frequentist Neyman-Pearson approach to hypothesis testing, you can, if you wish, shift conventional null and alternative hypotheses, making the latter the strawman and by ‘disproving’ it, assert the former.
The frequentist, Fisher, however, at least in his approach to testing of hypotheses, seems to have taken a strong view that the null hypothesis was quite different from any other and there was a strong asymmetry on inferences that followed from the application of significance tests.
Finally, to complete a quartet, the Bayesian geophysicist Jeffreys, inspired by Broad, specifically developed his approach to significance testing in order to be able to ‘prove’ scientific laws.
By considering the controversial case of equivalence testing in clinical trials, where the object is to prove that ‘treatments’ do not differ from each other, I shall show that there are fundamental differences between ‘proving’ and falsifying a hypothesis and that this distinction does not disappear by adopting a Bayesian philosophy. I conclude that falsificationism is important for Bayesians also, although it is an open question as to whether it is enough for frequentists.
In Search of Lost Infinities: What is the “n” in big data?Stephen Senn
In designing complex experiments, agricultural scientists, with the help of their statistician collaborators, soon came to realise that variation at different levels had very different consequences for estimating different treatment effects, depending on how the treatments were mapped onto the underlying block structure. This was a key feature of the Rothamsted approach to design and analysis and a strong thread running through the work of Fisher, Yates and Nelder, being expressed in topics such as split-pot designs, recovering inter-block information and fractional factorials. The null block-structure of an experiment is key to this philosophy of design and analysis. However modern techniques for analysing experiments stress models rather than symmetries and this modelling approach requires much greater care in analysis, with the consequence that you can easily make mistakes and often will.
In this talk I shall underline the obvious, but often unintentionally overlooked, fact that understanding variation at the various levels at which it occurs is crucial to analysis. I shall take three examples, an application of John Nelder’s theory of general balance to Lord’s Paradox, the use of historical data in drug development and a hybrid randomised non-randomised clinical trial, the TARGET study, to show that the data that many, including those promoting a so-called causal revolution, assume to be ‘big’ may actually be rather ‘small’. The consequence is that there is a danger that the size of standard errors will be underestimated or even that the appropriate regression coefficients for adjusting for confounding may not be identified correctly.
I conclude that an old but powerful experimental design approach holds important lessons for observational data about limitations in interpretation that mere numbers cannot overcome. Small may be beautiful, after all.
This year marks the 70th anniversary of the Medical Research Council randomised clinical trial (RCT) of streptomycin in tuberculosis led by Bradford Hill. This is widely regarded as a landmark in clinical research. Despite its widespread use in drug regulation and in clinical research more widely and its high standing with the evidence based medicine movement, the RCT continues to attracts criticism. I show that many of these criticisms are traceable to failure to understand two key concepts in statistics: probabilistic inference and design efficiency. To these methodological misunderstandings can be added the practical one of failing to appreciate that entry into clinical trials is not simultaneous but sequential.
I conclude that although randomisation should not be used as an excuse for ignoring prognostic variables, it is valuable and that many standard criticisms of RCTs are invalid.
The Rothamsted school meets Lord's paradoxStephen Senn
Lords ‘paradox’ is a notoriously difficult puzzle that is guaranteed to provoke discussion, dissent and disagreement. Two statisticians analyse some observational data and come to radically different conclusions, each of which has acquired defenders over the years since Lord first proposed his puzzle in 1967. It features in the recent Book of Why by Pearl and McKenzie, who use it to demonstrate the power of Pearl’s causal calculus, obtaining a solution they claim is unambiguously right. They also claim that statisticians have failed to get to grips with causal questions for well over a century, in fact ever since Karl Pearson developed Galton’s idea of correlation and warned the scientific world that correlation is not causation.
However, only two years before Lord published his paradox John Nelder outlined a powerful causal calculus for analyzing designed experiments based on a careful distinction between block and treatment structure. This represents an important advance in formalizing the approach to analysing complex experiments that started with Fisher 100 years ago, when he proposed splitting variability using the square of the standard deviation, which he called the variance, continued with Yates and has been developed since the 1960s by Rosemary Bailey, amongst others. This tradition might be referred to as The Rothamsted School. It is fully implemented in Genstat® but, as far as I am aware, not in any other package.
With the help of Genstat®, I demonstrate how the Rothamsted School would approach Lord’s paradox and come to a solution that is not the same as the one reached by Pearl and McKenzie, although given certain strong but untestable assumptions it would reduce to it. I conclude that the statistical tradition may have more to offer in this respect than has been supposed.
Presidents' invited lecture ISCB Vigo 2017
Discusses various issues to do with how randomised clinical trials should be analysed. See also https://errorstatistics.com/2017/07/01/s-senn-fishing-for-fakes-with-fisher-guest-post/
History of how and why a complex cross-over trial was designed to prove the equivalence of two formulations of a beta-agonist and what the eventual results were. Presented at the Newton Institute 28 July 2008. Warning: following the important paper by Kenward & Roger Biostatistics, 2010, I no longer think the random effects analysis is appropriate, although, in fact the results are pretty much the same as for the fixed effects analysis.
Techniques to optimize the pagerank algorithm usually fall in two categories. One is to try reducing the work per iteration, and the other is to try reducing the number of iterations. These goals are often at odds with one another. Skipping computation on vertices which have already converged has the potential to save iteration time. Skipping in-identical vertices, with the same in-links, helps reduce duplicate computations and thus could help reduce iteration time. Road networks often have chains which can be short-circuited before pagerank computation to improve performance. Final ranks of chain nodes can be easily calculated. This could reduce both the iteration time, and the number of iterations. If a graph has no dangling nodes, pagerank of each strongly connected component can be computed in topological order. This could help reduce the iteration time, no. of iterations, and also enable multi-iteration concurrency in pagerank computation. The combination of all of the above methods is the STICD algorithm. [sticd] For dynamic graphs, unchanged components whose ranks are unaffected can be skipped altogether.
Quantitative Data AnalysisReliability Analysis (Cronbach Alpha) Common Method...2023240532
Quantitative data Analysis
Overview
Reliability Analysis (Cronbach Alpha)
Common Method Bias (Harman Single Factor Test)
Frequency Analysis (Demographic)
Descriptive Analysis
Levelwise PageRank with Loop-Based Dead End Handling Strategy : SHORT REPORT ...Subhajit Sahu
Abstract — Levelwise PageRank is an alternative method of PageRank computation which decomposes the input graph into a directed acyclic block-graph of strongly connected components, and processes them in topological order, one level at a time. This enables calculation for ranks in a distributed fashion without per-iteration communication, unlike the standard method where all vertices are processed in each iteration. It however comes with a precondition of the absence of dead ends in the input graph. Here, the native non-distributed performance of Levelwise PageRank was compared against Monolithic PageRank on a CPU as well as a GPU. To ensure a fair comparison, Monolithic PageRank was also performed on a graph where vertices were split by components. Results indicate that Levelwise PageRank is about as fast as Monolithic PageRank on the CPU, but quite a bit slower on the GPU. Slowdown on the GPU is likely caused by a large submission of small workloads, and expected to be non-issue when the computation is performed on massive graphs.
Data Centers - Striving Within A Narrow Range - Research Report - MCG - May 2...pchutichetpong
M Capital Group (“MCG”) expects to see demand and the changing evolution of supply, facilitated through institutional investment rotation out of offices and into work from home (“WFH”), while the ever-expanding need for data storage as global internet usage expands, with experts predicting 5.3 billion users by 2023. These market factors will be underpinned by technological changes, such as progressing cloud services and edge sites, allowing the industry to see strong expected annual growth of 13% over the next 4 years.
Whilst competitive headwinds remain, represented through the recent second bankruptcy filing of Sungard, which blames “COVID-19 and other macroeconomic trends including delayed customer spending decisions, insourcing and reductions in IT spending, energy inflation and reduction in demand for certain services”, the industry has seen key adjustments, where MCG believes that engineering cost management and technological innovation will be paramount to success.
MCG reports that the more favorable market conditions expected over the next few years, helped by the winding down of pandemic restrictions and a hybrid working environment will be driving market momentum forward. The continuous injection of capital by alternative investment firms, as well as the growing infrastructural investment from cloud service providers and social media companies, whose revenues are expected to grow over 3.6x larger by value in 2026, will likely help propel center provision and innovation. These factors paint a promising picture for the industry players that offset rising input costs and adapt to new technologies.
According to M Capital Group: “Specifically, the long-term cost-saving opportunities available from the rise of remote managing will likely aid value growth for the industry. Through margin optimization and further availability of capital for reinvestment, strong players will maintain their competitive foothold, while weaker players exit the market to balance supply and demand.”
06-04-2024 - NYC Tech Week - Discussion on Vector Databases, Unstructured Data and AI
Discussion on Vector Databases, Unstructured Data and AI
https://www.meetup.com/unstructured-data-meetup-new-york/
This meetup is for people working in unstructured data. Speakers will come present about related topics such as vector databases, LLMs, and managing data at scale. The intended audience of this group includes roles like machine learning engineers, data scientists, data engineers, software engineers, and PMs.This meetup was formerly Milvus Meetup, and is sponsored by Zilliz maintainers of Milvus.
The Building Blocks of QuestDB, a Time Series Databasejavier ramirez
Talk Delivered at Valencia Codes Meetup 2024-06.
Traditionally, databases have treated timestamps just as another data type. However, when performing real-time analytics, timestamps should be first class citizens and we need rich time semantics to get the most out of our data. We also need to deal with ever growing datasets while keeping performant, which is as fun as it sounds.
It is no wonder time-series databases are now more popular than ever before. Join me in this session to learn about the internal architecture and building blocks of QuestDB, an open source time-series database designed for speed. We will also review a history of some of the changes we have gone over the past two years to deal with late and unordered data, non-blocking writes, read-replicas, or faster batch ingestion.
7. A Simple Example of ‘Invalid Inversion’
• Most women do not suffer from breast cancer
• It would be a mistake to conclude, however, that most breast cancer
victims are not women
• To do so would be to transpose the conditionals
• This is an example of invalid inversion
• Why is this important?
• People regularly confuse the probability of the data given the
hypothesis with the probability of the hypothesis given the data
• Misinterpretation of P-values is linked to this
7(c) Stephen Senn
9. Some Plausible Figures for the UK
Probability breast cancer given female = 550/31,418=0.018
9(c) Stephen Senn
10. Some Plausible Figures for the UK
Probability female given breast cancer =550/553=0.995
10(c) Stephen Senn
11. The difference is in the denominator
The numerator is the same
11(c) Stephen Senn
Invalid inversion is an error caused by mistaking the relevant marginal class
550/31418 or 550/553
12. A Little Maths
Unless ,
P A B
P A B
P B
P A B
P B A
P A
P B P A P A B P B A
So invalid inversion is equivalent to a confusion of the marginal probabilities. The
same joint probability is involved in the two conditional probabilities but different
marginal probabilities are involved
12(c) Stephen Senn
13. The Regression Analogue
Predicting Y from X is not the same as predicting X from Y.
2
2
XY
Y X
X
XY
X Y
Y
Note the similarity with the probability case.
The numerator (the covariance) is a statistic of joint variation.
The denominators (the variances) are statistics of marginal variation. These
marginal statistics are not the same.
13(c) Stephen Senn
The difference is in the denominator
The numerator is the same
17. Regression to the Mean
A Simulated Example
• Diastolic blood pressure (DBP)
• Mean 90mmHg
• Between patient variance 50mmHg2
• Within patient variance 15 mmHg2
• Boundary for hypertensive 95 mmHg
• Simulation of 1000 patients whose DBP at baseline
and outcome are shown
• Blue consistent normotensive
• Red Consistent hypertensive
• Orange hypertensive/normotensive or vice versa
17(c) Stephen Senn
20. (c) Stephen Senn 20
Mean at baseline and
outcome are the same
Mean at outcome is
lower than at baseline
All patients are hypertensive
at baseline
Many are not at outcome
If you know why the title of this talk is extremely stupid, then you clearly know something about control, data and reasoning: in short, you have most of what it takes to be a statistician. If you have studied statistics then you will also know that a large amount of anything, and this includes successful careers, is luck.
In this talk I shall try share some of my experiences of being a statistician in the hope that it will help you make the most of whatever luck life throws you, In so doing, I shall try my best to overcome the distorting influence of that easiest of sciences hindsight. Without giving too much away, I shall be recommending that you read, listen, think, calculate, understand, communicate, and do. I shall give you some example of what I think works and what I think doesn’t
In all of this you should never forget the power of negativity and also the joy of being able to wake up every day and say to yourself ‘I love the small of data in the morning’.
30 minutes presentation plus 5 minutes questions
This example is covered in chapter 4 of
Senn, S. J. (2003). Dicing with Death. Cambridge: Cambridge University Press.
See
Senn, S. J. (2013). Invalid inversion. Significance, 10(2), 40-42
Since we are calculating the probability of having breast cancer given that someone is female, we condition on being ‘female’. We thus strike out the column ‘male’ as being irrelevant.
The probability we require is the joint frequency ‘breast cancer’ and ‘female’ divide by the relevant marginal frequency ‘female’
Since we are calculating the probability of being female given that someone suffering from breast cancer, we condition on suffering from breast cancer ’. We thus strike out the column ‘not suffering from breast cancer ’ as being irrelevant.
The probability we require is the joint frequency ‘breast cancer’ and ‘female’ divide by the relevant marginal frequency ‘suffering from breast cancer ’
Extract of GenStat program
"To simulate regression to the mean"
"This version used to try and reproduce the numbers selected (285)in original version
of Significance paper"
"Set parameters"
SCALAR NSIM,mean,betvar,withvar,cut,lower,upper;VALUE=1000,90,50,15,95,60,120
TEXT xlabel,ylabel,title; VALUES='DBP at Baseline (mmHg)','DBP at Outcome (mmHg)','Diastolic blood pressure'
"Begin simulation"
FOR [NTIMES=1000]
GRANDOM [DISTRIBUTION=Normal; NVALUES=NSIM; SEED=0; MEAN=mean; VARIANCE=betvar] True
GRANDOM [DISTRIBUTION=Normal; NVALUES=NSIM; SEED=0; MEAN=0; VARIANCE=withvar] E1
CALCULATE X=True+E1
CALCULATE HBase=X>=cut
CALCULATE Check=SUM(HBase)
IF Check.EQ.285
PRINT Check; DECIMALS=0
EXIT [CONTROL=for]
ENDIF
ENDFOR
VARIATE [NVALUES=2]Xline1,Xline2,Xline3,Yline1,Yline2,Yline3
CALCULATE Xline1=cut
CALCULATE Yline1$[1],Yline1$[2]=lower,upper
CALCULATE Xline2$[1],Xline2$[2]=lower,upper
CALCULATE Yline2=cut
CALCULATE Xline3$[1],Xline3$[2]=lower, upper
CALCULATE Yline3$[1],Yline3$[2]=lower, upper
See
Senn, S. J. (2009). Three things every medical writer should know about statistics. The Write Stuff, 18(3), 159-162
These are prime numbers. The minimum block size is thus the product of them all and that is 105.
By the time the last patient has completed period two (say) many of the patients will have completed the whole trial.
The way to run such a trial is as an add-on trial. All patients receive the current therapy as standard and they receive either placebo or the new treatment in addition. Trials of HIV infection were often of this sort and (correctly) described as placebo controlled.
Senn, S. J. (2001). The Misunderstood Placebo. Applied Clinical Trials, 10(5), 40-46
See
Senn, S. J. (1998). Mathematics: governess or handmaiden? Journal of the Royal Statistical Society Series D-The Statistician, 47(2), 251-259