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Archive of posts filed under the Stan category.

Webinar: On Bayesian workflow

This post is by Eric. This Wednesday, at 12 pm ET, Aki Vehtari is stopping by to talk to us about Bayesian workflow. You can register here. Abstract We will discuss some parts of the Bayesian workflow with a focus on the need and justification for an iterative process. The talk is partly based on […]

Summer research jobs at Flatiron Institute

If you’re an undergrad or grad student and work in applied math, stats, or machine learning, you may be interested in our summer research assistant and associate positions at the Flatiron Institute’s Center for Computational Mathematics: Scientific computing summer positions Machine learning and statistics summer positions There is no deadline, but we’ll start reviewing applications […]

The Mets are hiring

Des McGowan writes: We are looking to hire multiple full time analysts/senior analysts to join the Baseball Analytics department at the New York Mets. The roles will involve building, testing, and presenting statistical models that inform decision-making in all facets of Baseball Operations. These positions require a strong background in complex statistics and data analytics, […]

Postdoc in precision medicine at Johns Hopkins using Bayesian methods

Aki Nishimura writes: My colleague Scott Zeger and I have a postdoc position for our precision medicine initiative at Johns Hopkins and we are looking for expertise in Bayesian methods, statistical computation, or software development. Expertise in Stan would be a plus!

Statisticians don’t use statistical evidence to decide what statistical methods to use. Also, The Way of the Physicist.

David Bailey, a physicist at the University of Toronto, writes: I thought you’d be pleased to hear that a student in our Advanced Physics Lab spontaneously used Stan to analyze data with significant uncertainties in both x and y. We’d normally expect students to use python and orthogonal distance regression, and STAN is never mentioned […]

Postdoc in Paris for Bayesian models in genetics . . . differential equation models in Stan

Julie Bertrand writes: The BIPID team in the IAME UMR1137 INSERM Université de Paris is opening a one-year postdoctoral position to develop Bayesian approaches to high throughput genetic analyses using nonlinear mixed effect models. The candidate will analyse longitudinal phenotype data using differential equation models on clinical trial data with Stan and perform simulation studies […]

Webinar: Some Outstanding Challenges when Solving ODEs in a Bayesian context

This post is by Eric. This Wednesday, at 12 pm ET, Charles Margossian is stopping by to talk to us about solving ODEs using Bayesian methods. You can register here. If you want to get a feel for the types of issues he will be discussing, take a look at his (and Andrew’s) recent case […]

Come work with me and David Shor !

Open positions on our progressive data team: Machine Learning engineer – https://grnh.se/6713732b4us Software Engineer – https://grnh.se/15ee5a2e4us Devops – https://grnh.se/aa2bef714us We are a diverse team of engineers, data scientists, statisticians, and political insiders who are closely connected to some of the most important decision makers in the progressive ecosystem. We worked with central players to develop strategy and direct […]

“Maybe we should’ve called it Arianna”

Katie Hafner wrote this obituary of Arianna Rosenbluth, original programmer of what is known as the Metropolis algorithm: Arianna Rosenbluth Dies at 93; Pioneering Figure in Data Science Dr. Rosenbluth, who received her physics Ph.D. at 21, helped create an algorithm that has became a foundation of understanding huge quantities of data. She died of […]

How to track covid using hospital data collection and MRP

Len Covello, Yajuan Si, and I write: The current way we track the prevalence of coronavirus infections is deeply flawed. Ideally, health officials would test random samples of citizens in each community in a systematic way. But throughout the pandemic, the United States has lacked the political will or funding to pursue it. Instead, testing […]

New research suggests: “Targeting interventions – including transmission-blocking vaccines – to adults aged 20-49 is an important consideration in halting resurgent epidemics and preventing COVID-19-attributable deaths.”

In recent weeks we’ve been hearing a lot about the priority of vaccinations. Should we be vaccinating older people first? Essential workers? Just vaccinate as many as possible without worrying about who gets it? Giving out the vaccine is partly about protecting people and partly about slowing the chains of transmission. The results of a […]

Routine hospital-based SARS-CoV-2 testing outperforms state-based data in predicting clinical burden.

Len Covello, Yajuan Si, Siquan Wang, and I write: Throughout the COVID-19 pandemic, government policy and healthcare implementation responses have been guided by reported positivity rates and counts of positive cases in the community. The selection bias of these data calls into question their validity as measures of the actual viral incidence in the community […]

How many infectious people are likely to show up at an event?

Stephen Kissler and Yonatan Grad launched a Shiny app, Effective SARS-CoV-2 test sensitivity, to help you answer the question, How many infectious people are likely to show up to an event, given a screening test administered n days prior to the event? Here’s a screenshot. The app is based on some modeling they did with […]

Hamiltonian Monte Carlo using an adjoint-differentiated Laplace approximation: Bayesian inference for latent Gaussian models and beyond

Charles Margossian, Aki Vehtari, Daniel Simpson, Raj Agrawal write: Gaussian latent variable models are a key class of Bayesian hierarchical models with applications in many fields. Performing Bayesian inference on such models can be challenging as Markov chain Monte Carlo algorithms struggle with the geometry of the resulting posterior distribution and can be prohibitively slow. […]

2 PhD student positions on Bayesian workflow! With Paul Bürkner!

Paul Bürkner writes: The newly established work group for Bayesian Statistics of Dr. Paul-Christian Bürkner at the Cluster of Excellence SimTech, University of Stuttgart (Germany), is looking for 2 PhD students to work on Bayesian workflow and Stan-related topics. The positions are fully funded for at least 3 years and people with a Master’s degree […]

Mister P for the 2020 presidential election in Belarus

An anonymous group of authors writes: Political situation Belarus is often called the “last dictatorship” in Europe. Rightly so, Aliaskandr Lukashenka has served as the country’s president since 1994. In the 26 years of his rule, Lukashenka has consolidated and extended his power, which is today absolute. Rigging referendums has been an effective means of […]

Bayesian Workflow

Aki Vehtari, Daniel Simpson, Charles C. Margossian, Bob Carpenter, Yuling Yao, Paul-Christian Bürkner, Lauren Kennedy, Jonah Gabry, Martin Modrák, and I write: The Bayesian approach to data analysis provides a powerful way to handle uncertainty in all observations, model parameters, and model structure using probability theory. Probabilistic programming languages make it easier to specify and […]

“Model takes many hours to fit and chains don’t converge”: What to do? My advice on first steps.

The above question came up on the Stan forums, and I replied: Hi, just to give some generic advice here, I suggest simulating fake data from your model and then fitting the model and seeing if you can recover the parameters. Since it’s taking a long time to run, I suggest just running your 4 […]

Stan’s Within-Chain Parallelization now available with brms

The just released R package brms version 2.14.0 supports within-chain parallelization of Stan. This new functionality is based on the recently introduced reduce_sum function in Stan, which allows to evaluate sums over (conditionally) independent log-likelihood terms in parallel, using multiple CPU cores at the same time via threading. The idea of reduce_sum is to exploit […]

Stan receives its second Nobel prize.

Aki writes: Nobel prize and other science prices are problematic and this is not endorsement of such prices, but this might be useful for someone who needs to tell (hype) about the impact of Stan (or just as another funny fact about Stan). Previously Stan was used in the the LIGO gravitational wave research awarded […]

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