• Advanced Courses in Life Sciences

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Live Online Course – 7th Edition

Introduction to Bayesian Inference in Practice

May 8th-12th, 2023

Live sessions will be recorded

Introduction to Bayesian Inference in Practice

Course overview & Programme

Most researchers in life sciences are exposed in their research to a multitude of methods and algorithms to test hypotheses, infer parameters, explore empirical data sets, etc.

Bayesian methods have become standard practice in several fields, (e.g. phylogenetic inference, evolutionary (paleo)biology, genomics), yet understanding how these Bayesian machinery works are not always trivial.

This course is based on the assumption that the easiest way to understand the principles of Bayesian inference and the functioning of the main algorithms is to implement these methods yourself.

The instructor will outline the relevant concepts and basic theory, but the focus of the course will be to learn how to do Bayesian inference in practice. He will show how to implement the most common algorithms to estimate parameters based on posterior probabilities, such as Markov Chain Monte Carlo samplers, and how to build hierarchical models.

He will also touch upon hypothesis testing using Bayes factors and Bayesian variable selection.

The course will take a learn-by-doing approach, in which participants will implement their own MCMCs using R or Python (templates for both languages will be provided).

After completion of the course, the participants will have gained a better understanding of how the main Bayesian methods implemented in many programs used in biological research work. Participants will also learn how to model at least basic problems using Bayesian statistics and how to implement the necessary algorithms to solve them.

Participants are expected to have some knowledge of R or Python (each can choose their preferred language), but they will be guided “line-by-line” in writing their script. The aim is that, by the end of the week, each participant will have written their own MCMC – from scratch! Participants are encouraged to bring own datasets and questions and we will (try to) figure them out during the course and implement scripts to analyze them in a Bayesian framework.

  • Introduction to probabilistic models and Bayes theorem. We’ll learn:
    • How to calculate the likelihood of any dataset under a simple model
    • The Bayes principles (what is a prior? What is a posterior probability?)
  • Write an R (or Python) script to compute the likelihood of data under Normal and Gamma models. 3D plots of the likelihood surface.
  • Basic structure of Markov Chain Monte Carlo, the most popular algorithm in Bayesian analysis.
  • MCMC, how it works, how to implement it. Based on the likelihood functions written on Monday, implement an MCMC to fit normal and gamma distributions.
  • What is the difference between modeling a pattern and modeling a process? When should we prefer one or the other? (practical) Analysis of global temperature data (provided) to estimate the existence of any climatic trends.
  • Hypothesis testing using marginal likelihoods. (practical) How to interpret and summarize the results of an MCMC, how to assess if it worked.
  • Bayesian tricks to avoid model testing: Hierarchical modeling, shrinkage, and Bayesian variable selection.
  • Continue working on the MCMC script and with own data.
  • Alternative algorithms in Bayesian analyses: Gibbs sampling and Approximate Bayesian Computation (ABC). Basic principles of machine learning.
  • Finalize the MCMC script and (if applicable) plan the future development of the methods implemented for analysis of own data.

Basic knowledge of Python or R and Statistics. All participants must have a personal computer (Windows, Macintosh), with webcam and headphones if possible, and access to a good internet connection.

Instructors

Daniele Silvestro instructor for Transmitting Science

Dr. Daniele Silvestro
University of Gothenburg
Sweden

Tobias Andermann instructor for Transmitting Science

Tobias Andermann
University of Gothenburg
Sweden

Dates & Schedule

May 8th-12th, 2023

13:00-17:00 (Madrid time zone)

Online live sessions from Monday to Friday; 13:00 to 17:00 (Madrid time zone).

The rest of the time will be taught with recorded classes and assignments, to be done between the live sessions.

Total course hours: 32.5

20 hours of online live lessons, plus 12.5 hours of assignments.

This course is equivalent to 2 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.

Language

English

This course will be delivered live online

This course will be taught using a combination of live (synchronous) sessions on Zoom and tasks to be completed in between live sessions on the Slack platform.

Live sessions will be recorded. Recordings will be made available to participants for a limited period of time. However, attendance to the live sessions is required.

Places

Places are limited to 18 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end.

Haris Saslis coordinator for Transmitting Science

Dr. Haris Saslis
Transmitting Science
Greece

Soledad De Esteban-Trivigno Transmitting Science coordinator

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Fees & Discounts

  • Course Fee
  • Early bird (until March 31st, 2023):
  • 486 €
    (388.80 € for Ambassador Institutions)
  • Regular (after March 31st, 2023):
  • 578 €
    (462.40 € for Ambassador Institutions)
  • Prices include VAT.
    After registration you will receive confirmation of your acceptance on the course.
    Payment is not required during registration.

We offer discounts on the Course Fee.

Discounts are not cumulative. Participants receive the highest appropriate discount.

We also offer the possibility of paying in two instalments. Please contact us to request this.

Former participants of Transmitting Science courses receive a 5% discount on the Course Fee.

20% discount on the Course Fee is offered to members of certain organisations (Ambassador Institutions). If you wish to apply for this discount, please indicate it in the Registration form (proof will be asked later). If you would like your institution to become a Transmitting Science Ambassador Institution, please contact us at communication@transmittingscience.com

Unemployed scientists, as well as PhD students without any grant or scholarship to develop their PhD, can benefit from a 40% discount on the Course Fee. This applies only to participants based in Spain. If you wish to ask for this discount, please contact us. The discount may apply for a maximum of 2 places, which will be covered by strict registration order.

Registration

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