• Advanced Courses in Life Sciences

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Online Course – 3rd Edition

Introduction to Bayesian Inference in Practice

August 17th-21st, 2020

Statistics and Bioinformatics

Statistics and Bioinformatics

This course will be delivered ONLINE: 15 hours of online live lessons,  plus 7.5 hours of recorded classes and assignments. A good internet connection is required to follow the course.

Introduction to Bayesian Inference in Practice

Course overview

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.

Requirements

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

Contact

courses@transmittingscience.com

LOCATION

This course will be delivered online.

Please check the schedule for the live online part, and be aware that it is GMT+1.

Date

August 17th-21st, 2020

LANGUAGE

English

COURSE LENGTH & ECTS

32.5 hours online.

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.

PLACES

Places are limited to 18 participants and will be occupied by strict registration order. If the course fills up there will be an assistant instructor to help during the practise time.

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

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

Program

  • 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.

Fees

  • Course Fee
  • Early bird (until July 31st, 2020):
  • 535 € *
    (428 € for Ambassador Institutions)
  • Regular (after July 31st, 2020):
  • 644 € *
    (515.20 € for Ambassador Institutions)
  • This includes course material (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com

Schedule

  • Monday to Friday (GMT+1):
    • 14:00 to 18:00 online live lessons.

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

Funding

Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Registration

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FORBIO members based in Norway do not need to pay the fee.