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Advanced Courses in Life Sciences

2nd Edition

Introduction to Bayesian Inference in Practice

May 6th-10th, 2019, Barcelona (Spain)

Statistics and Bioinformatics

Statistics and Bioinformatics Logo

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 this Bayesian machinery works is 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.

LOCATION

Can Carol

C/ Font de la Reina, 5
08786 Capellades, Barcelona (Spain)

How to get there

DATE

May 6th-10th, 2019

LANGUAGE

English

COURSE LENGTH & ECTS

32.5 hours on-site.

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 20 participants and will be occupied by strict registration order.

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

Instructors

Daniele Silvestro instructor for Transmitting Science

Dr. Daniele Silvestro
University of Gothenburg
Sweden

Tobias Hofmann instructor for Transmitting Science

Tobias Hofmann
University of Gothenburg
Sweden

Coordinators

Ana Rosa Gómez-Cano coordinator at Transmitting Science

Dr. Ana Rosa Gómez-Cano
Transmitting Science
Spain

Soledad De Esteban-Trivigno instructor at Transmitting Science

Dr. Soledad De Esteban-Trivigno
Transmitting Science
Spain

Requirements

Basic knowledge of Python or R and Statistics. All participants must bring their own personal laptop.

Program

Monday, April 6th, 2019.

  • Morning: 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?)
  • Afternoon: (practical) Write an R (or Python) script to compute the likelihood of data under Normal and Gamma models. 3D plots of the likelihood surface.

Tuesday, April 7th, 2019.

  • Morning: basic structure of Markov Chain Monte Carlo, the most popular algorithm in Bayesian analysis.
  • Afternoon: (practical) 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.

Wednesday, April 8th, 2019.

  • Morning: 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.
  • Afternoon: Hypothesis testing using marginal likelihoods. (practical) How to interpret and summarize the results of an MCMC, how to assess if it worked.

Thursday, April 9th, 2019.

  • Morning: Bayesian tricks to avoid model testing: Hierarchical modeling, shrinkage, and Bayesian variable selection.
  • Afternoon: (practical) Continue working on the MCMC script and with own data.

Friday, April 10th, 2019.

  • Morning: Alternative algorithms in Bayesian analyses: Gibbs sampling and Approximate Bayesian Computation (ABC). Basic principles of machine learning.
  • Afternoon: (practical) Finalize the MCMC script and (if applicable) plan the future development of the methods implemented for analysis of own data.

Fees

  • Course Fee
  • {{content-1}}
  • Early bird (until January 31st, 2019):
  • 535 *
  • Regular (after January 31st, 2019):
  • 665 *
  • This includes course material, coffee breaks and lunches (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.
  • Course Fee + Accommodation Package
  • {{content-1}}
  • Early bird (until January 31st, 2019):
  • 535 * + 330 = 865
  • Regular (after January 31st, 2019):
  • 665 * + 330 = 995
  • This includes course material, coffee breaks, transportation from and to Barcelona city, accommodation from Sunday to Friday, breakfasts, lunches and dinners (VAT included).
    * Participants from companies/industry will have an extra charge of 100 €.

We offer the possibility of paying in two instalments (contact the course coordinators). Discounts (see Funding below) are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Accommodation

Accommodation Package

If you take the Accommodation Package you will be hosted in the Rural House Can Carol, in single-sex shared dormitories (2 – 4 people) with bathroom en-suite.

If the number of participants exceeds the available rooms at Can Carol, some of them could be accommodated in the Hotel Tall del Conill, by registration order. The hotel is at 10 minutes walking, although transport will be provided in the morning and after dinner. Lunches and dinners will be with the whole group.

A supplemental charge will be added if you prefer to stay in a single room.

Accommodation is included from Sunday (check-in) to Friday (check-out). Breakfast, lunch and dinner are also provided during the week, starting from the dinner of Sunday to lunch of Friday (included).

Other accommodation options

If you do not want the Accommodation Package, accommodation is available in places other than Can Carol: Where to stay near the Venue.

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Rural House Can Carol

Rural House Can Carol (Capellades, Barcelona, Spain)

Schedule

Course Schedule
  • Monday to Friday:
    • 9:30 to 13:00 Lessons.
    • 13:00 to 14:00 Lunch (included).
    • 14:00 to 17:00 Lessons.
Accommodation Package Schedule
  • Sunday:
    • 19:00 Meeting point in Plaza Catalunya (Barcelona) to take the bus to Capellades. If you are planning to arrive later, you can find more information in How to get there.
    • 20:00 Registration in the Hotel.
    • 20:30 Dinner.
  • Monday to Thursday:
    • 8:00 to 9:00 Breakfast.
    • 20:30 Dinner.
  • Friday:
    • 8:00 to 9:00 Breakfast.
    • 17:30 Meeting point in the Hotel to take the bus to Barcelona city.
    • 19:00 Arrival at Plaza Catalunya (Barcelona).

The schedule is approximate; it is possible that the content of one day may run into the next and a working day may be longer than advertised.

Funding

Discounts

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

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

Spanish unemployed scientists, as well as Spanish PhD students 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 coordinators. That would apply for a maximum of 2 places and they will be covered by strict inscription order.

Discounts are not cumulative and apply only on the fee, not to Accommodation Package or other options.

Organizers

Transmitting Science Logo

Collaborators

Logo Ajuntament Capellades
Colegio Oficial de Biólogos de Castilla y León Logo
Colegio Oficial de Biólogos de Euskadi Logo
Colexio Oficial de Biólogos de Galicia Logo
Col·legi Oficial de Biòlegs de la Comunitat Valenciana Logo

Registration