636-0702-00L  Statistical Models in Computational Biology

SemesterSpring Semester 2020
LecturersN. Beerenwinkel
Periodicityyearly recurring course
Language of instructionEnglish



Courses

NumberTitleHoursLecturers
636-0702-00 VStatistical Models in Computational Biology
The lecture will be held either in Zurich or Basel and will be transmitted via videoconference to the second location.
Lecture will be streamed and recorded
2 hrs
Thu12:00-14:00ER SA TZ »
12:15-14:00BSB E 4 »
12:15-14:00HG D 16.2 »
N. Beerenwinkel
636-0702-00 UStatistical Models in Computational Biology
The tutorial will be held either in Zurich or Basel and will be transmitted via videoconference to the second location.
1 hrs
Thu14:00-15:00ER SA TZ »
14:15-15:00BSB E 4 »
14:15-15:00HG D 16.2 »
N. Beerenwinkel
636-0702-00 AStatistical Models in Computational Biology
Project work, no fixed presence required.
2 hrsN. Beerenwinkel

Catalogue data

AbstractThe course offers an introduction to graphical models and their application to complex biological systems. Graphical models combine a statistical methodology with efficient algorithms for inference in settings of high dimension and uncertainty. The unifying graphical model framework is developed and used to examine several classical and topical computational biology methods.
ObjectiveThe goal of this course is to establish the common language of graphical models for applications in computational biology and to see this methodology at work for several real-world data sets.
ContentGraphical models are a marriage between probability theory and graph theory. They combine the notion of probabilities with efficient algorithms for inference among many random variables. Graphical models play an important role in computational biology, because they explicitly address two features that are inherent to biological systems: complexity and uncertainty. We will develop the basic theory and the common underlying formalism of graphical models and discuss several computational biology applications. Topics covered include conditional independence, Bayesian networks, Markov random fields, Gaussian graphical models, EM algorithm, junction tree algorithm, model selection, Dirichlet process mixture, causality, the pair hidden Markov model for sequence alignment, probabilistic phylogenetic models, phylo-HMMs, microarray experiments and gene regulatory networks, protein interaction networks, learning from perturbation experiments, time series data and dynamic Bayesian networks. Some of the biological applications will be explored in small data analysis problems as part of the exercises.
Lecture notesno
Literature- Airoldi EM (2007) Getting started in probabilistic graphical models. PLoS Comput Biol 3(12): e252. doi:10.1371/journal.pcbi.0030252
- Bishop CM. Pattern Recognition and Machine Learning. Springer, 2007.
- Durbin R, Eddy S, Krogh A, Mitchinson G. Biological Sequence Analysis. Cambridge university Press, 2004

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits6 credits
ExaminersN. Beerenwinkel
Typesession examination
Language of examinationEnglish
RepetitionThe performance assessment is only offered in the session after the course unit. Repetition only possible after re-enrolling.
Mode of examinationoral 20 minutes
Additional information on mode of examinationRepetition possible only with re-enrollment, including projects.
The final grade is 70% oral session examination and 30% project. The practical projects are an integral part (60 hours of work, 2 credits) of the course. The project has to be re-run in case of a repetition.
This information can be updated until the beginning of the semester; information on the examination timetable is binding.

Learning materials

No public learning materials available.
Only public learning materials are listed.

Groups

No information on groups available.

Restrictions

There are no additional restrictions for the registration.

Offered in

ProgrammeSectionType
Biology MasterElective Compulsory Master Courses I: ComputationWInformation
Computational Biology and Bioinformatics MasterData ScienceWInformation
Data Science MasterInterdisciplinary ElectivesWInformation
Computer Science BachelorMinor CoursesWInformation
Computational Science and Engineering BachelorBiologyWInformation
Computational Science and Engineering MasterBiologyWInformation
Statistics MasterStatistical and Mathematical CoursesWInformation