Suchergebnis: Katalogdaten im Frühjahrssemester 2019

Computational Biology and Bioinformatics Master Information
More informations at: Link
Master-Studium (Studienreglement 2017)
Vertiefungsfächer
A total of 30 ECTS needs to be acquired in the Advanced Courses category. Thereof 18 ECTS in the Theory and 12 ECTS in the Biology category.
Theorie
At least 18 ECTS need to be acquired in this category.
NummerTitelTypECTSUmfangDozierende
252-0063-00LData Modelling and Databases Information W7 KP4V + 2UG. Alonso, C. Zhang
KurzbeschreibungData modelling (Entity Relationship), relational data model, relational design theory (normal forms), SQL, database integrity, transactions and advanced database engines
LernzielIntroduction to relational databases and data management. Basics of SQL programming and transaction management.
InhaltThe course covers the basic aspects of the design and implementation of databases and information systems. The courses focuses on relational databases as a starting point but will also cover data management issues beyond databases such as: transactional consistency, replication, data warehousing, other data models, as well as SQL.
LiteraturKemper, Eickler: Datenbanksysteme: Eine Einführung. Oldenbourg Verlag, 7. Auflage, 2009.

Garcia-Molina, Ullman, Widom: Database Systems: The Complete Book. Pearson, 2. Auflage, 2008.
401-0674-00LNumerical Methods for Partial Differential Equations
Nicht für Studierende BSc/MSc Mathematik
W8 KP2G + 2P + 4AR. Hiptmair
KurzbeschreibungDerivation, properties, and implementation of fundamental numerical methods for a few key partial differential equations: convection-diffusion, heat equation, wave equation, conservation laws. Implementation in C++ based on a finite element library.
LernzielMain skills to be acquired in this course:
* Ability to implement fundamental numerical methods for the solution of partial differential equations efficiently.
* Ability to modify and adapt numerical algorithms guided by awareness of their mathematical foundations.
* Ability to select and assess numerical methods in light of the predictions of theory
* Ability to identify features of a PDE (= partial differential equation) based model that are relevant for the selection and performance of a numerical algorithm.
* Ability to understand research publications on theoretical and practical aspects of numerical methods for partial differential equations.
* Skills in the efficient implementation of finite element methods on unstructured meshes.

This course is neither a course on the mathematical foundations and numerical analysis of methods nor an course that merely teaches recipes and how to apply software packages.
Inhalt1 Case Study: A Two-point Boundary Value Problem [optional]
1.1 Introduction
1.2 A model problem
1.3 Variational approach
1.4 Simplified model
1.5 Discretization
1.5.1 Galerkin discretization
1.5.2 Collocation [optional]
1.5.3 Finite differences
1.6 Convergence
2 Second-order Scalar Elliptic Boundary Value Problems
2.1 Equilibrium models
2.1.1 Taut membrane
2.1.2 Electrostatic fields
2.1.3 Quadratic minimization problems
2.2 Sobolev spaces
2.3 Variational formulations
2.4 Equilibrium models: Boundary value problems
3 Finite Element Methods (FEM)
3.1 Galerkin discretization
3.2 Case study: Triangular linear FEM in two dimensions
3.3 Building blocks of general FEM
3.4 Lagrangian FEM
3.4.1 Simplicial Lagrangian FEM
3.4.2 Tensor-product Lagrangian FEM
3.5 Implementation of FEM in C++
3.5.1 Mesh file format (Gmsh)
3.5.2 Mesh data structures (DUNE)
3.5.3 Assembly
3.5.4 Local computations and quadrature
3.5.5 Incorporation of essential boundary conditions
3.6 Parametric finite elements
3.6.1 Affine equivalence
3.6.2 Example: Quadrilaterial Lagrangian finite elements
3.6.3 Transformation techniques
3.6.4 Boundary approximation
3.7 Linearization [optional]
4 Finite Differences (FD) and Finite Volume Methods (FV) [optional]
4.1 Finite differences
4.2 Finite volume methods (FVM)
5 Convergence and Accuracy
5.1 Galerkin error estimates
5.2 Empirical Convergence of FEM
5.3 Finite element error estimates
5.4 Elliptic regularity theory
5.5 Variational crimes
5.6 Duality techniques [optional]
5.7 Discrete maximum principle [optional]
6 2nd-Order Linear Evolution Problems
6.1 Parabolic initial-boundary value problems
6.1.1 Heat equation
6.1.2 Spatial variational formulation
6.1.3 Method of lines
6.1.4 Timestepping
6.1.5 Convergence
6.2 Wave equations [optional]
6.2.1 Vibrating membrane
6.2.2 Wave propagation
6.2.3 Method of lines
6.2.4 Timestepping
6.2.5 CFL-condition
7 Convection-Diffusion Problems [optional]
7.1 Heat conduction in a fluid
7.1.1 Modelling fluid flow
7.1.2 Heat convection and diffusion
7.1.3 Incompressible fluids
7.1.4 Transient heat conduction
7.2 Stationary convection-diffusion problems
7.2.1 Singular perturbation
7.2.2 Upwinding
7.3 Transient convection-diffusion BVP
7.3.1 Method of lines
7.3.2 Transport equation
7.3.3 Lagrangian split-step method
7.3.4 Semi-Lagrangian method
8 Numerical Methods for Conservation Laws
8.1 Conservation laws: Examples
8.2 Scalar conservation laws in 1D
8.3 Conservative finite volume discretization
8.3.1 Semi-discrete conservation form
8.3.2 Discrete conservation property
8.3.3 Numerical flux functions
8.3.4 Montone schemes
8.4 Timestepping
8.4.1 Linear stability
8.4.2 CFL-condition
8.4.3 Convergence
8.5 Higher order conservative schemes [optional]
8.5.1 Slope limiting
8.5.2 MUSCL scheme
8.6. FV-schemes for systems of conservation laws [optional]

"optional" indicates that the corresponding topic might be skipped depending on the progress of the course.
SkriptThe lecture will be taught in flipped classroom format:
- Video tutorials for all thematic units will be published online.
- Solution of homework problems will be covered by video tutorials.
- Lecture documents and tablet notes accompanying the videos will be made available to the audience as PDF.
LiteraturChapters of the following books provide supplementary reading
(detailed references in course material):

* D. Braess: Finite Elemente,
Theorie, schnelle Löser und Anwendungen in der Elastizitätstheorie, Springer 2007 (available online).
* S. Brenner and R. Scott. Mathematical theory of finite element methods, Springer 2008 (available online).
* A. Ern and J.-L. Guermond. Theory and Practice of Finite Elements, volume 159 of Applied Mathematical Sciences. Springer, New York, 2004.
* Ch. Großmann and H.-G. Roos: Numerical Treatment of Partial Differential Equations, Springer 2007.
* W. Hackbusch. Elliptic Differential Equations. Theory and Numerical Treatment, volume 18 of Springer Series in Computational Mathematics. Springer, Berlin, 1992.
* P. Knabner and L. Angermann. Numerical Methods for Elliptic and Parabolic Partial Differential Equations, volume 44 of Texts in Applied Mathematics. Springer, Heidelberg, 2003.
* S. Larsson and V. Thomée. Partial Differential Equations with Numerical Methods, volume 45 of Texts in Applied Mathematics. Springer, Heidelberg, 2003.
* R. LeVeque. Finite Volume Methods for Hyperbolic Problems. Cambridge Texts in Applied Mathematics. Cambridge University Press, Cambridge, UK, 2002.

However, study of supplementary literature is not important for for following the course.
Voraussetzungen / BesonderesMastery of basic calculus and linear algebra is taken for granted.
Familiarity with fundamental numerical methods (solution methods for linear systems of equations, interpolation, approximation, numerical quadrature, numerical integration of ODEs) is essential.

Important: Coding skills and experience in C++ are essential.

Homework assignments involve substantial coding, partly based on a C++ finite element library. The written examination will be computer based and will comprise coding tasks.
401-3052-05LGraph Theory Information W5 KP2V + 1UB. Sudakov
KurzbeschreibungBasic notions, trees, spanning trees, Caley's formula, vertex and edge connectivity, blocks, 2-connectivity, Mader's theorem, Menger's theorem, Eulerian graphs, Hamilton cycles, Dirac's theorem, matchings, theorems of Hall, König and Tutte, planar graphs, Euler's formula, basic non-planar graphs, graph colorings, greedy colorings, Brooks' theorem, 5-colorings of planar graphs
LernzielThe students will get an overview over the most fundamental questions concerning graph theory. We expect them to understand the proof techniques and to use them autonomously on related problems.
SkriptLecture will be only at the blackboard.
LiteraturWest, D.: "Introduction to Graph Theory"
Diestel, R.: "Graph Theory"

Further literature links will be provided in the lecture.
Voraussetzungen / BesonderesStudents are expected to have a mathematical background and should be able to write rigorous proofs.


NOTICE: This course unit was previously offered as 252-1408-00L Graphs and Algorithms.
227-1034-00LComputational Vision (University of Zurich) Information
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: INI402

Mind the enrolment deadlines at UZH:
Link
W6 KP2V + 1UD. Kiper
KurzbeschreibungThis course focuses on neural computations that underlie visual perception. We study how visual signals are processed in the retina, LGN and visual cortex. We study the morpholgy and functional architecture of cortical circuits responsible for pattern, motion, color, and three-dimensional vision.
LernzielThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
InhaltThis course considers the operation of circuits in the process of neural computations. The evolution of neural systems will be considered to demonstrate how neural structures and mechanisms are optimised for energy capture, transduction, transmission and representation of information. Canonical brain circuits will be described as models for the analysis of sensory information. The concept of receptive fields will be introduced and their role in coding spatial and temporal information will be considered. The constraints of the bandwidth of neural channels and the mechanisms of normalization by neural circuits will be discussed.
The visual system will form the basis of case studies in the computation of form, depth, and motion. The role of multiple channels and collective computations for object recognition will
be considered. Coordinate transformations of space and time by cortical and subcortical mechanisms will be analysed. The means by which sensory and motor systems are integrated to allow for adaptive behaviour will be considered.
LiteraturBooks: (recommended references, not required)
1. An Introduction to Natural Computation, D. Ballard (Bradford Books, MIT Press) 1997.
2. The Handbook of Brain Theorie and Neural Networks, M. Arbib (editor), (MIT Press) 1995.
252-0220-00LIntroduction to Machine Learning Information Belegung eingeschränkt - Details anzeigen
Previously called Learning and Intelligent Systems.
W8 KP4V + 2U + 1AA. Krause
KurzbeschreibungThe course introduces the foundations of learning and making predictions based on data.
LernzielThe course will introduce the foundations of learning and making predictions from data. We will study basic concepts such as trading goodness of fit and model complexitiy. We will discuss important machine learning algorithms used in practice, and provide hands-on experience in a course project.
Inhalt- Linear regression (overfitting, cross-validation/bootstrap, model selection, regularization, [stochastic] gradient descent)
- Linear classification: Logistic regression (feature selection, sparsity, multi-class)
- Kernels and the kernel trick (Properties of kernels; applications to linear and logistic regression); k-nearest neighbor
- Neural networks (backpropagation, regularization, convolutional neural networks)
- Unsupervised learning (k-means, PCA, neural network autoencoders)
- The statistical perspective (regularization as prior; loss as likelihood; learning as MAP inference)
- Statistical decision theory (decision making based on statistical models and utility functions)
- Discriminative vs. generative modeling (benefits and challenges in modeling joint vy. conditional distributions)
- Bayes' classifiers (Naive Bayes, Gaussian Bayes; MLE)
- Bayesian approaches to unsupervised learning (Gaussian mixtures, EM)
LiteraturTextbook: Kevin Murphy, Machine Learning: A Probabilistic Perspective, MIT Press
Voraussetzungen / BesonderesDesigned to provide a basis for following courses:
- Advanced Machine Learning
- Deep Learning
- Probabilistic Artificial Intelligence
- Probabilistic Graphical Models
- Seminar "Advanced Topics in Machine Learning"
227-0558-00LPrinciples of Distributed Computing Information W6 KP2V + 2U + 1AR. Wattenhofer, M. Ghaffari
KurzbeschreibungWe study the fundamental issues underlying the design of distributed systems: communication, coordination, fault-tolerance, locality, parallelism, self-organization, symmetry breaking, synchronization, uncertainty. We explore essential algorithmic ideas and lower bound techniques.
LernzielDistributed computing is essential in modern computing and communications systems. Examples are on the one hand large-scale networks such as the Internet, and on the other hand multiprocessors such as your new multi-core laptop. This course introduces the principles of distributed computing, emphasizing the fundamental issues underlying the design of distributed systems and networks: communication, coordination, fault-tolerance, locality, parallelism, self-organization, symmetry breaking, synchronization, uncertainty. We explore essential algorithmic ideas and lower bound techniques, basically the "pearls" of distributed computing. We will cover a fresh topic every week.
InhaltDistributed computing models and paradigms, e.g. message passing, shared memory, synchronous vs. asynchronous systems, time and message complexity, peer-to-peer systems, small-world networks, social networks, sorting networks, wireless communication, and self-organizing systems.

Distributed algorithms, e.g. leader election, coloring, covering, packing, decomposition, spanning trees, mutual exclusion, store and collect, arrow, ivy, synchronizers, diameter, all-pairs-shortest-path, wake-up, and lower bounds
SkriptAvailable. Our course script is used at dozens of other universities around the world.
LiteraturLecture Notes By Roger Wattenhofer. These lecture notes are taught at about a dozen different universities through the world.

Distributed Computing: Fundamentals, Simulations and Advanced Topics
Hagit Attiya, Jennifer Welch.
McGraw-Hill Publishing, 1998, ISBN 0-07-709352 6

Introduction to Algorithms
Thomas Cormen, Charles Leiserson, Ronald Rivest.
The MIT Press, 1998, ISBN 0-262-53091-0 oder 0-262-03141-8

Disseminatin of Information in Communication Networks
Juraj Hromkovic, Ralf Klasing, Andrzej Pelc, Peter Ruzicka, Walter Unger.
Springer-Verlag, Berlin Heidelberg, 2005, ISBN 3-540-00846-2

Introduction to Parallel Algorithms and Architectures: Arrays, Trees, Hypercubes
Frank Thomson Leighton.
Morgan Kaufmann Publishers Inc., San Francisco, CA, 1991, ISBN 1-55860-117-1

Distributed Computing: A Locality-Sensitive Approach
David Peleg.
Society for Industrial and Applied Mathematics (SIAM), 2000, ISBN 0-89871-464-8
Voraussetzungen / BesonderesCourse pre-requisites: Interest in algorithmic problems. (No particular course needed.)
401-3632-00LComputational StatisticsW8 KP3V + 1UM. H. Maathuis
KurzbeschreibungWe discuss modern statistical methods for data analysis, including methods for data exploration, prediction and inference. We pay attention to algorithmic aspects, theoretical properties and practical considerations. The class is hands-on and methods are applied using the statistical programming language R.
LernzielThe student obtains an overview of modern statistical methods for data analysis, including their algorithmic aspects and theoretical properties. The methods are applied using the statistical programming language R.
Voraussetzungen / BesonderesAt least one semester of (basic) probability and statistics.

Programming experience is helpful but not required.
101-0178-01LUncertainty Quantification in Engineering Information W3 KP2GB. Sudret, S. Marelli
KurzbeschreibungUncertainty quantification aims at studying the impact of aleatory and epistemic uncertainty onto computational models used in science and engineering. The course introduces the basic concepts of uncertainty quantification: probabilistic modelling of data (copula theory), uncertainty propagation techniques (Monte Carlo simulation, polynomial chaos expansions), and sensitivity analysis.
LernzielAfter this course students will be able to properly pose an uncertainty quantification problem, select the appropriate computational methods and interpret the results in meaningful statements for field scientists, engineers and decision makers. The course is suitable for any master/Ph.D. student in engineering or natural sciences, physics, mathematics, computer science with a basic knowledge in probability theory.
InhaltThe course introduces uncertainty quantification through a set of practical case studies that come from civil, mechanical, nuclear and electrical engineering, from which a general framework is introduced. The course in then divided into three blocks: probabilistic modelling (introduction to copula theory), uncertainty propagation (Monte Carlo simulation and polynomial chaos expansions) and sensitivity analysis (correlation measures, Sobol' indices). Each block contains lectures and tutorials using Matlab and the in-house software UQLab (Link).
SkriptDetailed slides are provided for each lecture. A printed script gathering all the lecture slides may be bought at the beginning of the semester.
Voraussetzungen / BesonderesA basic background in probability theory and statistics (bachelor level) is required. A summary of useful notions will be handed out at the beginning of the course.

A good knowledge of Matlab is required to participate in the tutorials and for the mini-project.
263-2300-00LHow To Write Fast Numerical Code Information Belegung eingeschränkt - Details anzeigen
Number of participants limited to 84.

Prerequisite: Master student, solid C programming skills.

Takes place the last time in this form.
W6 KP3V + 2UM. Püschel
KurzbeschreibungThis course introduces the student to the foundations and state-of-the-art techniques in developing high performance software for mathematical functionality such as matrix operations, transforms, and others. The focus is on optimizing for a single core. This includes optimizing for the memory hierarchy, for special instruction sets, and the possible use of automatic performance tuning.
LernzielSoftware performance (i.e., runtime) arises through the complex interaction of algorithm, its implementation, the compiler used, and the microarchitecture the program is run on. The first goal of the course is to provide the student with an understanding of this "vertical" interaction, and hence software performance, for mathematical functionality. The second goal is to teach a systematic strategy how to use this knowledge to write fast software for numerical problems. This strategy will be trained in several homeworks and a semester-long group project.
InhaltThe fast evolution and increasing complexity of computing platforms pose a major challenge for developers of high performance software for engineering, science, and consumer applications: it becomes increasingly harder to harness the available computing power. Straightforward implementations may lose as much as one or two orders of magnitude in performance. On the other hand, creating optimal implementations requires the developer to have an understanding of algorithms, capabilities and limitations of compilers, and the target platform's architecture and microarchitecture.

This interdisciplinary course introduces the student to the foundations and state-of-the-art techniques in high performance mathematical software development using important functionality such as matrix operations, transforms, filters, and others as examples. The course will explain how to optimize for the memory hierarchy, take advantage of special instruction sets, and other details of current processors that require optimization. The concept of automatic performance tuning is introduced. The focus is on optimization for a single core; thus, the course complements others on parallel and distributed computing.

Finally a general strategy for performance analysis and optimization is introduced that the students will apply in group projects that accompany the course.
252-0526-00LStatistical Learning Theory Information W7 KP3V + 2U + 1AJ. M. Buhmann
KurzbeschreibungThe course covers advanced methods of statistical learning :
Statistical learning theory;variational methods and optimization, e.g., maximum entropy techniques, information bottleneck, deterministic and simulated annealing; clustering for vectorial, histogram and relational data; model selection; graphical models.
LernzielThe course surveys recent methods of statistical learning. The fundamentals of machine learning as presented in the course "Introduction to Machine Learning" are expanded and in particular, the theory of statistical learning is discussed.
Inhalt# Theory of estimators: How can we measure the quality of a statistical estimator? We already discussed bias and variance of estimators very briefly, but the interesting part is yet to come.

# Variational methods and optimization: We consider optimization approaches for problems where the optimizer is a probability distribution. Concepts we will discuss in this context include:

* Maximum Entropy
* Information Bottleneck
* Deterministic Annealing

# Clustering: The problem of sorting data into groups without using training samples. This requires a definition of ``similarity'' between data points and adequate optimization procedures.

# Model selection: We have already discussed how to fit a model to a data set in ML I, which usually involved adjusting model parameters for a given type of model. Model selection refers to the question of how complex the chosen model should be. As we already know, simple and complex models both have advantages and drawbacks alike.

# Statistical physics models: approaches for large systems approximate optimization, which originate in the statistical physics (free energy minimization applied to spin glasses and other models); sampling methods based on these models
SkriptA draft of a script will be provided;
transparencies of the lectures will be made available.
LiteraturHastie, Tibshirani, Friedman: The Elements of Statistical Learning, Springer, 2001.

L. Devroye, L. Gyorfi, and G. Lugosi: A probabilistic theory of pattern recognition. Springer, New York, 1996
Voraussetzungen / BesonderesRequirements:

knowledge of the Machine Learning course
basic knowledge of statistics, interest in statistical methods.

It is recommended that Introduction to Machine Learning (ML I) is taken first; but with a little extra effort Statistical Learning Theory can be followed without the introductory course.
227-0216-00LControl Systems II Information W6 KP4GR. Smith
KurzbeschreibungIntroduction to basic and advanced concepts of modern feedback control.
LernzielIntroduction to basic and advanced concepts of modern feedback control.
InhaltThis course is designed as a direct continuation of the course "Regelsysteme" (Control Systems). The primary goal is to further familiarize students with various dynamic phenomena and their implications for the analysis and design of feedback controllers. Simplifying assumptions on the underlying plant that were made in the course "Regelsysteme" are relaxed, and advanced concepts and techniques that allow the treatment of typical industrial control problems are presented. Topics include control of systems with multiple inputs and outputs, control of uncertain systems (robustness issues), limits of achievable performance, and controller implementation issues.
SkriptThe slides of the lecture are available to download.
LiteraturSkogestad, Postlethwaite: Multivariable Feedback Control - Analysis and Design. Second Edition. John Wiley, 2005.
Voraussetzungen / BesonderesPrerequisites:
Control Systems or equivalent
151-0566-00LRecursive Estimation Information W4 KP2V + 1UR. D'Andrea
KurzbeschreibungEstimation of the state of a dynamic system based on a model and observations in a computationally efficient way.
LernzielLearn the basic recursive estimation methods and their underlying principles.
InhaltIntroduction to state estimation; probability review; Bayes' theorem; Bayesian tracking; extracting estimates from probability distributions; Kalman filter; extended Kalman filter; particle filter; observer-based control and the separation principle.
SkriptLecture notes available on course website: Link
Voraussetzungen / BesonderesRequirements: Introductory probability theory and matrix-vector algebra.
401-3642-00LBrownian Motion and Stochastic Calculus Information W10 KP4V + 1UW. Werner
KurzbeschreibungThis course covers some basic objects of stochastic analysis. In particular, the following topics are discussed: construction and properties of Brownian motion, stochastic integration, Ito's formula and applications, stochastic differential equations and connection with partial differential equations.
LernzielThis course covers some basic objects of stochastic analysis. In particular, the following topics are discussed: construction and properties of Brownian motion, stochastic integration, Ito's formula and applications, stochastic differential equations and connection with partial differential equations.
SkriptLecture notes will be distributed in class.
Literatur- J.-F. Le Gall, Brownian Motion, Martingales, and Stochastic Calculus, Springer (2016).
- I. Karatzas, S. Shreve, Brownian Motion and Stochastic Calculus, Springer (1991).
- D. Revuz, M. Yor, Continuous Martingales and Brownian Motion, Springer (2005).
- L.C.G. Rogers, D. Williams, Diffusions, Markov Processes and Martingales, vol. 1 and 2, Cambridge University Press (2000).
- D.W. Stroock, S.R.S. Varadhan, Multidimensional Diffusion Processes, Springer (2006).
Voraussetzungen / BesonderesFamiliarity with measure-theoretic probability as in the standard D-MATH course "Probability Theory" will be assumed. Textbook accounts can be found for example in
- J. Jacod, P. Protter, Probability Essentials, Springer (2004).
- R. Durrett, Probability: Theory and Examples, Cambridge University Press (2010).
401-3602-00LApplied Stochastic Processes Information W8 KP3V + 1UV. Tassion
KurzbeschreibungPoisson-Prozesse; Erneuerungsprozesse; Markovketten in diskreter und in stetiger Zeit; einige Beispiele und Anwendungen.
LernzielStochastische Prozesse dienen zur Beschreibung der Entwicklung von Systemen, die sich in einer zufälligen Weise entwickeln. In dieser Vorlesung bezieht sich die Entwicklung auf einen skalaren Parameter, der als Zeit interpretiert wird, so dass wir die zeitliche Entwicklung des Systems studieren. Die Vorlesung präsentiert mehrere Klassen von stochastischen Prozessen, untersucht ihre Eigenschaften und ihr Verhalten und zeigt anhand von einigen Beispielen, wie diese Prozesse eingesetzt werden können. Die Hauptbetonung liegt auf der Theorie; "applied" ist also im Sinne von "applicable" zu verstehen.
LiteraturR. N. Bhattacharya and E. C. Waymire, "Stochastic Processes with Applications", SIAM (2009), available online: Link
R. Durrett, "Essentials of Stochastic Processes", Springer (2012), available online: Link
M. Lefebvre, "Applied Stochastic Processes", Springer (2007), available online: Link
S. I. Resnick, "Adventures in Stochastic Processes", Birkhäuser (2005)
Voraussetzungen / BesonderesPrerequisites are familiarity with (measure-theoretic) probability theory as it is treated in the course "Probability Theory" (401-3601-00L).
636-0530-00LHigh Performance ComputingW4 KP4Gexterne Veranstalter
Kurzbeschreibung
Lernziel
262-6220-00LMolecular Dynamics Simulations with Applications in Soft Matter
Findet dieses Semester nicht statt.
W3 KP3Vexterne Veranstalter
Kurzbeschreibung
Lernziel
262-0200-00LBayesian PhylodynamicsW4 KP2G + 2AT. Stadler, T. Vaughan
KurzbeschreibungHow fast was Ebola spreading in West Africa? Where and when did the epidemic outbreak start? How can we construct the phylogenetic tree of great apes, and did gene flow occur between different apes? Students will be able to perform their own phylodynamic analysis of genetic sequencing and independent data analysis to characterize future epidemic outbreaks or reconstruct parts of the tree of life.
LernzielAttendees will extend their knowledge of Bayesian phylodynamics obtained in the “Computational Biology” class (636-0017-00L) and will learn how to apply this theory to real world data. The main theoretical concepts introduced are:
* Bayesian statistics
* Phylogenetic and phylodynamic models
* Markov Chain Monte Carlo methods
Attendees will apply these concepts to a number of applications yielding biological insight into:
* Epidemiology
* Pathogen evolution
* Macroevolution of species
InhaltIn the first part of the semester, in each week, we will first present the theoretical concepts of Bayesian phylodynamics. The presentation will be followed by attendees using the software package BEAST v2 to apply these theoretical concepts to empirical data. We use previously published datasets on e.g. Ebola, Zika, Yellow Fever, Apes, and Penguins for analysis. Examples of these practical tutorials are available on Link.
In the second part of the semester, the students choose an empirical dataset of genetic sequencing data and possibly some non-genetic metadata. They then design and conduct a research project in which they perform Bayesian phylogenetic analyses of their dataset. The weekly class is intended to discuss and monitor progress and to address students’ questions very interactively. At the end of the semester, the students present their research project in an oral presentation. The content of the presentation, the style of the presentation, and the performance in answering the questions after the presentation will be marked.
SkriptLecture slides will be available on moodle.
LiteraturThe following books provide excellent background material:
• Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST.
• Yang, Z. 2014. Molecular Evolution: A Statistical Approach.
• Felsenstein, J. 2003. Inferring Phylogenies.
The tutorials in this course are based on our Summer School “Taming the BEAST”: Link
Voraussetzungen / BesonderesThis class builds upon the content which we taught in the Computational Biology class (636-0017-00L). Attendees must have either taken the Computational Biology class or acquired the content elsewhere.
261-5113-00LComputational Challenges in Medical Genomics Information Belegung eingeschränkt - Details anzeigen
Number of participants limited to 20.
W2 KP2SA. Kahles, G. Rätsch
KurzbeschreibungThis seminar discusses recent relevant contributions to the fields of computational genomics, algorithmic bioinformatics, statistical genetics and related areas. Each participant will hold a presentation and lead the subsequent discussion.
LernzielPreparing and holding a scientific presentation in front of peers is a central part of working in the scientific domain. In this seminar, the participants will learn how to efficiently summarize the relevant parts of a scientific publication, critically reflect its contents, and summarize it for presentation to an audience. The necessary skills to succesfully present the key points of existing research work are the same as needed to communicate own research ideas.
In addition to holding a presentation, each student will both contribute to as well as lead a discussion section on the topics presented in the class.
InhaltThe topics covered in the seminar are related to recent computational challenges that arise from the fields of genomics and biomedicine, including but not limited to genomic variant interpretation, genomic sequence analysis, compressive genomics tasks, single-cell approaches, privacy considerations, statistical frameworks, etc.
Both recently published works contributing novel ideas to the areas mentioned above as well as seminal contributions from the past are amongst the list of selected papers.
Voraussetzungen / BesonderesKnowledge of algorithms and data structures and interest in applications in genomics and computational biomedicine.
262-6240-00LDistributed Information Systems
*Mutually exclusive courses in the advanced course category: "Distributed Information Systems" (Uni Basel) and "Principles of Distributed Compution" (ETH Zürich)*
W4 KP2Vexterne Veranstalter
Kurzbeschreibung
Lernziel
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