# Search result: Catalogue data in Spring Semester 2020

Computational Biology and Bioinformatics Master More informations at: https://www.cbb.ethz.ch | ||||||

Core Courses Please note that the list of core courses is a closed list. Other courses cannot be added to the core course category in the study plan. Also the assignments of courses to core subcategories cannot be changed. Students need to pass at least one course in each core subcategory. A total of 40 ECTS needs to be acquired in the core course category. | ||||||

Bioinformatics Please note that all Bioinformatics core courses are offered in the autumn semester | ||||||

Biophysics | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |
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262-5100-00L | Protein Biophysics (University of Zurich)No enrollment to this course at ETH Zurich. Book the corresponding module directly at UZH. UZH Module Code: BCH304 Mind the enrolment deadlines at UZH: https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html | W | 6 credits | 3V + 1U | University lecturers | |

Abstract | The course includes a general introduction into protein structure and biophysics as well as into the usage of molecular dynamics simulations and other computational methods, protein structure and X-ray techniques, protein NMR for determining protein structure and dynamics as well as for folding studies and protein thermodynamics. | |||||

Objective | A 4 hour/week course on all aspects of protein biophysics. The course includes a general introduction into protein structure and biophysics as well as into the usage of molecular dynamics simulations and other computational methods, protein structure and X-ray techniques, protein NMR for determining protein structure and dynamics as well as for folding studies and protein thermodynamics. | |||||

Content | The lecture course consists of four parts: 1) non-covalent interactions, properties of water and hydrophobic effect, protein folding and misfolding, molecular dynamics simulations; 2) atomistic simulations of proteins 3) thermodynamics and kinetics of protein folding; 4) single molecule biophysics: single molecule fluorescence spectroscopy, fluorescence correlation spectroscopy, and applications to stochastic processes in biology. | |||||

151-0980-00L | Biofluiddynamics | W | 4 credits | 2V + 1U | D. Obrist, P. Jenny | |

Abstract | Introduction to the fluid dynamics of the human body and the modeling of physiological flow processes (biomedical fluid dynamics). | |||||

Objective | A basic understanding of fluid dynamical processes in the human body. Knowledge of the basic concepts of fluid dynamics and the ability to apply these concepts appropriately. | |||||

Content | This lecture is an introduction to the fluid dynamics of the human body (biomedical fluid dynamics). For selected topics of human physiology, we introduce fundamental concepts of fluid dynamics (e.g., creeping flow, incompressible flow, flow in porous media, flow with particles, fluid-structure interaction) and use them to model physiological flow processes. The list of studied topics includes the cardiovascular system and related diseases, blood rheology, microcirculation, respiratory fluid dynamics and fluid dynamics of the inner ear. | |||||

Lecture notes | Lecture notes are provided electronically. | |||||

Literature | A list of books on selected topics of biofluiddynamics can be found on the course web page. | |||||

Biosystems | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |

636-0016-00L | Computational Systems Biology: Stochastic Approaches | W | 4 credits | 3G | M. H. Khammash, A. Gupta | |

Abstract | This course is concerned with the development of computational methods for modeling, simulation, and analysis of stochasticity in living cells. Using these tools, the course explores the richness of stochastic phenomena, how it arises from the interactions of dynamics and noise, and its biological implications. | |||||

Objective | To understand the origins and implications of stochastic noise in living cells, and to learn the computational tools for the modeling, simulation, analysis, and identification of stochastic biochemical reaction networks. | |||||

Content | The cellular environment is abuzz with noise. A key source of this noise is the randomness that characterizes the motion of cellular constituents at the molecular level. Cellular noise not only results in random fluctuations (over time) within individual cells, but it is also a main source of phenotypic variability among clonal cell populations. Review of basic probability and stochastic processes; Introduction to stochastic gene expression; deterministic vs. stochastic models; the stochastic chemical kinetics framework; a rigorous derivation of the chemical master equation; moment computations; linear vs. nonlinear propensities; linear noise approximations; Monte Carlo simulations; Gillespie's Stochastic Simulation Algorithm (SSA) and variants; direct methods for the solution of the Chemical Master Equation; moment closure methods; intrinsic and extrinsic noise in gene expression; parameter identification from noise; propagation of noise in cell networks; noise suppression in cells; the role of feedback; exploiting noise; bimodality and stochastic switches. | |||||

Literature | Literature will be distributed during the course as needed. | |||||

Prerequisites / Notice | Students are expected to have completed the course `Mathematical modeling for systems biology (BSc Biotechnology) or `Computational systems biology (MSc Computational biology and bioinformatics). Concurrent enrollment in `Computational Systems Biology: Deterministic Approaches is recommended. | |||||

636-0111-00L | Synthetic Biology IAttention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L. | W | 4 credits | 3G | S. Panke, J. Stelling | |

Abstract | Theoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig | |||||

Objective | After the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see www.igem.ethz.ch). | |||||

Content | The overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems. | |||||

Lecture notes | Handouts during classes. | |||||

Literature | Mark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press Uri Alon, An Introduction to Systems Biology, Chapman & Hall | |||||

Prerequisites / Notice | 1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on https://bsse.ethz.ch/bpl/education/lectures/synthetic-biology-i/download.html as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact sven.panke@bsse.ethz.ch for access to material 2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (www.syntheticbiology.ethz.ch, http://www.igem.org). This competition is also the contents of the course Synthetic Biology II. https://bsse.ethz.ch/bpl/education/lectures/synthetic-biology-i/download.html | |||||

Data Science | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |

551-0364-00L | Functional GenomicsInformation for UZH students: Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH. Please mind the ETH enrolment deadlines for UZH students: Link | W | 3 credits | 2V | C. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers | |

Abstract | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. | |||||

Objective | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks. | |||||

Content | The curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced sequencing, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects. | |||||

Prerequisites / Notice | The Functional Genomics course will be taught in English. | |||||

636-0702-00L | Statistical Models in Computational Biology | W | 6 credits | 2V + 1U + 2A | N. Beerenwinkel | |

Abstract | The 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. | |||||

Objective | The 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. | |||||

Content | Graphical 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 notes | no | |||||

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 | |||||

636-0019-00L | Data Mining IIPrerequisites: Basic understanding of mathematics, as taught in basic mathematics courses at the Bachelor`s level. Ideally, students will have attended Data Mining I before taking this class. | W | 6 credits | 3G + 2A | K. M. Borgwardt | |

Abstract | Data Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. Building on the basic algorithms and concepts of data mining presented in the course "Data Mining I", this course presents advanced algorithms and concepts from data mining and the state-of-the-art in applications of data mining. | |||||

Objective | The goal of this course is that the participants gain an advanced understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications, and to enable them to conduct their own research projects in the domain of data mining. | |||||

Content | The goal of the field of data mining is to find patterns and statistical dependencies in large databases, to gain an understanding of the underlying system from which the data were obtained. In computational biology, data mining contributes to the analysis of vast experimental data generated by high-throughput technologies, and thereby enables the generation of new hypotheses. In this course, we will present advanced topics in data mining and its applications in computational biology. Tentative list of topics: 1. Dimensionality Reduction 2. Association Rule Mining 3. Text Mining 4. Graph Mining | |||||

Lecture notes | Course material will be provided in form of slides. | |||||

Literature | Will be provided during the course. | |||||

262-6190-00L | Machine Learning | W | 8 credits | 4G | external organisers | |

Abstract | ||||||

Objective | ||||||

252-0220-00L | Introduction to Machine Learning Limited number of participants. Preference is given to students in programmes in which the course is being offered. All other students will be waitlisted. Please do not contact Prof. Krause for any questions is this regard. If necessary, please contact studiensekretariat@inf.ethz.ch | W | 8 credits | 4V + 2U + 1A | A. Krause | |

Abstract | The course introduces the foundations of learning and making predictions based on data. | |||||

Objective | The 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. | |||||

Content | - 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) | |||||

Literature | Textbook: Kevin Murphy, Machine Learning: A Probabilistic Perspective, MIT Press | |||||

Prerequisites / Notice | Designed to provide a basis for following courses: - Advanced Machine Learning - Deep Learning - Probabilistic Artificial Intelligence - Seminar "Advanced Topics in Machine Learning" | |||||

636-0101-00L | Systems Genomics | W | 4 credits | 3G | N. Beerenwinkel, C. Beisel, S. Reddy | |

Abstract | This lecture course is an introduction to Systems Genomics. It addresses how fundamental questions in biological systems are studied and how the resulting data is statistically analyzed in order to derive predictive mathematical models. The focus is on viewing biology from a genomic perspective, which requires high-throughput experimental methods (e.g., RNA-seq, genome-scale screening, single-cell | |||||

Objective | The goal of this course is to learn how a detailed quantitative description of genome biology can be employed for a better understanding of molecular and cellular processes and function. Students will learn fundamental questions driving the field of Systems Genomics. They will also be introduced to traditional and advanced state-of-the-art technologies (e.g., CRISPR-Cas9 screening, droplet-microfluidic sequencing, cellular genetic barcoding) that are used to obtain quantitative data in Systems Genomics. They will learn how to use these data to develop mathematical models and efficient statistical inference algorithms to recognize patterns, molecular interrelationships, and systems behavior. Finally, students will gain a perspective of how Systems Genomics can be used for applied biological sciences (e.g., drug discovery and screening, bio-production, cell line engineering, biomarker discovery, and diagnostics). | |||||

Content | Lectures in Systems Genomics will alternate between lectures on (i) biological questions, experimental technologies, and applications, and (ii) statistical data analysis and mathematical modeling. Selected complex biological systems and the respective experimental tools for a quantitative analysis will be presented. Some specific examples are the use of RNA-sequencing to do quantitative gene expression profiling, CRISPR-Cas9 genome scale screening to identify genes responsible for drug resistance, single-cell measurements to identify novel cellular phenotypes, and genetic barcoding of cells to dissect development and lineage differentiation. Main Topics: -- Next-generation sequencing -- Transcriptomics -- Biological network analysis -- Functional and perturbation genomics -- Single-cell biology and analysis -- Genomic profiling of the immune system -- Genomic profiling of cancer -- Evolutionary genomics -- Genome-wide association studies Selected genomics datasets will be analyzed by students in the tutorials using the statistical programming language R and dedicated Bioconductor packages. | |||||

Lecture notes | The PowerPoint presentations of the lectures as well as other course material relevant for an active participation will be made available online. | |||||

Literature | -- Do K-A, Qin ZS & Vannucci M (2013) Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data, Cambridge University Press -- Klipp E. et al (2009) Systems Biology, Wiley-Blackwell -- Alon U (2007) An Introduction to Systems Biology, Chapman & Hall -- Zvelebil M & Baum JO (2008) Understanding Bioinformatics, Garland Science | |||||

Seminar Compulsory seminar. | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |

636-0704-00L | Computational Biology and Bioinformatics Seminar | O | 2 credits | 2S | J. Stelling, D. Iber, M. H. Khammash, J. Payne, T. Stadler, C. Uhler | |

Abstract | Computational Biology und Bioinformatik analysieren lebende Systeme mit Methoden der Informatik. Das Seminar kombiniert Präsentationen von Studierenden und Forschenden, um das sich schnell entwickelnde Gebiet aus der Informatikperspektive zu skizzieren. Themenbereiche sind Sequenzanalyse, Proteomics, Optimierung und Bio-inspired computing, Systemmodellierung, -simulation und -analyse. | |||||

Objective | Studying and presenting fundamental papers of Computational Biology and Bioinformatics. Learning how to make a scientific presentation and how classical methods are used or further developed in current research. | |||||

Content | Computational biology and bioinformatics aim at advancing the understanding of living systems through computation. The complexity of these systems, however, provides challenges for software and algorithms, and often requires entirely novel approaches in computer science. The aim of the seminar is to give an overview of this rapidly developing field from a computer science perspective. In particular, it will focus on the areas of (i) DNA sequence analysis, sequence comparison and reconstruction of phylogenetic trees, (ii) protein identification from experimental data, (iii) optimization and bio-inspired computing, and (iv) systems analysis of complex biological networks. The seminar combines the discussion of selected research papers with a major impact in their domain by the students with the presentation of current active research projects / open challenges in computational biology and bioinformatics by the lecturers. Each week, the seminar will focus on a different topic related to ongoing research projects at ETHZ, thus giving the students the opportunity of obtaining knowledge about the basic research approaches and problems as well as of gaining insight into (and getting excited about) the latest developments in the field. | |||||

Literature | Original papers to be presented by the students will be provided in the first week of the seminar. | |||||

Advanced Courses 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. Note that some of the lectures are being recorded: https://video.ethz.ch/lectures.html | ||||||

Theory At least 18 ECTS need to be acquired in this category. | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |

252-0063-00L | Data Modelling and Databases | W | 7 credits | 4V + 2U | C. Zhang | |

Abstract | Data modelling (Entity Relationship), relational data model, relational design theory (normal forms), SQL, database integrity, transactions and advanced database engines | |||||

Objective | Introduction to relational databases and data management. Basics of SQL programming and transaction management. | |||||

Content | The 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. | |||||

Literature | Kemper, Eickler: Datenbanksysteme: Eine Einführung. Oldenbourg Verlag, 7. Auflage, 2009. Garcia-Molina, Ullman, Widom: Database Systems: The Complete Book. Pearson, 2. Auflage, 2008. | |||||

401-0674-00L | Numerical Methods for Partial Differential EquationsNot meant for BSc/MSc students of mathematics. | W | 10 credits | 2G + 2U + 2P + 4A | R. Hiptmair | |

Abstract | Derivation, 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. | |||||

Objective | Main 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. | |||||

Content | 1 Second-Order Scalar Elliptic Boundary Value Problems 1.2 Equilibrium Models: Examples 1.3 Sobolev spaces 1.4 Linear Variational Problems 1.5 Equilibrium Models: Boundary Value Problems 1.6 Diffusion Models (Stationary Heat Conduction) 1.7 Boundary Conditions 1.8 Second-Order Elliptic Variational Problems 1.9 Essential and Natural Boundary Conditions 2 Finite Element Methods (FEM) 2.2 Principles of Galerkin Discretization 2.3 Case Study: Linear FEM for Two-Point Boundary Value Problems 2.4 Case Study: Triangular Linear FEM in Two Dimensions 2.5 Building Blocks of General Finite Element Methods 2.6 Lagrangian Finite Element Methods 2.7 Implementation of Finite Element Methods 2.7.1 Mesh Generation and Mesh File Format 2.7.2 Mesh Information and Mesh Data Structures 2.7.2.1 L EHR FEM++ Mesh: Container Layer 2.7.2.2 L EHR FEM++ Mesh: Topology Layer 2.7.2.3 L EHR FEM++ Mesh: Geometry Layer 2.7.3 Vectors and Matrices 2.7.4 Assembly Algorithms 2.7.4.1 Assembly: Localization 2.7.4.2 Assembly: Index Mappings 2.7.4.3 Distribute Assembly Schemes 2.7.4.4 Assembly: Linear Algebra Perspective 2.7.5 Local Computations 2.7.5.1 Analytic Formulas for Entries of Element Matrices 2.7.5.2 Local Quadrature 2.7.6 Treatment of Essential Boundary Conditions 2.8 Parametric Finite Element Methods 3 FEM: Convergence and Accuracy 3.1 Abstract Galerkin Error Estimates 3.2 Empirical (Asymptotic) Convergence of Lagrangian FEM 3.3 A Priori (Asymptotic) Finite Element Error Estimates 3.4 Elliptic Regularity Theory 3.5 Variational Crimes 3.6 FEM: Duality Techniques for Error Estimation 3.7 Discrete Maximum Principle 3.8 Validation and Debugging of Finite Element Codes 4 Beyond FEM: Alternative Discretizations [dropped] 5 Non-Linear Elliptic Boundary Value Problems [dropped] 6 Second-Order Linear Evolution Problems 6.1 Time-Dependent Boundary Value Problems 6.2 Parabolic Initial-Boundary Value Problems 6.3 Linear Wave Equations 7 Convection-Diffusion Problems [dropped] 8 Numerical Methods for Conservation Laws 8.1 Conservation Laws: Examples 8.2 Scalar Conservation Laws in 1D 8.3 Conservative Finite Volume (FV) Discretization 8.4 Timestepping for Finite-Volume Methods 8.5 Higher-Order Conservative Finite-Volume Schemes | |||||

Lecture notes | The lecture will be taught in flipped classroom format: - Video tutorials for all thematic units will be published online. - Tablet notes accompanying the videos will be made available to the audience as PDF. - A comprehensive lecture document will cover all aspects of the course. | |||||

Literature | Chapters 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. | |||||

Prerequisites / Notice | Mastery 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. | |||||

401-3052-05L | Graph Theory | W | 5 credits | 2V + 1U | B. Sudakov | |

Abstract | Basic notions, trees, spanning trees, Caley's formula, vertex and edge connectivity, 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 | |||||

Objective | The 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. | |||||

Lecture notes | Lecture will be only at the blackboard. | |||||

Literature | West, D.: "Introduction to Graph Theory" Diestel, R.: "Graph Theory" Further literature links will be provided in the lecture. | |||||

Prerequisites / Notice | Students 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. | |||||

227-1034-00L | Computational Vision (University of Zurich)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: https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html | W | 6 credits | 2V + 1U | D. Kiper | |

Abstract | This 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. | |||||

Objective | This 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. | |||||

Content | This 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. | |||||

Literature | Books: (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. | |||||

227-0558-00L | Principles of Distributed Computing | W | 7 credits | 2V + 2U + 2A | R. Wattenhofer, M. Ghaffari | |

Abstract | We 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. | |||||

Objective | Distributed 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. | |||||

Content | Distributed 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 | |||||

Lecture notes | Available. Our course script is used at dozens of other universities around the world. | |||||

Literature | Lecture 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 | |||||

Prerequisites / Notice | Course pre-requisites: Interest in algorithmic problems. (No particular course needed.) | |||||

401-3632-00L | Computational Statistics | W | 8 credits | 3V + 1U | M. H. Maathuis | |

Abstract | We 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. | |||||

Objective | The 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. | |||||

Content | See the class website | |||||

Prerequisites / Notice | At least one semester of (basic) probability and statistics. Programming experience is helpful but not required. | |||||

101-0178-01L | Uncertainty Quantification in Engineering | W | 3 credits | 2G | S. Marelli | |

Abstract | Uncertainty 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. | |||||

Objective | After 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. | |||||

Content | The 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 (www.uqlab.com). | |||||

Lecture notes | Detailed slides are provided for each lecture. A printed script gathering all the lecture slides may be bought at the beginning of the semester. | |||||

Prerequisites / Notice | A 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. | |||||

252-0526-00L | Statistical Learning Theory | W | 7 credits | 3V + 2U + 1A | J. M. Buhmann, C. Cotrini Jimenez | |

Abstract | The course covers advanced methods of statistical learning: - Variational methods and optimization. - Deterministic annealing. - Clustering for diverse types of data. - Model validation by information theory. | |||||

Objective | The course surveys recent methods of statistical learning. The fundamentals of machine learning, as presented in the courses "Introduction to Machine Learning" and "Advanced Machine Learning", are expanded from the perspective of statistical learning. | |||||

Content | - Variational methods and optimization. We consider optimization approaches for problems where the optimizer is a probability distribution. We will discuss concepts like maximum entropy, information bottleneck, and deterministic annealing. - Clustering. This is the problem of sorting data into groups without using training samples. We discuss alternative notions of "similarity" between data points and adequate optimization procedures. - Model selection and validation. This refers to the question of how complex the chosen model should be. In particular, we present an information theoretic approach for model validation. - Statistical physics models. We discuss approaches for approximately optimizing large systems, which originate in statistical physics (free energy minimization applied to spin glasses and other models). We also study sampling methods based on these models. | |||||

Lecture notes | A draft of a script will be provided. Lecture slides will be made available. | |||||

Literature | Hastie, 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 | |||||

Prerequisites / Notice | Knowledge of machine learning (introduction to machine learning and/or advanced machine learning) Basic knowledge of statistics. | |||||

227-0216-00L | Control Systems II | W | 6 credits | 4G | R. Smith | |

Abstract | Introduction to basic and advanced concepts of modern feedback control. | |||||

Objective | Introduction to basic and advanced concepts of modern feedback control. | |||||

Content | This 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. | |||||

Lecture notes | The slides of the lecture are available to download. | |||||

Literature | Skogestad, Postlethwaite: Multivariable Feedback Control - Analysis and Design. Second Edition. John Wiley, 2005. | |||||

Prerequisites / Notice | Prerequisites: Control Systems or equivalent |

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