# Search result: Catalogue data in Autumn Semester 2020

Cyber Security Master | ||||||

Minor | ||||||

Computational Science | ||||||

Core Courses | ||||||

Number | Title | Type | ECTS | Hours | Lecturers | |
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252-0535-00L | Advanced Machine Learning | W | 10 credits | 3V + 2U + 4A | J. M. Buhmann, C. Cotrini Jimenez | |

Abstract | Machine learning algorithms provide analytical methods to search data sets for characteristic patterns. Typical tasks include the classification of data, function fitting and clustering, with applications in image and speech analysis, bioinformatics and exploratory data analysis. This course is accompanied by practical machine learning projects. | |||||

Objective | Students will be familiarized with advanced concepts and algorithms for supervised and unsupervised learning; reinforce the statistics knowledge which is indispensible to solve modeling problems under uncertainty. Key concepts are the generalization ability of algorithms and systematic approaches to modeling and regularization. Machine learning projects will provide an opportunity to test the machine learning algorithms on real world data. | |||||

Content | The theory of fundamental machine learning concepts is presented in the lecture, and illustrated with relevant applications. Students can deepen their understanding by solving both pen-and-paper and programming exercises, where they implement and apply famous algorithms to real-world data. Topics covered in the lecture include: Fundamentals: What is data? Bayesian Learning Computational learning theory Supervised learning: Ensembles: Bagging and Boosting Max Margin methods Neural networks Unsupservised learning: Dimensionality reduction techniques Clustering Mixture Models Non-parametric density estimation Learning Dynamical Systems | |||||

Lecture notes | No lecture notes, but slides will be made available on the course webpage. | |||||

Literature | C. Bishop. Pattern Recognition and Machine Learning. Springer 2007. R. Duda, P. Hart, and D. Stork. Pattern Classification. John Wiley & Sons, second edition, 2001. T. Hastie, R. Tibshirani, and J. Friedman. The Elements of Statistical Learning: Data Mining, Inference and Prediction. Springer, 2001. L. Wasserman. All of Statistics: A Concise Course in Statistical Inference. Springer, 2004. | |||||

Prerequisites / Notice | The course requires solid basic knowledge in analysis, statistics and numerical methods for CSE as well as practical programming experience for solving assignments. Students should have followed at least "Introduction to Machine Learning" or an equivalent course offered by another institution. PhD students are required to obtain a passing grade in the course (4.0 or higher based on project and exam) to gain credit points. | |||||

636-0007-00L | Computational Systems Biology | W | 6 credits | 3V + 2U | J. Stelling | |

Abstract | Study of fundamental concepts, models and computational methods for the analysis of complex biological networks. Topics: Systems approaches in biology, biology and reaction network fundamentals, modeling and simulation approaches (topological, probabilistic, stoichiometric, qualitative, linear / nonlinear ODEs, stochastic), and systems analysis (complexity reduction, stability, identification). | |||||

Objective | The aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks. | |||||

Content | Biology has witnessed an unprecedented increase in experimental data and, correspondingly, an increased need for computational methods to analyze this data. The explosion of sequenced genomes, and subsequently, of bioinformatics methods for the storage, analysis and comparison of genetic sequences provides a prominent example. Recently, however, an additional area of research, captured by the label "Systems Biology", focuses on how networks, which are more than the mere sum of their parts' properties, establish biological functions. This is essentially a task of reverse engineering. The aim of this course is to provide an introductory overview of corresponding computational methods for the modeling, simulation and analysis of biological networks. We will start with an introduction into the basic units, functions and design principles that are relevant for biology at the level of individual cells. Making extensive use of example systems, the course will then focus on methods and algorithms that allow for the investigation of biological networks with increasing detail. These include (i) graph theoretical approaches for revealing large-scale network organization, (ii) probabilistic (Bayesian) network representations, (iii) structural network analysis based on reaction stoichiometries, (iv) qualitative methods for dynamic modeling and simulation (Boolean and piece-wise linear approaches), (v) mechanistic modeling using ordinary differential equations (ODEs) and finally (vi) stochastic simulation methods. | |||||

Lecture notes | http://www.csb.ethz.ch/education/lectures.html | |||||

Literature | U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006. Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2010. B. Ingalls, Mathematical modeling in systems biology: an introduction. MIT Press, 2013 | |||||

Electives | ||||||

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

252-0543-01L | Computer Graphics | W | 8 credits | 3V + 2U + 2A | M. Gross, M. Papas | |

Abstract | This course covers some of the fundamental concepts of computer graphics generation of photorealistic images from digital representations of 3D scenes and image-based methods for recovering digital scene representations from captured images. | |||||

Objective | At the end of the course the students will be able to build a rendering system. The students will study the basic principles of rendering and image synthesis. In addition, the course is intended to stimulate the students' curiosity to explore the field of computer graphics in subsequent courses or on their own. | |||||

Content | This course covers fundamental concepts of modern computer graphics. Students will learn about 3D object representations and the details of how to generate photorealistic images from digital representations of 3D scenes. Starting with an introduction to 3D shape modeling, geometry representation and texture mapping, we will move on to the physics of light transport, acceleration structures, appearance modeling and Monte Carlo integration. We will apply these principles for computing light transport of direct and global illumination due to surfaces and participating media. We will end with an overview of modern image-based capture and image synthesis methods, covering topics such as geometry and material capture, light-fields and depth-image based rendering. | |||||

Lecture notes | no | |||||

Literature | Books: High Dynamic Range Imaging: Acquisition, Display, and Image-Based Lighting Multiple view geometry in computer vision Physically Based Rendering: From Theory to Implementation | |||||

Prerequisites / Notice | Prerequisites: Fundamentals of calculus and linear algebra, basic concepts of algorithms and data structures, programming skills in C++, Visual Computing course recommended. The programming assignments will be in C++. This will not be taught in the class. | |||||

261-5100-00L | Computational Biomedicine Number of participants limited to 60. | W | 5 credits | 2V + 1U + 1A | G. Rätsch, V. Boeva, N. Davidson | |

Abstract | The course critically reviews central problems in Biomedicine and discusses the technical foundations and solutions for these problems. | |||||

Objective | Over the past years, rapid technological advancements have transformed classical disciplines such as biology and medicine into fields of apllied data science. While the sheer amount of the collected data often makes computational approaches inevitable for analysis, it is the domain specific structure and close relation to research and clinic, that call for accurate, robust and efficient algorithms. In this course we will critically review central problems in Biomedicine and will discuss the technical foundations and solutions for these problems. | |||||

Content | The course will consist of three topic clusters that will cover different aspects of data science problems in Biomedicine: 1) String algorithms for the efficient representation, search, comparison, composition and compression of large sets of strings, mostly originating from DNA or RNA Sequencing. This includes genome assembly, efficient index data structures for strings and graphs, alignment techniques as well as quantitative approaches. 2) Statistical models and algorithms for the assessment and functional analysis of individual genomic variations. this includes the identification of variants, prediction of functional effects, imputation and integration problems as well as the association with clinical phenotypes. 3) Models for organization and representation of large scale biomedical data. This includes ontolgy concepts, biomedical databases, sequence annotation and data compression. | |||||

Prerequisites / Notice | Data Structures & Algorithms, Introduction to Machine Learning, Statistics/Probability, Programming in Python, Unix Command Line | |||||

636-0017-00L | Computational Biology | W | 6 credits | 3G + 2A | T. Stadler, T. Vaughan | |

Abstract | The aim of the course is to provide up-to-date knowledge on how we can study biological processes using genetic sequencing data. Computational algorithms extracting biological information from genetic sequence data are discussed, and statistical tools to understand this information in detail are introduced. | |||||

Objective | Attendees will learn which information is contained in genetic sequencing data and how to extract information from this data using computational tools. The main concepts introduced are: * stochastic models in molecular evolution * phylogenetic & phylodynamic inference * maximum likelihood and Bayesian statistics Attendees will apply these concepts to a number of applications yielding biological insight into: * epidemiology * pathogen evolution * macroevolution of species | |||||

Content | The course consists of four parts. We first introduce modern genetic sequencing technology, and algorithms to obtain sequence alignments from the output of the sequencers. We then present methods for direct alignment analysis using approaches such as BLAST and GWAS. Second, we introduce mechanisms and concepts of molecular evolution, i.e. we discuss how genetic sequences change over time. Third, we employ evolutionary concepts to infer ancestral relationships between organisms based on their genetic sequences, i.e. we discuss methods to infer genealogies and phylogenies. Lastly, we introduce the field of phylodynamics, the aim of which is to understand and quantify population dynamic processes (such as transmission in epidemiology or speciation & extinction in macroevolution) based on a phylogeny. Throughout the class, the models and methods are illustrated on different datasets giving insight into the epidemiology and evolution of a range of infectious diseases (e.g. HIV, HCV, influenza, Ebola). Applications of the methods to the field of macroevolution provide insight into the evolution and ecology of different species clades. Students will be trained in the algorithms and their application both on paper and in silico as part of the exercises. | |||||

Lecture notes | Lecture slides will be available on moodle. | |||||

Literature | The course is not based on any of the textbooks below, but they are excellent choices as accompanying material: * Yang, Z. 2006. Computational Molecular Evolution. * Felsenstein, J. 2004. Inferring Phylogenies. * Semple, C. & Steel, M. 2003. Phylogenetics. * Drummond, A. & Bouckaert, R. 2015. Bayesian evolutionary analysis with BEAST. | |||||

Prerequisites / Notice | Basic knowledge in linear algebra, analysis, and statistics will be helpful. Programming in R will be required for the project work (compulsory continuous performance assessments). We provide an R tutorial and help sessions during the first two weeks of class to learn the required skills. However, in case you do not have any previous experience with R, we strongly recommend to get familiar with R prior to the semester start. For the D-BSSE students, we highly recommend the voluntary course „Introduction to Programming“, which takes place at D-BSSE from Wednesday, September 12 to Friday, September 14, i.e. BEFORE the official semester starting date http://www.cbb.ethz.ch/news-events.html For the Zurich-based students without R experience, we recommend the R course Link, or working through the script provided as part of this R course. |

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