Search result: Catalogue data in Autumn Semester 2017

Computational Biology and Bioinformatics Master Information
More informations at: https://www.cbb.ethz.ch/
Master Studies (Programme Regulations 2017)
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.
Data Science
NumberTitleTypeECTSHoursLecturers
636-0018-00LData Mining IW6 credits3G + 2AK. M. Borgwardt
AbstractData Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. This course provides an introduction to the key problems, concepts, and algorithms in data mining, and the applications of data mining in computational biology.
ObjectiveThe goal of this course is that the participants gain an understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications.
ContentThe 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 the algorithmic foundations of data mining and its applications in computational biology. The course will feature an introduction to popular data mining problems and algorithms, reaching from classification via clustering to feature selection. This course is intended for both students who are interested in applying data mining algorithms and students who would like to gain an understanding of the key algorithmic concepts in data mining.

Tentative list of topics:

1. Distance functions
2. Classification
3. Clustering
4. Feature Selection
Lecture notesCourse material will be provided in form of slides.
LiteratureWill be provided during the course.
Prerequisites / NoticeBasic understanding of mathematics, as taught in basic mathematics courses at the Bachelor's level.
401-6282-00LStatistical Analysis of High-Throughput Genomic and Transcriptomic Data (University of Zurich)
No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH.
UZH Module Code: STA426

Mind the enrolment deadlines at UZH:
https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html
W5 credits3GH. Rehrauer, M. Robinson
AbstractA range of topics will be covered, including basic molecular biology, genomics technologies and in particular, a wide range of statistical and computational methods that have been used in the analysis of DNA microarray and high throughput sequencing experiments.
Objective-Understand the fundamental "scientific process" in the field of Statistical Bioinformatics
-Be equipped with the skills/tools to preprocess genomic data (Unix, Bioconductor, mapping, etc.) and ensure reproducible research (Sweave)
-Have a general knowledge of the types of data and biological applications encountered with microarray and sequencing data
-Have the general knowledge of the range of statistical methods that get used with microarray and sequencing data
-Gain the ability to apply statistical methods/knowledge/software to a collaborative biological project
-Gain the ability to critical assess the statistical bioinformatics literature
-Write a coherent summary of a bioinformatics problem and its solution in statistical terms
ContentLectures will include: microarray preprocessing; normalization; exploratory data analysis techniques such as clustering, PCA and multidimensional scaling; Controlling error rates of statistical tests (FPR versus FDR versus FWER); limma (linear models for microarray analysis); mapping algorithms (for RNA/ChIP-seq); RNA-seq quantification; statistical analyses for differential count data; isoform switching; epigenomics data including DNA methylation; gene set analyses; classification
Lecture notesLecture notes, published manuscripts
Prerequisites / NoticePrerequisites: Basic knowlegde of the programming language R, sufficient knowledge in statistics

Former course title: Statistical Methods for the Analysis of Microarray and Short-Read Sequencing Data
252-0535-00LMachine Learning Information W8 credits3V + 2U + 2AJ. M. Buhmann
AbstractMachine 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.
ObjectiveStudents will be familiarized with the most important 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. A machine learning project will provide an opportunity to test the machine learning algorithms on real world data.
ContentThe 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:

- Bayesian theory of optimal decisions
- Maximum likelihood and Bayesian parameter inference
- Classification with discriminant functions: Perceptrons, Fisher's LDA and support vector machines (SVM)
- Ensemble methods: Bagging and Boosting
- Regression: least squares, ridge and LASSO penalization, non-linear regression and the bias-variance trade-off
- Non parametric density estimation: Parzen windows, nearest nieghbour
- Dimension reduction: principal component analysis (PCA) and beyond
Lecture notesNo lecture notes, but slides will be made available on the course webpage.
LiteratureC. 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 / NoticeThe course requires solid basic knowledge in analysis, statistics and numerical methods for CSE as well as practical programming experience for solving assignments.
Students should at least have followed one previous course offered by the Machine Learning Institute (e.g., CIL or LIS) or an equivalent course offered by another institution.
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