[BBC] Registration open: BioSB Course Pattern Recognition (5th edition) - 25-29 September 2017

[Femke Francissen]

*BioSB Course Pattern Recognition (5th edition)*



*Date:  25-29 September 2017*

*Location: AMC, Amsterdam*

*Course Coordinator: Perry Moerland (AMC)*


Website: http://biosb.nl/education/course-portfolio/pattern-recognition/

Registration:
http://biosb.nl/education/course-portfolio/pattern-recognition/enrollment/


Please note that this course is free of charge for PhDs who are or
become a member
of the  BioSB research school
<http://biosb.nl/about/members/biosb-membership-information/>.



*Description*



Many problems in bioinformatics require classification: prediction of the
class to which a certain object (i.e. a gene, protein, cell, patient, …)
belongs. This calls for algorithms that can assign the most likely label
(discrete output) to an object, given one or more measurements on that
object. For most interesting problems, the underlying physics are too
complex to explicitly design such an algorithm. In such cases, often a
machine learning approach is taken: an algorithm is constructed, with
parameters that are tuned based on an available dataset of training
examples. The algorithm should predict the labels for these examples as
well as possible, yet still generalize, i.e. perform well on objects not
seen before. Some examples of classification problems in bioinformatics are
gene finding (sequence in, gene presence out), diagnostics (gene expression
data in, diagnosis out), data integration (measurements in, probability of
interaction out), etc.

In this course, we will introduce basic techniques from the fields of
pattern recognition and machine learning to solve such problems. We will
introduce the pattern recognition pipeline: measuring, feature extraction
and selection, classification and evaluation. The course is a mixture of
theory sessions and lab courses. During the lab courses Matlab will be used
and a brief introduction to Matlab will be provided. The course has to be
completed afterwards with a 5-10 page report describing the analysis of a
biological dataset using some of the methods taught in the course.

The structure of the course is as follows:

   - *Monday *(Introduction; Marcel Reinders): Introduction to pattern
   recognition: measurements, features, classification. Supervised vs.
   unsupervised learning, relation to regression. Bayesian framework: risk,
   cost; evaluation: ROCs, cross-validation. Density estimation: histograms,
   nearest neighbour, Parzen, Gaussian Bayesian classification.
   - *Tuesday* (Classification; Perry Moerland): Parametric classifiers:
   (D)LDA, (D)QDA. Nonparametric classifiers: k-NN, Parzen. Discriminant
   analysis: LDA, logistic regression. Decision trees and random forests.
   - *Wednesday* (Feature selection and extraction; Lodewyk Wessels):
   Feature selection: criteria, search algorithms (forward, backward, branch &
   bound). Sparse classifiers: Ridge, LASSO. Feature extraction: PCA, Fisher.
   Embeddings: MDS.
   - *Thursday* (Clustering and HMMs; Perry Moerland): Hierarchical
   clustering. Agglomerative clustering. Model-based clustering:
   mixtures-of-Gaussians, Expectation-Maximization. Hidden Markov models.
   - *Friday* (Selected advanced topics; Marcel Reinders): Artificial
   neural networks. Support vector machines. Classifier ensembles. Complexity
   and regularisation. Deep learning.

*Target audience *


The course is aimed at PhD students with a background in bioinformatics,
computer science or a related field, life sciences. Participants from the
private sector are also welcome. A working knowledge of basic statistics
and linear algebra is assumed. Preparation material on statistics and
linear algebra will be distributed before the course, to be studied by
students missing the required background.


*Learning objectives*


After having followed this course, the student has a good understanding of
basic pattern recognition and machine learning techniques and is able to
recognize what method is most applicable to data analysis problems (s)he
encounters in bioinformatics applications.


This course is part of the Education Programme of BioSB
<http://biosb.nl/education/course-portfolio-2/>, the Netherlands
Bioinformatics and Systems Biology Research School, which offers training
and education for in bioinformatics and systems biology.



More information about BioSB can be found at www.biosb.nl.




*​*
*​*
*Femke Francissen*
Community manager
BioSB Research School

*NEW V*isiting address (as of 1 July 2017): Jaarbeurs Innovation Mile
(JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht
*NEW **Postal address *(as of 1 July 2017): Postbus 8500 | 3503 RM Utrecht

E-mail: femke.francissen at biosb.nl
Mobile: +31 6 17 90 4888
Skype: femke.francissen
Website: www.biosb.nl
LinkedIn link <http://nl.linkedin.com/in/femkefrancissen>
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