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Seminar: Applied Machine Learning: Annalisa Marsico

This document summarizes the goals and structure of a seminar on applied machine learning. The course aims to provide both soft skills like evaluating research papers and hard skills like learning machine learning methods and how to apply them to biological questions. Students will give presentations on papers they have read and evaluated. The instructor provides guidelines for compressing papers into concise summaries while retaining key information. Topics to be covered include feature selection, unsupervised learning, random forests, SVMs, neural networks, active learning, semi-supervised learning, and multi-task learning, with a focus on biological and bioinformatics applications.

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Shubha Shivaprakash
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55 views

Seminar: Applied Machine Learning: Annalisa Marsico

This document summarizes the goals and structure of a seminar on applied machine learning. The course aims to provide both soft skills like evaluating research papers and hard skills like learning machine learning methods and how to apply them to biological questions. Students will give presentations on papers they have read and evaluated. The instructor provides guidelines for compressing papers into concise summaries while retaining key information. Topics to be covered include feature selection, unsupervised learning, random forests, SVMs, neural networks, active learning, semi-supervised learning, and multi-task learning, with a focus on biological and bioinformatics applications.

Uploaded by

Shubha Shivaprakash
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Seminar: Applied Machine Learning

Annalisa Marsico
OWL RNA Bionformatics group
Max Planck Institute for Molecular Genetics
Free University of Berlin
SoSe 2015
Goals of this course - I

• Soft skills
– Learn how to evaluate a research paper
– Learn what makes a paper good
– Learn how to get your paper published
– Learn how to give a scientific talk
– Learn to be critical / evaluate
Goals of this course - II

• Hard skills
– Get an overview of the Methods in Machine
Learning field & the applications to
Biology/Bioinformatics
– Learn how basic concepts / algorithms/
statistical methods are applied and extended
in this field
– Learn how to ask the right biological question
and choose the right Machine Learning
method ‚to solve it‘
Course design
• Today -> overview on the topics, assignment of
papers
• Student presentations
– Each student will choose a paper and will give a
presentation
– Two presentations per term (30-40 minutes + 15
minutes questions)
– Discussion: questions, critical assessmnet
Presentation guidelines
Compression with minimal loss of information

1. Understand the context & data used


2. Identify the important question/motivation
3. Focus on the method
4. Summarize shortly the main findings
– Forget about unimportant details
5. Evaluate and think about possible future
directions
Advices / Help
• Read your paper twice before saying ‚I don‘t understand it‘

• Read the supplementary material

• Do not try to understand every detail but the general idea has to be
clear

• Main objective: lively interesting talk that promotes discussion

• Come anytime to me with questions (write me 3-4 days before)


[email protected]
Tel: +49 30 8413 1843
where: MPI for Molecular Genetics, Ihnestrasse 63-73, Room 1.3.07

• send me your presentation one week before your talk

• Get feedback and give feedback (also to me )


Practical information
Day First talk Second talk
April 16 Introduction Introduction
April 23 Girls‘ Day Girls‘ Day
April 30
May 07
May 14
May 21
May 28
June 04
June 11
June 18
June 25
July 07
July 09 backup backup
Link to the Seminar webpage

http://www.molgen.mpg.de/3415218/Seminar-Applied-Machine-Learning
Topics
General machine learning papers
1. Assessing the accuracy of prediction algorithms for classification: an overview
2. An introduction to ROC analysis
3. A Study of Cross-Validation and Bootstrap for Accuracy Estimation
and Model Selection

Feature selection
1. A review of feature selection techniques in bioinformatics
2. Novel unsupervised feature filtering of biological data
Topics
Unsupervised Learning (applications to Bioinformatics)
1. Cluster analysis of gene expression data: A Survey
2. Biclustering algorithms for Biological data analysis: A Survey

Random Forests (applications to Bioinformatics)


1. Simple decision rules for classifying human cancers from gene expression profiles
2. Prediction of protein - protein interactions using random decision forest framework
3. Detection and interpretation of expression quantitative trait loci (eQTL).
4. RFECS: A Random-Forest Based Algorithm for Enhancer Identification
from Chromatin State
Topics
Classification with Support Vector Machines (SVMs)
1. The spectrum kernel: A string Kernel for SVM protein classification
2. Kernel-based machine learning protocol for predicting DNA-binding proteins
3. A boosting approach for motif modeling using ChIP-chip data

Neural Networks and deep Learning


1. Gene prediction in metagenomic fragments: A large scale machine
learning approach
2. Beyond the ‘best’ match: machine learning annotation of protein sequences
by integration of different sources of information
3. Deep learning of the tissue-regulated splicing code
Topics
Active Learning (applications to Bioinformatics)
1. Predicting positive p53 cancer rescue regions using Most Informative
Positive (MIP) active learning
2. Active Learning with Support Vector Machine applied to Gene Expression
Data for Cancer Classification

Semi-supervised Learning (applications to Bioinformatics)


1. Semi-supervised learning improves gene expression-based prediction
of cancer recurrence
2. Matching experiments across species using expression values
and textual information

Multi-task Learning (applications to Bioinformatics)


1. Probabilistic multi-class multi-kernel learning: on protein fold recognition and
remote homology detection
2. Integrating sequence, expression and interaction data to determine
condition-specific miRNA regulation.

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