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27.03.2017: Machine Learning Coffee seminar "Learning to Rank: Applications to Bioinformatics"

27.03.2017 09:15–10:00

HIIT seminar

Exactum D123, Kumpula

Hiroshi Mamitsuka
 

Learning to Rank: Applications to Bioinformatics


Abstract: Learning To Rank (LTR) has been developed in information retrieval for ranking documents regarding the relevance to a given query. Typically LTR builds a ranking model from given relevant (or irrelevant) query-document pairs. Generally, in some respect, LTR can be thought as an attempt to solve a multilabel classification problem, where queries are labels. A lot of settings in bioinformatics can be turned into multilabel classification problems having relatively similar properties. One typical example is biomedical document annotation. Currently PubMed, a database of 26 million biomedical citations, has around 30,000 keywords, called MeSH (Medical Subject Headings) terms, i.e. labels in multilabel classification, where the number of articles per MeSH term is extremely diverse, ranging from only 20 to more than eight million. This large, biased dataset already goes beyond the general sense of settings expected by regular multilabel classifiers. In this talk, I will start with introduction and a brief review of LTR. I then raise three bioinformatics multilabel classification problems that share real data-derived, practical properties, which hamper the application of regular multilabel classifiers. Finally I will show that LTR nicely addresses such large-scale, challenging bioinformatics multilabel classification problems.

 
A large portion of this talk appeared in ISMB in 2015 and 2016.
 
Machine Learning Coffee seminars are weekly seminars held jointly by the Aalto University and the University of Helsinki. The seminars aim to gather people from different fields of science with interest in machine learning. Seminars will be held on Mondays at 9 am at Aalto University and the University of Helsinki every other week. At Aalto University, talks will be held in Konemiehentie 2, seminar room T5 and at the University of Helsinki in Kumpula, seminar room D123, unless otherwise noted. Talks will begin at 9:15 am and porridge and coffee will be served from 9:00 am.
 
Following talks:
April 3, Otaniemi: Mikko Kivelä: Multilayer networks
April 10th, Kumpula: Markus Heinonen, Spectral Kernels
April 17th, *no talk* (Easter break) 
 
Welcome!