iSimp: A Sentence Simplification System for Biomedical Text

54 Pages·2012·0.51 MB·English

iSimp: A Sentence Simplification System
for Biomedical Text
Yifan Peng, Catalina O. Tudor, Manabu Torii
Cathy H. Wu, and K. Vijay-Shanker
Computer & Information Sciences
University of Delaware
Oct 6, 2012
Outline
1 Introduction and motivation
2 iSimp: what to simplify, and how
3 Evaluation
4 Summary and future work
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
Complexity of sentences is a challenge
iSimp simplifies the text so that the existing text mining tools can
be improved
This topic is still new, though we are not the first one (Miwa,
2010; Jonnalagadda, 2010; Siddharthan, 2003)
Introduction
Lots of text mining applications are developed for biomedical text
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
iSimp simplifies the text so that the existing text mining tools can
be improved
This topic is still new, though we are not the first one (Miwa,
2010; Jonnalagadda, 2010; Siddharthan, 2003)
Introduction
Lots of text mining applications are developed for biomedical text
Complexity of sentences is a challenge
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
This topic is still new, though we are not the first one (Miwa,
2010; Jonnalagadda, 2010; Siddharthan, 2003)
Introduction
Lots of text mining applications are developed for biomedical text
Complexity of sentences is a challenge
iSimp simplifies the text so that the existing text mining tools can
be improved
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
Introduction
Lots of text mining applications are developed for biomedical text
Complexity of sentences is a challenge
iSimp simplifies the text so that the existing text mining tools can
be improved
This topic is still new, though we are not the first one (Miwa,
2010; Jonnalagadda, 2010; Siddharthan, 2003)
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
How do we extract relations?
• PKC phosphorylates GAP-43 on serine 41.
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
• It was suggested that Yak1 phosphorylates
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
Sentences
Crf1 to promote its nuclear entry.
Word ... ProteinA p✿h✿✿o✿s✿p✿✿h✿o✿r✿y✿l✿a✿t✿e✿s✿ ProteinB ...
Sequence
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
Design rules for all possible variations
There are TOO many variations
Improve deep representations of sentences
Parsers become error-prone for long and complex sentences
Parsers will be less efficient for long sentences
Simplify sentences to reduce variations
They are same because of subject – object relation
Three alternative ways
Raf-1 phosphorylates and activates MEK1 , which in turn
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
phosphorylates and activates the MAP kinases/extracellular
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
Sentence
signal regulated kinases, ERK1 and ERK2.
Word ... ProteinA p✿h✿✿o✿s✿p✿h✿o✿r✿y✿l✿a✿t✿e✿s ProteinB ...
Sequence
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
Design rules for all possible variations
There are TOO many variations
Improve deep representations of sentences
Parsers become error-prone for long and complex sentences
Parsers will be less efficient for long sentences
Simplify sentences to reduce variations
Three alternative ways
Raf-1 phosphorylates and activates MEK1 , which in turn
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
phosphorylates and activates the MAP kinases/extracellular
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
Sentence
signal regulated kinases, ERK1 and ERK2.
Word ... ProteinA p✿h✿✿o✿s✿p✿h✿o✿r✿y✿l✿a✿t✿e✿s ProteinB ...
Sequence
They are same because of subject – object relation
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text
Improve deep representations of sentences
Parsers become error-prone for long and complex sentences
Parsers will be less efficient for long sentences
Simplify sentences to reduce variations
Three alternative ways
Raf-1 phosphorylates and activates MEK1 , which in turn
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
phosphorylates and activates the MAP kinases/extracellular
✿✿✿✿✿✿✿✿✿✿✿✿✿✿✿
Sentence
signal regulated kinases, ERK1 and ERK2.
Word ... ProteinA p✿h✿✿o✿s✿p✿h✿o✿r✿y✿l✿a✿t✿e✿s ProteinB ...
Sequence
They are same because of subject – object relation
Design rules for all possible variations
There are TOO many variations
Yifan Peng, et. al. iSimp: A Sentence Simplification Systemfor Biomedical Text