Sentence Filtering for Information Extraction in Genomics, a Classification Problem
PKDD '01 Proceedings of the 5th European Conference on Principles of Data Mining and Knowledge Discovery
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ACM SIGKDD Explorations Newsletter
Beyond the bag of words: a text representation for sentence selection
AI'06 Proceedings of the 19th international conference on Advances in Artificial Intelligence: Canadian Society for Computational Studies of Intelligence
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The Bacteria Gene Renaming (RENAME) task is a supporting task in the BioNLP Shared Task 2011 (BioNLP-ST'11). The task consists in extracting gene renaming acts and gene synonymy reminders in scientific texts about bacteria. In this paper, we present in details our method in three main steps: 1) the document segmentation into sentences, 2) the removal of the sentences exempt of renaming act (false positives) using both a gene nomenclature and supervised machine learning (feature selection and SVM), 3) the linking of gene names by the target renaming relation in each sentence. Our system ranked third at the official test with 64.4% of F-measure. We also present here an effective post-competition improvement: the representation as SVM features of regular expressions that detect combinations of trigger words. This increases the F-measure to 73.1%.