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Protein Word Detection using Text Segmentation Techniques

G. Devi
Sutanu Chakraborti
BioNLP 2017, Vancouver, Canada, August 4, 2017, Association for Computational Linguistics, pp. 238-246 (to appear)


Literature in Molecular Biology is abundant with linguistic metaphors. In particular, there have been works in the past that attempt to draw parallels between linguistics and biology, driven by the fundamental premise that proteins have a language of their own. Since word detection is fundamental to the decipherment of any unknown language, we attempt to establish a problem mapping from natural language text to protein sequences at the level of words. Towards this end, we explore the use of an unsupervised text segmentation algorithm to the task of extracting ”biological words” from protein sequences. We also demonstrate the effectiveness of using domain knowledge to complement data driven approaches in the text segmentation task, as well as in its biological counterpart.