Protein Word Detection Using Text Segmentation Techniques

Authors

Ashish V. Tendulkar, Google Inc., IndiaFollow
Sutanu Chakraborti, Department of CSE IIT Madras 600036, IndiaFollow
Ganesh Devi, Department of CSE IIT Madras 600036, IndiaFollow

Document Type

Article

Abstract

Literature in Molecular Biology is abundant with linguistic metaphors. There has 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 crucial 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 for the task of extracting "biological words” from protein sequences. We demonstrate the effectiveness of using domain knowledge to complement data-driven approaches in the text segmentation task, as well as in its biological counterpart. We also propose a novel extrinsic evaluation measure for protein words through protein family classification.

Recommended Citation

Tendulkar, Ashish V.; Chakraborti, Sutanu; and Devi, Ganesh (2025) "Protein Word Detection Using Text Segmentation Techniques," Journal of Global Awareness: Vol. 6: No. 1, Article 6.
Available at: https://scholar.stjohns.edu/jga/vol6/iss1/6