Understanding the Language of Life: Identifying and Characterizing the Language Units in Protein Sequences

ongoing

"Proteins play a key role in biological processes that govern and maintain life. Although they are three-dimensional entities, they can be represented in textual form as sequences of amino acids that largely determine their structures and functions. By analogy with natural (human) languages, we can consider proteins as written with a language, which we refer to in this proposal as the ""language of life"". Natural languages can be read and understood by humans. However, we cannot yet understand the language of life. We do not even know what the vocabulary is, i.e., what the basic language units are (analogous to words in human languages). Textual representation of proteins has enabled the application of natural language processing (NLP) techniques to the study of proteins, and breakthrough results have been achieved in various downstream tasks such as protein structure prediction. However, these efforts remain only at the ""processing level"" of the language of life. The main goal of this project is to go beyond the level of language processing and open new research horizons for understanding the language of life. Using my expertise in NLP and bioinformatics, I will pursue the following objectives: (i) develop innovative methods to determine the language units (i.e., the vocabulary) of the language of life; (ii) identify the characteristics of this language as well as its variability among species; (iii) develop novel methods to identify and characterize the functions of the language units. This research will lay the foundation for a new field of research, molecular language understanding, which aims to develop methods for understanding the messages encoded in molecular sequences. The ultimate goal of this project is to decipher the language of life, which will lead to groundbreaking consequences for understanding life and health, and will shed light to the development of novel prevention, diagnosis, and treatment strategies for diseases."