We welcome you to CDS-KIAC talk on 05 August 2024 (Monday). The details are as below:
Speaker: Dr. Kumaresh, post doctoral researcher, Eddy Lab at Harvard University.
Title: “Protein Sequence Annotation using Language Models”
Date and Time: August 05, 2024, 3:30 PM
Venue: #421, SERC Auditorium
Abstract:
Protein function inference relies on annotating protein domains via sequence similarity, often modeled through profile Hidden Markov Models (profile HMMs), which capture evolutionary diversity within related domains. However, profile HMMs make strong simplifying independence assumptions when modeling residues in a sequence. Here, we introduce PSALM (Protein Sequence Annotation with Language Models), a hierarchical approach that relaxes these assumptions and uses representations of protein sequences learned by protein language models to enable high-sensitivity, high-specificity residue-level protein sequence annotation. We validate PSALM’s performance on a curated set of “ground truth” annotations determined by a profile HMM-based method and highlight PSALM as a promising alternative for protein sequence annotation.
Bio of Speaker:
Kumaresh is a post doctoral researcher in the Eddy Lab at Harvard University working on machine learning models for annotating, understanding and analyzing protein sequences. He has a PhD from Harvard University where he worked in systems neuroscience, building models of decision making and attentional switching using zebrafish as a model organism. Kumaresh’s undergraduate and Masters training is in Computer Science and Electrical Engineering from IIIT Bangalore and he brings this strong computational background to tackle complex real world biological problems.
ALL ARE WELCOME
