Master’s Thesis at the College of Information Technology Explores the Use of Augmented Random Search for Multiple Sequence Alignment

Duhaa Fadill Abbas
The Department of Software at the College of Information Technology – University of Babylon hosted the defense of a master’s thesis by student Buraq Ghassan Hamza, entitled “Using Augmented Random Search For Multiple Sequence Alignment”, under the supervision of Dr. Muhannad Mohammed Jassim. The defense took place at 9:00 a.m. on Thursday, August 28, 2025, in the College’s Conference Hall.

The thesis focused on the significance of Multiple Sequence Alignment (MSA) and its vital role in computational biology, including phylogenetic analysis, structural biology, and genome characterization. Accurate alignment of biological sequences is essential for identifying conserved regions, understanding functional relationships, and inferring evolutionary history.

The researcher highlighted that traditional sequence alignment methods, despite their wide adoption, face limitations in efficiency and scalability, particularly when applied to large or complex datasets. To address these challenges, the study proposed the adoption of the Augmented Random Search (ARS) algorithm—a reinforcement learning-based approach characterized by its simplicity and effectiveness in high-dimensional optimization tasks.

In this research, the MSA task was formulated as a “black-box” optimization problem, where the system explores the alignment space by introducing random modifications and evaluating their quality using standard metrics such as the Sum-of-Pairs (SP) score and the Column Score (CS), both of which are scientifically recognized measures for assessing alignment accuracy and biological relevance.