Doctor of Philosophy in

Course description: This course provides a broad overview of bioinformatics for single cell omics technologies, a new and fast-growing family of biological assays that enables measuring the molecular contents of individual cells with very high resolution and is key to advancing precision medicine. The course starts with an accessible introduction to basic molecular biology: the cell structure, the central dogma of molecular biology, the flow of biological information in the cell, the different types of molecules in the cell, and how we can measure them. This course then introduces students to the diverse landscape of biological data, including its types and characteristics and explores the foundational principles of single-cell omics bioinformatics, encompassing key methodologies, tools, and computational workflows, with an emphasis on the development of foundation models for single cell omics data.

Course description: This interdisciplinary course is designed for students and professionals with a background in machine learning who seek to understand the fundamentals of molecular biology. The course explores key biological concepts and their applications to machine learning, particularly in the fields of bioinformatics, genomics, and computational biology. By bridging the gap between molecular biology and machine learning, students will gain the knowledge to apply machine learning techniques to biological data and solve complex problems in medicine, genetics, and drug discovery.

Course description: Computational biology has become an important discipline in the intersection of computing, mathematics, biology and medicine. Biological data sets produced by modern biotechnologies are large and hence they can only be understood by using mathematical modeling and computational techniques. Starting from analysis of genetic sequences, the field has progressed towards analysis and modeling of entire biological systems. A way of abstracting the vast amount of biomedical information is by modeling and analyzing these data by using networks (or graphs). Such approaches have been used to model phenomena in other research domains, apart from computational and systems biology and medicine.

Course description: This interdisciplinary graduate course introduces students to the core concepts, tools, and emerging methods in computational genomics and epigenomics. It is designed for students from biology, computer science, machine learning, and related fields who are interested in applying their skills to cutting-edge questions in biology and medicine. Students will explore how genomic and epigenomic data, such as DNA, RNA, chromatin accessibility, and methylation, are generated and analyzed using statistical and machine learning techniques. The course covers foundational topics such as genome organization, gene regulation, and high-throughput sequencing technologies. It extends to advanced applications including multi-omic data integration, deep learning for genomics, and cancer omics.
Course description: This course examines the intersection of artificial intelligence (AI) and computer systems, focusing on how systems enable efficient AI workloads and how AI techniques enhance system performance. The course covers fundamental principles and emerging trends in system design, hardware-software co-design, resource management, and AI-driven system optimization. Through lectures, hands-on labs, and research projects, students will explore techniques for scaling AI applications, improving system efficiency, and integrating AI into traditional computing environments. By engaging with real-world case studies and cutting-edge frameworks, students will develop the skills needed to contribute to the rapidly evolving field of AI systems in both academia and industry. 

This course provides the students a comprehensive introduction to artificial intelligence. It builds upon fundamental concepts in machine learning. Students will learn about supervised and unsupervised learning, various learning algorithms, and the basics of the neural network, deep learning, and reinforcement learning.

This course provides a comprehensive overview of different concepts and methods related to deep learning. Students will first learn the foundations of deep learning, after which they will be introduced to a series of deep models: convolutional neural networks, autoencoders, recurrent neural network, and deep generative models. Students will work on case studies of deep learning in different fields such as computer vision, medical imaging, natural language processing, etc.

This course provides a comprehensive introduction to the basics of human visual system and color perception, image acquisition and processing, linear and nonlinear image filtering, image features description and extraction, classification, and segmentation strategies. Moreover, students will be introduced to quality assessment methodologies for computer vision and image processing algorithms.
Prerequisite courses:  CS7101 Algorithms and Data Structures 

Course description: This course discusses the advanced concepts in operating system design and implementation. The operating system provides a convenient and efficient interface between user programs and the hardware of the computer on which they run. 

The course provides a comprehensive introduction to the concepts, principles and methods of geometry-aware computer vision which helps in describing the shape and structure of the world. In particular, the objective of the course is to introduce the formal tools and techniques that are necessary for estimating depth, motion, disparity, volume, pose and shapes in 3D scenes.

This course provides a comprehensive overview of different concepts and methods related to visual object recognition and detection. In particular, the students will learn a large family of successful and recent state-of-the-art architectures of deep neural networks to solve the tasks of visual recognition, detection, and tracking.

This course is an introductory course on data mining, which is the process of discovering patterns in large data sets involving methods at the intersection of machine learning, statistics, and database systems.
Course description: This course provides an overview of foundational principles and contemporary topics in information security. Students will examine system protection strategies, structural security frameworks, software resilience, and detection of security threats. The course integrates theoretical concepts with practical applications to enhance the understanding of securing complex information systems. 

This course is an introductory course on big data processing, which is the process of analyzing and utilizing big data. The course involves methods at the intersection of parallel computing, machine learning, statistics, database systems, etc.

This course is an introductory course on Information Retrieval (IR). The explosive growth of available digital information (e.g., Web pages, emails, news, Tweets, Wikipedia pages) demands intelligent information agents that can sift through all available information and find out the most valuable and relevant information. Web search engines, such as Google and Bing, are several examples of such tools. This course studies the basic principles and practical algorithms used for information retrieval and text mining. It will cover algorithms, design, and implementation of modern information retrieval systems. Topics include: retrieval system design and implementation, text analysis techniques, retrieval models (e.g., Boolean, vector space, probabilistic, and learning-based methods), search evaluation, retrieval feedback, search log mining, and applications in web information management.

This course covers the fundamentals of theoretical statistics, which are the foundation for the analysis of the properties of machine learning algorithms. Covered topics include statistical models, statistical inference, maximum likelihood estimation, optimal hypothesis testing, decision theory and Bayesian inference, non-parametric statistics, and Bootstrap, (generalized) linear model and high dimensional statistics. All necessary tools from Probability theory: deviation inequalities, type of convergence, law of large numbers, central limit theorem, properties of the Gaussian distribution (etc) will be introduced whenever needed and their proofs given at the end of each chapter.

This course provides a graduate-level introduction to the principles and methods of medical imaging, with thorough grounding in the physics of the imaging problems. This course covers the fundamentals of X-ray, CT, MRI, ultrasound, and PET imaging. In addition, the course provides an overview of 3D geometry of medical images and a few classical problems in medical images analysis including classification, segmentation, registration, quantification, reconstruction and radiomics.

Assumed knowledge: Basic concepts in linear algebra, calculus, probability, and statistics. Programming in Python or similar language. 

Course description: This course provides a comprehensive introduction to natural language processing (NLP). It builds upon fundamental concepts in mathematics, specifically probability and statistics, linear algebra, and calculus, and assumes familiarity with programming. 

This course provides a comprehensive introduction to machine learning. It builds upon fundamental concepts in mathematics, specifically probability and statistics, linear algebra, and calculus. Students will learn about supervised and unsupervised learning, various learning algorithms, and basics of learning theory, graphical models, and reinforcement learning.

Course description: Master’s thesis research exposes students to an unsolved research problem, where they are required to propose new solutions and contribute towards the body of knowledge. Students pursue an independent research study, under the guidance of a supervisory panel, for a period of one (1) year. Master’s thesis research helps train graduates to pursue more advanced research in their Ph.D. degree. Further, it enables graduates to independently pursue an industrial project involving research component independently.

Assumed knowledge: Prior to undertaking an internship, students must have successfully completed 24 credit hours. 

Course description: The MBZUAI Internship (up to six weeks) with industry is intended to provide the student with hands-on experience, blending practical experiences with academic learning.