Aqib Hasnain

Aqib Hasnain

PhD Candidate in Mechanical Engineering

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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

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A computational understanding of Uniform Manifold Approximation and Projection (UMAP)

18 minute read

Published:

Uniform Manifold Approximation and Projection (UMAP) is a nonlinear dimensionality reduction technique developed by McIness et al. in 2018. Though its use is often called into question in the biological sciences, it has become a key visualization tool for many computational biologists wanting to tease apart important differences between cellular transcription or genetic profiles. While UMAP has been widely adopted as the state-of-the-art in nonlinear dimensionality reduction, it is often poorly understood by its users, leading to its misuse. The difficulty in understanding UMAP is in part due to the tremendous effort by the original authors in exposing mathematical ideas that ground UMAP as the first graph-based approach with theoretical understanding of its functionality. The authors use ideas from Riemannian geometry and algebraic topology to construct the theoretical framework on which UMAP is built. It is then good news that UMAP can be thoroughly understood from an entirely computational perspective.

Metric spaces of microbial essential gene landscapes

18 minute read

Published:

Essential genes are those which are crucial for survival of an organism in a given context. This post will introduce manifold and metric learning to characterize and classify essential genes from the chaos game representation of a genetic sequence.

portfolio

publications

talks

teaching

Thermosciences I, II, III – Teaching assistant

Course, UC Santa Barbara, Department of Mechanical Engineering, 2017

TA’d for the three quarter-series of courses on thermodynamics and heat transfer. Main responsibilities were answering student’s questions, hosting office hours, and grading. I was also responsible for delivering two lectures, the first on thermodynamic lookup tables and how to perform single and double interpolation, and the second on radiative heat transfer analysis using view factors.

Biological Control – Teaching assistant

Course, UC Santa Barbara, Department of Mechanical Engineering, 2020

This course taught dynamical systems analysis of biological systems and design of synthetic biological circuits to both graduate and undergraduate students. Main responsibilities were answering student’s questions, hosting office hours, and grading. I was also responsible for delivering two lectures on recently developed techniques for gene regulatory network reconstruction e.g. dynamic mode decomposition.