Optimal Transport Materials

A compilation of notes, slides, and code on the topic of optimal transport.

Background and Overview

For a comprehensive summary of the background of Optimal Transport (OT) and its applications in computational biology, refer to the following Nature article:

• Optimal transport for single-cell and spatial omics

Specialized Applications in Computational Biology

For more specialized applications of OT in computational biology, consider the following articles:

• Optimal transport improves cell–cell similarity inference in single-cell omics data

• Learning single-cell perturbation responses using neural optimal transport

• Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition

• Optimal Transport for Latent Integration with An Application to Heterogeneous Neuronal Activity Data

• Mapping cells through time and space with moscot

These resources provide in-depth insights into specific applications of OT in various areas of computational biology.

Books on Optimal Transport

For a deeper understanding of the background, mathematics, and computational aspects of OT, the following books are highly recommended:

• Computational Optimal Transport
  • This book provides a comprehensive introduction to the computational aspects of OT, including algorithms and applications.
• Optimal Transport for Applied Mathematicians
  • This book offers a rigorous mathematical treatment of OT theory, suitable for researchers in related fields.

These books serve as excellent resources for those looking to deepen their understanding of the theoretical foundations and practical implementations of OT.