Sayali Alatkar, Computer Sciences graduate student, and Biostatistics and Medical Informatics professor Daifeng Wang (also CS affiliate) have had their paper accepted to ISMB/ECCB 2025 proceedings. ISMB is the annual international conference on Intelligent Systems for Molecular Biology and is the flagship meeting of the International Society for Computational Biology (ISCB). It is one of the top conferences in computational biology. ECCB is the European Conference on Computational Biology, which has joined forces with ISMB to become the largest bioinformatics and computational biology conference in the world. This is the first research paper from UW-Madison to be accepted to the ISMB/ECCB proceedings in several years.
Alatkar and Wang’s paper, ARTEMIS integrates autoencoders and Schrödinger Bridges to predict continuous dynamics of gene expression, cell population and perturbation from time-series single-cell data, details how they developed a machine learning model called ARTEMIS (trAjectory infeRence wiTh unbalancEd dynaMic optImal tranSport) to model how cells change over time during processes such as organ development and disease progression. Alatkar says, “ARTEMIS analyzes snapshots of gene expression from single cells to infer continuous cellular trajectories, estimate cell population changes, and identify potential genes that may influence these dynamic processes.”
The team applied their model to biological processes such as pancreatic development, cancer cell transitions, and embryogenesis, where it accurately predicted missing cell states, tracked changes in cell populations, and prioritized genes potentially driving cellular dynamics.
The conference, which will be the 33rd for ISMB and the 24th for EECB, will be held in July in Liverpool, UK. The principal focus of the joint ISMB/ECCB conference is on the development and application of advanced computational methods to address biological problems, and brings together researchers from computer science, bioinformatics, computational biology, molecular biology, mathematics, statistics, and related fields. “I’m looking forward to presenting our work at ISMB,” says Alatkar. “It’s a great opportunity to share our research and connect with others in the field.”
Congratulations to Alatkar and Wang!