Our preprint on STARLING - a new method for clustering highly multiplexed imaging data while accounting for segmentation errors - is now up on bioRxiv along with a corresponding twitter thread.

Congratulations to Hassaan, Michael, and Chengxin whose paper understanding the impacts of dataset imbalanced on single-cell data integration is now published in Nature Biotechnology.

Congratulations to Michael and Sean whose work understanding the impact of active and self-supervised learning on efficient annotation of single-cell expression data has been published in Nature Communications.

Welcome to Sarah Asbury who joins as a graduate student developing methods to map T cell exhaustion from multi-modal data.

Congratulations to Cindy and Alina for their new preprint on automated machine learning for scRNA-seq analysis!.

Congratulations to Shanza for being awarded a 3 year Canada Graduate Scholarships — Doctoral award and to Michael for being awarded a TFRI MOHCCN Data Science fellowship.

Congratulations to Alina who's work published in TMLR has been accepted in the journal track of the 2023 AutoML conference.

Welcome to Haifen Chen and Kevin Sun who join as a Research Associate and NSERC summer student respectively. Haifen will be working on a range of collaborations around single-cell and spatial omics, and Kevin will be working on methods development for learning cell representations from highly-multiplexed imaging data.

Kieran will be presenting at AACR 2023 in Orlando, Florida at the “Multiplexed Imaging: Ready for Prime Time?” educational session.

Congratulations to Alina Selega whose paper on Multi-objective Bayesian optimization of heuristic objectives has been accepted to Transactions on Machine Learning Research (TMLR). You can read the paper here.

We have a new preprint on Multi-Objective Bayesian Optimization methods over heuristic objectives with applications in genomics. Check out the paper and the tweetorial.

• Cindy Fang will be presenting our work on predicting what pipeline is best to analyze a scRNA-seq dataset at Bioc 2022.
• Jett Lee will be presenting our work on segmentation error aware clustering for highly multiplexed imaging at the MLSCB COSI at ISMB 2022.
• Kieran is presenting at the Stanford Computational and Systems Immunology Seminar on August 2nd.

Chengxin Yu will be in San Diego at RECOMB 22 and the CCB satellite to present our work on using single-cell counterfactuals to dynamically evaluate the accuracy of bulk RNA-seq deconvolution methods.

We are looking for an undergraduate student researcher to join us for a summer internship to build classification models of YAP-dependent cancer subtypes via the University of Toronto Data Science Institute SUDS program. Please see here for details and eligibility, our project is entitled AI classification of cancer patients into novel YAP-dependent subtypes. The deadline to apply is February 7th and applications may be submitted here.

Welcome to Darren Chan who joins as a PhD student jointly supervised by Hartland Jackson.

A big welcome to Morris Greenberg who joins as a PhD student in statistical sciences co-supervised with Radu Craiu and Eunice Poon who joins for the term as an undergraduate co-op student.

Our work on automated cell type assignment for highly multiplexed imaging data has been published in Cell Systems. Congratulations to Michael, Jinyu, Sunyun, and Shanza.

Congratulations to Cait and Chengxin on receiving Ontario Graduate Scholarships and to Shanza for receiving a OSOTF award!

Welcome to Benjamin Zheng and Sean Gong who join the lab as an Amgen scholar and for BCB 330 projects respectively.

Congratulations to Alina Selega who has been selected for the 2021 Vector Institute Postgraduate Affiliate Program.

We have been awarded a 5 year CIHR project grant (with Hartland Jackson and Daniel Schramek) to use computational and experimental approaches to understand immune escape in pancreatic cancers. Congratulations all!

Welcome to Alina Selega who joins as a postdoctoral fellow to work on AutoML approaches for biomedical data analysis.

Kieran is speaking at the Stanford Center for Biomedical Informatics Research Colloquium on January 21st.

Joanne Leung has been awarded an AAI Intersect Fellowship. Congratulations!

Kieran has been awarded a 5 year Canada Research Chair in Machine Learning for Translational Biomedicine from CIHR.

Congratulations to Michael Geuenich who will be staying on in the lab to complete his PhD working on machine learning models for cancer genomics.

Welcome to Shanza Ayub and Chengxin Yu who join as PhD students in the Computational Biology in Molecular Genetcs (CBMG) program, and to Aisha Faruqui and Cindy Fang who join as undergraduate research students for 2020-2021!

We have been awarded a 5 year NSERC Discovery grant Accelerating biological discovery with automated machine learning for single-cell data analysis to develop and apply AutoML methods in the field of single-cell data analysis.

Welcome Sunyun Lee who is a 3rd year Toronto Computer Science student, who joins the lab having won an NSERC Undergraduate Student Research Award!

Welcome Michael Geuenich who joins the lab as a summer student before continuing his PhD in Molecular Genetics here in Toronto.

Our review paper Computational modelling in single-cell cancer genomics: methods and future directions is now online as a preprint.

We are pleased to host the second workshop on single-cell cancer genomics (SCANGEN) at ISMB2020. Abstract submission is open until June 5th.

Welcome Jinyu Hou who is a UofT CS student and joins the lab for a summer project in machine learning modelling of spatial proteomics data.