Michael He, Ph.D., BPharm (Hons)

**Is single-cell data integration a solved problem? ** Lots of great methods, but still not quite yet! Specifically, Check Dataset Imbalance! 🎉 Excited to announce that our study on dataset imbalances in single-cell analysis just hit Nature Biotechnology (@NatureBiotech)! 🎉 Dive into our paper titled "Characterizing the impacts of dataset imbalance on single-cell data integration" here: nature.com/articles/s41587-0… 🔬 We've thoroughly assessed how dataset imbalances can twist the results of single-cell integration and batch-correction, affecting everything from cell-type classification to differential expression. Our work doesn't just highlight the issue; it offers solid solutions! 🧩 Starting with balanced PBMC data, we uncovered how changing cell-type balance disrupts integration results. But, when we cluster similar cell-types hierarchically, the magic happens – stability is dramatically improved! 📊 We didn't stop there. Our research extends to how these imbalances influence crucial downstream analyses. The impact? Statistically significant changes that could sway biological conclusions. 🛠️ To empower researchers, we've developed a suite of guidelines and introduced innovative balanced clustering metrics. Our tools are designed to navigate the tricky waters of dataset imbalance, ensuring accurate, meaningful results. Check out our full tutorial: github.com/hsmaan/Iniquitate… 🧬 And, for a cherry on top, we've redefined benchmarking standards with new metrics that ensure fair and nuanced interpretation of integration results. Future benchmarking, we've got you covered! Explore our balanced clustering package: github.com/hsmaan/balanced-c… 🔧 Our comprehensive toolkit, including code, data, and detailed documentation, is now fully open-source! We're setting new standards for method development and benchmarking in single-cell integration, with an eye on the broader horizon of representation learning. Get all the goodies here: github.com/hsmaan/Iniquitate Huge congratulations to all the authors, especially the first author, Hassaan Maan, a PhD student I co-supervise with @kieranrcampbell, who almost single-handedly led this project! @UHN @MBPatUofT @VectorInst @UofTCompSci @UofT_LMP @pmcc_ai @UHNAIHUB