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Today, let’s remember Allen Newell, who was born on this day in 1927. Newell received the #ACMTuringAward in 1975 with co-recipient Herbert A. Simon for making basic contributions to #AI, the psychology of human cognition, and list processing. youtu.be/vpfAOBbtGTo

CMU Carnival never gets old. The weather is not great but the energy is unmistakable. Carnegie Mellon University

Honored to receive the Allen Newell Award for Research Excellence CMU School of Computer Science. Newell’s approach to research- tackling real-world problems with precision, meaningful impact, and a commitment to excellence - has been a hallmark of Carnegie Mellon University. Truly grateful for this recognition

Integrating spatial transcriptomics across platforms is hard - different gene panels, sparse data. We introduce LLOKI, using optimal transport + single-cell FMs for unified ST integration. Work led by Ellie Haber (Machine Learning Dept. at Carnegie Mellon) & Lane Fellow Spencer Krieger biorxiv.org/content/10.110…

Cellular interactions span scales and shape cell states & tissue function. We introduce STEAMBOAT, a multiscale attention model for spatial omics that reveals how cells interact - from local contact to long-range signals. Led by Lane Fellow Shaoheng Liang. biorxiv.org/content/10.110…

STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues biorxiv.org/content/10.110…

Enjoyed giving a guest lecture today at MIT for the course “Generative AI for Biology”. This fall at CMU CMU School of Computer Science, I will be launching a similar course with my colleague Lei Li: Generative AI for Biomedicine (02541 / 02741 / 11481 / 11781).

I like big classrooms and even brighter shoes

Final version of our paper eLife - the journal (led by Andrew Belmont): Major nuclear locales define nuclear genome organization and function beyond A and B compartments. elifesciences.org/articles/99116

Had a wonderful time in Seoul for #RECOMB2025 RECOMB Conference Series. Proud of Shaoheng Liang and Ellie Haber from my group — both delivered fantastic presentation !

I got an email that started with "Hi Dr. Massachusetts." For the record, my last name is indeed Ma - not that MA.

The short talk and scholarship deadlines for the Keystone Symposia AI in Molecular Biology meeting in September are coming up fast, May 20th. Looking forward to seeing the submissions! keystonesymposia.org/conferences/co…

We introduce #POPARI, an interpretable, spatially-aware factor-based model for multi-sample #spatialtranscriptomics. Huge kudos to Shahul Alam for his incredible effort (yes, 80+ equations!). In collaboration with Sophia Liu and Fei Chen Lab. biorxiv.org/content/10.110…

Enjoyed #CZBiohubCHI Scientific Advisory Board meeting. Incredible science happening under the leadership of Shana Kelley Chan Zuckerberg Biohub Network - where tech, biology, and AI are being catalyzed under one roof. Photo credit: Ankur Singh

We introduce EYKTHYR, a computational method that integrates gene expression and chromatin accessibility in a spatially aware model to identify transcription factors shaping spatial gene programs. Led by Lane Fellow Spencer Krieger #spatialtranscriptomics biorxiv.org/content/10.110…