Eric and Wendy Schmidt Center

🍀 Happy St. Patrick’s Day! You’re in luck today – we have a great MIA meeting lined up for this Wednesday, March 19, featuring Andrew White and Sam Cox, both from FutureHouse and University of Rochester. 📅 March 19 💬 Andrew White 🏫 FutureHouse, University of Rochester 💡 9 am: A progress report on the automation of science 💬 Sam Cox 🏫 FutureHouse, University of Rochester 💡 10 am: Automating chemistry with LLM-based agents 🗓️ Add to your calendar: https://lnkd.in/eANtKa5u Both talks will be in person at the Broad (Acadia, M1) and broadcast over Zoom. If you do not have a Broad badge, please arrive at the 75 Ames St. entrance 10 minutes early with an ID to check in with security. We will escort folks up at 8:55 and 9:55 am; please email mia-team@broadinstitute.org if you arrive outside of these times. Broad Institute of MIT and Harvard #UniversityofRochester #FutureHouse #SchmidtCenter #ModelsInferenceAlgorithms #MIA #AndrewWhite #SamCox 🧑🏫 Read the abstracts: broad.io/MIA 💌 Join our mailing list for updates and Zoom links: bit.ly/MIACast 📺 Watch previous talks: broad.io/MIAPlaylist  🗓️ View our calendar: broad.io/ewsc-calendar

Traditionally, models of neural circuit development proposed two phases: genetically-driven neural wiring, followed by environmentally driven pruning and refinement. But this is inconsistent with certain innate behaviors; many animals, for example, are capable of complex problem solving just after birth. In a perspective piece, Dániel Barabási, André Ferreira Castro (University of Cambridge), and Florian Engert (Harvard University) propose a new three-system model for neural circuit formation. In the first system, development patterns neural circuits, defining innate understanding. In the second, “Eureka” learning events rapidly update existing knowledge. In the third, synapses are perpetually fine-tuned. #BroadInstitute #Science #ScienceNews #Research #ScientificResearch

For our next MIA meeting this Wednesday, March 12, we look forward to hosting Rishwanth Raghu and Dr. Ellen Zhong, both from Princeton University, who will talk about deep learning methods for reconstruction of structural landscapes from cryoEM and cryoET images. 📅 Wednesday, March 12, 2025 📍Acadia (75 Ames St, M1) and virtually 💬 Rishwanth Raghu 🏫 Ph.D. student, Princeton University’s Department of Computer Science 💡 Primer, 9 am: Heterogeneous reconstruction in cryo-EM 💬 Ellen Zhong 🏫 Assistant Professor, Princeton University’s Department of Computer Science 💡 Seminar, 10 am: Machine learning for visualizing structural landscapes inside the cell 🧑🏫 Abstracts: broad.io/MIA 💌 Mailing list: bit.ly/MIACast 📺 Previous talks: broad.io/MIAPlaylist  🗓️ Calendar of events: broad.io/ewsc-calendar Both talks will be in person at the Broad (Acadia, M1) and broadcast over Zoom. If you do not have a Broad badge, please arrive at the 75 Ames St. entrance 10 minutes early with an ID to check in with security. We will escort folks up at 8:55 and 9:55 am; please email mia-team@broadinstitute.org if you arrive outside of these times. Broad Institute of MIT and Harvard, Eric and Wendy Schmidt Center, Princeton Computer Science #SchmidtCenter #ModelsInferenceAlgorithms #MIA #RishwanthRaghu #EllenZhong

I feel very excited -- and proud -- to be giving a talk at this conference!

⚡ News “flash” – we have a great lineup of speakers for tomorrow’s MIA flash talks, featuring two Eric and Wendy Schmidt Center postdoctoral fellows. See you tomorrow! 📅 Wednesday, March 5 📍Acadia (75 Ames St, M1) and virtually 9:00 am 💬 Isabella Boyle 🏫 Senior Computational Associate, Cancer Data Science, Broad Institute 💡 GeneTEA: gene-term enrichment with natural language processing 💬 Pia Francesca Rissom 🏫 Visiting Scholar, Iqbal Lab | Ladders 2 Cures Accelerator, Broad Institute 💡 Comparing protein language models through embedding space comparison 💬 Viktoria Schuster 🏫 Postdoctoral Fellow, Eric and Wendy Schmidt Center, Broad Institute 💡 Interpreting gene expression models with sparse autoencoders 10:00 am 💬 Phillip Nicol 🏫 Ph.D. student, Irizarry Lab, Harvard School of Public Health 💡 Identifying spatially variable genes by projecting to morphologically relevant coordinates 💬 Uthsav Chitra 🏫 Postdoctoral Fellow, Eric and Wendy Schmidt Center, Broad Institute 💡 Mapping the topography of spatial gene expression with interpretable deep learning 💬 Barış Ekim 🏫 Ph.D. student, Berger Lab, MIT and Popic Lab, Broad Institute 💡 Minimizer-space computation in genomics 🧑🏫 See the full MIA schedule and learn more at broad.io/MIA. The flash talks will be in person at the Broad (Acadia, M1) and broadcast over Zoom. If you do not have a Broad badge, please arrive at the 75 Ames St. entrance 10 minutes early with an ID to check in with security. We will escort folks up at 8:55 and 9:55 am; please email mia-team@broadinstitute.org if you arrive outside of these times. Broad Institute of MIT and Harvard #SchmidtCenter #ModelsInferenceAlgorithms #MIA #IsabellaBoyle #PhillipNicol #FrancescaRissom #UthsavChitra #VikiSchuster #BarisEkim #CancerDataScience #IqbalLab #L2C #IrizarryLab #HarvardSchoolPublicHealth #BergerLab #MIT #PopicLab

🧠✨ Congratulations to Eric and Wendy Schmidt Center postdoctoral fellow Dániel Barabási on his recent first-author paper in Nature Reviews Neuroscience, co-authored by Florian Engert and André Ferreira Castro! His work introduces a new framework for neural circuit formation, integrating genetics, development, plasticity, and learning. Challenging conventional views that prioritize learning and plasticity, this perspective proposes three distinct systems that guide circuit assembly – from genetically driven development to single-shot learning and continuous recalibration. 🔍 Learn more about how this perspective reshapes our understanding of brain adaptability: https://lnkd.in/emw3nb6y 📖 Read the full paper: https://lnkd.in/ef8hSbH5 Broad Institute of MIT and Harvard #SchmidtCenter #BroadInstitute #HarvardMCB #DanielBarabasi #BrainResearch #AIandBiology #ComputationalResearch #ScienceResearch #NatureReviewsNeuroscience

MIA update – next week (Wednesday, February 26), we’re excited to welcome Robert Patro and Noor Pratap Singh, both from the University of Maryland’s Department of Computer Science and Center for Bioinformatics and Computational Biology. 📅 Wednesday, February 26 📍Acadia (75 Ames St, M1) and virtually 💬 Rob Patro 💡 Primer, 9 am: Counting is not easy: Assessing and quantifying uncertainty in abundance inferences from high-throughput sequencing data 💬 Noor Pratap Singh 💡 Seminar, 10 am: Uncertainty-aware analysis of RNA-Seq data using a tree-based framework 🧑🏫 Abstracts: broad.io/MIA 💌 Mailing list: bit.ly/MIACast 📺 Previous talks: broad.io/MIAPlaylist  🗓️ Calendar of events: broad.io/ewsc-calendar Both talks will be in person at the Broad (Acadia, M1) and broadcast over Zoom. If you do not have a Broad badge, please arrive at the 75 Ames St. entrance 10 minutes early with an ID to check in with security. We will escort folks up at 8:55 and 9:55 am; please email mia-team@broadinstitute.org if you arrive outside of these times. Broad Institute of MIT and Harvard, Department of Computer Science, UMD #SchmidtCenter #ModelsInferenceAlgorithms #MIA #RobPatro #NoorPratapSingh

In a new study published in Nature Communications, Eric and Wendy Schmidt Center’s Hannah Schlueter and Director Caroline Uhler introduce #PORCELAN, a statistical framework that automatically detects gene expression patterns linked to lineage progression. This method provides a systematic way to study how gene expression and cell state memory evolve through cell divisions, offering new insights into processes such as cancer progression. 🧬 Learn more: https://lnkd.in/egrvi5Ax Broad Institute of MIT and Harvard, MIT EECS, MIT Institute for Data, Systems, and Society (IDSS), MIT Laboratory for Information and Decision Systems (LIDS) #BroadInstitute #SchmidtCenter #MIT #MITEECS #MITIDSS #MITLIDS #CarolineUhler #HannahSchlueter #ScienceNews #ScienceResearch #SingleCellResearch #GeneExpression #ComputationalBiology

Hannah Schlueter and Caroline Uhler developed a computational method, PORCELAN, that combines representation learning, tree-likeness scores, and a permutation strategy to compare lineage relationships between single cells with their relationships in another paired modality such as gene expression. They validated PORCELAN on simulated gene expression data paired with lineage information and applied it to recent datasets on lung cancer and embryogenesis in a mouse model and C. elegans. PORCELAN identified biologically meaningful patterns and genes, demonstrating its potential utility and versatility. Read more in Nature Communications. #BroadInstitute #Science #ScienceNews #Research #ScientificResearch