The Pittsburgh Supercomputing Center is pleased to present a Machine Learning and Big Data workshop.

This workshop will focus on topics including big data analytics and machine learning with Spark, as well as deep learning.

This will be an IN PERSON event hosted by various satellite sites, there WILL NOT be a direct to desktop option for this event. SBU's Institute for Advanced Computational Science (IACS) is one of those satellite sites!

Location: IACS Conference Room #2

Interested applicants must first have an ACCESS ID. If you don't have the ID, please visit this page to create one: ACCESS USER REGISTRATION.


Once you have an ACCESS ID, please login (see top right here) then register here.

Join us for an engaging panel discussion featuring researchers who participated in our inaugural AI JAM session on February 26th. Our panelists will share their firsthand experiences using large language models to tackle complex scientific problems, with a special focus on prompt engineering strategies, discussing both breakthroughs and challenges encountered during this collaborative initiative. Learn how these cutting-edge AI tools are being applied to real-world research questions and discover insights that could inform your own scientific endeavors. Attendees are encouraged to come prepared with questions about prompt engineering for the panel discussion.

Moderator: Adolfy Hoisie, Deputy Director, Computing and Data Sciences

Kevin Yager, Group Leader, AI-Accelerated Nanoscience, Center for Functional Nanomaterials
Lingda Li, Associate Computational Scientist, Systems, Architecture and Computing Technologies, Computing and Data Sciences
Liguo Wang, Director of Scientific Operations, Laboratory for BioMolecular Structure (LBMS), National Synchrotron Light Source II
Weiguo Yin, Physicist, Condensed Matter Theory, Condensed Matter Physics and Materials Science Department

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1606837837?pwd=Tc0mwQqLXpDfYOIaoaurmpLD2mMlzS.1 (Meeting ID)

Passcode: 822553

Abstract: Recent advances in Spatial Transcriptomics (ST) pair histology images with spatially resolved gene expression profiles, enabling predictions of gene expression across different tissue locations based on image patches. This opens up new possibilities for enhancing whole slide image (WSI) prediction tasks with localized gene expression. However, existing methods do not fully leverage the interactions between different tissue locations, which are crucial for accurate joint prediction. To address this, we introduce MERGE (Multi-faceted hiErarchical gRaph for Gene Expressions), which combines a multi-faceted hierarchical graph construction strategy with graph neural networks (GNN) to improve gene expression predictions from WSIs. By clustering tissue image patches based on both spatial and morphological features, and incorporating intra- and inter-cluster edges, our approach fosters interactions between distant tissue locations during GNN learning. As an additional contribution, we evaluate different data smoothing techniques that are necessary to mitigate artifacts in ST data, often caused by technical imperfections. We advocate for adopting gene-aware smoothing methods that are more biologically justified. Experimental results on gene expression prediction show that our GNN method outperforms state-of-the-art techniques on multiple metrics such as mean squared error (MSE), mean absolute error (MAE), and pearson correlation coefficient (PCC). Qualitative analysis establishes the effectiveness of MERGE in capturing cancer marker genes, thus consolidating its utility in diagnostics. As an extension of this work, we use MERGE in a setting with an uncertainty calibration branch to perform robust gene expression smoothing. We show that using patch-wise uncertainty from an uncertainty calibration model and the gene expression predictions from MERGE to enrich the ground truth gene expression matrix, results in better alignment with pathologist annotations, thus establishing that the smoothing is biologically informed.

Speaker: Aniruddha Ganguly

Location: Virtual Zoom Meeting


https://stonybrook.zoom.us/j/5474847973?pwd=Sng0Q2h1c1d3cm9sbFBmYUczMHZNdz09
Meeting ID: 547 484 7973
Passcode: 206739

You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes three short talks on AI research happening at BNL, followed by an open mixer over coffee and snacks for everyone to network and discuss all things AI. The first half hour will consist of presentations that will be available via ZOOM, and the second half hour will be for in person only networking.

Join us every other Tuesday at noon in CDSD's Training Room (building 725, 2nd floor) to learn about interesting AI methods and applications, engage with potential collaborators, prepare for pending FASST funding calls, and build a community of AI for Science at BNL.

Tuesday, January 7, 2025, 12:00 pm -- CDS, Bldg. 725, Training Room

Speakers

Jianda Chen, EBNN - Improving the stability and accuracy of PDE-ML hybrid AGCMs

Boyang Li, CDS - Accelerating Materials Discovery using Machine Learning

Jaehye on Do, NPP Isotopes - Using LLMs for Isotopes Research and Production

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1615289117?pwd=Hqkbj9itxWrFnkhZ8rQXHPInO2gxdF.1

Meeting ID: 161 528 9117
Passcode: 991382


Abstract: This talk shows how machine learning can address challenges in Astrophysics. We specifically focus on black hole simulations and supernova observations. First, we present a super-resolution technique for black hole simulations that avoids the need for high-resolution labels by leveraging the Hamiltonian and momentum constraints from general relativity. This method reduces constraint violations by one to two orders of magnitude. Next, we introduce Maven, a multimodal foundation model for supernova science. Using contrastive learning to align photometric and spectroscopic data, Maven achieves state-of-the-art results in classification and redshift estimation by pre-training on synthetic data and fine-tuning on real observations.

Bio: Thomas Helfer is a computational physicist specializing in deep learning and physics. Currently based at the Institute for Advanced Computational Science at Stony Brook University, Thomas was previously a postdoctoral fellow at Johns Hopkins and did his PhD with Eugene Lim at King's College in London. In his work, he looks to bridge topics; in his PhD, he bridged theoretical particle physics and gravitational waves. Now, in his postdoctoral work, he aims to find novel applications of deep learning in astrophysics.

*please note: this seminar will be held in a hybrid format*


Location: IACS Seminar Room OR Join Zoom Meeting
https://stonybrook.zoom.us/j/98617630652?pwd=tb4hplPgb3bTTifPCJTCcsn3P9vX8y.1

Meeting ID: 986 1763 0652
Passcode: 882994

Subject: RADIOLOGY GRAND ROUNDS CT Colonography: An Effective Test for Colorectal Cancer Screening- Judy Yee, M.D.
When: Wednesday, May 12, 2021 12:00 PM-1:00 PM (UTC-05:00) Eastern Time (US & Canada).
Where: JOIN ZOOM MEETING

 

Judy Yee, MD

Chair, Department of Radiology

Professor, Department of Radiology

Abdominal Imaging

 

Join Zoom Meeting

https://einsteinmed.zoom.us/j/97782190723?pwd=clMzMys2SlZjZzJId1hUNzMyVUQ2UT09

 

Meeting ID: 977 8219 0723

Passcode: 101083