You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes one short talk 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.

At our Oct 7 Mixer, BNL's newly minted interim director, John Hill will be present to give opening remarks and kick us off on a new year of impactful scientific AI collaborations.

Abstract: Weather extremes and strong seasonal-to- subseasonal variability pose growing challenges to urban populations, infrastructure, and energy systems. Yet, most cities remain data deserts: routine weather observations are sparse, with stations concentrated at airports rather than within the urban core. This lack of coverage limits our ability to monitor and predict fine-scale urban weather patterns precisely where they matter most. We present a new AI-driven framework for optimal sensor placement and urban weather monitoring. Unlike traditional approaches, our method leverages physics- based simulations together with Bayesian experimental design principles, but does so using a computationally efficient variational inference strategy that makes large-scale optimization tractable. This allows us to guide sensor networks in a way that minimizes information loss while capturing spatiotemporal variability at city scales. Applied to Phoenix, Arizona, our framework outperforms random sensor placement strategies, especially when only a limited number of sensors can be deployed. Importantly, the same AI models that guide sensor placement also function as a real-time nowcasting tool, providing urban weather information over the entire domain, beyond sensor locations. Together, these capabilities offer a scalable pathway to reduce urban data deserts, enhance monitoring of weather extremes, and improve resilience planning for energy, transportation, and public health systems.

Biography: Dr. Katia Lamer is an atmospheric scientist and the Director of the Center for Multiscale Applied Sensing at Brookhaven National Laboratory. Originally from Canada, she earned her B.S. and M.S. in Atmospheric and Oceanic Sciences from McGill University and a Ph.D. in Meteorology from Penn State University. Her research focuses on atmospheric boundary layer processes and remote sensing technologies, with a strong emphasis on data science. At Brookhaven, she is known for her work with the CMAS mobile observatories and its facility that connect fundamental atmospheric science to real-world applications, improving weather prediction, environmental monitoring, and urban climate resilience. Her work has been featured in public outlets such as New Scientist and Wired. Dr. Lamer also serves as an invited member of the World Meteorological Organization's Data Assimilation and Observing Systems Working Group, and the American Meteorological Society's Boundary Layer and Turbulence Committee. puting, communications and sensing, all enabled by AI.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1604383624?pwd=ffQ5cUPNxTI7nzClKQO6cnsNbhF9Vf.1

Meeting ID: 160 438 3624 | Passcode: 558449



Date of Event

Joel H. Saltz, MD, PhD
SUNY Distinguished Professor Cherith Professor and Founding Chair
Department of Biomedical Informatics
Stony Brook University

Apostolos K. Tassiopoulos, MD, FACS
Professor of surgery and vice chair for quality and outcomes Chief of the Division of Vascular and Endovascular Surgery
Director of the Stony Brook Vascular Center Stony Brook Medicine

Title: Clinical applications of artificial intelligence to improve diagnosis and risk stratification for patients with aortic aneurysms

Time: Wednesday, Feb 17, 2021 3 pm - 4 pm

Join Zoom Meeting
https://stonybrook.zoom.us/j/95617197636?pwd=KytzZ2pVRG9SZGpKZUtpNXJISj...
Meeting ID: 956 1719 7636 Passcode: 924293


Abstract: This talk is about the two ends of LLM training: pre-training and in-deployment learning. I will present an approach to disentangle knowledge from skill in model pre-training. This brings about a new class of LLMs that externalize knowledge, with dramatically different characteristics from common LLMs along dimensions of scale, factuality, and updateability. On the other end, I will discuss two in-deployment learning methods. I will describe how in-context learning abilities extend beyond supervised settings, showing that LLMs display in-context reinforcement learning from rewards. Finally, if time allows, I will describe continual learning from implicit interaction signals, demonstrating that LLMs can retrospectively decode latent interaction cues by observing how humans respond to their outputs.

Bio: Yoav Artzi is an Associate Professor in the Department of Computer Science and Cornell Tech at Cornell University, a visiting faculty researcher at Google DeepMind, and arXiv's associate faculty director. His research focuses on language modeling and learning in interactive and situated scenarios. His work was acknowledged by awards and honorable mentions at ACL, EMNLP, NAACL, and IROS, as well as a TACL test-of-time award. Yoav holds a B.Sc. from Tel Aviv University and a Ph.D. from the University of Washington.

Location: NCS 120

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: Computational pathology has revolutionized cancer diagnosis and research through the analysis of digitized whole slide images (WSIs). However, the giga-pixel size of these images presents profound technical challenges, creating two intertwined bottlenecks: computational inefficiency and label inefficiency. The immense data scale makes standard end-to-end (E2E) training of deep neural networks infeasible due to prohibitive GPU memory requirements, while the reliance on expert pathologists for annotations makes obtaining high-quality labeled data a tedious and expensive process. This proposal confronts these dual challenges by developing a series of novel model architectures, training paradigms, and self-supervised learning methods designed to create a more efficient and effective framework for WSI analysis.

To improve computational efficiency, this proposal first introduces a locally supervised learning paradigm that enables E2E training on entire WSIs by partitioning a network into gradient-isolated modules, circumventing the memory bottleneck of backpropagation. Second, it presents Prompt-MIL, a parameter-efficient fine-tuning framework that reduces the number of trainable parameters, memory consumption, and training time by fine-tuning only few prompts to guide large pre-trained models. Third, this work advances the efficient architecture on WSIs by developing novel State-Space Models (SSMs). It proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy inherent in 1D models. Fourth, to address the inefficiency of multi-directional scans in Mamba models, including 2DMamba, it presents Locally Bi-directional Mamba (LBMamba), which introduces a novel, hardware-aware local backward scan that integrates bi-directional scan into a single forward pass, significantly improving throughput performance trade-off. Lastly, it proposes an extension to the LBMamba, warp-level Bi-directional Mamba (WLBMamba) that extends the thread-level bidirectional scan to warp-level bidirectional scan that further improves the throughput performance trade-off.

To improve label efficiency, this proposal proposes a Precise Location-based Matching strategy for self-supervised dense contrastive learning. By allowing a local patch in one augmented view to match multiple overlapping patches in another, creates a more accurate correspondence, leading to superior feature representations for dense prediction tasks like segmentation and detection.

In summary, this proposal presents a holistic investigation into the efficiency bottlenecks in computational pathology. Through these combined contributions in model architecture, training paradigms, and self-supervised learning, this work establishes a more scalable, efficient, and powerful computational framework for analyzing giga-pixel pathology images.

Speaker: Jingwei Zhang

Location: Old Computer Science Room 2114

Zoom: https://stonybrook.zoom.us/j/95187903649?pwd=tV0CNxLu1QKqw7hGmcE1h0rJ2C6n1b.1
Meeting ID: 951 8790 3649 | Passcode: 488916

The Future Histories Studio at Stony Brook University and Guggenheim New York are collaborating to present a day-long symposium on October 24 at the Simons Center for Geometry and Physics. This conference will explore urgent questions at the intersection of artificial intelligence, machine learning, and the human, and is co-organized by Noam Segal, LG Electronics Associate Curator at Guggenheim New York. In this role, Noam plays an important part in researching these topics, promoting a deeper understanding of the ways in which contemporary artists use new technologies, and developing and supporting the Guggenheim's engagement with technology-based art under the LG Guggenheim Art and Technology Initiative.

The event examines the profound transformations brought by automation--how AI compels us to rethink cognition, agency, and the conditions of reason itself. As these systems become ever more embedded in daily life--largely invisible yet deeply consequential--they challenge the very foundations of subjectivity and governance. We are surrounded by logics we cannot fully access, yet which shape our realities, while new forms of alterity arise--distinct modes of reasoning that propose collective unknowns beyond established frameworks of knowledge.

This emerging terrain invites us to consider cognitive plurality, where biological and technological intelligences generate new categories, concepts, and understandings. Once unique to humans--art, authorship, judgment, invention--are now co-articulated with systems of computation and planetary-scale infrastructure. The symposium brings together artists, scholars, and technologists to probe the cultural, philosophical, and ecological implications of this entanglement.

The concept of neurodiversity has shown that neurological differences such as autism, ADHD, and dyslexia are not deficits but variations that enrich collective life. Extending this to machines can be provocative: just as neurodivergence unsettles fixed definitions of intelligence, so too AI challenges anthropocentric assumptions about cognition. Yet the analogy is limited. Neurodiversity is rooted in the lived struggles of human communities, while machines neither think nor struggle. Human cognition involves perception, learning, memory, and reasoning through embodied experience. Machine cognition, by contrast, is computational pattern recognition and statistical modeling, without consciousness or lived context, and with only narrow forms of sensing.

For this reason, the symposium advances a broader framework of cognitive diversity or technodiversity--a recognition of proliferating intelligences, human, machinic, and hybrid, as part of a shared ecology. This shift calls for new models of creativity, responsibility, and collaboration that honor the irreducibility of human thought while engaging the radical alterity of machine logics.

Location: Stony Brook Simons Center for Geometry and Physics, Della Pietra Family Auditorium

This event is co organized by the Guggenheim New York

How to Do Spectral Learning at Scale for Science and Engineering

Abstract: Spectral decompositions such as singular value decompositions (SVDs) and eigenvalue decompositions (EVDs) are central tools across a vast swath of scientific computing and machine learning, with abundant engineering applications. Yet many modern methods for learning such decompositions in high dimensions struggle with instability, bias, and poor scalability, even when approximation power is not the limiting factor. I argue that these difficulties are not intrinsic to spectral problems, but instead arise from a shared reliance on Rayleigh-quotient-based constrained optimization, which forces explicit orthogonality handling through penalties, normalization, or whitening.
To address these challenges, I present a reformulation based on unconstrained variational objectives that implicitly encode spectral structure, eliminating the need for orthogonalization and ad-hoc regularization. This perspective leads to a conceptually simpler and scalable parametric framework for learning ordered spectral representations via nested optimization. The resulting framework is well matched to diverse settings in science and engineering. As examples, I demonstrate its effectiveness on eigenvalue problems for linear PDEs such as the Schrödinger equation, spectral (Koopman) analysis of nonlinear dynamical systems such as molecular dynamics, and structured representation learning with deep neural nets. Collectively, these examples illustrate how abandoning Rayleigh-quotient-based formulations resolves long-standing optimization pathologies across domains.

Bio: Jongha (Jon) Ryu is a postdoctoral associate at MIT EECS. He received his Ph.D. in Electrical and Computer Engineering from UC San Diego. His research develops statistical and mathematical foundations for scientific machine learning, with a focus on scalable spectral methods, efficient generative modeling, and reliable uncertainty quantification for scientific and engineering systems.

Location: NCS 120
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The next AI Institute seminar speaker will be Chao Chen of Biomedical Informatics, on Monday November 29 at noon via zoom:

https://stonybrook.zoom.us/j/96233844681?pwd=aVVsUnIzMWJDMHRqVXcrQU5HMjFVQT09

He will be talking on the Detection of Trojan Attacks to Deep Neural Networks - A Topological Perspective, with his abstract and bio below.


Abstract: Deep neural networks are known to have security issues. One particular threat is the Trojan attack. It occurs when the attackers stealthily manipulate the model's behavior through Trojaned training samples, i.e., samples with special trigger injected and labels altered. To identify a Trojaned model at deployment is challenging, due to limited access to the training data. We propose to identify Trojaned neural networks using methods from topological data analysis. In particular, we propose to (1) inspect high-order topological features of the neuron interactions and (2) reverse engineer the injected triggers using a topological loss. These approaches take different angles and reveal insights into the behavior of neural networks when their strong memorialization power is exploited maliciously. The work has been accepted to NeurIPS'21. I will also briefly mention other research directions from my group, including incorporating topological information into deep image analysis, topology-inspired graph neural networks, and robust training of neural networks with label noise. These works have been published in ICLR, ICML, NeurIPS, ECCV, ICCV and AAAI in recent years.
Bio: Dr. Chao Chen is an assistant professor of Biomedical Informatics at Stony Brook University. His research interests span topological data analysis (TDA), machine learning and biomedical image analysis. He develops principled learning methods inspired by the theory from TDA, such as persistent homology and discrete Morse theory. These methods address problems in biomedical image analysis, robust machine learning, and graph neural networks from a unique topological view. His research results have been published in major machine learning, computer vision, and medical image analysis conferences. He is serving as an area chair for MICCAI, AAAI, CVPR and NeurIPS.