University Libraries Presents: The Library AI Club is a welcoming space for students, faculty, and staff to explore AI in a supportive, low-pressure environment. Meeting every two weeks, the club features discussions, collaborative projects, guest speakers, and hands-on experiments. Join us to learn, share ideas, and engage with AI responsibly and creatively. We'd love to see you at an upcoming meeting!
Location: Melville Library, Scholarly Communication Seminar Room
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. 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.
We meet once a month at noon in CDSD's Training Room (building 725, room 2-124) 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.
Multilayer machine-learning framework for screening catalytic activity and selectivity
Abstract: Machine learning (ML) studies based on quantum chemical datasets have emerged as a powerful tool for accelerating catalyst discovery. However, their potential applications remain limited by high costs, low data quality, and restricted reliability. Here, we report a multilayer binary classification framework (MLBC) for screening catalytic performance in multistep processes with ML models. Key features include low-cost synthetic data generation via kinetic Monte Carlo simulations, high-quality data that capture catalytic behavior under reaction conditions, robust treatment of imbalanced data distributions, and descriptor selection that enhances reliability and interpretability. Using carbon dioxide (CO 2 ) hydrogenation to methanol (CH 3 OH) on copper (Cu)-based catalysts as a case study, the MLBC framework outperforms conventional ML models by demonstrating high reliability and strong generalization in classifying systems with activity and methanol selectivity exceeding those of Cu. In addition, feature analysis reveals that control over the critical transition steps between competing pathways governs activity and selectivity in CO 2 hydrogenation.
In addition to our speaker, we will have a number of CDS staff in attendance with expertise in AI methods and applications including image analysis, foundation models development, and inverse problem solving.
Biography: Dr. Wenjie Liao is a research associate in the Chemistry Division at Brookhaven National Laboratory, where he develops computational and machine-learning approaches to understand and improve heterogeneous catalysts. He earned his Ph.D. from Stony Brook University. His research focuses on identifying active sites, mapping reaction pathways, and predicting catalyst performance, with the goal of accelerating the discovery of more efficient catalysts for energy and chemical transformations.
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
Please Note: Due to a funding shortfall, we are for the time being no longer able to provide pizza and sodas for these events. We will have coffee though, and all are of course welcome to bring their lunch.
CSE 600 Seminar Series | Fall 2025
Speaker: Jiawei (Joe) Zhou
Speaker: Jiawei (Joe) Zhou
The Hudson River Estuary (HRE) and New York Bight (NYB) are closely connected, with HRE acting as crucial areas where many NYB marine species spawn and grow. Understanding how these biotic and abiotic environments interact, especially with rapid climate change, is key to better managing fisheries and conserving ecosystems. To better understand the HRE-NYB ecosystem, we develop a comprehensive ecosystem model that links physical and biological processes. Using data from long-term monitoring programs, we analyze ecological patterns and identify key factors regulating the ecosystem. We use this information to develop a model that mimics the food web from tiny plankton to large predators in the ecosystem. This model can help us better understand how changes in the environment, like rising temperatures, and human activities such as fishing affect marine lives and ecosystem over time. The insights from this model can support smarter fisheries management and efforts to conserve marine ecosystems in the HRE-NYB region.
IACS Student Seminar Speaker: Xiangyan Yang, Dept. of Applied Math & Statistics
Location: IACS Seminar Room or Zoom
Join Zoom Meeting: https://stonybrook.zoom.us/j/91650247483?pwd=fvAGEwadplJh7jFC5RWcdvZ5NWPJth.1
Meeting ID: 916 5024 7483
Passcode: 631055
IACS Student Seminar Speaker: Xiangyan Yang, Dept. of Applied Math & Statistics
Location: IACS Seminar Room or Zoom
Join Zoom Meeting: https://stonybrook.zoom.us/j/91650247483?pwd=fvAGEwadplJh7jFC5RWcdvZ5NWPJth.1
Meeting ID: 916 5024 7483
Passcode: 631055
Abstract: Computational pathology has revolutionized cancer diagnosis and research through the analysis of digitized whole slide images (WSIs). However, their giga-pixel size creates two intertwined bottlenecks: computational inefficiency, as prohibitive GPU memory makes standard end-to-end (E2E) training infeasible, and label inefficiency, as expert annotation is tedious and expensive. This dissertation confronts both challenges through novel architectures, training paradigms, and self-supervised learning methods for efficient WSI analysis.
To improve computational efficiency, this dissertation 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 training only a few prompts to guide large pre-trained models, reducing trainable parameters, memory, and training time. Third, this work proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy in 1D models. Fourth, it presents Locally Bi-directional Mamba (LBMamba), whose hardware-aware local backward scan integrates bi-directional scanning into a single forward pass, improving the throughput-performance trade-off of Mamba models.
To improve label efficiency, this dissertation proposes a precise location based matching strategy for self-supervised dense contrastive learning, which allows a local patch in one augmented view to match multiple overlapping patches in another, producing more accurate correspondences and superior features for dense prediction tasks like segmentation and detection. Additionally, to better scale multi-channel cell imaging modalities, this dissertation introduces ChannelSFormer, a channel-agnostic vision transformer that disentangles spatial and channel-wise reasoning through divided attention and channel class token, enabling effective representation learning across variable channel configurations in both self-supervised and supervised settings.
In summary, this dissertation 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: NCS 220
Zoom: https://stonybrook.zoom.us/j/93175806292?pwd=xbtxnQyYGoThz5B1DyJxJxPF9lxiJE.1
Meeting ID: 931 7580 6292
Passcode: 314091
To improve computational efficiency, this dissertation 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 training only a few prompts to guide large pre-trained models, reducing trainable parameters, memory, and training time. Third, this work proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy in 1D models. Fourth, it presents Locally Bi-directional Mamba (LBMamba), whose hardware-aware local backward scan integrates bi-directional scanning into a single forward pass, improving the throughput-performance trade-off of Mamba models.
To improve label efficiency, this dissertation proposes a precise location based matching strategy for self-supervised dense contrastive learning, which allows a local patch in one augmented view to match multiple overlapping patches in another, producing more accurate correspondences and superior features for dense prediction tasks like segmentation and detection. Additionally, to better scale multi-channel cell imaging modalities, this dissertation introduces ChannelSFormer, a channel-agnostic vision transformer that disentangles spatial and channel-wise reasoning through divided attention and channel class token, enabling effective representation learning across variable channel configurations in both self-supervised and supervised settings.
In summary, this dissertation 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: NCS 220
Zoom: https://stonybrook.zoom.us/j/93175806292?pwd=xbtxnQyYGoThz5B1DyJxJxPF9lxiJE.1
Meeting ID: 931 7580 6292
Passcode: 314091
Abstract: Humans perceive the world around them by recognizing global patterns and structures such as object parts, branches, their spatial arrangement, and so on. Most deep learning models, however, take a fundamentally local approach. They process images pixel-by-pixel rather than focusing on structures as a whole. While these models indeed perform well on many tasks, the local (pixel-level) versus global (structure-level) disconnect makes them harder to interpret and control.
Topology, in a general sense, is a mathematical language for describing structure. It delineates how different parts of an image relate to one another, capturing both individual structures and their overall layout. Preserving topology enforces structural correctness and, by extension, semantic validity.
In this thesis, we investigate how topological constraints can be used to bridge the gap between local and global understanding. We use topology to inform the design of deep learning models that are explicitly structure-aware. Our thesis focuses on dense prediction tasks, which include image segmentation, uncertainty estimation, and generative modeling. First, we introduce a topological interaction module for semantic segmentation that encodes containment and exclusion constraints directly into the learning process. This preserves anatomical hierarchies and improves multi-class consistency. Next, since segmentation models can never be truly perfect, we address the need for reliable uncertainty estimation to identify error-prone regions. Unlike conventional pixel-wise uncertainty maps, which tend to be noisy and difficult to interpret, we propose reasoning at the level of structural units--branches and connections--which are more visually discernible and actionable. Finally, we leverage topology for generative modeling. We propose a topology-guided diffusion framework that can be controlled using structural attributes like object count and connectivity.
Together, these contributions establish a unified approach to topology-informed, structure-preserving dense prediction models. By integrating topological reasoning with deep networks, this thesis advances models that are not only accurate, but also structurally consistent, interpretable, and controllable. The results from this thesis have been published in ECCV, NeurIPS, and ICLR.
Speaker: Saumya Gupta
Location: New Computer Science (NCS) 120
Zoom: https://stonybrook.zoom.us/j/
Topology, in a general sense, is a mathematical language for describing structure. It delineates how different parts of an image relate to one another, capturing both individual structures and their overall layout. Preserving topology enforces structural correctness and, by extension, semantic validity.
In this thesis, we investigate how topological constraints can be used to bridge the gap between local and global understanding. We use topology to inform the design of deep learning models that are explicitly structure-aware. Our thesis focuses on dense prediction tasks, which include image segmentation, uncertainty estimation, and generative modeling. First, we introduce a topological interaction module for semantic segmentation that encodes containment and exclusion constraints directly into the learning process. This preserves anatomical hierarchies and improves multi-class consistency. Next, since segmentation models can never be truly perfect, we address the need for reliable uncertainty estimation to identify error-prone regions. Unlike conventional pixel-wise uncertainty maps, which tend to be noisy and difficult to interpret, we propose reasoning at the level of structural units--branches and connections--which are more visually discernible and actionable. Finally, we leverage topology for generative modeling. We propose a topology-guided diffusion framework that can be controlled using structural attributes like object count and connectivity.
Together, these contributions establish a unified approach to topology-informed, structure-preserving dense prediction models. By integrating topological reasoning with deep networks, this thesis advances models that are not only accurate, but also structurally consistent, interpretable, and controllable. The results from this thesis have been published in ECCV, NeurIPS, and ICLR.
Speaker: Saumya Gupta
Location: New Computer Science (NCS) 120
Zoom: https://stonybrook.zoom.us/j/
Kate Armstrong, a Vancouver-based artist, writer, and independent curator, will explore the role of AI in art and creativity through three AI-driven projects: KEKE Terminal, Botto, and Sasha Stiles' AI collaborator Technelegy. She will compare these projects to historical artistic movements and investigate AI's role as an autonomous creative agent, the function of community participation, and the shifting dynamics of authorship.
Location: Humanities Institute Room 1008
Location: Humanities Institute Room 1008
This event brings together people with interests in Computer Vision theory and techniques and examines current research issues in the field.
Each seminar consists of multiple short talks (around 15 minutes) by several students.
Join Zoom Meeting:
https://stonybrook.zoom.us/j/93547152068?pwd=WVpoRVgzelBXeloxdXVEakNSb2M5UT09
Meeting ID: 935 4715 2068 | Passcode: 481832
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.
Embodied Intelligence at Scientific User Facilities
Abstract: This presentation explores the active work integrating artificial intelligence and robotics at the National Synchrotron Light Source II, and a perspective for the future. Through various case studies, we highlight the optimization of operations, improved experimental outcomes, and the orchestration of distributed multimodal experiments. This ongoing development includes collaborators from across the light and neutron sources in the DOE complex. We will elaborate on the open-source Bluesky project, and its capabilities to support adaptive and autonomous experiments. Additionally, we will discuss how Bluesky can be integrated with open-source robotic control software to unlock new flexible automation for autonomous scientific research, which scales to new experiments and continues to leverage human ingenuity.
Biography: Dr. Phillip M. Maffettone is an Associate Computational Scientist in the Data Science and Systems Integration Division at NSLS-II. His research focuses on accelerating scientific discovery at user facilities through the integration of robotics, artificial intelligence (AI), and advanced experiment orchestration systems. He leads the N3XTware project, constructing the software architecture for the next 12 beamlines to be built at NSLS-II. Prior to this he built the brain on the world's first mobile robotic scientist at the University of Liverpool, and later spearheaded the machine learning platform for a biotechnology start-up, BigHat Biosciences. He holds a DPhil in Inorganic Chemistry from the University of Oxford and a B.S. in Chemical Engineering from the University at Buffalo.
Location: CDS, Bldg. 725, Training Room
Link: https://bnl.zoomgov.com/j/16049713 31?pwd=nc5CV3cOFrdYxordFieP W07tIDmwYb.1
Meeting ID: 160 497 1331
Passcode: 289875
When: Thu: 10/28/2021, 10 am
Where: NCS Room 220, or
Zoom: https://stonybrook.zoom.
Deep Surface MeshesPascal FuaEPFLGeometric Deep Learning has recently made striking progress with the advent of Deep Implicit Fields (SDFs). They allow for detailed modeling of watertight surfaces of arbitrary topology while not relying on a 3D Euclidean grid, resulting in a learnable 3D surface parameterization that is not limited in resolution. Unfortunately, they have not yet reached their full potential for applications that require an explicit surface representation in terms of vertices and facets because converting the SDF to such a 3D mesh representation requires a marching-cube algorithm, whose output cannot be easily differentiated with respect to the SDF parameters. In this talk, I will discuss our approach to overcoming this limitation and implementing convolutional neural nets that output complex 3D surface meshes while remaining fully-differentiable and end-to-end trainable. I will also present applications to single view reconstruction, physically-driven Shape optimization, and bio-medical image segmentation.
Bio:
Pascal Fua received an engineering degree from Ecole Polytechnique, Paris, in 1984 and a Ph.D. in Computer Science from the University of Orsay in 1989. He joined EPFL (Swiss Federal Institute of Technology) in 1996 where he is a Professor in the School of Computer and Communication Science and head of the Computer Vision Lab. Before that, he worked at SRI International and at INRIA Sophia-Antipolis as a Computer Scientist. His research interests include shape modeling and motion recovery from images, analysis of microscopy images, and Augmented Reality. He has (co)authored over 300 publications in refereed journals and conferences. He has received several ERC grants. He is an IEEE Fellow and has been an Associate Editor of IEEE journal Transactions for Pattern Analysis and Machine Intelligence. He often serves as program committee member, area chair, and program chair of major vision conferences and has cofounded three spinoff companies.