Title: Building foundation models for scientific data Seminar

Speaker: Ruben Ohana, Ph.D. and Michael McCabe, Ph.D - Flatiron Institute, New York

Abstract: Foundation models are very large architectures trained on large-scale datasets and can be used to transfer knowledge from a domain to another. Scientific data, particularly numerical simulations of partial differential equations (PDEs), presents unique challenges due to its complexity and the need for domain expertise to assess prediction quality, complicating the building of the first foundation models in this field. In this talk, we will develop our approach of building foundation models for scientific data, highlighting the requirements and expectations for achieving meaningful results. We will also introduce The Well, a comprehensive collection of datasets encompassing multi-scale simulations of fluid dynamics, astrophysics, and biological systems. The Well serves as a foundation for developing models that generalize across diverse physical phenomena, aiming to accelerate scientific discovery through large-scale learning.

Join Zoom Meeting: https://bnl.zoomgov.com/j/1606898802?pwd=GbbPiLGHlEokDskxjeFheMFWfuboxO.1
Meeting ID: 160 689 8802
Passcode: 281575

Please join us this Friday, February 13th for the CSE 600 seminar given by Associate Professor Debswapna Bhattacharya, from the Department of Computer Science at Virginia Tech.

Abstract: Building a model of a biological system that can provide actionable hypotheses to form a solid foundation for experimental and theoretical analyses is one of the key challenges in biology and medicine. In this talk, I will present my group's ongoing work in developing, evaluating, and disseminating a new generation of computational methods for biomolecular modeling powered by artificial intelligence (AI) and machine learning (ML). First, I will introduce a new generation of AI/ML methods for improved modeling and characterization of protein-nucleic acid assemblies by deep graph learning using embeddings from biological large language models (LLMs) as well as geometric attention-enabled pairing of heterogeneous biological LLMs, a previously unexplored avenue. Then, I will present a novel generative deep learning model based on equivariant flow matching for end-to-end generation of all-atom RNA 3D structural ensemble. Finally, I will outline my future research directions on attaining atomic-level accuracy in computational modeling of biomolecules and their assemblies at scale.

Speaker: Debswapna Bhattacharya is an Associate Professor in the Department of Computer Science at Virginia Tech. He received his Ph.D. in Computer Science from the University of Missouri-Columbia in 2016. Before joining Virginia Tech in 2022, he was an Assistant Professor at Auburn University from 2017 to 2021. His research interests lie at the intersection of computational biology and machine learning, with a particular focus on artificial intelligence for computational structural biology, specifically in modeling and characterization of biomolecular structures and interactions. His research group has been developing novel computational and data-driven methods, software, and information systems for diverse biomolecular modeling problems, ranking among the best methods in community-wide blind assessments and serving the worldwide community of biomedical users. He received various research awards (NSF CAREER Award, NIH Maximizing Investigators' Research Award, NSF National AI Research Resource Award) and numerous institutional honors (National Distinction and Outstanding Contributor at Virginia Tech, Ginn Faculty Fellowship at Auburn University, Outstanding Engineering Faculty Award at Auburn University).
Location: NCS 120
The 39th Annual AAAI Conference on Artificial Intelligence will be held from February 25 to March 4, 2025 in Philadelphia, Pennsylvania, USA. More information can be found here.

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.

Abstract: Two-dimensional (2D) materials such as graphene, hBN, and TMDs offer atomically sharp interfaces and unprecedented tunability when vertically assembled into van der Waals heterostructures. These stacks have enabled discoveries ranging from moiré superconductivity and correlated insulators to quantum emitters and next-generation nanoelectronic devices. Yet constructing high-quality heterostructures remains largely artisanal: researchers manually identify exfoliated flakes, align a polymer stamp by eye, and finely adjust temperature and contact geometry through tacit skill. This manual workflow is difficult to reproduce, scales poorly, and prevents systematic exploration of the enormous combinatorial space of materials, twist angles, and interfacial conditions. AutoLab is an autonomous platform that translates this tacit human expertise into programmable, feedback-driven control. Instead of pressing flakes with predefined trajectories, AutoLab uses machine vision to detect polymer-wafer contact, dynamically regulates contact evolution through closed-loop actuation and temperature control, and captures high-quality flakes with the cleanliness and precision of expert manual fabrication. The system integrates perception, decision making, and motion planning into a single robotic framework, enabling reproducible stacking, wafer-level coverage, and accelerated discovery. Beyond 2D materials, AutoLab illustrates a broader paradigm for AI-native scientific automation: codifying human experimental reasoning into algorithms that interrogate data in real time, adaptively adjust instrumentation, and generate scalable, high-fidelity datasets. Such platforms could generalize to diverse research domains--quantum device fabrication, optical alignment, surface science, autonomous microscopy, and other workflows where expert intuition currently limits throughput and reproducibility. By bridging artisanal manipulation and robotic autonomy, AutoLab points toward a future where scientific discovery is accelerated by machines that not only execute instructions, but learn, respond, and collaborate with human scientists.

Biography: Dr. Yutao Li is a research associate from Department of Condensed Matter Physics and Material Science, Brookhaven National Laboratory. He has 8 years of experience in 2D material sample fabrication, and investigation in their electronic transport, optical and mechanical properties.

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.

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



New York Scientific Data Summit (NYSDS) is a premier annual conference that brings together researchers and thought leaders from academia, national labs and industry to exchange ideas and foster collaboration focused on data-driven science and technology. Co-hosted by Brookhaven National Laboratory and the Institute for Advanced Computational Science (IACS) at Stony Brook University, NYSDS 2025 will take place on September 11-12, 2025, in the SUNY Global Center in New York City.

NYSDS 2025 will spotlight artificial intelligence (AI), machine learning (ML) and robotics - fields currently at a pivotal point with transformative impacts on science and technology. From accelerating computationally demanding simulations to discerning signals from noisy data, AI/ML has become an integral part of the scientific workflows. Despite many advances, challenges remain to ensure that AI/ML applications are reliable, explainable and trustworthy.

Robotics, a growing field that couples AI with physically actuated mechanical bodies, has seen increased interest in areas spanning science, technology and manufacturing. The need for real-time decision-making and control, along with the intricate morphology of robots, makes robotics an intriguing application of AI, advanced computing and optimization.


This NYSDS 2025 is open to the public. To be eligible to attend, all participants must register online by August 30, 2025. For questions or assistance with registering, please contact the Summit Coordinator.

Register here.

Abstract: Anxiety disorders are characterized by persistent and excessive form of fear and worry that interferes with daily functioning, distinguishing it from the adaptive anxiety that helps individuals respond to challenges. Despite affecting millions worldwide and costing a significant public health burden, anxiety disorders still remain underdiagnosed than actual prevalence due to lack of understanding and stigmatization. Leveraging machine learning (ML) and natural language processing (NLP) approaches can help bridge this gap by enabling scalable and accessible mental health assessments, offering a data-driven understanding of anxiety from individual and societal perspectives, and shedding light on societal stigmas toward mental health conditions. At the same time, advancing ML and NLP techniques for anxiety research presents unique technical challenges, such as effectively modeling linguistic markers of anxiety and ensuring interpretability in mental health predictions.

This dissertation investigates anxiety from both individual and societal perspectives using artificial intelligence. First, we explore individual manifestations of anxiety through three methodological advancements: (1) integrating contextual and discourse-level embeddings to improve language-based anxiety prediction using Facebook posts and selfreported surveys; (2) enhancing cognitive dissonance detection in Twitter dataset with transfer learning and active learning; and (3) developing longitudinal representation learning approaches that achieve both predictive utility and interpretability of adolescent psychopathology. Finally, we extended our analysis to societal dimension of anxiety by identifying and categorizing social norms expressed in Reddit and Twitter posts and examining their associations with anxiety. By combining data-driven methods with psychological insights, this work studies anxiety from various angles - capturing both individual experiences and societal influences - offering a step toward a more comprehensive understanding of its causes and manifestations.

Speaker: Swanie Juhng

https://stonybrook.zoom.us/j/98905245099?pwd=M7rI7aNfNio281qyebEUdNPBcSiK7Y.1
University Libraries Present: Analyzing quantitative data can feel overwhelming without the right tools. In this workshop, SBU Libraries' Data Literacies Lead, Ahmad Pratama will show you how to master the basics of exploratory data analysis for quantitative data using Python. This workshop covers several techniques to help you uncover patterns and insights in your datasets.

Online RSVP via link: https://stonybrook.zoom.us/meeting/register/vEPycmDrQoGjFqkmsYHgxw