Abstract:
Coarse grained (CG) models alleviate the drawbacks of all-atom simulations. The latter still pose challenges because they are computationally expensive and give access to limited spatiotemporal scales, despite the use of modern high-performance computing clusters. CG models ignore some of the atomistic degrees of freedom, leading to fewer interatomic interactions, hence less computing time. Introducing such models emphasizes the need to properly manage these multiple scales, by carefully deriving potentials and reconstructing conformations from their CG representations, usually with the help of Machine Learning. Following a bottom-up and force matching approach, we train a Physics-Informed Neural Network to extract the CG force field parameters from all-atom simulation data. We verify our approach by applying it to fibrin monomers to study multiple-fibrin polymerization in solution at the microsecond scale, after modifying the force field to incorporate further non-bonded interactions, not present in the training data. Access to these scales will allow us to study the effects of some of the molecules' components. Furthermore, we modify recent solutions in data-driven protein backmapping. Taking advantage of the developments in graph neural networks and variational inference, we introduce an intermediate step in the all-atom reconstruction of a molecule given its CG configuration, in an attempt to more accurately de-coarsen structures whose atom-to-CG-beads ratio is very high. The combined effect of our new forward and inverse coarse graining methodology will enable the in silico study of many phenomena that are highly dynamic and intrinsically multiscale.

Bio:
Georgios Kementzidis is a third year PhD student in the Department of Applied Mathematics and Statistics at Stony Brook University. His advisor is Dr. Yuefan Deng. His research interests lie at the intersection of Computational Science, molecular dynamics (MD) simulations, and Machine Learning (ML) applications to Computational Biophysics. He is particularly interested in coarse-graining and multi-scale simulations.

*Note: this seminar will be held in-person (food provided on a first-come, first serve basis) and online*

Join Zoom Meeting https://stonybrook.zoom.us/j/99510099036?pwd=EyowuLBGvUVLZDBlG6F6chkMICFOZ7.1
Meeting ID: 995 1009 9036
Passcode: 132419
The overall purpose of this seminar is to bring together people with interests in Computer Vision theory and techniques and to examine current research issues. This course will be appropriate for people who already took a Computer Vision graduate course or already had research experience in Computer Vision. To enroll in this course, you must either: (1) be in the PhD program or (2) receive permission from the instructors.

Each seminar will consist of multiple short talks (around 10 minutes) by multiple people. Students can register for 1 credit for CSE 656. Registered students must attend and present a minimum of 2 or 3 talks. Everyone else is welcome to attend. Fill in https://forms.gle/pCVXovgfMfQwGqG38 to subscribe to our mailing list for further announcement.
Abstract:
Artificial intelligence (AI)-based methods and computational materials science continue to make inroads into accelerated materials design and development. I will review Al-enabled advances made in the subfield of polymer informatics, with a particular focus on the design of application-specific practical polymeric materials. I will describe exemplar design attempts within a few critical and emerging application spaces, including materials designs for storing, producing, and conserving energy, and those that can prepare us for a sustainable economy powered by recyclable and/or biodegradable polymers. Al- powered workflows help efficiently search the staggeringly large chemical and configurational space of materials, using modern machine-learning (ML) algorithms to solve forward and inverse materials design problems. A practical informatics-based design protocol involves creating a set of application-specific target property criteria, building ML model predictors for those relevant target properties, enumerating or generating a tangible population of viable polymers, and selecting candidates that meet design recommendations. The protocol will be demonstrated for several energy and sustainability-related applications. Finally, I will offer an outlook on the lingering obstacles that must be overcome to achieve widespread adoption of informatics-driven protocols in industrial-scale materials development.

Speaker Bio:
Prof. Ramprasad is the Regents' Entrepreneur, Michael E. Tennenbaum Family Chair and Georgia Research Alliance Eminent Scholar in the School of Materials Science & Engineering at the Georgia Institute of Technology. He is also the CEO and co-founder of Matmerize, Inc. His area of expertise is the development and application of computational and machine learning tools to accelerate sustainable materials development aimed at energy production, storage and utilization. Prof. Ramprasad received his B. Tech. in Metallurgical Engineering at the Indian Institute of Technology, Madras, India, an M.S. degree in Materials Science & Engineering at the Washington State University, and a Ph.D. degree also in Materials Science & Engineering at the University of Illinois, Urbana-Champaign.
Prof. Ramprasad is a Fellow of the Materials Research Society, a Fellow of the American Physical Society, an elected member of the Connecticut Academy of Science and Engineering, and the recipient of the Alexander von Humboldt Fellowship and the Max Planck Society Fellowship for Distinguished Scientists. He has authored or co-authored over 300 peer-reviewed journal articles, 8 book chapters and 8 patents, and has delivered over 300 invited talks at Universities and Conferences worldwide. He is a member of the Editorial Advisory Boards of npj Computational Materials, ACS Materials Letters and Journal of Physical Chemistry A/B/C. He created and chaired the inaugural 2022 Gordon Research Conference on Computational Materials Science and Engineering.

Location: Room 301, Engineering Building

Launching a University-Wide AI Innovation Institute:

Last spring, the Office of the Provost led a group of over 30 faculty, staff, and administrators to consider how we can expand and leverage our strengths in AI research and discovery. The resulting recommendation was to launch a university-wide AI Innovation Institute (AI3), which would expand the Institute for AI-driven Discovery and Innovation established in 2018 from a department-level institute within the College of Engineering and Applied Science (CEAS) to the university-wide AI Innovation Institute reporting to the provost.

As a university-wide enterprise, the AI Innovation Institute (AI3) is intended to accelerate, coordinate, and organize AI innovation and education across Stony Brook. The institute will serve to empower the entire university community and beyond, catalyzing core AI research, curriculum innovation, and societal change in the ever-evolving landscape of knowledge work.

The AI Town Hall, led by AI3 Interim Director Skiena, is an open house event that will provide an overview of the major AI initiatives on campus, including the new AI Seed Grant program and Stony Brook's role in New York State's Empire AI program. The session will include time for questions and discussion about the future of AI at Stony Brook.

Abstract: Sub-grid turbulence is challenging to resolve in climate models; therefore, it is parameterized. Traditionally, turbulent parameterizations have relied on physics-based and equation-based approaches. However, ad hoc and uncertain components in these parameterizations introduce uncertainty in future climate predictions. Recently, data-driven techniques have emerged as an alternative for modeling sub-grid fluxes. I will demonstrate the use of machine learning to model vertical turbulent fluxes in the ocean surface boundary layer and its impact on reducing biases in NOAA's Geophysical Fluid Dynamics Laboratory ocean climate model.

I will show how neural networks, trained to predict the eddy diffusivity profile from high-fidelity yet computationally expensive turbulence schemes, enhance the vertical mixing scheme in the climate model. These networks replace ad hoc components while maintaining the conservation principles of the standard ocean model equations. The enhanced scheme outperforms its predecessor by reducing biases in the mixed-layer depth and modestly improving tropical upper-ocean stratification in ocean-only global simulations. Furthermore, simplified equations that can replace the neural networks show similar improvements but with lower computational cost and better interpretability. They point to structural deficiencies in the baseline parameterization. This work is one of the first successful applications of machine learning to improve a sub-grid parameterization of turbulent mixing in ocean climate models.

IACS Seminar Speaker: Aakash Sane, Princeton University

Location: IACS Seminar Room or Zoom

Join Zoom Meeting: https://stonybrook.zoom.us/j/97764942108?pwd=MzCWupCe3L9mKdrgfO2bJg3GBbvXuf.1
Meeting ID: 977 6494 2108
Passcode: 519324
The Future Histories Studio welcomes Moontae Lee, LG AI Research.


Generative AI is transforming how we understand, create, and interact with information. Large Language Models (LLMS) comprehend contexts, answer non-trivial questions, and spark creative ideas. This talk introduces the evolution of these models, highlighting the most recent advancements in planning, reasoning, and evaluation. The talk also touches on the criticalconsiderations for both model developers and users, carefully addressing limitations of LLMs as well as ethical and societal implications. Finally, the talk provides ongoing directions in researchand production: from the rise of personalized AI agents to the future frontiers of AI.

Moontae Lee is the Director of the Superintelligence Lab at LG AI Research and an Assistant Professor of Information and Decision Sciences at the University of Illinois Chicago. His journey with Large Language Models began as a visiting scholar at Microsoft Research in 2019, continuously consulting the Deep Learning Group at Redmond until joining LG. He holds a PhD in Computer Science from Cornell, an MS from Stanford, and BS degrees in Computer Science, Mathematics, and Psychology from Sogang University. He has been an area chair for major AI conferences and earned recognition in Operations Research and Computational Social Science, including awards from INFORMS and Amazon.

His research interests include:
● Computational Creativity, Algorithmic Awareness
● Retrieval-Augmented Generation and Evaluation
● Code Generation, Reasoning, Planning
● Fine-grained Alignment from Human/AI Feedback in Generative AI
● Large Time-series Models, Diffusion/Consistency
● Machine Unlearning
● Ranking Monopoly, Voting Fairness
● AI Safety, Ethics, and Market Impacts

Join us in person @ Future Histories Studio Staller Center for the Arts, 4222
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