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
Educational objectives:
1. Explain how AI represents a Cognitive Revolution in academic medicine, redefining thefundamental limits of human cognition and knowledge work.
2. Differentiate between superficial AI adoption (innovation theatre) and truetransformationthrough AI-native institutional design.
3. Analyze how AI fundamentally reshapes clinical, research, and educational work-from dataentry to verification, recall to recognition, and hypothesis generation to evaluation-andidentify implications for redesigning academic health systems.
Speaker: Jiajie Zhang, Ph.D.,Dean, Professor, and Glassell Family FoundationDistinguished Chair in Informatics Excellence,D. Bradley McWilliams School of BiomedicalInformatics, UTHealth Houston
Location: MART Building, Room: 7M-0602 (7th Floor)
1. Explain how AI represents a Cognitive Revolution in academic medicine, redefining thefundamental limits of human cognition and knowledge work.
2. Differentiate between superficial AI adoption (innovation theatre) and truetransformationthrough AI-native institutional design.
3. Analyze how AI fundamentally reshapes clinical, research, and educational work-from dataentry to verification, recall to recognition, and hypothesis generation to evaluation-andidentify implications for redesigning academic health systems.
Speaker: Jiajie Zhang, Ph.D.,Dean, Professor, and Glassell Family FoundationDistinguished Chair in Informatics Excellence,D. Bradley McWilliams School of BiomedicalInformatics, UTHealth Houston
Location: MART Building, Room: 7M-0602 (7th Floor)
Fantastic Futures is an international conference series organized by AI4LAM as one of the most important global events at the intersection of AI and cultural heritage, shaping how memory institutions adapt to rapidly evolving technologies while maintaining public trust.
The conference brings together professionals, researchers, technologists, and cultural‑heritage institutions to explore how AI can support organizational workflows, users services and data preservation, access, discovery, as well as innovation in the cultural‑heritage sector:
- Librarians, archivists, museum professionals and all other GLAM enthusiasts
- Technologists working on cultural‑heritage applications, AI researchers and developers
- Digital humanists, researchers of cultural heritage
- University professors, students, and librarians
- Policy and ethics experts, governmental employees
- Strategic leaders and innovation managers
To register, visit AI4LAM's official website.
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/
Meeting ID: 986 1763 0652
Passcode: 882994
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.
Title: AI-Driven Target Selection Methods for Touch and Gaze Input
Abstract: Accurately selecting targets is an essential aspect of Human-Computer Interaction. Erroneous selections can cause tedious undo and redo actions. Additionally, some selection errors are non-reversible and can lead to undesirable consequences. However, high-accuracy target selection remains a challenge on touchscreen devices due to the small target size and imprecise touch inputs, and in gaze interaction because of the gaze tracking noise and no easy-to-use selection action. We first propose ReLM, a Reinforcement Learning-based Method for touchscreen target selection. ReLM can automatically show suggestions and require a second touch if the input is ambiguous, and can directly select a target candidate when the input is certain. Our empirical evaluation shows that ReLM reduces the error rate from 6.92% to 1.63%, and the selection time from 2.23s to 1.59s over Shift, an existing suggestion-based method. Compared to BayesianCommand, a direct selection-based method, our ReLM reduces the error rate from 3.64% to 0.89%, while increasing the selection time by only 200 ms. Secondly, we investigate how to improve target selection performance for gaze interaction. We propose BayesGaze, an eye-gaze based target selection method. It accumulates the signal of each gaze point for selecting a target calculated by Bayes Theorem, and uses a threshold mechanism to determine the target selection. Our investigation shows that BayesGaze improves target selection accuracy and speed over a dwell-based selection method, and the Center of Gravity Mapping method.
All are welcome. Here is the zoom meeting link:
https://stonybrook.zoom.us/j/93130953411?pwd=Rm5IRlVPQ3M0cHJsTXpCVFljUlFGUT09 Meeting ID: 931 3095 3411Passcode: 999413
Abstract: Accurately selecting targets is an essential aspect of Human-Computer Interaction. Erroneous selections can cause tedious undo and redo actions. Additionally, some selection errors are non-reversible and can lead to undesirable consequences. However, high-accuracy target selection remains a challenge on touchscreen devices due to the small target size and imprecise touch inputs, and in gaze interaction because of the gaze tracking noise and no easy-to-use selection action. We first propose ReLM, a Reinforcement Learning-based Method for touchscreen target selection. ReLM can automatically show suggestions and require a second touch if the input is ambiguous, and can directly select a target candidate when the input is certain. Our empirical evaluation shows that ReLM reduces the error rate from 6.92% to 1.63%, and the selection time from 2.23s to 1.59s over Shift, an existing suggestion-based method. Compared to BayesianCommand, a direct selection-based method, our ReLM reduces the error rate from 3.64% to 0.89%, while increasing the selection time by only 200 ms. Secondly, we investigate how to improve target selection performance for gaze interaction. We propose BayesGaze, an eye-gaze based target selection method. It accumulates the signal of each gaze point for selecting a target calculated by Bayes Theorem, and uses a threshold mechanism to determine the target selection. Our investigation shows that BayesGaze improves target selection accuracy and speed over a dwell-based selection method, and the Center of Gravity Mapping method.
All are welcome. Here is the zoom meeting link:
https://stonybrook.zoom.us/j/
Abstract: Graphs are a universal language of science. Molecules, materials, quantum systems, and knowledge bases can all be naturally represented as graphs. This talk explores how graph-based artificial intelligence is emerging as a powerful engine for scientific discovery. Using molecular design as a guiding example, we examine how modern graph AI enables machines not only to analyze complex scientific structures but also to generate new ones. We will discuss graph neural networks for learning predictive models of molecular properties, graph generative models for constructing novel chemical structures, and emerging multimodal graph-language models that support inverse design and synthesis planning. Together, these advances make graph AI more scalable, interpretable, and data-efficient--key capabilities for real-world scientific discovery. As artificial intelligence enters the era of foundation models, the next frontier lies in multimodal reasoning. Scientific knowledge is not purely textual; it is expressed through structures, code, and experimental data. By integrating graph representations with large language models, we move toward AI systems that can reason across multiple modalities and engage with scientific knowledge in its native forms. Looking ahead, we envision AI systems that behave less like tools and more like collaborators in the scientific process--generating hypotheses, designing candidate structures, planning experiments, interpreting results, and iteratively refining ideas through cycles of success and failure. In this vision, multimodal and agentic AI will enable scientists to explore vast and previously inaccessible design spaces, accelerating breakthroughs across domains ranging from drug discovery and materials innovation to software systems and quantum technologies.
Bio: Jie Chen is an interdisciplinary researcher working at the intersection of computing and mathematics, with a current focus on foundation models and AI agents for scientific discovery. His research integrates machine learning, statistics, scientific computing, and numerical linear algebra, with contributions spanning graph neural networks, multimodal graph LLMs, graph structure learning, scalable Gaussian processes, graph coarsening, and matrix functions. He is widely recognized for transformative contributions to graph-based deep learning and large-scale statistical modeling, and for bridging theory with real-world scientific and engineering applications. Dr. Chen has led externally funded, multi-institutional research programs supported by Shell, Evonik, and the U.S. Department of Energy, with applications in materials discovery, financial forensics, and power system resilience. He previously served as a Senior Research Scientist and Manager at IBM Research and the MIT-IBM Watson AI Lab, and as a Postdoctoral Fellow at Argonne National Laboratory. He has published extensively in top-tier AI, statistics, and applied mathematics venues, and his work has been recognized by multiple IBM Outstanding Technical Achievement Awards and the SIAM Student Paper Prize. He earned his Ph.D. in Computer Science from the University of Minnesota and his B.S. in Mathematics with honors from Zhejiang University.
Location: NCS 120
Bio: Jie Chen is an interdisciplinary researcher working at the intersection of computing and mathematics, with a current focus on foundation models and AI agents for scientific discovery. His research integrates machine learning, statistics, scientific computing, and numerical linear algebra, with contributions spanning graph neural networks, multimodal graph LLMs, graph structure learning, scalable Gaussian processes, graph coarsening, and matrix functions. He is widely recognized for transformative contributions to graph-based deep learning and large-scale statistical modeling, and for bridging theory with real-world scientific and engineering applications. Dr. Chen has led externally funded, multi-institutional research programs supported by Shell, Evonik, and the U.S. Department of Energy, with applications in materials discovery, financial forensics, and power system resilience. He previously served as a Senior Research Scientist and Manager at IBM Research and the MIT-IBM Watson AI Lab, and as a Postdoctoral Fellow at Argonne National Laboratory. He has published extensively in top-tier AI, statistics, and applied mathematics venues, and his work has been recognized by multiple IBM Outstanding Technical Achievement Awards and the SIAM Student Paper Prize. He earned his Ph.D. in Computer Science from the University of Minnesota and his B.S. in Mathematics with honors from Zhejiang University.
Location: NCS 120
Abstract: The rapid growth of observational data presents unprecedented opportunities to enhance both the predictability and mechanistic understanding of Earth systems. However, fully harnessing big Earth data needs computational frameworks that bridge the gap between physics-based models and machine learning. In this talk, I will first demonstrate how AI methods can significantly improve the prediction of environmental systems. Despite their predictive accuracy, machine learning models often lack physical interpretability, limiting their ability for scientific inquiry. To address this, I will introduce the developed hybrid, differentiable modeling framework that unifies physical models with machine learning in an end-to-end trainable system. This framework autonomously learns from large observations while maintaining physical clarity. The machine learning components can be seamlessly embedded into physical backbones to assimilate multi-source data, support automatic parameterization, and represent uncertain processes. I will showcase applications of this framework in simulating and understanding the terrestrial water cycle and its interactions with ecosystems at continental and global scales. This talk will highlight how differentiable modeling not only improves the modeling ability in both data-rich and data-scarce scenarios, but also provides a systematic pathway to enhancing model structures, deciphering uncertain physical relations, and facilitating knowledge discovery in Earth system sciences.
IACS Seminar Speaker: Dapeng Feng, Stanford Univeristy
Location: IACS Seminar Room
IACS Seminar Speaker: Dapeng Feng, Stanford Univeristy
Location: IACS Seminar Room
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
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