A SBU Libraries workshop led by Ahmad Pratama, SBU Libraries Data Literacies Lead. In this hands-on session, participants will learn how to transform unstructured text into data for systematic analysis using Python and/or R, covering cleaning, tokenization, and pattern detection. The workshop compares traditional computational text analysis against Generative AI approaches, evaluating what each method reveals (or misses) when working with text corpora.

Register to attend the online event.

CSE 656 Seminars in Computer Vision - Wednesdays 11:30am-12:50pm, Room NCS 120

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 CSE656. 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.
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.

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Abstract: Drawing on group-theoretic and information-theoretic foundations, we propose information lattice learning (ILL) as a general framework to learn rules of a signal (e.g., an image or a probability distribution). In our definition, a rule is a coarsened signal used to help us gain one interpretable insight about the original signal. To make full sense of what might govern the signal's intrinsic structure, we seek multiple disentangled rules arranged in a hierarchy, called a lattice. Compared to representation/rule-learning models optimized for a specific task (e.g., classification), ILL focuses on explainability: it is designed to mimic human experiential learning and discover rules akin to those humans can distill and comprehend. We will detail the mathematical foundations and algorithms of ILL, and illustrate how it addresses the fundamental question what makes X an X by creating rule-based explanations designed to help humans understand. Our focus is on explaining X rather than (re)generating it. We show ILL's efficacy and interpretability on benchmarks and assessments, as well as a demonstration of ILL-enhanced classifiers achieving human-level digit recognition using only one or a few MNIST training examples (1-10 per class). We present applications in knowledge discovery, using ILL to distill music theory from scores and chemical laws from molecules and further revealing connections between them. We close with some early work on understanding the principles that govern scattering amplitudes in Super Yang-Mills theory, rather than just predicting them.

Biography: Lav R. Varshney is the Della Pietra Infinity Professor and inaugural director of the AI Innovation Institute at Stony Brook University. He is co-founder and CEO of Kocree, Inc., a startup company building novel human-controllable AI for discovery and creativity, and chief scientist of Ensaras, Inc., a startup company focused on AI and wastewater treatment. He holds appointments at RAND Corporation and at Brookhaven National Laboratory. He was previously on the faculty of the University of Illinois Urbana-Champaign, a visiting scholar at Northwestern's Kellogg School of Management, a principal research scientist at Salesforce Research AI, and a research staff member at IBM Research. He is a former White House staffer, having served on the National Security Council staff as a White House Fellow, where he contributed to national AI and wireless communications policy. His research interests include information theory and artificial intelligence. He received his B.S. degree from Cornell University and his S.M. and Ph.D. degrees from the Massachusetts Institute of Technology.

Location: Room 102
Abstract: Foundation models brought a paradigm shift on representation learning and the deep learning community. In my talk, I will examine the role of foundation models in medical imaging, focusing on their potential to unify diverse tasks through large-scale, generalist architectures. While these models achieve strong performance, their deployment in healthcare raises challenges related to data limitations, privacy, validation, and trust. We will also discuss domain-specific models for imaging, along with efficient adaptation techniques to adapt such models on domains that they have not been trained on. The presentation will also address key issues of reliability and interpretability, highlighting approaches like conformal prediction and counterfactual intervention to improve uncertainty estimation and model transparency. Overall, the talk will emphasize that despite their promise, foundation models require robust evaluation and trustworthy design to ensure safe and effective use in clinical settings.

Speaker: Maria Vakalopoulou is an assistant professor (MCF) in applied mathematics at CentraleSupelec, University Paris Saclay in France and the group leader of the biomathematics group of MICS Laboratory focusing on mathematical modeling in Life Sciences. She is affliated with Inria Saclay in France and Archimedes Unit in Greece. Her main research interest include the development of computational methods for image perception focusing on earth observation and medical applications. Before that, she was a postdoctoral student at CentraleSupelec, where she worked with Nikos Paragios. She completed her PhD at the Remote Sensing Laboratory at the School of Rural, Surveying and Geo-Informatics Engineering of the National Technical University of Athens under the supervision of Konstantinos Karantzalos.

Location: NCS 220
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