Stony Brook Radiology Department Invites you to the AI Research Seminar


Abstract: This talk traces the evolution of AI in neuroradiology through three connected stages: Precision Care, General Medical Intelligence, and Discovery. It moves from multimodal deep learning for stroke outcome prediction, to large-scale foundation models and agent-based medical AI, to imaging biomarkers such as brain aging derived from routine scans. It closes with early-stage work on Galen, a framework for reproducible, scalable, and transparent biomedical imaging AI development and analysis.

Speaker: Yongkai Liu, PhD, Instructor, Department of Radiology (Neuroimaging & Neurointervention), Stanford University

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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: Large Language Models (LLMs) have revolutionized how people interact with knowledge, offering unprecedented opportunities to accelerate the pace of scientific discovery. In this talk, I will discuss my research on the synergy between LLMs and scientific knowledge--specifically how these models extract, induce, and verify knowledge to automate the research lifecycle. First, I will cover our work on improving knowledge extraction from vast scientific literature, focusing on enabling models to comprehend long documents in a cost-efficient and comprehensive manner. I will describe a novel paradigm for representing document-level structured information as question-answer pairs and how we address the challenges of long-context understanding by leveraging global context through retrieval-augmented modeling. Next, I present our pioneering work on using LLMs for new scientific hypothesis generation. We introduce a framework employing reinforcement learning with fine-grained reward modeling and adaptive controllers.
This approach balances novelty, feasibility, and effectiveness to generate inspiring and actionable research hypotheses. Finally, I will discuss work on the first LLM Scientist for machine learning research. I will demonstrate how LLMs can move beyond hypothesis generation to participate in the execution and validation of scientific hypotheses, ensuring that the discovered knowledge is not only innovative but also grounded and verified.

Bio: Xinya Du is a tenure-track assistant professor at UT Dallas Computer Science Department. He earned a Ph.D. degree from Cornell University and was a Postdoctoral Research Associate at the University of Illinois (UIUC). He has also worked at Microsoft Research, Google Research, and Allen Institute AI. His research is on large language models, deep learning, and their applications in science.His work has been published in leading NLP and ML conferences (ACL, ICLR, NeurIPS). His research has received multiple recognitions, including a Best Paper Award at AAAI AI for Research and a Best Poster Award at ICML AI for Science workshop. His work was included in the list of Most Influential ACL Papers and has been covered by major media like New Scientist. He was named a Spotlight Rising Star in Data Science by the University of Chicago and is the recipient of several prestigious awards, including the Amazon Research Award, Cisco Research Award, Open Philanthropy Award, and the NSF CAREER Award.

Location: NCS 120

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.

Machine Learning for Seismic Low Frequency Extrapolation

Abstract: The cycle skipping problem that plagues seismic inversion can be mitigated by utilizing low-frequency seismic data, which captures the kinematics of wave propagation, in conjunction with a reasonable initial velocity model. However, seismic sources and receivers are band-limited and cannot provide signals down to 0 Hz. To improve solution of the seismic inverse problem one can synthesize the missing low-frequency content by solving a regression problem using machine learning (ML). The recorded high-frequency (HF) seismic data is the input and the ML models are trained to predict the missing low-frequency (LF) seismic data. Deep learning models utilizing convolutional neural networks (CNNs) and generative adversarial networks (GANs) demonstrate important capabilities for LF extrapolation. However, such models require powerful hardware and careful training. We explore the feasibility of using less costly ML models such as a random forest, Gaussian process surrogates, and gradient boosting as alternatives to computationally expensive deep learning models.

Biography: Sue Minkoff is Chair of Applied Mathematics at Brookhaven National Laboratory. From 2012-2024 she was a Professor of Mathematical Sciences and an Affiliated Professor in the Departments of Sustainable Earth Systems Sciences and Science and Mathematics Education at the University of Texas at Dallas. From 2000-2012 she served on the faculty in the Department of Mathematics and Statistics at the University of Maryland, Baltimore County. She received her doctorate in Computational and Applied Mathematics from Rice University. From 1995-1997 she was a National Science Foundation-Industrial postdoc joint with the University of Texas at Austin and British Petroleum, and from 1997-2000 she held the von Neumann Fellowship in the Mathematics Department at Sandia National Labs. In 2000 Minkoff was promoted to Senior Member of the Technical Staff in Sandia's Geophysics Department. Minkoff's research interests include scientific computing, inverse problems, uncertainty quantification and digital twins modeling, Earth science, and photonics.

Location: CDS, Bldg. 725, Training Room

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Face Editing with Machine Learning presented by Zhixin Shu

ABSTRACT: The face is the most informative feature of humans and has been a long-standing research topic in Computer Vision and Graphics. Images of faces are also ubiquitous in photography and social media, and people have devoted significant resources to capturing and editing face images. Face editing can be broadly viewed as the encoding, manipulation and the decoding of some representations for face images. The challenges are that we want to manipulate an image in a controllable way and generate results that are both desirable and as realistic as possible. This thesis explores different Machine Learning-based face-editing approaches. I discuss the role of machine learning for achieving desirable edits by learning both the physical aspects as well as the statistical manifold of human faces. In my work for eye-editing, I discuss the importance of understanding multiple physical elements of a face image, such as shape, illumination, pose, etc. In a deep-learning-based approach, I introduce image formation domain knowledge to the construction and training of a neural network. This network provides transparent access to the disentangled representations of the aforementioned physical properties. With this network, we can achieve various face editing tasks in forms of representation manipulation. After that, I introduce Deforming Autoencoders, a network that learns to disentangle shape and appearance in an unsupervised manner. This disentanglement is beneficial for the learning of some other factors of variations, such as illumination and facial expression. In an extension of Deforming Autoencoders, we incorporate non-rigid structure-from-motion to learn a 3D morphable model for faces that only requires an image set for training. At last, I describe an image-to-image network for 3D face reconstruction, which also utilizes structure-from-motion in deep learning. With real face images in training, this network not only reconstructs 3D faces more accurately than prior art but also has better generalization ability in real-life testing cases.
Abstract: Theory-internal work on opacity in phonology has been focused on the challenges these interactions present for one theory (rules, constraints) versus another. But there has also been interest in studying the formal, invariant properties of opaque and other process interactions (Chandlee et al. 2018; Bakovic and Blumenfeld 2024), though these works crucially differ in their underlying assumptions. In this talk I will recontextualize Chandlee et al. (2018)'s result that opaque maps are ISL in light of Bakovic and Blumenfeld (2024)'s recent formal typology of process interactions, and this recontextualization will provide an answer to an open question about the k-value of an interaction map. I will then discuss the implications of this collective formal understanding of opacity for a recent model of lexicon and phonological grammar learning (i.e., Hua and Jardine 2021, Chandlee and Jardine to appear).


Speaker: Prof. Jane Chandlee, Associate Professor in the Department of Linguistics at Haverford College

Location: IACS Seminar room.
Abstract: The capacity to adapt machine learning models to various contexts, information, and objectives is particularly valuable. In this thesis, I focus on developing Class Conditional Guided Models. These are models that can be adaptively biased towards a class of interest via a conditional input. My primary focus lies in the efficiency of these models. They are constructed to require training only once, with the ability to quickly and conveniently adapt during testing time without necessitating fine-tuning or retraining.
Firstly, I propose RelationVAE, a novel generative model designed for few-shot scenarios, utilizing the prior knowledge of class similarity relationships. RelationVAE is designed to condition on the embeddings of the neighbor classes (i.e. classes with similarity relationships), to generate more reliable samples by making them more similar to the neighbor class. This enables adaptation of the generative model to the provided prior knowledge about class relationships.
As a second focus, I introduce scGAN, a shadow segmentation technique that enables adaptation to varying shadow distributions in different testing environments. scGAN is designed to condition on a sensitivity parameter, a scalar, to control the amount of the shadow detected. In the testing phase, the parameter is set to appropriate values, allowing the model to quickly adapt to specific test environments.
In my third contribution, I propose S-SEG, a methodology for fine-grained counting allowing adaptation to different granularities of fine-grained classes. In fine-grained problems, the distinction between classes is subtle and inconsistent across images, leading to variations in the granularity of the target class from one image to another. S-SEG is designed to be conditioned on an additional input, the sensitivity parameter, to control the granularities of the target class during inference.
My fourth contribution is a text-to-image synthesis method which allows controlling the number of the generated objects of a target class. I propose to generate an intermediate condition, the density map, which reflects the number of objects, together with their layout. This intermediate condition is used to effectively guide the generative model to generate objects with accurate counts.

Speaker: Vu Nguyen

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Speaker: Heather J. Lynch


Bio:  Dr. Heather J. Lynch is an Associate Professor of Ecology & Evolution at Stony Brook University. Prior to Stony Brook, Dr. Lynch was an Adjunct Professor of Applied Math and Statistics at UC Santa Cruz and a Research Scientist in the Biology Department at the University Maryland. Dr. Lynch received her A.B. in Physics from Princeton University in 2000, an A.M. in Physics from Harvard University in 2004, and a Ph.D. in Organismal and Evolutionary Biology from Harvard University in 2006. Dr. Lynch's research is focused on spatial population dynamics of Antarctic penguins, with a particular focus on statistical and mathematical models to integrate patchy time series with remote sensing imagery. These data will allow Dr. Lynch and colleagues to develop mathematical models to explore how coloniality constrains the colonization and extinction of individual habitat patches and, ultimately, the metapopulation dynamics of colonial seabirds.