Abstract: Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology.

Speaker: Qin Ren

Location: https://stonybrook.zoom.us/j/97458849045?pwd=SREklaxa7EFhKaK6TeRXgQPH64vrQJ.1&jst=2
CSE 600 Seminar Series | Fall 2025

Abstract: Imagine machines that can see the invisible: drones locating wildfire survivors, cameras predicting building failures, and smartphones detecting skin tumors. These applications lie beyond today's vision systems, which focus only on human-visible information. In this talk, I argue that a wealth of scene information is hidden in light properties invisible to the human eye, such as the travel time of photons and polarization of light waves. I will present how co- designing camera hardware, graphics models, and learning algorithms unlocks these invisible properties to create superhuman vision systems. I will present three superhuman vision capabilities: seeing around blind corners, turning objects into cameras, and extracting internal stress fields. By analyzing faint light reflections on diffuse walls and shiny objects, we create virtual cameras that reveal scenes hidden from the line of sight - enabling autonomous systems to navigate safely. Using the polarization of light, we recover mechanical stress fields hidden inside objects - opening new possibilities for non-destructive material characterization. These capabilities point toward a future where machines can see the invisible: around us, beneath our bodies, and beyond our scientific understanding.

Bio:
Akshat Dave is an Assistant Professor in the Department of Computer Science at Stony Brook
University, USA. His research lies at the intersection of applied optics, computer vision, and
machine learning. His work has been recognized by Rice University's Best Thesis Award, Optica Best Paper Prize, SIGGRAPH Asia Doctoral Consortium, and fellowships by Qualcomm, Texas Instruments, and INK Global Foundation. Prior to Stony Brook, he was a Postdoctoral Associate at MIT Media Lab. He holds a Ph.D. from Rice University and a Masters and a Bachelors from Indian Institute of Technology Madras.

George Em Karniadakis received his SM and PhD from Massachusetts Institute of Technology. He was appointed lecturer in the Department of Mechanical Engineering at MIT in 1987 and subsequently he joined the Center for Turbulence Research at Stanford/Nasa Ames. He joined Princeton University as assistant professor in the Department of Mechanical and Aerospace Engineering and as associate faculty in the program of applied and computational mathematics. He was a visiting professor at Caltech in 1993 in the Aeronautics Department and joined Brown University as associate professor of applied mathematics in the Center for Fluid Mechanics in 1994. After becoming a full professor in 1996, he continues to be a visiting professor and senior lecturer of Ocean/Mechanical Engineering at MIT. He is an AAAS fellow (2018), fellow of the Society for Industrial and Applied Mathematics (2010), fellow of the American Physical Society (2004), fellow of the American Society of Mechanical Engineers (2003) and associate fellow of the American Institute of Aeronautics and Astronautics (2006). He received the Alexander von Humboldt award in 2017, the Ralf E Kleinman award (2015), the J. Tinsley Oden Medal (2013), and the CFD award (2007) from the US Association in Computational Mechanics. His h-index is 103, and he has been cited over 52,000 times.


Abstract:
Karniadakis will present a new approach to develop a data-driven, learning-based framework for predicting outcomes of physical and biological systems, governed by PDEs, and for discovering hidden physics from noisy data. He will introduce a deep learning approach based on neural networks (NNs) and generative adversarial networks (GANs). He will also introduce new NNs that learn functionals and nonlinear operators from functions and corresponding responses for system identification. Unlike other approaches that rely on big data, here we learn from small data by exploiting the information provided by the physical conservation laws, which are used to obtain informative priors or regularize the neural networks. He will demonstrate the power of PINNs for several inverse problems in fluid mechanics, solid mechanics and biomedicine including wake flows, shock tube problems, material characterization, brain aneurysms, etc., where traditional methods fail due to lack of boundary and initial conditions or material properties. He will also present a new NN, DeepM&Mnet, which uses DeepOnets as building blocks for multiphysics problems, and he will demonstrate its unique capability in a 7-field hypersonics application.  

To register and for more information, click here.  
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

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.

At our Oct 7 Mixer, BNL's newly minted interim director, John Hill will be present to give opening remarks and kick us off on a new year of impactful scientific AI collaborations.

Abstract: Weather extremes and strong seasonal-to- subseasonal variability pose growing challenges to urban populations, infrastructure, and energy systems. Yet, most cities remain data deserts: routine weather observations are sparse, with stations concentrated at airports rather than within the urban core. This lack of coverage limits our ability to monitor and predict fine-scale urban weather patterns precisely where they matter most. We present a new AI-driven framework for optimal sensor placement and urban weather monitoring. Unlike traditional approaches, our method leverages physics- based simulations together with Bayesian experimental design principles, but does so using a computationally efficient variational inference strategy that makes large-scale optimization tractable. This allows us to guide sensor networks in a way that minimizes information loss while capturing spatiotemporal variability at city scales. Applied to Phoenix, Arizona, our framework outperforms random sensor placement strategies, especially when only a limited number of sensors can be deployed. Importantly, the same AI models that guide sensor placement also function as a real-time nowcasting tool, providing urban weather information over the entire domain, beyond sensor locations. Together, these capabilities offer a scalable pathway to reduce urban data deserts, enhance monitoring of weather extremes, and improve resilience planning for energy, transportation, and public health systems.

Biography: Dr. Katia Lamer is an atmospheric scientist and the Director of the Center for Multiscale Applied Sensing at Brookhaven National Laboratory. Originally from Canada, she earned her B.S. and M.S. in Atmospheric and Oceanic Sciences from McGill University and a Ph.D. in Meteorology from Penn State University. Her research focuses on atmospheric boundary layer processes and remote sensing technologies, with a strong emphasis on data science. At Brookhaven, she is known for her work with the CMAS mobile observatories and its facility that connect fundamental atmospheric science to real-world applications, improving weather prediction, environmental monitoring, and urban climate resilience. Her work has been featured in public outlets such as New Scientist and Wired. Dr. Lamer also serves as an invited member of the World Meteorological Organization's Data Assimilation and Observing Systems Working Group, and the American Meteorological Society's Boundary Layer and Turbulence Committee. puting, communications and sensing, all enabled by AI.

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

Abstract: This dissertation addresses the methodological disconnect between Natural Language Processing (NLP) and human-centric analysis by shifting the unit of analysis from document to human behavior in two broad respects: (i) time-ordering: modeling documents as sequential person-indexed behavioral observations, and (ii) person-level semantics: evaluation and explainability of models by their latent structure of psychological constructs rather than just its predictive accuracy against narrow proxy measures. First, we consider the most basic implication of language as a person's behaviors when measuring their psychological constructs: relationship between language sample size and model's predictive performance. We empirically show that the state-of-the-art transformers are often over-parameterized for typical NLP dataset sizes and can be reduced in dimensionality without performance loss. Establishing the author as the unit of analysis naturally allows us to treat their behavior as a time-ordered sequence. Second, we introduce a longitudinal evaluation framework that establishes ecologically valid evaluation settings, namely, cross-sectional and prospective generalization, and separates error measurement of the model into within-person dynamics and between-person differences. We demonstrate that traditional NLP evaluations based on random document splits can yield reversed conclusions under ecologically valid generalization settings. To address this, we develop models that capture the trajectory of mental states (e.g., mood shifts) rather than static traits. Third, moving into person-level semantics, we evaluate the latent structure of large language models using a novel machine behavior analytic framework. We find that while GPT-4 achieves high predictive correlation with self-reports, its latent symptoms structure diverges from clinical understanding. Finally, we propose a method for modeling multidimensional behaviors, embedding concurrent behavioral signals alongside language to predict future states. Taken together, this work suggests that operationalizing language as behavior advances NLP methods into a rigorous instrument for valid psychological inquiry.

Speaker: Adithya Ganesan

Location: Join Zoom Meeting (ID: 99021939129, Passcode: 569493)
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Place:  https://stonybrook.zoom.us/j/99167126152?pwd=TFpEYzM0aFhiOFJxSFJEb1JSS3YyQT09  

Time: 3 PM EST - Dec, 16th, 2020 

Abstract: 

Shadows provide useful cues to analyze visual scenes but also hamper many computer vision algorithms such as image segmentation, object detection, or tracking. For those reasons, shadow detection and shadow removal have been well-studied in computer vision.

Early work on shadow detection and removal focused on physical illumination models of shadows. These methods can express, identify, and remove shadows in a physically plausible manner. However, these models are often hard to optimize and are slow during inference due to their reliance on hand-designed image features. Recently, deep-learning approaches have achieved breakthroughs in performance for both shadow detection and removal. They learn to extract useful features through training while being extremely efficient during inference. However, these models are data-dependent, opaque, and ignore the physical aspects of shadows. Thus they often lack generalization and produce inconsistent results.

We propose incorporating physical illumination constraints of shadows into deep-learning models. These constraints force the networks to more closely follow the physics of shadows, enabling them to systematically and realistically modify shadows in images. For shadow detection, we present a novel Generative Adversarial Network (GAN) based model where the generator learns to generate images with realistic attenuated shadows that can be used to train a shadow detector. For shadow removal, we propose a method that uses deep-networks to estimate the unknown parameters of a shadow image formation model that removes shadows. The system outputs high-quality shadow-free images with little or no image artifacts and achieves state-of-the-art performance in shadow removal when trained on a fully-supervised setting. Moreover, the system is easy to train and constrain since the shadow removal mapping is strictly defined by the simplified illumination model with interpretable parameters. Thus, it can be trained even with a much weaker form of supervision signal. In particular, we show that we can use two sets of patches, shadow and shadow-free, to train our shadow decomposition framework via an adversarial system. These patches are cropped from the shadow images themselves.
Therefore, this is the first deep-learning method for shadow removal that can be trained without any shadow-free images, providing an alternative solution to the paired data dependency issue. The advantage of this training scheme is even more pronounced when tested on a novel domain such as video shadow removal where the method can be fine-tuned on a testing video with only the shadow masks generated by a pre-trained shadow detector and further improves shadow removal results.