Abstract: Computational pathology has revolutionized cancer diagnosis and research through the analysis of digitized whole slide images (WSIs). However, their giga-pixel size creates two intertwined bottlenecks: computational inefficiency, as prohibitive GPU memory makes standard end-to-end (E2E) training infeasible, and label inefficiency, as expert annotation is tedious and expensive. This dissertation confronts both challenges through novel architectures, training paradigms, and self-supervised learning methods for efficient WSI analysis.
To improve computational efficiency, this dissertation first introduces a locally supervised learning paradigm that enables E2E training on entire WSIs by partitioning a network into gradient-isolated modules, circumventing the memory bottleneck of backpropagation. Second, it presents Prompt-MIL, a parameter-efficient fine-tuning framework training only a few prompts to guide large pre-trained models, reducing trainable parameters, memory, and training time. Third, this work proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy in 1D models. Fourth, it presents Locally Bi-directional Mamba (LBMamba), whose hardware-aware local backward scan integrates bi-directional scanning into a single forward pass, improving the throughput-performance trade-off of Mamba models.
To improve label efficiency, this dissertation proposes a precise location based matching strategy for self-supervised dense contrastive learning, which allows a local patch in one augmented view to match multiple overlapping patches in another, producing more accurate correspondences and superior features for dense prediction tasks like segmentation and detection. Additionally, to better scale multi-channel cell imaging modalities, this dissertation introduces ChannelSFormer, a channel-agnostic vision transformer that disentangles spatial and channel-wise reasoning through divided attention and channel class token, enabling effective representation learning across variable channel configurations in both self-supervised and supervised settings.
In summary, this dissertation presents a holistic investigation into the efficiency bottlenecks in computational pathology. Through these combined contributions in model architecture, training paradigms, and self-supervised learning, this work establishes a more scalable, efficient, and powerful computational framework for analyzing giga-pixel pathology images.

Speaker: Jingwei Zhang

Location: NCS 220

Zoom: https://stonybrook.zoom.us/j/93175806292?pwd=xbtxnQyYGoThz5B1DyJxJxPF9lxiJE.1
Meeting ID: 931 7580 6292
Passcode: 314091
The North East AI Agents Day Organizing Committee invites you to '2026 AI Agents Day.'

The goal of this workshop is to offer a comprehensive overview of AI agents, bring ML, Systems, and HCI research communities together to share progress, discuss common problems and evaluation setups, and identify opportunities for collaboration. We aim to bring together attendees from diverse disciplines to foster interdisciplinary collaboration and discuss open research questions.

Location: Jane Street Offices, New York

Register here.

Jerome Liang, PhD 

Professor of Radiology, Biomedical Engineering, Electric and Computer Engineering, and Computer Science 

Co-Director of Research 

Department of Radiology 


Artificial intelligence, machine learning and computer-aided diagnosis in cancer Imaging 

February 11, 2021 

12:00pm - 1:00pm 

Virtual Seminar - Zoom 

https://stonybrook.zoom.us/j/98155629970?pwd=YzRvcnJnTlNTT1E5ak1oZEJvWTZHQT09 

Meeting ID: 981 5562 9970 

Passcode: 950410 

Host: 

Wei Zhao, PhD 

Professor of Radiology and Biomedical Engineering 

Educational Objectives  

Upon completion, participants should be able to:  

(1) Learn different medical image representations of cancer attributes, such as heterogeneity, high tendency to grow, etc.  

(2) Learn how computer (machine) can be trained (or programmed) to recognize the image representations.  

(3) Learn how artificial intelligence can drive the machine learning to maximize the performance of computer-aided diagnosis (CADx).  

Disclosure Statement  

In compliance with the ACCME Standards for Commercial Support, everyone who is in a position to control the content of an educational activity provided by the School of Medicine is expected to disclose to the audience any relevant financial relationships with any commercial interest that relates to the content of his/her presentation.  

 

The speaker, Jerome Liang, PhD, the planners; and the CME provider have no relevant financial relationship with a commercial interest (defined as any entity producing, marketing, re-selling, or distributing health care goods or services consumed by, or used on, patients), that relates to the content that will be discussed in the educational activity.  

 

CONTINUING MEDICAL EDUCATION CREDITS  

The School of Medicine, State University of New York at Stony Brook, is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.  

 

The School of Medicine, State University of New York at Stony Brook designates this live activity for a maximum of 1.0 AMA PRA Category 1 Credits™. Physicians should only claim credit commensurate with the extent of their participation in the activity.  

 

Should you be logging in Zoom by using your tablet or mobile device, please be sure to add your Full Name and/or Email for CME credit. 

Abstract: Large Language Models (LLMs) have transitioned from standalone prediction interfaces into integrated systems that incorporate content protection, external knowledge retrieval, and multi-step reasoning. While these functional layers expand model capabilities, they also introduce complex, inter-component dependencies that create novel and systemic security risks. This research provides a systematic deconstruction of the structural vulnerabilities emerging across these functional layers.

In this proposal, we evaluate the security boundaries of LLM systems through three pivotal dimensions:
The Content Layer: We present Watermark under Fire, revealing the inherent fragility of content-based tracing mechanisms under adaptive perturbations and highlighting the limitations of surface-level safety measures.
The Retrieval Layer: We introduce GraphRAG under Fire to examine the security of topology-aware knowledge integration. We reveal how graph-based indexing can be exploited as a structural lever for high-success poisoning attacks.
The Reasoning Layer: We detail AutoRAN, the first framework demonstrating the hijacking of internal safety reasoning in Large Reasoning Models (LRMs). This work proves that the transparency of the reasoning process itself creates a critical and exploitable attack surface.

Collectively, these studies demonstrate a systemic failure of add-on safety mechanisms in securing the broader LLM ecosystem. By identifying recurring patterns of exploitation across different system layers, this research provides the necessary foundation for transitioning from reactive patching to a more unified and architecturally-grounded approach to AI trustworthiness.

Speaker: Jiacheng Liang

Zoom: https://stonybrook.zoom.us/j/6669990420?pwd=dkY0eEw5YXpPSWo3RUE4OE1oVW90UT09&omn=97367037382
Meeting ID: 666 999 0420
Passcode: 075299
Abstract: Recent work in NLP uses debates between multiple LLMs to arrive at a more accurate conclusion. Earlier chain-of-thought prompting also shows improvements in accuracy when the model is asked to provide step-by-step reasoning in its response. Many publications since have developed strategies to improve the reasoning of model output with the goal of generating a more accurate result. However, even when asked to provide problem solving steps, the content of the reasoning provided by models is not well studied for all tasks and sometimes contains errors or conflicting statements even when the final result is correct. In fact, when evaluated across reasoning tasks, evidence shows that LLMs are not learning how to reason but are instead mimicking relevant solutions from their training sets.
By studying and evaluating the argumentation that LLMs provide, we can determine factors that may benefit or hinder the model's ability to give a complete, cohesive, and thorough answer. While there are signs that LLMs pattern match, finding where, when, and why this fails is valuable, as there may be ways to help the model imitate solutions that are more relevant to the task it is attempting to solve. Determining when pattern matching is not enough could show an area of improvement for future generations of LLMs. This research may separately aid in work on human-(AI)agent and inter-agent interaction. Specifically, frameworks could be used to determine when and why other models or humans are convinced by LLM-generated responses and which argument methods cause other models to change their response. Our current research in systematic versus heuristic cues shows that large language models sometimes present systematic or heuristic reasoning patterns based on prompting. Future research aims to explore other methods of classifying argumentation.

Speaker: Kiera Gross

Joining link: https://meet.google.com/xae-ywpv-udo
Professor Nanpeng Yu from UC Riverside present Machine Learning and Big Data Analytics in Power Distribution Systems.

Abstract: The electric utility industry is being swamped by petabytes of data coming from various sources such as smart meters, phasor measurement units, SCADA systems, geographical information systems and customer management systems. The primary and secondary value embedded in the complex and heterogeneous data sets from power distribution systems is immense. However, algorithms and applications for unlocking the potential of big data in power systems are at an early stage of development. This talk discusses the recent advancement of machine learning algorithms and big data analytics methods in power distribution systems. In particular, we will explain how to develop hybrid algorithms, which synergistically combine the merits of state-of-the-art machine learning algorithms and physical model-based methods. We will take a deep dive into the following applications: network topology identification, electricity theft detection, estimation of behind-the-meter solar generation and data-driven distribution system controls.

Bio: Dr. Nanpeng Yu received his B.S. in Electrical Engineering from Tsinghua University, Beijing, China, in 2006. Dr. Yu received his M.S. degrees in Electrical Engineering and Economics and Ph.D. degree from Iowa State University in 2010. Before joining University of California, Riverside, Dr. Yu was a senior power system planner and project manager at Southern California Edison from Jan, 2011 to July 2014.

Currently, he is an Associate Professor in the Department of Electrical and Computer Engineering at the University of California, Riverside, CA. Dr. Yu is the recipient of the Regents Faculty Fellowship and Regents Faculty Development award from University of California. He received multiple best paper awards from IEEE Power and Energy Society General Meeting, IEEE Power and Energy Society Grand International Conference and Exposition Asia and the Second International Conference on Green Communications, Computing and Technologies.

Dr. Yu is the director of Smart City Innovation Laboratory at UC Riverside. He currently serves as the vice chair of the distribution system operation and planning subcommittee of IEEE Power and Energy Society and the co-chair for IEEE Big Data Applications in Power Distribution Networks Task Force. Dr. Yu currently serves as the associate editor for IEEE Transactions on Smart Grid and International Transactions on Electrical Energy Systems.

Abstract:

Conventional approaches to scientific discovery often prioritize building larger sensors, gathering more data, and scaling up computational power. In this talk, I will present a complementary perspective: extracting insights hidden in the data we already have. The key lies in using AI not as a black-box predictor, but as a tool for interpreting data through its underlying physical process.

I will demonstrate how AI, when integrated with the physics of light propagation, can serve as a computational lens to overcome fundamental limitations in fields ranging from biomedicine to astrophysics. Specifically, I will showcase two compelling applications: non-invasive imaging through scattering biological tissues, and detecting faint exoplanets against the overwhelming brightness of their host stars.

These methods represent a departure from traditional learning-based approaches that rely on fitting models to training labels and hoping for generalization. Instead, with physics-informed strategies that decode how light propagates, we can transform raw measurements into scientifically meaningful insights--without requiring costly hardware upgrades or human-annotated datasets. Finally, I will outline future directions for combining AI with physical principles, enabling us to unlock more phenomena once considered hidden and accelerating discoveries in healthcare, astronomy, and beyond.

Short Bio:

Brandon Y. Feng is a Postdoctoral Associate at MIT Computer Science and Artificial Intelligence Laboratory (CSAIL) and a Visiting Scientist at the Harvard-Smithsonian Center for Astrophysics. His research bridges artificial intelligence and physics to expand the limits of human and machine vision. He develops AI-driven methods that reveal hidden patterns in complex visual data, driving breakthroughs in areas such as exoplanet detection and imaging through scattering tissues. His work has been published in top venues, including Science Advances, CVPR, ICCV, ECCV, and NeurIPS, and has been featured in Science.org, New Scientist, and Phys.org. He holds a Ph.D. in Computer Science from the University of Maryland, along with a B.A. in Computer Science and Statistics and an M.S. in Statistics from the University of Virginia.

Location: NCS 220
DeepMath Conference on the Mathematical Theory of Deep Neural Networks Recent advances in deep neural networks (DNNs), combined with open, easily-accessible implementations, have made DNNs a powerful, versatile method used widely in both machine learning and neuroscience. These advances in practical results, however, have far outpaced a formal understanding of these networks and their training. The dearth of rigorous analysis for these techniques limits their usefulness in addressing scientific questions and, more broadly, hinders systematic design of the next generation of networks. Recently, long-past-due theoretical results have begun to emerge from researchers in a number of fields. The purpose of this conference is to give visibility to these results, and those that will follow in their wake, to shed light on the properties of large, adaptive, distributed learning architectures, and to revolutionize our understanding of these systems.​​​
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https://stonybrook.zoom.us/meeting/register/tJMvd-irqTotGtQONZqerPf_TnhXcx8t2sA1