Le Hou Dissertation Defense: Deep Learning for Digital Histopathology across Multiple Scales

ABSTRACT: Histopathology is the study of tissue changes caused by diseases such as cancer. It plays a crucial role in disease diagnosis, survival analysis and development of new treatments. Using computer vision techniques, I focus on multiple tasks for automated analysis in digital histopathology images, which are challenging because histopathology images are heterogeneous and complex, due to the large variation of hundreds of cancer types in gigapixel resolution. In this thesis, I show how histopathology image analysis tasks can be viewed in three scales: Whole Slide Image (WSI)-level, patch-level and cellular-level, and present my contributions in each resolution level.

BIO: WSI-level analysis such as classifying WSIs into cancer types is challenging, because conventional classification methods such as off-the-shelf deep learning models cannot be applied directly on gigapixel WSIs due to computational limitations. I contribute a patch-based deep learning method that classifies gigapixel WSIs into cancer types and subtypes with close-to-human performance. This method is useful for computer-aided diagnosis. At patch-level, I contribute a novel method for histopathology image patch classification. On the task of identifying Tumor Infiltrating Lymphocyte (TIL) regions, the prediction result of this method correlates to the survival rate of patients. At cellular-level, I contribute novel methods for nucleus classification and roundness regression, which are interpretable features for histopathology studies. With this method, I generated a large-scale dataset of segmented nuclei, in WSIs from a large publicly available digital histopathology image dataset, to help advance histopathology research.

Imagine machines that can see beyond human limitations--drones locating hidden survivors, cameras predicting structural failures, or medical devices detecting tumors beneath the skin. Traditional vision systems are constrained by the boundaries of human perception, missing vast information present in light interactions. This talk explores the development of advanced vision systems that capture underutilized dimensions of light, model intricate light-scene interactions, and extract hidden 3D information--around corners, beneath surfaces, and at high speeds. By jointly developing novel imaging hardware, efficient rendering models, and physics-based learning algorithms, we aim to transcend conventional vision capabilities--unlocking critical applications in autonomous navigation, structural monitoring, and non-invasive medical imaging.

Speaker Bio:


Akshat Dave is a Postdoctoral Associate at MIT Media Lab in the Camera Culture group working with Prof. Ramesh Raskar. He received his Ph.D. from Rice University ECE Department in 2023 where he was advised by Prof. Ashok Veeraraghavan. His research lies at the intersection of applied optics, computer graphics, and computer vision. His research focuses on developing vision systems that go beyond human perception. His work has been recognized by Rice University's Best Thesis Award, OSA Best Paper Prize, and fellowships by Texas Instruments and Qualcomm.
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Abstract: Computational pathology has revolutionized cancer diagnosis and research through the analysis of digitized whole slide images (WSIs). However, the giga-pixel size of these images presents profound technical challenges, creating two intertwined bottlenecks: computational inefficiency and label inefficiency. The immense data scale makes standard end-to-end (E2E) training of deep neural networks infeasible due to prohibitive GPU memory requirements, while the reliance on expert pathologists for annotations makes obtaining high-quality labeled data a tedious and expensive process. This proposal confronts these dual challenges by developing a series of novel model architectures, training paradigms, and self-supervised learning methods designed to create a more efficient and effective framework for WSI analysis.

To improve computational efficiency, this proposal 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 that reduces the number of trainable parameters, memory consumption, and training time by fine-tuning only few prompts to guide large pre-trained models. Third, this work advances the efficient architecture on WSIs by developing novel State-Space Models (SSMs). It proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy inherent in 1D models. Fourth, to address the inefficiency of multi-directional scans in Mamba models, including 2DMamba, it presents Locally Bi-directional Mamba (LBMamba), which introduces a novel, hardware-aware local backward scan that integrates bi-directional scan into a single forward pass, significantly improving throughput performance trade-off. Lastly, it proposes an extension to the LBMamba, warp-level Bi-directional Mamba (WLBMamba) that extends the thread-level bidirectional scan to warp-level bidirectional scan that further improves the throughput performance trade-off.

To improve label efficiency, this proposal proposes a Precise Location-based Matching strategy for self-supervised dense contrastive learning. By allowing a local patch in one augmented view to match multiple overlapping patches in another, creates a more accurate correspondence, leading to superior feature representations for dense prediction tasks like segmentation and detection.

In summary, this proposal 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: Old Computer Science Room 2114

Zoom: https://stonybrook.zoom.us/j/95187903649?pwd=tV0CNxLu1QKqw7hGmcE1h0rJ2C6n1b.1
Meeting ID: 951 8790 3649 | Passcode: 488916

OVERVIEW


This workshop, Expanding Horizons in AI with HPC, aims to explore the dynamic intersection of AI and HPC, focusing on how advanced computing can accelerate AI research and applications. As AI models become more complex and data-intensive, traditional computing systems struggle to meet the demand for scalability, efficiency, and speed. HPC offers a solution by providing the necessary infrastructure for training large-scale models, enhancing AI algorithms, and enabling breakthroughs in fields such as deep learning, natural language processing, and autonomous systems.

Through a combination of expert presentations and panel discussions, participants will gain insights into the latest developments in AI-HPC integration. Attendees will also engage in discussions on the future trends, challenges, and ethical considerations surrounding the use of HPC in AI.

The workshop is designed for AI researchers, data scientists, engineers, and HPC professionals seeking to enhance their understanding of how high-performance computing can drive innovation and expand the potential of AI in solving complex, real-world problems.

The workshop will be held at the Wang Center at Stony Brook University.

https://you.stonybrook.edu/hpcai/

PROGRAM

The program features sessions on HPC Architectures for AI, AI Applications in HPC, LLM's in HPC, and AI in HPC Workflows, and open student presentations. The tentative program and list of confirmed speakers is available at https://you.stonybrook.edu/hpcai/program/.

CALL FOR STUDENT PRESENTATIONS & PARTICIPATION

We are excited to offer students the opportunity to present their work in the area of high-performance scientific computing and artificial intelligence at the workshop. We are calling for students to submit their talk proposals (Name + Title) by April 15 to hpc_ai_workshop@stonybrook.edu. The committee will select the best submission to be presented at the workshop. Accepted speakers will be notified by April 22, 2025.

All students, regardless of whether they are presenting, may reach out to hpc_ai_workshop@stonybrook.edu for financial support to cover travel and lodging costs.

REGISTRATION

Registration is available at https://www.eventbrite.com/e/expanding-horizons-in-ai-with-hpc-tickets-1256469978529?aff=oddtdtcreator until May 2nd. The registration fee covers the workshop participation and the social event in the evening of May 9.

Regular registration: $200
Student registration: $100


IMPORTANT NOTE

The registration fee was meant to cover the room rent, catering, and dinner. Thanks to an RF seed grant, we are able to drop the registration fees for SBU students and staff/faculty. We still ask for an informal registration via email to hpc_ai_workshop@stonybrook.edu until April 27, so we can plan for catering and dinner.
Please get in touch with us if you have already registered as an SBU student/faculty/staff member for the workshop so we can handle any reimbursement.

The program is now online at https://you.stonybrook.edu/hpcai/program/.

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.

AI and Edge Processing Co-Design for Radiation Detectors

Abstract: Artificial Intelligence (AI) offers exciting new opportunities for enhancing the performance of radiation detectors, ultimately leading to improved physics outcomes. Furthermore, with the explosive growth in data rates being seen by next-generation radiation detectors, deployment of AI algorithms at the edge by embedding intelligence within or near the detector front-end can be transformative. Such integration enables real-time data filtering, noise suppression, feature extraction, and adaptive control, while reducing downstream bandwidth and power consumption. This talk will cover three efforts that bring AI to the forefront of detector technology. First, we demonstrate how AI-based algorithms can be used for position reconstruction in virtual Frisch-grid (VFG) detectors by compensating for charge transport distortions and detector non- uniformities, leading to significantly enhanced fidelity in imaging of gamma-ray interactions. Second, we present a smart readout application specific integrated circuit (ASIC) that combines digital signal processing with co-designed artificial neural networks to enable on-chip regression and classification of detector signals, while meeting stringent constraints on accuracy, speed, and area. Finally, we introduce our recent efforts related to the development of electro-photonic processing architectures that integrate CMOS electronics and silicon photonics for near-sensor AI acceleration. These architectures aim to leverage cross-disciplinary co-design from algorithms to hardware, to achieve low latency and energy-efficient processing of detector data.

Biography: Dr. Prashansa Mukim is an early-career researcher in the Instrumentation Department at BNL, where she works on the design of front-end electronics for extreme environments and the development of co-design methodologies for novel processing modalities and beyond-CMOS technologies. Prior to joining BNL, she was a post-doctoral researcher at the National Institute of Standards and Technology (NIST) in Maryland, where she focused on characterizing the properties of CMOS circuits at cryogenic temperatures and applications of spintronic devices for neuromorphic computing. She received her Ph.D. in Electrical and Computer Engineering from the University of California, Santa Barbara, in 2021.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1608585935?pwd=UemgEkqijfNf3vIJIGuOa2MdjsunaT.1

Meeting ID: 160 858 5935
Passcode: 076033

Abstract: The advent of ChatGPT has redrawn the boundary of pedagogical discourse, where the dyadic configuration of teacher-student has, for many, become triadic -- one that includes AI as an relevant third party, not to be missed or dismissed. Within applied linguistics, AI-focused research has predominantly targeted the teaching and learning of writing (Fang & Han, 2025). The work on AI and speaking, on the other hand, has largely involved perception studies documenting its positive impact on learners' willingness to communicate (Goh & Aryadoust, 2025). In this talk, I explore the role of AI in the teaching and learning of speaking, and in particular, the development of interactional competence. Based on a corpus of learner-AI interactions, I demonstrate the ways in which ChatGPT excels and fails at acting as a useful conversation partner, with a view towards furthering our ongoing deliberation on the affordances and constraints of AI in language education.

Speaker: Hansun Zhang Waring (Teachers College, Columbia University)

Hansun Zhang Waring is Professor of Linguistics and Education at Columbia University and founder The Language and Social Interaction Working Group (LANSI). As an applied linguist and a conversation analyst, Hansun is interested in all things interaction -- (second language) pedagogical interaction, communication with the public, parent-child interaction, and human-AI interaction (HAI). Her work has appeared in leading journals in applied linguistics and discourse analysis as well as numerous book volumes, some of which she (co-)authored or co-edited. She is on the editorial boards of Chinese Language and Discourse (CLD), Classroom Discourse (CD), and International Review of Applied Linguistics (IRAL).

Location: Wang Center, Lecture Hall #1

If you need special accommodation, please contact chikako.nakamura@stonybrook.edu.