Abstract: Many foundation models for digital pathology have been released recently. Benchmarking available methods then becomes paramount to get a clearer view of the research landscape. For this reason, we introduce THUNDER, a tile-level benchmark for digital pathology foundation models, allowing for efficient comparison of many models on diverse datasets with a series of downstream tasks, studying their feature spaces and assessing the robustness and uncertainty of predictions informed by their embeddings. Such foundation models are often used as feature extractors and combined with Multiple Instance Learning (MIL) aggregators at downstream time. Such aggregation must be efficient and reliable. We will focus on two specific examples of this: (I) HistAug, a fast and efficient generative model for controllable augmentations in the latent space of foundation models to perform data augmentation for MIL, and (ii) CAR-MIL, a method based on counterfactual attention regularisation to improve the reliability of attention maps of MIL methods.

Short-bio: Pierre Marza is a Postdoctoral Researcher at CentraleSupelec in the Biomathematics team of the MICS lab, studying Computer Vision and Deep Learning for Medical Imaging, with a focus on Digital Pathology. Prior to this, he was a PhD student at INSA Lyon, in the LIRIS and CITI labs, advised by Christian Wolf, and co-advised by Laetita Matignon and Olivier Simonin. He studied Visual Navigation, Embodied AI, Spatial Reasoning, more specifically how to learn to represent 3D space, generalize to new environments and master diverse tasks from light supervision.

Location: NCS 220

Zoom: https://stonybrook.zoom.us/j/94798224254?pwd=CFraer25qnpORbJ14aAVHRwaSJOjJM.1
Research challenges in using computer vision in robotics systems Abstract The past decade has seen a remarkable increase in the level of performance of computer vision techniques, including with the introduction of effective deep learning techniques. Much of this progress is in the form of rapidly increasing performance on standard, curated datasets. However, translating these results into operational vision systems for robotics applications remains a formidable challenge. This talk with explore some of the fundamental questions at the boundary between computer vision and robotics that need to be addressed. This includes introspection/self-awareness of performance, anytime algorithms for computer vision, multi-hypothesis generation, rapid learning and adaptation. The discussion will be illustrated by examples from autonomous air and ground robots.

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.

Abstract: The increasing complexity and volume of data from electron microscopy necessitates advanced computational tools for timely and accurate analysis. In this talk, I will present several machine learning (ML) models developed to interpret diverse datasets from transmission electron microscopy (TEM). First, I demonstrate segmentation models for labelling regions of interest from in situ TEM images, such as atomic column positions or reaction sites that allow atomic-level quantitative analysis of data. Second, I introduce a self-supervised CNN model for denoising of low-dose HRTEM images, enabling clearer visualization of atomic features without sacrificing temporal resolution. Finally, a transformer-based model trained to predict copper oxidation states directly from their electron energy loss spectroscopy spectra will be introduced. Together, these projects showcase the power of tailored ML solutions to extract quantitative insights from complex microscopy data.

Biography: Brian Lee is a research associate working for the Electron Microscopy group and Theory and Computation group at the Center for Functional Nanomaterials. Previously, he has received PhD in Mechanical Engineering from Duke University and worked as a postdoc at Purdue University. His research focuses on applying machine learning and simulation techniques for materials science.

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

Join us to share your thoughts about teaching, learning, and AI!

The landscape of higher education is rapidly evolving with the integration of Artificial Intelligence (AI). Through the Institute on AI, Pedagogy, and the Curriculum with AAC&U, we are exploring ways that we can better address AI in teaching and learning. We want to hear your experiences, your concerns, and your ideas.

This is an open discussion for all faculty and staff to share their perspectives on the opportunities and challenges AI presents in our academic environment.

We'll be exploring critical questions like:
  • In the age of AI, what are the opportunities you see for enriching the classroom and curriculum? How can it enhance student learning or your professional practice?
  • What are the most significant challenges and concerns that AI raises for you regarding academics, student integrity, or your workload?
  • What resources (tools, training, technical support, policy guidance, etc.) do you need to feel confident and successful in the age of AI?
Date: Monday, December 1st
Time: 12:30pm-1:45pm
Location: West Campus - Melville Library, Special Collections Seminar Room (the room is to the left at the top of the first flight of stairs from the Melville lobby)
or
Date: Wednesday, December 3rd
Time: 10:30am-11:45am
Location: East Campus - HSC 2-154

Please register in advance so we can confirm the room.

Note: Videos will not be shared publicly and comments will only be shared in aggregate.

Your input is vital. From pedagogy to assessment, your insights will be critical. We look forward to a thoughtful and productive conversation!
  • Dr. Rose Tirotta-Esposito (Assistant Provost; Director of CELT)
  • Dr. Elizabeth Hewitt (Associate Professor in the Department of Technology and Society (DTS) in the College of Engineering and Applied Sciences)
  • Chris Kretz (Associate Librarian and Head of Academic Engagement at SBU Libraries)
  • Prof. Rajiv Lajmi (Assistant Professor in the School of Health Professions and Chair of Applied Health Informatics)
  • Dr. Matthew Salzano (Assistant Professor in the Department of Communication in the School of Communication and Journalism)
Join a faculty development program to support instructors across campus with navigating/integrating AI in their courses. We're inviting interested faculty to participate in the grant project called Fostering Writing-to-Learn Skills with Critical AI Literacy: A Faculty Development and Student Support Program (funded through the AI3 Institute).

Time commitment and completion requirements :

  • Attend four sessions and a final symposium on the following dates/times:

    • Friday, September 12 from 11am - 12:30pm over Zoom

    • Friday, September 26 from 11am - 12:30pm over Zoom

    • Friday, October 10 from 11am - 12:30pm over Zoom

    • Friday, October 24 from 11am - 12:30pm over Zoom

    • Friday, November 14 from 10am - 1pm in Wang 201 - please note that this is an in person session only

  • Engage with online materials in Brightspace prior to each of the sessions (mainly to update a syllabus, assignment, or teaching strategy that you can share and discuss at the workshop)

Contact: Shyam Sharma, Christine Fena, and Rose Tirotta-Esposito with questions.

https://docs.google.com/document/d/1b51tvfK0HSOkCW7cwYq2nyyeeHtvBZYC7_XHv7Av8wQ/edit?tab=t.0
Educational objectives:
  1. Techniques involving data driven inferences from multi-omics data
  2. Interdisciplinary approaches to uncover aspects of tumor biology
  3. Computational genomics method development, benchmarking, and validation


Speaker: Dr. Subhajyoti De, PhDProfessor, Cancer SystemsBiology and Pathology,Rutgers Cancer Institute,The State University of New Jersey

Location: MART Building, Room 7M-0602 (7th Floor)

Remote Access: https://stonybrook.zoom.us/j/95617197636?pwd=KytzZ2pVRG9SZGpKZUtpNXJISjNjZz09
Meeting ID: 95617197636 | Passcode: 924293

Join the Office of Educational Effectiveness' upcoming workshop on the transformative potential of AI tools to enhance program assessment. Learn how to leverage AI to create targeted learning objectives, detailed rubrics, and precise benchmarks that will elevate the quality and effectiveness of your program assessment process. Join in-person on Oct. 17 at 10:30 am or virtually on Oct. 21 at 12 pm.

Register in advance: https://calendar.stonybrook.edu/site/office-educational-effectiveness/event/leveraging-ai-in-assessment-zoom/

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.