The Provost's Lecture Series features talks by SUNY Distinguished Academy faculty members at Stony Brook University, showcasing the outstanding research and scholarship that is taking place at our institution.

Joe Mitchell

SUNY Distinguished Professor, Applied Mathematics and Statistics
Chair, Department of Applied Mathematics and Statistics, College of Engineering and Applied Sciences

A Case for Algorithms: A Computational Geometer's Perspective

Algorithms are all around us in every smart device and technology that has consumed our daily lives. As a computational geometer, I study algorithms to solve problems that involve a geometric perspective on data. I have observed that practically every technology and field of study has a need for effective algorithms involving geometric data. I reflect on some favorite algorithmic problems that are easy to visualize, but challenging to solve, and argue that the formal study of algorithms remains essential in the age of AI.

Reception to follow immediately after the talks.

Register here.

You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes three short talks 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.

Speakers

Kriti Chopra, Computing & Data Sciences (CDS)
Thomas Flynn, Computing & Data Sciences (CDS)
Wenjie Liao, Chemistry Division

Tuesday, January 7, 2025, 12:00 pm -- CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1615289117?pwd=Hqkbj9itxWrFnkhZ8rQXHPInO2gxdF.1

Meeting ID: 161 528 9117
Passcode: 991382

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.

Uncertainty-Aware Adaptation of LLMs for Protein-Protein Interaction Analysis

Abstract: Identification of protein-protein interactions (PPIs) helps derive cellular mechanistic understanding, particularly in the context of complex conditions such as neurodegenerative disorders, metabolic syndromes, and cancer. Large Language Models (LLMs) have demonstrated remarkable potential in predicting protein structures and interactions via automated mining of vast biomedical literature; yet their inherent uncertainty remains a key challenge for deriving reproducible findings, critical for biomedical applications. In this study, we present an uncertainty-aware adaptation of LLMs for PPI analysis, leveraging fine-tuned LLaMA-3 and BioMedGPT models. To enhance prediction reliability, we integrate LoRA ensembles and Bayesian LoRA models for uncertainty quantification (UQ), ensuring confidence- calibrated insights into protein behavior. Our approach achieves competitive performance in PPI identification across diverse disease contexts while addressing model uncertainty, thereby enhancing trustworthiness and reproducibility in computational biology. These findings underscore the potential of uncertainty-aware LLM adaptation for advancing precision medicine and biomedical research.

Biography: Sanket is a research staff member in the Applied Mathematics department within the Computing and Data Sciences Directorate at Brookhaven National Laboratory. Previously, he was the Amalie Emmy Noether Postdoctoral Fellow in the same department. He earned his Ph.D. in Statistics from Michigan State University.. Sanket's research interests span Bayesian statistics, uncertainty quantification (UQ), deep learning, Markov Chain Monte Carlo (MCMC), variational inference, and sparsity methods. He also focuses on dimensionality reduction, surrogate modeling, hybrid physical-data driven models, and active learning, with applications across climate science, materials science, and life sciences.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1605691898?pwd=xC7GebG7Kvzxa4AjPSIxJw7e9IZtoY.1

Meeting ID: 160 569 1898
Passcode: 303888

Title:Deep Contextual Modeling for Natural Language Understanding, Generation, and Grounding Zoom instructions: Join Zoom Meeting https://stonybrook.zoom.us/j/645050299?pwd=TVJVRkc3dlhxdDF5d00xWGlDQkovZz09 Meeting ID: 645 050 299 Password: 810247 One tap mobile +16468769923,,645050299#,,#,810247# US (New York) +13126266799,,645050299#,,#,810247# US (Chicago) Dial by your location +1 646 876 9923 US (New York) +1 312 626 6799 US (Chicago) +1 301 715 8592 US +1 346 248 7799 US (Houston) +1 408 638 0968 US (San Jose) +1 669 900 6833 US (San Jose) +1 253 215 8782 US Meeting ID: 645 050 299 Password: 810247 Find your local number: https://stonybrook.zoom.us/u/aemTiJMXu6 Abstract: Natural language is a fundamental form of information and communication. In both human-human and human-computer communication, people reason about the context of text and world state to understand language and produce language response. In this talk, I present several deep neural network based systems that first understand the meaning of language grounded in various contexts where the language is used, and then generate effective language responses in different forms for information access and human-computer communication. First, I will introduce Speaker Interaction RNNs for addressee and response selection in multi-party conversations based on explicit representations for different discourse participants. Then, I will present a text summarization approach for generating email subject lines by optimizing quality scores in a reinforcement learning framework. Finally, I will show an editing-based multi-turn SQL query generation system towards intelligent natural language interfaces to databases. Bio:Rui Zhang is a final year Ph.D. student at Yale University advised by Professor Dragomir Radev. His research interest lies in various natural language processing problems in understanding, generation, and grounding. He has been working on (1) End-to-End Neural Modeling for Entities, Sentences, Documents, and Multi-party Multi-turn Dialogues, (2) Text Summarization for Emails, News, and Scientific Articles, (3) Cross-lingual Information Retrieval for Low-Resource Languages, (4) Context-Dependent Text-to-SQL Semantic Parsing in Human-Computer Interaction. Rui Zhang has published papers and served as Program Committee members at top-tier NLP and AI conferences including ACL, NAACL, EMNLP, AAAI, CoNLL. During his Ph.D., He has done research internships at IBM Thomas J. Watson Research Center, Grammarly Research, and Google AI. He was a graduate student at the University of Michigan and got his bachelor's degrees at both the University of Michigan and Shanghai Jiao Tong University from the UM-SJTU Joint Institute.
Over the past decade, Artificial Intelligence (AI) has made stunning advances, from mastering language to solving the structure of proteins. These breakthroughs arise from more than forty years of work in neural networks, where ideas from neuroscience have inspired solutions in AI. In this lecture, Anthony Zador, MD, PhD, will explore how reverse engineering the brain's computations has driven progress in both fields, and how this back-and-forth between neuroscience and AI is set to grow even stronger -- with brain-inspired designs driving new AI advances while AI tools transform our understanding of how the brain works.

Speaker:
Dr. Zador works at the intersection of neuroscience and artificial intelligence. He is the Alle Davis Harris Professor of Biology at Cold Spring Harbor Laboratory, where he served as Chair of Neuroscience. He was named one of Foreign Policy's 100 Leading Global Thinkers and is a recipient of the Brain Research Foundation Fellowship, the Gill Symposium Transformative Investigator Award, and the Allen Distinguished Investigator Award.

Watch online at stonybrook.edu/live

Visual Analytics and Machine Learning for Biomedical Imaging Diagnosis

 

Arie Kaufman

 

We present an integrated approach using visual analytics and machine learning (ML) to diagnose abnormalities in 3D radiological imaging and biological microscopes. The primary example will involve 3D virtual pancreatography (VP), a novel visualization-ML procedure and application for non-invasive diagnosis and classification of pancreatic lesions, the precursors of pancreatic cancer. Currently, non-invasive screening of patients is performed through visual inspection of 2D axis-aligned CT images, though the relevant features are often not clearly visible nor automatically detected. VP is an end-to-end visual diagnosis system that includes an ML-based automatic segmentation of the pancreatic gland and the lesions, a semi-automatic approach to extract the primary pancreatic duct, an ML-based automatic classification of lesions into four prominent types, and specialized 3D and 2D exploratory visualizations of the pancreas, lesions and surrounding anatomy. We combine volume rendering with pancreas- and lesion-centric visualizations and measurements for effective diagnosis. We designed VP through close collaboration and feedback from expert radiologists, and evaluated it on multiple real-world CT datasets with various pancreatic lesions and case studies examined by the expert radiologists. Other applications include virtual colonoscopy, COVID-19, pathology, brain neurites, etc.


Biography: Arie Kaufman is Distinguished Professor and formerChair of the Department of Computer Science at Stony Brook University, where he is also Director of the Center for Visual Computing (CVC), and Chief Scientist at the Center of Excellence in Wireless and Information Technology (CEWIT). 

He received his PhD in Computer Science at Ben-Gurion University of the Negev in 1977.   He is known for his work in visualization, graphics, virtual reality, user interfaces, multimedia, and their applications, especially in bio-medicine. He is especially well known for his work on the 3-dimensional virtual colonoscopy, a revolutionary low-risk technique for colon cancer screening, and for pioneering the use of Graphics Processing Units (GPUs) and GPU-clusters. In 2012, he presided over the development and opening of the Reality Deck, the largest virtual reality display in the world, at Stony Brook University.

Kaufman was the founding Editor in Chief of IEEE Transactions on Visualization and Computer Graphics (TVCG), co-founded the IEEE Visualization Conference and Volume Graphics series, and is currently the director of IEEE Computer Society Technical Committee on Visualization and Graphics. He is an IEEE Fellow, ACM Fellow, winner of many awards, including the IEEE Visualization Career Award, and member of the European Academy of Sciences.



Steven Skiena is inviting you to a scheduled Zoom meeting.

Topic: AI Seminar: Arie Kaufman
Time: Apr 21, 2021 10:00 AM Eastern Time (US and Canada)

Join Zoom Meeting
https://stonybrook.zoom.us/j/96017498640?pwd=SE0rdHB6ZVlCM2ZpY2RnRUxyVnR3Zz09

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
What AI tools are available to help with the scholarly research process? Are they helpful? What do they do and is it worth the time and energy to try them out? Join librarian Christine Fena to explore and compare established and emerging AI research tools such as Elicit, Scite, Consensus, and Undermind. The online workshop will provide a starting point to understanding what these tools are, the basics of how they work, and how AI research assistants might bring changes to your search process in the future. All are welcome!



Register here via Zoom.