Please join us this Friday, February 13th for the CSE 600 seminar given by Associate Professor Debswapna Bhattacharya, from the Department of Computer Science at Virginia Tech.

Abstract: Building a model of a biological system that can provide actionable hypotheses to form a solid foundation for experimental and theoretical analyses is one of the key challenges in biology and medicine. In this talk, I will present my group's ongoing work in developing, evaluating, and disseminating a new generation of computational methods for biomolecular modeling powered by artificial intelligence (AI) and machine learning (ML). First, I will introduce a new generation of AI/ML methods for improved modeling and characterization of protein-nucleic acid assemblies by deep graph learning using embeddings from biological large language models (LLMs) as well as geometric attention-enabled pairing of heterogeneous biological LLMs, a previously unexplored avenue. Then, I will present a novel generative deep learning model based on equivariant flow matching for end-to-end generation of all-atom RNA 3D structural ensemble. Finally, I will outline my future research directions on attaining atomic-level accuracy in computational modeling of biomolecules and their assemblies at scale.

Speaker: Debswapna Bhattacharya is an Associate Professor in the Department of Computer Science at Virginia Tech. He received his Ph.D. in Computer Science from the University of Missouri-Columbia in 2016. Before joining Virginia Tech in 2022, he was an Assistant Professor at Auburn University from 2017 to 2021. His research interests lie at the intersection of computational biology and machine learning, with a particular focus on artificial intelligence for computational structural biology, specifically in modeling and characterization of biomolecular structures and interactions. His research group has been developing novel computational and data-driven methods, software, and information systems for diverse biomolecular modeling problems, ranking among the best methods in community-wide blind assessments and serving the worldwide community of biomedical users. He received various research awards (NSF CAREER Award, NIH Maximizing Investigators' Research Award, NSF National AI Research Resource Award) and numerous institutional honors (National Distinction and Outstanding Contributor at Virginia Tech, Ginn Faculty Fellowship at Auburn University, Outstanding Engineering Faculty Award at Auburn University).
Location: NCS 120
Optimization and Machine Learning - presented by Yifan Sun

Abstract: Optimization is a growing topic of interest in the machine learning community. It starts out as an option to check in Tensorflow (SGD? Adam? Adagrad?), but as we get more into the how and why of these options, we uncover many fundamental principles relating to operations research, control theory, and dynamical systems, dating back as far as the Cold World era. 

In this talk I will give a broad overview of some of the important optimization themes in machine learning. I will try to give connections between tools we are used to seeing in popular packages 
and fundamental optimization concepts like duality, convexity, contractive operators, etc. While we cannot hope to completely cover this diverse research area, I hope to provide a glimpse of this exciting research area that is permeating more and more into the machine learning world. 

Bio: Yifan Sun received her PhD in Electrical Engineering from the University of California Los Angeles in 2015, with research focusing on convex optimization and semidefinite programming. She was then Technicolor Research and Innovation, focusing on machine learning and 
data science applications. More recently, she completed two postdocs focusing on optimization, at the University of British Columbia in Vancouver, Canada and INRIA, in Paris, France.

We invite faculty to deliver a 10-minute presentation during our afternoon session at the CELT Symposium on April 11, 2025. Showcase how you use emerging technology (i.e. AI, VR, etc.) to support diverse student populations and enhance learning experiences. Share your innovative strategies and inspire others!

CELT Symposium Theme: A New Era of Inclusivity and Innovation in Higher Education

https://t.e2ma.net/click/5w0gph/5wwlu4oe/9v63j6
The Center of Excellence in Wireless and Information Technology (CEWIT) will host the 16th International Conference on Emerging Technologies for a Smarter World (CEWIT2020) virtually on November 5, 2020. The conference will center on the four major fields which are penetrating our business and personal lives: Machine Learning, Artificial Intelligence, Blockchain and Computational Medicine. For more info visit: https://www.cewit.org/.

The International Conference on Machine Learning (ICML) is the premier gathering of professionals dedicated to the advancement of the branch of artificial intelligence known as machine learning.

ICML is globally renowned for presenting and publishing cutting-edge research on all aspects of machine learning used in closely related areas like artificial intelligence, statistics and data science, as well as important application areas such as machine vision, computational biology, speech recognition, and robotics.

ICML is one of the fastest growing artificial intelligence conferences in the world. Participants at ICML span a wide range of backgrounds, from academic and industrial researchers, to entrepreneurs and engineers, to graduate students and postdocs.


For more information and registration, visit the official website.
West Campus - SAC- Student Activities Center - Ballrooms A & B 100 Nicolls Road Stony Brook NY 11794 Job Fair.jpg The Career Center invites Alumni Employers and Job Seekers to the IT/Computer Science Job and Internship Fair this spring. Job Seekers: A job fair is an opportunity for you to present yourself professionally in person to a potential employer, while showcasing your communication skills. Get more information Alumni Employers: Held in both the fall and spring semesters, this event is ideal for employers looking to fill internship, co-op, part-time and full-time opportunities in the field of information technology (i.e. Software Engineering, Network Administration, Web Development, etc.). Register here to recruit top SBU talent.
CSE 600 Seminar Series | Fall 2025


Abstract: Vision-language models that see and describe the world are now part of our daily lives, from internet search and accessibility tools to content generation and automatic moderation. However, as these models grow and become more widely used, their limitations have also become increasingly visible. In particular, it has been shown that these models are unable to reliably perform complex tasks that require abstraction and compositional reasoning. For example, they struggle to decompose an image or text into entities, attributes, and relations, and then reason over new combinations of these elements. As a result, we see generated content full of hallucinations, privacy leaks in images, and different types of biases in the model outputs.In this talk, I will outline a research agenda that aims to build trustworthy vision-language models in the age of generative AI. I will begin with compositional reasoning: how natural language inference can be used to decompose complex instructions and captions into atomic, verifiable statements, improving both evaluation and model behavior on tasks that require multi-step reasoning. I will then discuss how synthetic data and simulated environments can be used to train more reliable models, and how they can also stress-test models beyond standard benchmarks, revealing when models drop attributes, break object relations, or fail under distribution shifts. I will also share recent work on using hallucination correction as a signal to improve video-language alignment, and on privacy-preserving image understanding for blind and low-vision users. I will conclude with possible ways we can systematically probe, debug, and repair these models, turning synthetic perception into something we can trust in real-world deployments.



Speaker: Paola Cascante-Bonilla is a tenure-track Assistant Professor in the Department of Computer Science at Stony Brook University (SUNY). Before that, she was a Postdoctoral Associate at the University of Maryland Institute for Advanced Computer Studies (UMIACS), developing methods and metrics related to trustworthy machine learning. She received her Ph.D. in Computer Science at Rice University in 2024, working on Computer Vision, Natural Language Processing, and Machine Learning.Her research focuses on developing systems that enable compositional reasoning and common-sense inference through vision and language, while tackling issues such as cultural biases, data distribution, explainability, and trustworthy AI. Additionally, Cascante-Bonilla creates simulated environments for embodied agents to learn in a safe, controlled setting, aiming to facilitate effective collaboration and problem-solving for complex tasks by leveraging the implicit knowledge of large-scale pre-trained deep learning models.
Cascante-Bonilla is the recipient of the Ken Kennedy Institute SLB Graduate Fellowship (2022/23), she was selected as a Future Faculty Fellow by Rice's George R. Brown School of Engineering (2023) and as a Rising Star in EECS (2023).
Location: NCS 120

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

AI is everywhere and so are the privacy concerns that come with it. At its core, the most common forms of AI we use today are online digital services and thus inherit the usual privacy risks. We'll take a look at indirect prompt injection- a technique that can trick AI tools into revealing or extracting private information as well as techniques being used in academic contexts to manipulate systems and even mislead researchers.

Register here for the online session.
The Empirical Methods in Natural Language Processing (EMNLP) conference is a premier international academic conference in the field of artificial intelligence and natural language processing (NLP). Organized annually by the Association for Computational Linguistics (ACL) special interest group on linguistic data (SIGDAT), it focuses on research that uses empirical methods to solve language processing problems.

For more information, and registration, visit the official website.