AI Innovation Institute

CSE 600 Seminar Series | Fall 2025

Speakers: Jessica Roman, Simone Binneman, Michalis Polychronakis

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.

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.

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

Speakers

Maria Zawadowicz, EBNN--ML for Atmospheric Aerosol Research

Mohammad Atif, CDS--An Extensible Digital Twin Framework

Guang Zhao, CDS--Pareto Prompt Optimization

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

Meeting ID: 161 528 9117
Passcode: 991382

Join Klaus Mueller, professor of computer science and interim chair of the Department of Technology and Society, as he hosts Sucheta Lahiri.

Lahiri leads the AI Ethics and Risk Management function at Oxy, where she is responsible for ensuring that the company's AI solutions are developed and deployed in a manner that is ethical, efficient, trustworthy, safe, sustainable, and human-centered. She holds a doctorate from Syracuse University, along with two master's degrees in Applied Statistics and Information Science earned in India.

Zoom: https://stonybrook.zoom.us/j/7851507944?omn=98268154363#success

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