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

Abstract: Retrieval-augmented generation (RAG) systems empower large language models (LLMs) to access external knowledge during inference. Recent advances have enabled LLMs to act as search agents via reinforcement learning (RL), improving information acquisition through multi-turn interactions with retrieval engines. However, existing approaches either optimize retrieval using search-only metrics (e.g., NDCG) that ignore downstream utility or fine-tune the entire LLM to jointly reason and retrieve--entangling retrieval with generation and limiting the real search utility and compatibility with frozen or proprietary models. In this work, we propose s3, a lightweight, model-agnostic framework that decouples the searcher from the generator and trains the searcher using a Gain Beyond RAG reward: the improvement in generation accuracy over naïve RAG. s3 requires only 2.4k training samples to outperform baselines trained on over 70 × more data, consistently delivering stronger downstream performance across six general QA and five medical QA benchmarks.

Speaker: Peter Zeng

Location: CS2311
Join us as we celebrate this year's Brook & Beyond Challenge finalists.
The Office for Research and Innovation invites you to hear about the two-month journey in which the Brook & Beyond team supported eight cohorts in bringing their bold ideas from the lab to the marketplace. It's an energizing evening that highlights the collaboration, creativity, and entrepreneurial spirit driving discovery across the University.
Meet this year's award recipients, hear pitches from the emerging founders, and applaud their achievements.
Connect, celebrate, and be part of the momentum shaping the future of innovation at
Stony Brook University.
Refreshments will be served. Registration is required.
Register Here.
We live in a new scientific paradigm: the Big Data era, in which a lot of data is available for almost anything. In this new paradigm, the driving force is to use data directly to learn about chemical and physics systems employing artificial intelligence. This paradigm has proven helpful in simulating realistic physical, biological, and chemical models, yielding impressive results. Similarly, the insight gained in these situations can be used to improve our understanding of fundamental processes. In that regard, we want to answer the question: Can a machine learn chemistry? The answer to this question is still debatable, but we will show our ideas and methods to find the answer. We will also discuss our results on predicting atom-diatom reactions and other avenues and work in progress in our group.

Please register for the STEM Speaker Series: Can a Machine learn Chemistry here.
Abstract:

What is the nature of linguistic knowledge, and how is it acquired from limited data? In recent years, the program of subregular linguistics has identified formal language classes expressive enough to account for most phenomena in natural language but also sufficiently limited to be efficiently learned from positive data. An advantage to these formal learning algorithms is that they come with mathematically proven guarantees about their performance, and it is easy to reason about how and why they behave the way they do.

In this talk, I discuss the Multi Tier-based 2-Strictly Local Inference Algorithm (MT2SLIA), which probably learns the syntactically relevant class of 2-Factor Muti Tier-based Strictly Local (2FMSTL) tree languages. This algorithm efficiently learns from a polynomially-sized sample of positive data by identifying missing substructures and generalizing these as constraints over tiers in a principled manner.

I will introduce a working prototype implementation of this algorithm and demonstrate its behavior on a curated sample of natural language data to show how it can learn relevant syntactic patterns.

Bio:

Logan Swanson is a third year PhD student in the Department of Linguistics at Stony Brook University. He is advised by Dr. Jefferey Heinz and Dr. Thomas Graf. His interests include learning theory, computational syntax, and language change. His current research focuses on understanding the learning-theoretic elements of natural language by designing, implementing, and testing learning algorithms for linguistically relevant formal language classes.

*Please note: this seminar will be held in person (IACS Seminar Room w/ food provided) and online.

Join Zoom Meeting
https://stonybrook.zoom.us/j/95707958315?pwd=6ITUJ0ffCXjRJb4wpt0KMDTApfSLZ0.1

Meeting ID: 957 0795 8315
Passcode: 920473

Join us for an engaging panel discussion featuring researchers who participated in our inaugural AI JAM session on February 26th. Our panelists will share their firsthand experiences using large language models to tackle complex scientific problems, with a special focus on prompt engineering strategies, discussing both breakthroughs and challenges encountered during this collaborative initiative. Learn how these cutting-edge AI tools are being applied to real-world research questions and discover insights that could inform your own scientific endeavors. Attendees are encouraged to come prepared with questions about prompt engineering for the panel discussion.

Moderator: Adolfy Hoisie, Deputy Director, Computing and Data Sciences

Kevin Yager, Group Leader, AI-Accelerated Nanoscience, Center for Functional Nanomaterials
Lingda Li, Associate Computational Scientist, Systems, Architecture and Computing Technologies, Computing and Data Sciences
Liguo Wang, Director of Scientific Operations, Laboratory for BioMolecular Structure (LBMS), National Synchrotron Light Source II
Weiguo Yin, Physicist, Condensed Matter Theory, Condensed Matter Physics and Materials Science Department

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1606837837?pwd=Tc0mwQqLXpDfYOIaoaurmpLD2mMlzS.1 (Meeting ID)

Passcode: 822553

The overall purpose of this seminar is to bring together people with interests in Computer Vision theory and techniques and to examine current research issues. This course will be appropriate for people who already took a Computer Vision graduate course or already had research experience in Computer Vision. To enroll in this course, you must either: (1) be in the Ph.D. program or (2) receive permission from the instructors. Each seminar will consist of multiple short talks (around 15 minutes) by multiple students. Students can register for 1 credit for CSE656. Registered students must attend and present a minimum of 2 talks. Registered students must attend in person. Up to 3 absences will be excused. Everyone else is welcome to attend. The seminar will be taught by Prof. Chao Chen, chao.chen.1@stonybrook.edu.
The New York Academy of Sciences Presents AI for Materials: From Discovery to Production - A Virtual Symposium

Event Description: This interdisciplinary symposium covers the application of artificial intelligence (AI) throughout the entire life cycle of new materials -- from materials simulations and synthesis to translating research into high-volume industrial production.

Event Link & Registration: nyas.org/AI4Materials2020
Communication-Efficient Heterogeneity-Aware Machine Learning System and Architecture by Xuehai Qian

ABSTRACT: The key success of deep learning is the increasing size of models that can achieve high accuracy. At the same time, it is difficult to train the complex models with large data sets. Therefore, it is crucial to accelerate training with distributed systems and architectures, where communication and heterogeneity are two key challenges. In this talk, I will present two heterogeneity-aware decentralized training protocols without communication bottleneck. Specifically, Hop supports arbitrary iteration gap between workers by novel queue-based synchronization which can tolerate heterogeneity with system techniques. Prague uses randomized communication to tolerate heterogeneity with a new training algorithm based on partial reduce -- an efficient communication primitive. If time permits, I will present the systematic tensor partitioning for training on heterogeneous accelerator arrays (e.g., GPU/TPU). We believe that our principled approaches are crucial for achieving high-performance and efficient distributed training.

BIO: Xuehai Qian is an assistant professor at University of Southern California. His research interests include domain-specific systems and architectures, performance tuning and resource management of cloud systems and parallel computer architectures. He received his PhD from the University of Illinois Urbana Champaign and was a postdoc at UC Berkeley. He is the recipient of W.J Poppelbaum Memorial Award at UIUC, NSF CRII and CAREER Award, and the inaugural ACSIC (American Chinese Scholar In Computing) Rising Star Award.

Abstract: Much like other AI for Science domains, polymer design poses significant challenges. It requires grounding in empirical data and physical laws, precise handling of domain-specific structured representations, and compositional reasoning over multiple interacting constraints--all while working with limited data.

To address these limitations, we introduce PolyBench, a large-scale benchmark comprising over 125K polymer design and analysis tasks grounded in verified experimental and synthetic data. PolyBench includes tasks created from a wide range of data sources and presents diverse structural, property-driven, and synthesis-oriented reasoning problems. Tasks in PolyBench are organized from simple to complex analytical reasoning problems, enabling generalization tests and includes diagnostic probes to evaluate model capabilities. Additionally, to support effective domain alignment, we propose a knowledge-augmented reasoning distillation framework that enriches the dataset with structured chain-of-thought supervision derived from expert-informed reasoning strategies.

Small language models (7B-14B parameters) trained on PolyBench substantially outperform comparably sized baselines and, in many cases, exceed the performance of larger closed-source frontier models on polymer reasoning tasks, while also demonstrating improved transfer to external polymer benchmarks. Last, we conduct a diagnostic study that reveals a compositionality gap: despite strong performance on decomposed sub-questions, models struggle to integrate multiple interacting constraints and intermediate reasoning steps, highlighting fundamental limitations in current scientific language models.

Speaker: Dikshya Mohanty

Location: NCS 115/Online

Zoom: https://stonybrook.zoom.us/j/94746001760?pwd=BCAd8gu7cXLn3PXM6kkbh11V6r0Mr7.1
Meeting ID: 947 4600 1760 Passcode: 987917