AI Innovation Institute

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

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.

Experiencing Machine Learning in Collider-Accelerator Control System

Abstract: The Relativistic Heavy Ion Collider (RHIC) at Collider-Accelerator Department (C-AD) of BNL provides the world's only high-energy polarized proton beam. It is in the unique position to study where nuclei obtain their spin. During 25 years of operation at RHIC, the C-AD controls group has developed its own control system to tune the accelerator performance, which contains millions of control points. The successful operation of this system will highly affect the machine performance. RHIC's successor, the Electron-Ion Collider (EIC), will be one of the most complex scientific instruments ever built, with the capability of colliding polarized proton and electron beams. The increasing complexity of instruments will require new, sophisticated control methods/tools to tune and optimize the accelerator performance. In this talk, I will summarize some projects developed in recent years that utilize machine learning in the C-AD controls group.

Biography: Dr. Yuan Gao is an assistant scientist at the Collider-Accelerator Department (C-AD) at Brookhaven, primarily working on developing new machine learning schemes in the control group to enhance system performance. His research interests include game theory, algorithm design, anomaly detection, and simulation modeling.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1604302440?pwd=0x2I95PIvbkkzIi6rA0MNnon5k2sux.1

Meeting ID: 160 430 2440
Passcode: 478223

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

Sanket Jantre
Tao Zhang
Xi Yu

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

Abstract:

It is known that models like large language models (LLMs) can often suggest colloquial plans given verbal descriptions of tasks, yet they are unable to reliably provide executable and verifiable plans given formally specified environments. In this talk, I will discuss a strand of efforts to have LLMs generate accurate and explainable plans in textual simulations. Instead of directly generating the plan or actions, LLMs are prompted to generate Planning Domain Definition Language (PDDL) that specifies the environment (domain file) and the task (problem file), which can then be deterministically solved with an off-the-shelf planner. In a 3-phase study, my collaborators and I first observed that it is possible but very challenging for LLMs to generate long-form code such as PDDL domain and problem files given textual specifications. Next, we devise methodologies for LLMs to iteratively generate and refine problem files while exploring a partially-observed, simulated, textual environment. Finally, we show that domain files are even more difficult to generate correctly, even on well-established planning tasks such as BlocksWorld. Finally, I will discuss ongoing efforts to improve said ability of structured generation and promising frontiers to explore.

Bio:
Li Harry Zhang is an assistant professor at Drexel University, focusing on Natural Language Processing (NLP) and artificial intelligence (AI). He obtained his PhD degree from the University of Pennsylvania advised by Prof. Chris Callison-Burch. Prior, he obtained his Bachelor's degree at the University of Michigan mentored by Prof. Rada Mihalcea and Prof. Dragomir Radev. His current research uses large language models (LLMs) to reason and plan via symbolic and structured representations. He has published more than 20 peer-reviewed papers in NLP and AI conferences, such as ACL, EMNLP, and AACL, that have been cited more than 1,000 times. He also consistently serves as Area Chair, Session Chair, and reviewer in those venues. Being a musician, producer, and content creator having over 50,000 subscribers, he is also passionate in the research of AI music and creativity.