Abstract:
Quantifying similarity is a central notion in science and data analysis, pervading everything from phylogenetic trees to the foundation of clustering. Unfortunately, despite being examined and applied for decades, traditional similarity and distance metrics have fundamental drawbacks. The key problem is that all of them are only defined over pairs of objects, so they scale quadratically when one tries to compare N objects. The present explosion in the amount of data available to us requires new ways to process information, and while some current algorithms can handle millions of points, we need alternatives applicable to billions. This is what motivated us to develop a new framework that can compare any number of objects at the same time. With this, we achieve an unprecedented linear scaling when comparing multiple objects. Here we will discuss the main properties of this formalism, along with its applications in drug design and to the analysis of Molecular Dynamics (MD) simulations. Our indices have proven to be incredibly versatile when applied to chemical space exploration and visualization, allowing us to rigorously quantify the chemical diversity of very large molecular libraries. This has led to the creation of several algorithms to sample important regions in chemical space, including a more efficient way of identifying the prevalence of activity cliffs. Additionally, our indices provide a convenient route to sample complex MD trajectories, allowing to identify representative structures very efficiently. Moreover, we can also cluster biological ensembles in a more robust way than with standard algorithms, which has led to our group's work on MDANCE, a very flexible and efficient open-source clustering module. Drop by if you want to know how we clustered one billion molecules!


Speaker:
Assistant Professor, Department of Chemistry and Quantum Theory Project
University of Florida, Gainesville
Website: https://quintana.chem.ufl.edu/

Location:
Laufer Center Lecture Hall 101
The IEEE / CVF Computer Vision and Pattern Recognition Conference (CVPR) is the premier annual computer vision event comprising the main conference and several co-located workshops and short courses. With its high quality and low cost, it provides an exceptional value for students, academics and industry researchers.



Location: Colorado Convention Center


New York Scientific Data Summit (NYSDS) is a premier annual conference that brings together researchers and thought leaders from academia, national labs and industry to exchange ideas and foster collaboration focused on data-driven science and technology. Co-hosted by Brookhaven National Laboratory and the Institute for Advanced Computational Science (IACS) at Stony Brook University, NYSDS 2025 will take place on September 11-12, 2025, in the SUNY Global Center in New York City.

NYSDS 2025 will spotlight artificial intelligence (AI), machine learning (ML) and robotics - fields currently at a pivotal point with transformative impacts on science and technology. From accelerating computationally demanding simulations to discerning signals from noisy data, AI/ML has become an integral part of the scientific workflows. Despite many advances, challenges remain to ensure that AI/ML applications are reliable, explainable and trustworthy.

Robotics, a growing field that couples AI with physically actuated mechanical bodies, has seen increased interest in areas spanning science, technology and manufacturing. The need for real-time decision-making and control, along with the intricate morphology of robots, makes robotics an intriguing application of AI, advanced computing and optimization.


This NYSDS 2025 is open to the public. To be eligible to attend, all participants must register online by August 30, 2025. For questions or assistance with registering, please contact the Summit Coordinator.

Register here.

Join us at the Center for Excellence in Learning and Teaching (CELT) for an interactive Zoom workshop on Generative AI designed for faculty and staff interested in enhancing teaching and assessment practices, increasing student engagement, and navigating the rapidly evolving landscape of AI tools. Participants will be introduced to common AI tools, explore potential instructional uses, and discuss key considerations such as academic integrity, transparency, and equity.

Register now: https://stonybrook.zoom.us/meeting/register/6js1eP64T1ys8tyU57EJ7Q#/registration

As part of a grant project funded by the AI3 Institute, a group of instructors participated in a faculty development program, Fostering Writing-to-Learn Skills with Critical AI Literacy: A Faculty Development and Student Support Program. This program was developed to support instructors across campus with navigating/integrating AI in their courses specifically around writing intensive/involved assignments. We would like to invite anyone interested to the culmination of this program, a mini-symposium, where the participants will share practical changes they made or are making around writing intensive/involved assignments and AI.

Location: Wang 201

A light lunch will be served. Please register by Friday, November 7th.

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
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.