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
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

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.

Embodied Intelligence at Scientific User Facilities

Abstract: This presentation explores the active work integrating artificial intelligence and robotics at the National Synchrotron Light Source II, and a perspective for the future. Through various case studies, we highlight the optimization of operations, improved experimental outcomes, and the orchestration of distributed multimodal experiments. This ongoing development includes collaborators from across the light and neutron sources in the DOE complex. We will elaborate on the open-source Bluesky project, and its capabilities to support adaptive and autonomous experiments. Additionally, we will discuss how Bluesky can be integrated with open-source robotic control software to unlock new flexible automation for autonomous scientific research, which scales to new experiments and continues to leverage human ingenuity.

Biography: Dr. Phillip M. Maffettone is an Associate Computational Scientist in the Data Science and Systems Integration Division at NSLS-II. His research focuses on accelerating scientific discovery at user facilities through the integration of robotics, artificial intelligence (AI), and advanced experiment orchestration systems. He leads the N3XTware project, constructing the software architecture for the next 12 beamlines to be built at NSLS-II. Prior to this he built the brain on the world's first mobile robotic scientist at the University of Liverpool, and later spearheaded the machine learning platform for a biotechnology start-up, BigHat Biosciences. He holds a DPhil in Inorganic Chemistry from the University of Oxford and a B.S. in Chemical Engineering from the University at Buffalo.

Location: CDS, Bldg. 725, Training Room

Link: https://bnl.zoomgov.com/j/16049713 31?pwd=nc5CV3cOFrdYxordFieP W07tIDmwYb.1

Meeting ID: 160 497 1331
Passcode: 289875

The Institute for AI-Driven Discovery and Innovation hosts Dr. Mary
Simoni for a talk on her music and its intersection with AI, as part
of the Music and AI Seminars series.

The event will be held on Thursday, December 10, 2020, at 3:00 PM.

Abstract: Mary Simoni, Dean of Humanities, Arts & Social Sciences at
Rensselaer Polytechnic Institute will discuss her research in the use
of computer algorithms and technology in the composition and
performance of music. The talk will feature compositions inspired by
Augmented Transition Networks (ATNs), employ motion tracking to
control synthesis parameters, and a work in progress that employs
machine learning using training data that juxtaposes classical music
with COVID-19. During this talk, participants will be introduced to
several technologies that support music information retrieval, machine
learning, and algorithmic composition such as jSymbolic, Weka, and
Common Music.

Zoom details below:
https://stonybrook.zoom.us/j/98236706900?pwd=bDFEZFZtaHBWU0cyL0wxK3UrdUpIdz09
Meeting ID: 982 3670 6900
Passcode: 133945  

Abstract: Traditional questionnaires remain the primary method for assessing psychological outcomes and beliefs, capturing individuals' and populations' inner states. This dissertation presents an alternative computational method that overcomes key limitations in current mental health monitoring, particularly in spatiotemporal resolution, responses to major events, and automatic belief identification. By analyzing ∼1 billion Tweets from 2 million geo-located users, we created a big data pipeline for estimating depression and anxiety at the county-week level. These Language-Based Mental Health Assessments (LBMHA) demonstrated higher reliability and validity than traditional survey measures. Our approach effectively captured mental health trends and highlighted significant increases in mental illness following major events. Using the LBMHA pipeline, we conducted quasi-experiments, research designs that simulate randomized control trials, to generate explanations for mental health changes due to COVID-19 incidence/death. Utilizing these time-series analyses, we conducted discontinuity forecasting for community-specific anxiety shifts using statistical learning via ensemble and contextual models. To likewise investigate individual internal states, we created a novel task and annotated dataset for self belief language identification. Our fine-tuned language model for self-belief classification, despite its relatively small scale, outperformed GPT-4o. The self belief topics identified by our model successfully predicted depression, anxiety, and stress, offering insights into the relationship between self-conceptualization and mental health. The adoption of scalable language-based assessments with modern distributed computation presents a promising avenue for advancing community and individual mental health research.

Speaker: Siddharth Mangalik

https://stonybrook.zoom.us/j/91251321639?pwd=faggV5jZ7ByFDCFmnLXD3HiYxjQ1Eb.1&jst=2
Abstract: Datalog is a powerful language for expressing recursive computations through rules: Horn clauses in first order logic. Although effective at expressing queries over existential properties, Datalog and many of its popular implementations struggle with queries that involve more complex aggregates, requiring users to apply verbose, non-composable, and/or inefficient workarounds. Recent work on lattice-based datalogs addresses many of these concerns for aggregates that can be encoded as lattices (e.g., min or max), but more general aggregates like count remain problematic. In this talk, I will argue that this is not a fundamental limitation of Datalog, but rather from its model of truth: Both datalog semantics and evaluation rules make heavy use of the fact that insertion is both monotone and idempotent. Once a fact is known to be true, it can not be retracted, nor can further discoveries of the same fact alter its truth. Monotonicity is critical for forward progress under Datalog's ``open world'' model, as it allows us to safely assert the truth of a body. Meanwhile, idempotence makes it easier to reason about evaluation, as we need only guarantee that each head atom will be derived at-least-once. Unfortunately, more general aggregates like sum() are neither idempotent, nor monotone. I will introduce Hedgelog, a strict generalization of Datalog that uses general monoids as a basis for truth. I will show that this generalization remains compatible with Datalog's open world model, how it enables cleaner and more composable datalog programs, and how the underlying monoid relations open the door to interesting datastructure-level optimizations.

Bio: Oliver Kennedy is an associate professor at the University at Buffalo. He earned his PhD from Cornell University in 2011 and now leads the Online Data Interactions (ODIn) lab, which operates at the intersection of databases and programming languages. Oliver is the recipient of an NSF CAREER award, an IEEE Region 1 Technological Innovation Award, UB's Exceptional Scholar Award, and several UB SEAS teaching awards. Oliver is also one of the founding board members of Breadcrumb Analytics. Several of Oliver's papers have been invited to Best of compilations from SIGMOD and VLDB. The ODIn lab is currently exploring (i) how we can leverage database techniques like incremental view maintenance to make compilers faster, (ii) how to make it easier for data scientists to track how sources of uncertainty, ambiguity, and/or bias affect analyses, and (iii) how to streamline the interfaces --- both human and software --- between different tools for data science, like python, sql, and spreadsheets.

Location: NCS 120