The Future of Learning: Rethinking Practice in a Changing World

Thursday, March 26, 2026 (Workshops)
Friday, March 27, 2026 (Symposium)

Open to Stony Brook University Faculty, Staff, and Graduate Students. Hosted by the Center for Excellence in Learning and Teaching, Office of the Provost.

Thursday, March 26, 2026
Workshop: AI Tools and Techniques
  • Open to all faculty & staff
  • Hands-on, exploratory
  • Registration only limited to the size of the room
  • Location: In-person, TBD
  • Time: 10 AM - 12 PM
  • Registration required

Friday, March 27, 2026
Keynote: Teaching and Thinking with AI
  • Faculty, TAs, postdocs, and academic staff
  • In-person on-campus conference venue
  • Location: SAC Balroom
  • Time: 9 AM - 3 PM
  • Registration required

Keynote Speaker: José Antonio Bowen

José Antonio Bowen has been leading innovation and change for over 40 years at Stanford, Georgetown and the University of Southampton (UK), as a dean at Miami University and SMU and as President of Goucher College. Bowen has worked as a musician with Stan Getz, Dave Brubeck, and many others and his symphony was nominated for the Pulitzer Prize in Music (1985).
Bowen holds four degrees from Stanford and has written over 100 scholarly articles and books, including the Cambridge Companion to Conducting (2003), Teaching Naked (2012 and the winner of the Ness Award for Best Book on Higher Education), Teaching Naked Techniques with C. Edward Watson (2017) and Teaching Change: How to Develop Independent Thinkers using Relationships, Resilience and Reflection (Johns Hopkins University Press, 2021).
Bowen has appeared in The New York Times, Forbes, The Wall Street Journal, and has three TED talks. Stanford honored him as a Distinguished Alumni Scholar (2010) and he has presented keynotes and workshops at more than 300 campuses and conferences 46 states and 17 countries around the world. In 2018, he was awarded the Ernest L. Boyer Award (for significant contributions to American higher education). He is a senior fellow for the American Association of Colleges and Universities.

Register here.
Abstract: Molecular learning has become an emerging field of AI, driving breakthroughs in drug discovery, protein design, and materials design. For high-stakes scientific tasks, however, predictive accuracy alone is not sufficient: models must also be interpretable and trustworthy. Our work aims to study molecular learning under a unified explainability perspective across two major model families: Graph Neural Networks (GNNs) and Large Language Models (LLMs).

GNNs are natural choices for molecular graphs and achieve strong performance on many molecular tasks. To enhance explainability, many GNN explanation methods have been proposed and work well for 2D GNNs. However, 3D GNNs introduce two key challenges: producing chemically meaningful substructures and reducing fidelity loss caused by dense geometric graphs. To address these challenges, I present two methods. 3DGraphX decomposes dense 3D graphs into chemically meaningful 3D motifs, enabling compact explanations that align with chemical intuition. EDMA introduces an energy-based discrete mask approximation approach to reduce the discrepancy between the soft mask optimized during training and the hard mask used for explanation, improving explanation fidelity.

LLMs present different characteristics and challenges compared with GNNs. LLMs can provide a certain level of explanation through step-by-step reasoning, and their natural-language outputs are easy for humans to understand and interpret. However, because LLMs are trained for general-purpose tasks, their performance on scientific tasks often lags behind specialized GNNs. To improve performance, existing methods guide LLMs by providing suggestions through brief feedback, retrieval-augmented generation (RAG), or planner agents. However, these approaches face several limitations, such as vague guidance, introduced bias problems, and high computational cost. To fill the gap, I propose RL-Guider, a lightweight reinforcement-learning agent that converts evaluation feedback into input-specific guidance for molecular optimization. RL-Guider improves over time by accumulating historical experience and transfers efficiently across different LLMs while preserving interpretability.

Together, these efforts aim to provide explanations that are scientifically meaningful and faithful, while also preserving or improving performance on molecular tasks to better meet real scientific needs.

Speaker: Xufeng Liu

Location: New Computer Science-1-Room 115
Abstract: In this talk, we take a step back and argue that many varied and seemingly unrelated attacks on the web are actually symptoms of one deeper problem that has existed since the web's inception. Whether it is attacks due to expired domain names, cloaking done by malicious websites, malvertising, or even our growing distrust of the news can be largely attributed back to the issue of stateless linking. Stateless linking refers to the absence of any integrity guarantees between the time that a link for a remote resource was created, to a future time when this link is resolved by web clients. We draw on 10+ years of research to demonstrate how stateless linking and the resulting lack of content integrity is the true culprit for many of our past, current, and likely future web problems. Successfully tackling this one really challenging problem, has the potential of solving many of our web woes.

Bio: Nick Nikiforakis is affiliated with the National Security Institute. He received his PhD in Computer Science from KU Leuven in Belgium. He received his MSc, in Parallel and Distributed Systems and BSc in Computer Science from the University of Crete, Greece. His research focuses on web security and privacy, software security, and intrusion detection.

Location: NCS 120
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 PhD program or (2) receive permission from the instructors.

Each seminar will consist of multiple short talks (around 10 minutes) by multiple people. Students can register for 1 credit for CSE 656. Registered students must attend and present a minimum of 2 or 3 talks. Everyone else is welcome to attend. Fill in https://forms.gle/pCVXovgfMfQwGqG38 to subscribe to our mailing list for further announcement.

  • CEWIT's 6th annual hackathon sponsored by Major League Hacking, Hack@CEWIT2022, is taking place virtually on February 18-20, 2022. This year's theme is Hacking Into the Metaverse and will focus on NFT's, Blockchain, Crypto, and the Metaverse. To find out more about the event, mentoring, sponsoring, or to register, visit:

  • https://www.cewit.org/programs/events/hack.php

Nam Nguyen

4-5pm, Dec 17 2020

https://stonybrook.zoom.us/j/94214254415?pwd=K1VoQml4cFdlVW51VW41dWtid2tJdz09



The molecular mechanisms and functions in complex biological systems
currently remain elusive. Recent high-throughput techniques, such as
next-generation sequencing, have generated a wide variety of
multiomics datasets that enable the identification of biological
functions and mechanisms via multiple facets. However, integrating
these large-scale multiomics data and discovering functional insights
are, nevertheless, challenging tasks. To address these challenges,
machine learning has been broadly applied to analyze multiomics. In
particular, multiview learning is more effective than previous
integrative methods for learning data's heterogeneity and revealing
cross-talk patterns. Although it has been applied to various contexts,
such as computer vision and speech recognition, multiview learning has
not yet been widely applied to biological data--specifically,
multiomics data. Therefore, we have developed a framework called
multiview empirical risk minimization (MV-ERM) for unifying multiview
learning methods (Nguyen, et al., PLoS Computational Biology, 2020).
MV-ERM enables potential applications to understand multiomics
including genomics, transcriptomics, and epigenomics, in an aim to
discover the functional and mechanistic interpretations across omics.
Based on MV-ERM, we have developed the following methods:
ManiNetCluster, Varmole and ECMarker.



(1) ManiNetCluster (Nguyen, et al., BMC Genomics, 2019) is a manifold
learning method which simultaneously aligns and clusters gene networks
(e.g., co-expression) to systematically reveal the links of genomic
function between different phenotypes. Specifically, ManiNetCluster
employs manifold alignment to uncover and match local and non-linear
structures among networks, and identifies cross-network functional
links. We demonstrated that ManiNetCluster better aligns the
orthologous genes from their developmental expression profiles across
model organisms than state-of-the-art methods. This indicates the
potential non-linear interactions of evolutionarily conserved genes
across species in development. Furthermore, we applied ManiNetCluster
to time series transcriptome data measured in the green alga
Chlamydomonas reinhardtii to discover the genomic functions linking
various metabolic processes between the light and dark periods of a
diurnally cycling culture;



(2) Varmole (Nguyen, et al., Bioinformatics, 2020) is an interpretable
deep learning method that simultaneously reveals genomic functions and
mechanisms while predicting phenotype from genotype. In particular,
Varmole embeds multi-omic networks into a deep neural network
architecture and prioritizes variants, genes and regulatory linkages
via biological drop-connect without needing prior feature selections.
With an application to schizophonia, we demonstrate that Varmole
provides an effective alternative for recent statistical methods that
associate functional omic data (e.g. gene expression) with genotype
and phenotype and that link variants to individual genes in population
studies such as genome-wide association study;



(3) ECMarker (Jin*, Nguyen*, et al., Bioinformatics, 2020) is an
interpretable and scalable machine learning model that predicts gene
expression biomarkers for disease phenotypes and simultaneously
reveals underlying regulatory mechanisms. Particularly, ECMarker is
built on the integration of semi- and discriminative- restricted
Boltzmann machines, a neural network model for classification allowing
lateral connections at the input gene layer. With application to the
gene expression data of non-small cell lung cancer (NSCLC) patients,
we found that ECMarker not only achieved a relatively high accuracy
for predicting cancer stages but also identified the biomarker genes
and gene networks implying the regulatory mechanisms in lung cancer
development.



Finally, we propose a novel multiview learning method, Malignomics, to
predict phenotypes from heterogeneous multi-omic features. Malignomics
will first align multi-omic features by deep manifold alignment onto a
common latent space, better predicting nonlinear relationships across
omics. This deep alignment aims to preserve both global consistency
and local smoothness across omics and reveal higher-order nonlinear
interactions (i.e., manifolds) among cross-omic features. Second, it
uses these manifold structures to regularize the classifiers for
predicting phenotypes. This manifold-regularization allows
highlighting cross-omic feature manifolds and prioritizing the
features and interactions for the phenotypes. The prioritized
multi-omic features will further reveal underlying phenotypic
functions and mechanisms and thus enhance the biological
interpretation of Malignomics. We will apply Malignomics to
multi-omics data in neuropsychiatric disorders, and prioritize gene
regulatory networks linking risk variants, regulatory elements, and
genes for the disorders. We will also compare Malignomics with the
state-of-the-arts, and investigate how the manifold regulation will
potentially improve understanding of multi-omics functions and
predicting diseases.

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. 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.

We meet every other Tuesday at noon in CDSD's Training Room (building 725, room 2-124) 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.

Abstract: Identifying model Hamiltonians is a vital step toward creating predictive models of materials. W​e combined Bayesian optimization with the EDRIXS numerical package to infer Hamiltonian parameters from resonant inelastic X-ray scattering (RIXS) spectra within the single atom approximation. To evaluate the efficacy of our method, we tested it on experimental RIXS spectra for several materials and demonstrated that it can reproduce results obtained from hand-fitted parameters to a precision similar to expert human analysis while providing a more systematic mapping of parameter space. Our work provides a key first step toward solving the inverse scattering problem to extract effective multi- orbital models from information-dense RIXS measurements, which can be applied to a host of quantum materials.

Biography: Marton Lajer is a postdoctoral researcher at the Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory. Marton​ obtained his PhD in theoretical physics at the Eotvos Lorand University, Hungary, in 2021. He was a​ junior research fellow at the Wigner Research Centre for Physics in Budapest before joining BNL in September 2022. His background spans various analytical and performance-critical numerical methods, mostly in the context of low- dimensional quantum field theories and quantum many-body systems. His research currently focuses on incorporating AI-enhanced methods to various problems in inelastic spectroscopy.

In addition to our speaker, we will have a number of CDS staff in attendance with expertise in AI methods and applications including image analysis, foundation models development, and inverse problem solving.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1604383624?pwd=ffQ5cUPNxTI7nzClKQO6cnsNbhF9Vf.1

Meeting ID: 160 438 3624
Passcode: 558449

Please Note: Due to a funding shortfall, we are for the time being no longer able to provide pizza and sodas for these events. We will have coffee though, and all are of course welcome to bring their lunch.

Zoom Link: https://stonybrook.zoom.us/j/98533029054?pwd=5FXO6lWGTJssCADEYkYbA7sjaacPRX.1

Meeting ID: 985 3302 9054

Passcode: 436997

Abstract:

Semantic segmentation, the task of assigning a semantic label to each pixel in an image, is a fundamental problem in the field of Computer Vision. with crucial applications in domains like autonomous driving, drone imagery and medical image analysis. Despite advancements in deep learning architectures, state-of-the-art models still heavily depend on large-scale pixel-level annotations, which are costly and time-consuming to acquire. To address this issue, Semi-Supervised Segmentation (SSS) has emerged as a promising solution, leveraging a small set of labeled images alongside a larger corpus of unlabeled data to reduce the annotation burden. In this proposal, I aim to investigate the challenges of SSS and propose approaches to address them. Existing SSS methods rely on a teacher-student framework to generate pseudo-labels for unlabeled images, which are then used for model training. However, this approach presents two major challenges. Pixel-level consistency fails to effectively capture contextual information, and pseudo-labels are noisy, especially in the early stages of training. To address the challenge of noisy pseudo-labels, existing methods rely on confidence-based thresholding to identify reliable pseudo-labels. However, during early training phases, when the model is poorly calibrated, this approach can select high-confidence but noisy pseudo-labels. To address this, we propose a novel approach that reduces reliance on model confidence to select reliable pseudo-labels. Our method employs an ensemble of a segmentation model and an object detection model to select more reliable pseudo-labels, which are then used to weight pseudo-labels using rank statistics, reducing the influence of noisy labels in training. Next, to address both the challenge of capturing contextual information and noisy pseudo-labels I introduce a novel Multi-scale Patch-based Multi-label Classifier (MPMC), which incorporates patch-level contextual information and reduces the impact of noisy pixel pseudo-labels by using the predictions of the patch-level Multi-label classifier to detect noisy labels, enhancing overall segmentation performance. While my work so far has focused on effectively utilizing unlabeled data to improve segmentation performance, as part of our future work, I will explore the use of textual information, such as category descriptions, for segmentation tasks. In limited labeled data scenarios it is more challenging to align visual features with textual features from large language models (LLMs).

Abstract: Jailbreak attacks circumvent LLMs' built-in safeguards by concealing harmful queries within adversarial prompts. While most existing defenses attempt to mitigate the effects of adversarial prompts, they often prove inadequate as adversarial prompts can take arbitrary, adaptive forms. This paper introduces RobustKV, a novel jailbreak defense that takes a fundamentally different approach by selectively removing critical tokens of harmful queries from key-value (KV) caches. Intuitively, for an adversarial prompt to be effective, its tokens must achieve sufficient `importance' (measured by attention scores), which consequently lowers the importance of tokens in the concealed harmful query. Therefore, by carefully evicting the KVs of low-ranked tokens, RobustKV minimizes the harmful query's presence in the KV cache, thus preventing the LLM from generating informative responses. Extensive evaluation using benchmark datasets and models demonstrates that RobustKV effectively counters state-of-the-art jailbreak attacks while maintaining the LLM's performance on benign queries. Notably, RobustKV creates an interesting effectiveness-evasiveness dilemma for the adversary, leading to its robustness against adaptive attacks.

Speaker: Tanqiu Jiang

Where: NCS 220 and Zoom (https://stonybrook.zoom.us/j/6406956411)