University Libraries Present: Analyzing quantitative data can feel overwhelming without the right tools. In this workshop, SBU Libraries' Data Literacies Lead, Ahmad Pratama will show you how to master the basics of exploratory data analysis for quantitative data using Python. This workshop covers several techniques to help you uncover patterns and insights in your datasets.

Online RSVP via link: https://stonybrook.zoom.us/meeting/register/vEPycmDrQoGjFqkmsYHgxw



Abstract: Trustworthy AI deployment in high-stakes domains requires systems that are fair, private, robust, and controllable as they scale. Yet these demands are often pursued through ad-hoc approaches, lacking a systematic understanding of the inherent trade-offs between competing objectives. We add fairness regularizers and hope bias decreases. We train on massive datasets and hope the model learns the underlying logic of how concepts combine, rather than memorizing statistical shortcuts. We encrypt data and hope the resulting computational overhead remains manageable. But hope isnot a science.
In this talk, I argue that what trustworthy AI lacks is not better heuristics but a deeper science of what these properties fundamentally cost and what is achievable. Before we can fix a system, we must map the terrain: what trade-offs are unavoidable, what regions of performance areunreachable, and how far current methods fall from what is actually achievable. My research builds this map across fairness, privacy, robustness, and controllability, following a common methodology: diagnose where models fail, characterize the fundamental limits any method must obey, and design systems that approach those limits. I will present this framework, its extension to scientific applications where we replace statistical constraints with physical laws to ensure AI systems remain grounded in reality, and a vision for scaling these principles to the rapidly expanding ecosystem of composed and interacting AI systems.


Bio: Dr. Vishnu Boddeti is an Associate Professor in the Department of Computer Science and Engineering at Michigan State University, where he leads the Human Analysis Lab (HAL). His research develops mathematical frameworks for trustworthy AI, spanning fairness, privacy, robustness, and physics-informed learning, with an emphasis on characterizing fundamental limits and building systems that achieve them. His work has been supported by NSF, NIST, DARPA, ONR, Ford, and others, and recognized with a Meta Research Award (2021). His research has been featured on the cover of Nature, recognized as an Editor's Highlight in Nature Communications, and received multiple best paper awards, including the 2024 IEEE-CCF Cloud Computing Best Paper Award and the TMLR Outstanding Certification Finalist (2023). He serves as Senior Area Editor for IEEE Transactions on Information Forensics and Security and completed his PhD in ECE from Carnegie Mellon University in 2012.

Location: NCS 120
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
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.
Join Zoom Meeting
https://stonybrook.zoom.us/j/98079526509?pwd=Wkt5eURhVDN5VE56TUloS2h5V1Jodz09

Meeting ID: 980 7952 6509
Passcode: 949941



Abstract Over the last decade, artificial neural networks have undergone a revolution, catalyzed by better
supervised learning algorithms. However, in stark contrast to young animals (including humans), training such
networks requires enormous numbers of labeled examples, leading to the belief that animals must rely instead
mainly on unsupervised learning. The reason is that most animal behavior is not the result of clever learning
algorithms--supervised or unsupervised-- but is encoded in the genome. Specifically, animals are born with
highly structured brain connectivity, which enables them to learn very rapidly. Because the wiring diagram is
far too complex to be specified explicitly in the genome, it must be compressed through a genomic
bottleneck. I will describe results showing how the genomic bottleneck algorithm can lead to dramatic
compression of networks and better generalization, particularly for rapid transfer in supervised and
reinforcement learning.

Anthony Zador is professor of neuroscience at CSHL.

This course is designed to help you approach AI with clarity and intention. Explore how to ask better questions, apply critical judgment to AI-generated outputs, and use these tools to support--not replace--human decision-making. With the right prompts, a thoughtful lens, and a focus on impact, AI can help reduce friction and free you to focus on what matters most: people, purpose, and leadership.

Audience: Any current or aspiring leader who currently uses AI and is interested in bringing their skills to the next level.

Register here.