AI Innovation Institute

Join Stony Brook University's Center for Excellence in Learning and Teaching (CELT) for a bootcamp on how to use AI to enhance your teaching and courses. This event will demonstrate how ChatGPT, Microsoft Copilot, and other generative AI platforms can support you in crafting learning.

Register here.

Abstract: Recent advances in Spatial Transcriptomics (ST) pair histology images with spatially resolved gene expression profiles, enabling predictions of gene expression across different tissue locations based on image patches. This opens up new possibilities for enhancing whole slide image (WSI) prediction tasks with localized gene expression. However, existing methods do not fully leverage the interactions between different tissue locations, which are crucial for accurate joint prediction. To address this, we introduce MERGE (Multi-faceted hiErarchical gRaph for Gene Expressions), which combines a multi-faceted hierarchical graph construction strategy with graph neural networks (GNN) to improve gene expression predictions from WSIs. By clustering tissue image patches based on both spatial and morphological features, and incorporating intra- and inter-cluster edges, our approach fosters interactions between distant tissue locations during GNN learning. As an additional contribution, we evaluate different data smoothing techniques that are necessary to mitigate artifacts in ST data, often caused by technical imperfections. We advocate for adopting gene-aware smoothing methods that are more biologically justified. Experimental results on gene expression prediction show that our GNN method outperforms state-of-the-art techniques on multiple metrics such as mean squared error (MSE), mean absolute error (MAE), and pearson correlation coefficient (PCC). Qualitative analysis establishes the effectiveness of MERGE in capturing cancer marker genes, thus consolidating its utility in diagnostics. As an extension of this work, we use MERGE in a setting with an uncertainty calibration branch to perform robust gene expression smoothing. We show that using patch-wise uncertainty from an uncertainty calibration model and the gene expression predictions from MERGE to enrich the ground truth gene expression matrix, results in better alignment with pathologist annotations, thus establishing that the smoothing is biologically informed.

Speaker: Aniruddha Ganguly

Location: Virtual Zoom Meeting


https://stonybrook.zoom.us/j/5474847973?pwd=Sng0Q2h1c1d3cm9sbFBmYUczMHZNdz09
Meeting ID: 547 484 7973
Passcode: 206739

18th Annual Engineering Ball Flowerfield, St. James, NY Thursday April, 2nd, 7:00 to 10:00 pm Pick up your tickets in 231 Engineering (Monday - Friday, 10:00 am to 4 pm) Presenting Partner: L3Harris

Abstract: The rapid growth of observational data presents unprecedented opportunities to enhance both the predictability and mechanistic understanding of Earth systems. However, fully harnessing big Earth data needs computational frameworks that bridge the gap between physics-based models and machine learning. In this talk, I will first demonstrate how AI methods can significantly improve the prediction of environmental systems. Despite their predictive accuracy, machine learning models often lack physical interpretability, limiting their ability for scientific inquiry. To address this, I will introduce the developed hybrid, differentiable modeling framework that unifies physical models with machine learning in an end-to-end trainable system. This framework autonomously learns from large observations while maintaining physical clarity. The machine learning components can be seamlessly embedded into physical backbones to assimilate multi-source data, support automatic parameterization, and represent uncertain processes. I will showcase applications of this framework in simulating and understanding the terrestrial water cycle and its interactions with ecosystems at continental and global scales. This talk will highlight how differentiable modeling not only improves the modeling ability in both data-rich and data-scarce scenarios, but also provides a systematic pathway to enhancing model structures, deciphering uncertain physical relations, and facilitating knowledge discovery in Earth system sciences.


IACS Seminar Speaker: Dapeng Feng, Stanford Univeristy

Location: IACS Seminar Room

The next AI Institute seminar speaker will be Chao Chen of Biomedical Informatics, on Monday November 29 at noon via zoom:

https://stonybrook.zoom.us/j/96233844681?pwd=aVVsUnIzMWJDMHRqVXcrQU5HMjFVQT09

He will be talking on the Detection of Trojan Attacks to Deep Neural Networks - A Topological Perspective, with his abstract and bio below.


Abstract: Deep neural networks are known to have security issues. One particular threat is the Trojan attack. It occurs when the attackers stealthily manipulate the model's behavior through Trojaned training samples, i.e., samples with special trigger injected and labels altered. To identify a Trojaned model at deployment is challenging, due to limited access to the training data. We propose to identify Trojaned neural networks using methods from topological data analysis. In particular, we propose to (1) inspect high-order topological features of the neuron interactions and (2) reverse engineer the injected triggers using a topological loss. These approaches take different angles and reveal insights into the behavior of neural networks when their strong memorialization power is exploited maliciously. The work has been accepted to NeurIPS'21. I will also briefly mention other research directions from my group, including incorporating topological information into deep image analysis, topology-inspired graph neural networks, and robust training of neural networks with label noise. These works have been published in ICLR, ICML, NeurIPS, ECCV, ICCV and AAAI in recent years.
Bio: Dr. Chao Chen is an assistant professor of Biomedical Informatics at Stony Brook University. His research interests span topological data analysis (TDA), machine learning and biomedical image analysis. He develops principled learning methods inspired by the theory from TDA, such as persistent homology and discrete Morse theory. These methods address problems in biomedical image analysis, robust machine learning, and graph neural networks from a unique topological view. His research results have been published in major machine learning, computer vision, and medical image analysis conferences. He is serving as an area chair for MICCAI, AAAI, CVPR and NeurIPS.

Abstract: In this talk, we will discuss what a CS PhD entails and the traits and habits that are important for success in PhD programs and future careers. While the talk is targeted to first-year PhD students, PhD students at all levels should derive from it.

Bio: Samir Das is a professor in the Department of Computer Science at Stony Brook
University. He is currently serving as the department chair. He is well recognized in the
community for his research in wireless networks and systems.

Location: NCS120

Come learn of the exciting research being done across so many fields using AI! The recipients of AI3's seed awards will present their work in our showcase on November 17, 2025 and we would love to see you there!

The schedule is listed below.

Location: New Computer Science Room 120

Session 1 - 10:30 AM to 11:45

Kevin Reed, PI, Introducing the AI Techniques in Assessing the Future Changes of Extreme Precipitation and Associated Flood Risks
Co-PIs: Tangnyu Song, Ishrat Dollan
Consultant: Jayesh Rathi

Ruwen Qin, PI, AI-Assisted Analysis of Materials in Recycling Streams
Consultant: Vismay Vora

Giuseppe Gazzola, PI, Using AI to Investigate National Literatures: Italy, France, Spain 1733- 1794
Consultant: Jayesh Rathi

Joseph Lemelin, PI, IAE2^3: AI Ecologies
Co-PIs: Katherine Johnston, Aruna Balasubramanian, Matthew Salzano

Niranjan Balasubramanian, Co-PI, Molecular Foundations for Sustainability: Data Analytics for Sustainable Cellulose Scaffolding Modifications to Remediate Diverse Water Contamination Challenges
PI: Benjamin Hsiao, Co-PI: I. V. Ramakrishnan

Owen Rambow, PI,Achieving Common Ground Through Language and Vision in Mixed-Initiative Human-Machine Communication Via zoom
Co-PI Susan Brennan

Session 2 - 12:30 PM to 1:45

Jack McSweeney, PI, Developing Machine Learning Approaches to Classify Internal Waves
Consultant: Vismay Vora

Eric Josephs, PI, Learning Design Rules to Personalize Precision CRISPR Gene Therapies with Interpretable AI
Consultant: Deboparna Banerjee

Shyam Sharma, PI, Fostering Writing-to-Learn Skills through Critical AI Literacy: A Faculty Development and Student Support Program
Co-PIs: Rose Tirotta-Esposito, Christine Fena

Ritwik Banerjee, PI, A Pragmatic Approach to AI for Digital Media Integrity: Combating Complex Misinformation Through Fallacies and Propaganda
Co-PI: Ruobing Li

Ziyu Shu, Co-PI, Novel Clinical Applications of Deep Image Prior-based CT Image Reconstruction
PI: Xin Qian, Co-PIs: Tiezhi Zhang, Zhaozheng Yin

Prateek Prasanna, Co-PI, An Artificial Intelligence-Driven Clinical Decision Support Tool for the Management of Abdominal Aortic Aneurysm
PI: Apostolos Tassiopoulos, Co-PI's: Mary Saltz, Janos Hajagos, Tahsin Kurc

Presenters will give a 5-minute talk with 2 minutes for Q & A.

CSE 600 Seminar Series | Fall 2025



Abstract:

We often talk about AI as if it begins with a dataset and ends with an application. But behind every model lie two sets of actors who are rarely acknowledged in technical documentation: the workers who train AI systems and the researchers who try to make sense of them. This talk brings both groups into view.
Dr. Ben Zhang will offer an on-the-ground examination of the prevailing values and invisible labor that underpin commercial AI production and data production. Drawing on ethnographic research inside AI data annotation centers in China, he introduces the concept of precision labor to unpack the labor dimension of constructing, managing, and performing technical accuracy. This concept highlights the hidden and excessive labor required to reconcile the ambiguity and uncertainty involved in AI training. A precision labor lens challenges the legitimacy and sustainability of the relentless pursuit of technical accuracy, raising new questions about its consequences and implications.
On the other end of the pipeline, as LLMs become embedded in society, social scientists like Dr. Jieshu Wang is scrutinizing their potential biases while employing them as research tools. She will present her recent work auditing LLM responses across different contexts, revealing that LLMs exhibit varying levels of environmental awareness and disproportionately reward institutional prestige in peer-review simulations. She also demonstrates how LLMs can serve as useful tools in social-science pipelines, e.g., extracting location information, inferring demographics, parsing citations, mapping social networks, and analyzing occupational data.
By placing these two worlds side by side - the labor of training AI and the scholarly efforts to study it - we show why responsible AI should go beyond the deployment phase - emphasizing fairness audits, and model explainability. It requires reimaging the values, labor regimes, and social science practices that shape AI systems from annotation to analysis.


Bios:

Dr. Jieshu Wang is an interdisciplinary researcher studying the human and social dimensions of artificial intelligence (AI) and how people can thrive in an AI-integrated future. She combines computational methods with qualitative insights to trace technology trends and understand their broader societal impact. She earned her Ph.D. in Human and Social Dimensions of Science and Technology from Arizona State University, after earlier degrees in Civil Engineering, Economics, and Science and Technology Studies. She has also worked as a patent examiner, an editor at a popular science magazine, and co-founded Synced (机器之心), an AI-focused media company in China. Her research looks both backward and forward. Backward-looking, she examines how AI are created, who creates them, and who is missing from the process. Forward-looking, she studies how AI is transforming the way we live, connect, invent, work, and adapt, as well as how AI might help address challenges such as climate change and workforce transitions.
Dr. Ben Zhang is an Assistant Professor in the Department of Technology. His research explores the production and sociotechnical impacts of AI systems in critical areas such as work, health, and sustainability. Drawing from his background in Human-Computer Interaction (HCI), Human-Centered AI, and Science and Technology Studies (STS), he employs a life-cycle-centered approach to holistically examine the promises and harms of these systems and to inform the design of responsible AI infrastructures across their development, deployment, and governance. Ben received his Ph.D. in Information Science from the University of Michigan. Ben's work has been supported by competitive awards and fellowships, including the University of Michigan Rackham Predoctoral Fellowship and the Weizenbaum Fellowship. His research has appeared in premier computing venues, including ACM CHI, ACM CSCW, and AAAI ICWSM.

Location: NCS 120