AI Innovation Institute

Abstract: The capacity to adapt machine learning models to various contexts, information, and objectives is particularly valuable. In this thesis, I focus on developing Class Conditional Guided Models. These are models that can be adaptively biased towards a class of interest via a conditional input. My primary focus lies in the efficiency of these models. They are constructed to require training only once, with the ability to quickly and conveniently adapt during testing time without necessitating fine-tuning or retraining.
Firstly, I propose RelationVAE, a novel generative model designed for few-shot scenarios, utilizing the prior knowledge of class similarity relationships. RelationVAE is designed to condition on the embeddings of the neighbor classes (i.e. classes with similarity relationships), to generate more reliable samples by making them more similar to the neighbor class. This enables adaptation of the generative model to the provided prior knowledge about class relationships.
As a second focus, I introduce scGAN, a shadow segmentation technique that enables adaptation to varying shadow distributions in different testing environments. scGAN is designed to condition on a sensitivity parameter, a scalar, to control the amount of the shadow detected. In the testing phase, the parameter is set to appropriate values, allowing the model to quickly adapt to specific test environments.
In my third contribution, I propose S-SEG, a methodology for fine-grained counting allowing adaptation to different granularities of fine-grained classes. In fine-grained problems, the distinction between classes is subtle and inconsistent across images, leading to variations in the granularity of the target class from one image to another. S-SEG is designed to be conditioned on an additional input, the sensitivity parameter, to control the granularities of the target class during inference.
My fourth contribution is a text-to-image synthesis method which allows controlling the number of the generated objects of a target class. I propose to generate an intermediate condition, the density map, which reflects the number of objects, together with their layout. This intermediate condition is used to effectively guide the generative model to generate objects with accurate counts.

Speaker: Vu Nguyen

Zoom: https://stonybrook.zoom.us/j/97114455337?pwd=Z4rB9dWcstlahUIs8PRrvQ9b2ZK2Df.1
Meeting ID: 971 1445 5337
Passcode: 272300

CVPR 2020 - Seattle, Washington - Strong possibility this will be held remotely - http://cvpr2020.thecvf.com/

2020 Annual Conference of the Association for Computational Linguistics Online format - https://acl2020.org/

AI Seminar: Computational Pathology: Deep Learning, Classification and
Predicting the Future  - Joel Saltz

Abstract:  Pathologists have been looking at tissue through microscopes since the 1800s.  During each pathologist's career,  he or she views slides having  roughly 1,000,000,000,000 cells. Deep learning methods are rapidly being developed to assimilate the huge amount of information walked inside of tissue images and to use this information to predict outcomes and responses to treatments.

Stony Brook is a leader in this type of multi-disciplinary work. I will provide an overview of Stony Brook computational Pathology efforts and articulate how these have the potential to create biomedical advances as well as to drive development of new computer science. 


Bio: Dr. Joel Saltz is a leader in research on advanced information technologies for large scale data science and biomedical/scientific research. He has developed innovative pathology informatics methods, including: the first published whole slide virtual microscope system; pioneering pathology computer-aided diagnosis techniques; and methods for decomposing pathology images into features and linking those features to cancer omics, response to treatment and outcome. He has broken new ground in big data through development of the filter-stream based DataCutter system, the map-reduce style Active Data Repository and the inspector-executor runtime compiler framework. He has also been an active contributor in clinical informatics, having developed
predictive models for hospital readmissions, point of care laboratory testing quality assurance systems, decision support systems for electrophoresis interpretation and graphical user interfaces to support clinical data warehouse queries. Dr. Saltz has been a pioneer in establishing the field of biomedical informatics; he founded and built two highly successful departments of biomedical informatics, one at Ohio State University and one at Emory University. In 2013, he came to Stony Brook as Vice President for Clinical Informatics and Founding Department Chair of Biomedical Informatics - to create a living laboratory for biomedical informatics and to create a third unique biomedical informatics department dually housed in the School of Medicine and the College of Engineering. Dr. Saltz is trained both as a computer scientist and as a physician through the MSTP program at Duke University. He has deep experience in computer science, having served on the computer science faculties at Yale University and the University of Maryland. He completed his residency in clinical
pathology at Johns Hopkins University and he is a practicing, board-certified clinical pathologist. 

Abstract: Humans perceive the world around them by recognizing global patterns and structures such as object parts, branches, their spatial arrangement, and so on. Most deep learning models, however, take a fundamentally local approach. They process images pixel-by-pixel rather than focusing on structures as a whole. While these models indeed perform well on many tasks, the local (pixel-level) versus global (structure-level) disconnect makes them harder to interpret and control.

Topology, in a general sense, is a mathematical language for describing structure. It delineates how different parts of an image relate to one another, capturing both individual structures and their overall layout. Preserving topology enforces structural correctness and, by extension, semantic validity.

In this thesis, we investigate how topological constraints can be used to bridge the gap between local and global understanding. We use topology to inform the design of deep learning models that are explicitly structure-aware. Our thesis focuses on dense prediction tasks, which include image segmentation, uncertainty estimation, and generative modeling. First, we introduce a topological interaction module for semantic segmentation that encodes containment and exclusion constraints directly into the learning process. This preserves anatomical hierarchies and improves multi-class consistency. Next, since segmentation models can never be truly perfect, we address the need for reliable uncertainty estimation to identify error-prone regions. Unlike conventional pixel-wise uncertainty maps, which tend to be noisy and difficult to interpret, we propose reasoning at the level of structural units--branches and connections--which are more visually discernible and actionable. Finally, we leverage topology for generative modeling. We propose a topology-guided diffusion framework that can be controlled using structural attributes like object count and connectivity.

Together, these contributions establish a unified approach to topology-informed, structure-preserving dense prediction models. By integrating topological reasoning with deep networks, this thesis advances models that are not only accurate, but also structurally consistent, interpretable, and controllable. The results from this thesis have been published in ECCV, NeurIPS, and ICLR.

Speaker: Saumya Gupta

Location: New Computer Science (NCS) 120


Zoom: https://stonybrook.zoom.us/j/93643318604?pwd=kv8DagpbayzizivU29UCYItnlzlYRM.1&jst=2

NLP Reading Group | Fall 2025

The Natural Language Processing Reading Group at Stony Brook University meets weekly to discuss recent research papers in NLP and related fields.
Join the Google Group here.