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

This is Stony Brook's quantum moment. Join us for a spotlight on the core achievements and research excellence of faculty across the Colleges of Arts and Sciences (CAS), and Engineering and Applied Sciences (CEAS) - and their collaborative advancements in quantum science and technology. Learn about the real world impact of their enduring work, their leadership in translating foundational science into entrepreneurial opportunities, and their impetus for making connections to next generation innovation.

Presented by: Catherine Chen, Ph.D., Research Development Associate

Welcome remarks: President Andrea Goldsmith

Panel moderators: Dean David Wrobel, CAS, and Dean Andrew Singer, CEAS

Presentations and panel featuring our faculty:

  • Jennifer Cano, CAS, Physics and Astronomy

  • P. Scott Carney, CEAS, Mechanical Engineering

  • Hyeongrak Chuck Choi, CEAS, Electrical and Computer Engineering

  • Eden Figueroa, CAS, Physics and Astronomy

  • Humanshu Gupta, CEAS, Computer Science

  • Angela Kelly, CAS, Physics and Astronomy

Location: Theatre at the Charles B. Wang Center, Stony Brook University

Reserve your tickets by March 26!

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

Abstract: This talk shows how machine learning can address challenges in Astrophysics. We specifically focus on black hole simulations and supernova observations. First, we present a super-resolution technique for black hole simulations that avoids the need for high-resolution labels by leveraging the Hamiltonian and momentum constraints from general relativity. This method reduces constraint violations by one to two orders of magnitude. Next, we introduce Maven, a multimodal foundation model for supernova science. Using contrastive learning to align photometric and spectroscopic data, Maven achieves state-of-the-art results in classification and redshift estimation by pre-training on synthetic data and fine-tuning on real observations.

Bio: Thomas Helfer is a computational physicist specializing in deep learning and physics. Currently based at the Institute for Advanced Computational Science at Stony Brook University, Thomas was previously a postdoctoral fellow at Johns Hopkins and did his PhD with Eugene Lim at King's College in London. In his work, he looks to bridge topics; in his PhD, he bridged theoretical particle physics and gravitational waves. Now, in his postdoctoral work, he aims to find novel applications of deep learning in astrophysics.

*please note: this seminar will be held in a hybrid format*


Location: IACS Seminar Room OR Join Zoom Meeting
https://stonybrook.zoom.us/j/98617630652?pwd=tb4hplPgb3bTTifPCJTCcsn3P9vX8y.1

Meeting ID: 986 1763 0652
Passcode: 882994

The International Conference on Machine Learning (ICML) is the premier gathering of professionals dedicated to the advancement of the branch of artificial intelligence known as machine learning.

ICML is globally renowned for presenting and publishing cutting-edge research on all aspects of machine learning used in closely related areas like artificial intelligence, statistics and data science, as well as important application areas such as machine vision, computational biology, speech recognition, and robotics.

ICML is one of the fastest growing artificial intelligence conferences in the world. Participants at ICML span a wide range of backgrounds, from academic and industrial researchers, to entrepreneurs and engineers, to graduate students and postdocs.


For more information and registration, visit the official website.
ICB&DD 19th Annual Symposium

Iwao Ojima, Director, ICB&DD
Ivet Bahar Chair, Organizing Committee
Dima KozakovCo-Chair, OrganizingCommittee

There will be poster sessions on projects conducted in the ICB&DD member's laboratories aswell as other laboratories in the area. Awards will be given to the best three posters.

Please see the link for the registration and poster sessions in:
https://www.stonybrook.edu/commcms/icbdd/https://forms.gle/Wh4UzVx9U4HWStXb8