Jerome Liang, PhD 

Professor of Radiology, Biomedical Engineering, Electric and Computer Engineering, and Computer Science 

Co-Director of Research 

Department of Radiology 


Artificial intelligence, machine learning and computer-aided diagnosis in cancer Imaging 

February 11, 2021 

12:00pm - 1:00pm 

Virtual Seminar - Zoom 

https://stonybrook.zoom.us/j/98155629970?pwd=YzRvcnJnTlNTT1E5ak1oZEJvWTZHQT09 

Meeting ID: 981 5562 9970 

Passcode: 950410 

Host: 

Wei Zhao, PhD 

Professor of Radiology and Biomedical Engineering 

Educational Objectives  

Upon completion, participants should be able to:  

(1) Learn different medical image representations of cancer attributes, such as heterogeneity, high tendency to grow, etc.  

(2) Learn how computer (machine) can be trained (or programmed) to recognize the image representations.  

(3) Learn how artificial intelligence can drive the machine learning to maximize the performance of computer-aided diagnosis (CADx).  

Disclosure Statement  

In compliance with the ACCME Standards for Commercial Support, everyone who is in a position to control the content of an educational activity provided by the School of Medicine is expected to disclose to the audience any relevant financial relationships with any commercial interest that relates to the content of his/her presentation.  

 

The speaker, Jerome Liang, PhD, the planners; and the CME provider have no relevant financial relationship with a commercial interest (defined as any entity producing, marketing, re-selling, or distributing health care goods or services consumed by, or used on, patients), that relates to the content that will be discussed in the educational activity.  

 

CONTINUING MEDICAL EDUCATION CREDITS  

The School of Medicine, State University of New York at Stony Brook, is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.  

 

The School of Medicine, State University of New York at Stony Brook designates this live activity for a maximum of 1.0 AMA PRA Category 1 Credits™. Physicians should only claim credit commensurate with the extent of their participation in the activity.  

 

Should you be logging in Zoom by using your tablet or mobile device, please be sure to add your Full Name and/or Email for CME credit. 

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 Ph.D. program or (2) receive permission from the instructors. Each seminar will consist of multiple short talks (around 15 minutes) by multiple students. Students can register for 1 credit for CSE656. Registered students must attend and present a minimum of 2 talks. Registered students must attend in person. Up to 3 absences will be excused. Everyone else is welcome to attend. The seminar will be taught by Prof. Chao Chen, chao.chen.1@stonybrook.edu.
The IEEE / CVF Computer Vision and Pattern Recognition Conference (CVPR) is the premier annual computer vision event comprising the main conference and several co-located workshops and short courses. With its high quality and low cost, it provides an exceptional value for students, academics and industry researchers.



Location: Colorado Convention Center
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.
Abstract: DeepSeek-R1-Zero has shown that reinforcement learning (RL) at scale can directly enhance the reasoning capabilities of LLMs without supervised fine-tuning. In this work, we critically examine R1-Zero-like training by analyzing its two core components: base models and RL. We investigate a wide range of base models, including DeepSeek-V3-Base, to understand how pretraining characteristics influence RL performance. Our analysis reveals that DeepSeek-V3-Base already exhibit ''Aha moment'', while Qwen2.5 base models demonstrate strong reasoning capabilities even without prompt templates, suggesting potential pretraining biases. Additionally, we identify an optimization bias in Group Relative Policy Optimization (GRPO), which artificially increases response length (especially for incorrect outputs) during training. To address this, we introduce Dr. GRPO, an unbiased optimization method that improves token efficiency while maintaining reasoning performance. Leveraging these insights, we present a minimalist R1-Zero recipe that achieves 43.3% accuracy on AIME 2024 with a 7B base model, establishing a new state-of-the-art.

Speaker: Md. Saqib Hasan

Location: CS2311
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

You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes three short talks on AI research happening at BNL, followed by an open mixer over coffee and snacks for everyone to network and discuss all things AI. 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.

Join us every other Tuesday at noon in CDSD's Training Room (building 725, 2nd floor) 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.

Speakers

Kriti Chopra, Computing & Data Sciences (CDS)
Thomas Flynn, Computing & Data Sciences (CDS)
Wenjie Liao, Chemistry Division

Tuesday, January 7, 2025, 12:00 pm -- CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1615289117?pwd=Hqkbj9itxWrFnkhZ8rQXHPInO2gxdF.1

Meeting ID: 161 528 9117
Passcode: 991382

Professor Nanpeng Yu from UC Riverside present Machine Learning and Big Data Analytics in Power Distribution Systems.

Abstract: The electric utility industry is being swamped by petabytes of data coming from various sources such as smart meters, phasor measurement units, SCADA systems, geographical information systems and customer management systems. The primary and secondary value embedded in the complex and heterogeneous data sets from power distribution systems is immense. However, algorithms and applications for unlocking the potential of big data in power systems are at an early stage of development. This talk discusses the recent advancement of machine learning algorithms and big data analytics methods in power distribution systems. In particular, we will explain how to develop hybrid algorithms, which synergistically combine the merits of state-of-the-art machine learning algorithms and physical model-based methods. We will take a deep dive into the following applications: network topology identification, electricity theft detection, estimation of behind-the-meter solar generation and data-driven distribution system controls.

Bio: Dr. Nanpeng Yu received his B.S. in Electrical Engineering from Tsinghua University, Beijing, China, in 2006. Dr. Yu received his M.S. degrees in Electrical Engineering and Economics and Ph.D. degree from Iowa State University in 2010. Before joining University of California, Riverside, Dr. Yu was a senior power system planner and project manager at Southern California Edison from Jan, 2011 to July 2014.

Currently, he is an Associate Professor in the Department of Electrical and Computer Engineering at the University of California, Riverside, CA. Dr. Yu is the recipient of the Regents Faculty Fellowship and Regents Faculty Development award from University of California. He received multiple best paper awards from IEEE Power and Energy Society General Meeting, IEEE Power and Energy Society Grand International Conference and Exposition Asia and the Second International Conference on Green Communications, Computing and Technologies.

Dr. Yu is the director of Smart City Innovation Laboratory at UC Riverside. He currently serves as the vice chair of the distribution system operation and planning subcommittee of IEEE Power and Energy Society and the co-chair for IEEE Big Data Applications in Power Distribution Networks Task Force. Dr. Yu currently serves as the associate editor for IEEE Transactions on Smart Grid and International Transactions on Electrical Energy Systems.
Abstract: Making large language models usable requires post-training methods that align models to human values, robustly handle underspecified inputs, and generalize to diverse instructions. This talk addresses the challenge of developing responsible AI through post-training from the following angles. First, I address contextual robustness. Preference data, for example, is often underspecified, and I show how underspecification in preference data can lead to diverging preferences. Standard reward models fail to properly handle these disagreements, often making decisive choices even when human annotators are split. I argue that more consequential outputs demand more context, and propose clarification question generation as one solution. Second, I will discuss how we can train models to be better instruction followers. I will show that most models severely overfit on a small set of instruction-following constraints and are not able to generalize well to unseen output constraints. I propose to train models with reinforcement learning from verifiable rewards for verifiable instruction following, and show how this leads to improved generalization on constraint following. Throughout the presentation, I will outline how I have applied these insights into developing open generative models, like Tülu and OLMo, and I will conclude with my research agenda for responsible post-training: critical AI evaluation, broader generalization, and expanding what models can reliably do.


Bio: Valentina Pyatkin is a postdoctoral researcher at the Allen Institute for AI and the University of Washington, advised by Prof. Hanna Hajishirzi and Prof. Yejin Choi. Additionally, she is part- time affiliated with the ETH AI Center, where she mentors students and works on post-training for the Swiss AI Initiative. She obtained her PhD in Computer Science from Bar Ilan University. Her work has been awarded an ACL Outstanding Paper Award and the ACL Best Theme Paper Award, and has been supported by a Schmidt Sciences Postdoctoral Award. During her doctoral studies, she conducted research internships at Google and the Allen Institute for AI, where she received the AI2 Outstanding Intern of the Year Award.

Location: NCS 120