Abstract: Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology.

Speaker: Qin Ren

Location: https://stonybrook.zoom.us/j/97458849045?pwd=SREklaxa7EFhKaK6TeRXgQPH64vrQJ.1&jst=2
Abstract: Monocular surface normal estimators trained on large-scale RGB-normal data often perform poorly in the edge cases of reflective, textureless, and dark surfaces. Polarization encodes surface orientation independently of texture and albedo, offering a physics-based complement for these cases. Existing polarization methods, however, require multi-view capture or specialized training data, limiting generalization. We introduce Poppy, a training-free framework that refines normals from any frozen RGB backbone using single-shot polarization measurements at test time. Keeping backbone weights frozen, Poppy optimizes per-pixel offsets to the input RGB and output normal along with a learned reflectance decomposition. A differentiable rendering layer converts the refined normals into polarization predictions and penalizes mismatches with the observed signal. Across seven benchmarks and three backbone architectures (diffusion, flow, and feed-forward), Poppy reduces mean angular error by 23-26% on synthetic data and 6-16% on real data. These results show that guiding learned RGB-based normal estimators with polarization cues at test time refines normals on challenging surfaces without retraining.

Speaker: Irene Kim

Location: NCS 115
AI + Music Seminar - The meeting will consist of introductions and organizational discussions, aimed at understanding participants' interests. We'll discuss what the seminars can focus on going forward.

Designed for faculty, staff, presidents, provosts, academic leaders, student affairs professionals, IT specialists, librarians, researchers, administrators, institutional decision-makers, and other higher education stakeholders, the conference highlights practical strategies institutions can implement now while exploring longer-term governance, policy, and ethical considerations. Participants will leave with concrete tools, cross-institutional insights, and collaborative connections that support mission-aligned AI innovation.

Hosted by: AAC&U

Location: Atlanta, GA and Virtual

Register here.

IACS Research Theme: Human Centered Computing Seminar

Abstract: The AI art platform Artbreeder hosts daily remix parties where users build on each other's work, creating transparent evolutionary chains of images from a single seed. This study analyzes 130,882 images from 368 remix parties to identify the drivers of novelty, complexity, and competitive success. The results reveal an interesting tension: while more novel parent images produce more novel and complex children and attract more likes, users paradoxically prefer to remix images that are less novel and complex. At the group level, larger remix parties produce more novelty at the cost of lower complexity. Additionally, images tend to converge towards common thematic attractors (e.g., steampunk scenes, alien architecture, furries) over the course of remix parties. These results provide quantitative insights into collective creativity--the production of novelty by groups of people--a typically opaque aspect of human cultural evolution.

Speaker: Dr. Mason Youngblood

Location: Institute for Advanced Computational Science, Seminar Room
Hyperscale Verification in Microsoft Azure talk by Nikolaj Bjorner

Abstract: Cloud providers are increasingly embracing network verification for managing complex datacenter network infrastructure. Microsoft's Azure cloud infrastructure integrates the SecGuru tool, which leverages the Z3 Satisfiability Modulo Theories solver, for checking network access
control lists. It also integrates a verifier that uses both custom verification algorithms and Z3 that checks correctness of forwarding tables in Azure data-centers. These tools assure that the network is configured to preserve desired intent over hundreds of thousands of network devices. We describe our experiences building and running SecGuru for network verification in Azure.

Finally we mention recent advances in Z3, including a distributed version of Z3 that scales with Azure's elastic cloud. It integrates recent advances in lookahead and distributed SAT solving for Z3's
engines for SMT. A different recent advance includes integration of DNNs to learn variable branching strategies for high-performance SAT solvers, including MiniSAT, Glucose and Z3's SAT solver.

Bio: Nikolaj Bjorner is a Principal Researcher at Microsoft Research, Redmond, working in the area of Automated Theorem Proving and Software Engineering. His current main line of work is around the state-of-the art theorem prover Z3, which is used as a foundation of several software engineering tools. Z3 received the 2015 ACM SIGPLAN Software System award and most influential tool paper in the first 20 years of TACAS in 2014, and test of time award at ETAPS 2018. Together with Leonardo de Moura received the CADE 2019 Herbrand award for contributions to SMT and applications. Previously, he developed the DFSR, Distributed File System - Replication, and Remote Differential
Compression protocols, RDC, part of Windows Server since 2005 and before that worked on distributed file sharing systems at a startup, and program synthesis and transformation systems at the Kestrel Institute. He received his Master's and PhD degrees in computer science from Stanford University.
Hosted by the College of Business faculty and staff, this virtual session will explore how our MS in Business Analytics & Intelligence program can enable you to become a future leader with AI expertise. This session will also cover the program's benefits, curriculum, cost, and admission requirements.

Register here.


Dates: 

Wednesday, March 3, 2021 - 6:00pm to 7:30pm

Location: 

Zoom - contact events@cs.stonybrook.edu for Zoom info.

Event Description: 

Women in Computer Science (WiCS), the Society of Women Engineers (SWE), and the Stony Brook Robotics Team (SBRT) are collaborating to host an event called Inspiring Women in STEM Academia: A Community Dialogue to address the lack of female representation in STEM academia. 
 

All are invited to attend so they may gain a better understanding of the challenges faced by their female colleagues and hear perspectives on how they can offer support in the workplace. Given the shockingly disproportionate number of female professionals in STEM academia, we feel that this event would be extremely beneficial for male faculty to listen to and amplify their voices.

It will begin with a discussion panel consisting of Stony Brook professors and faculty who will provide valuable insight into the issue. From there, we will split into smaller discussion groups where student and faculty attendees will be able to voice their opinions, hear about the thoughts/experiences of others, and participate in an engaging discussion with panelists.

The event will be held on March 3rd from 6:00 - 7:30 PM on Zoom.
 

The following Stony Brook faculty will be panelists:

Dr. Aruna Balasubramanian - Computer Science Professor, WiCS Advisor, WPhD Advisor

Dr. Xinwei Mao - Civil Engineering Assistant Professor

Urszula Zalewski - Director of Experiential Learning, Career Center Advisor (Healthcare)

Dr. Heather Lynch - Ecology and Evolution Professor, Lynch Lab for Quantitative Ecology

Karen Kernan - URECA Director, Simons Summer Research Program Director

Dr. Eszter Boros - Chemistry Assistant Professor, Boros Lab

Dr. Maria Nagan - Chemistry Lecturer, Nagan Research Lab

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

Discover how Google Gemini can help you draft lesson plans, generate discussion questions, design activities, and create course materials in a fraction of the time.

You have a workshop to plan, need an engaging activity, and a stack of content to create, but not enough time? Google Gemini, available through your SBU Google account, can help you brainstorm, draft, and refine lesson plans, learning objectives, discussion prompts, rubrics, and more. This session is designed for anyone who is interested in using Gemini to help generate learning activities.

In this session, you will:

  1. Access Google Gemini using your SBU Google account
  2. Write effective prompts for lesson planning and content creation
  3. Generate and refine learning objectives, discussion questions, and activities
  4. Create or improve course materials such as rubrics, instructions, and assessment ideas
  5. Apply best practices for reviewing and adapting AI-generated content

Register here.