The Renaissance School Of Medicine Department of Scientific Affairs and its Single Cell Genomics facility are excited to host a special seminar and discussion on AI and single cell genomics analysis:

With the decreasing cost of sequencing, many biobanks and large research cohorts have moved to whole genome sequencing (WGS) and single-cell RNA-seq. However, making use of this deluge of data remains a challenge. I will discuss statistical and deep learning approaches that we are exploring to address the challenge of noncoding variant interpretation, including our work as part of the Alzheimer's disease sequencing project.

Speaker: David A. Knowles, PhD. Asst. Professor of Computer Science, Interdisciplinary Appointee in Systems Biology, Columbia University Core Faculty Member, New York Genome Center

Join us in person: Health Science Tower Level 3, Lecture Hall 5
Join librarian Christine Fena for an interactive workshop that invites you to explore AI tools firsthand, not just as users, but as critical investigators. Through playful experimentation and collaborative discovery, you'll uncover inherent biases, probe algorithmic flaws, and gain a deeper understanding of AI's limitations and societal impacts.

Location: Melville Library, Central Reading Room, Lab B

https://library.stonybrook.edu/library-events/critiquing-ai/
Abstract: Anxiety disorders are characterized by persistent and excessive form of fear and worry that interferes with daily functioning, distinguishing it from the adaptive anxiety that helps individuals respond to challenges. Despite affecting millions worldwide and costing a significant public health burden, anxiety disorders still remain underdiagnosed than actual prevalence due to lack of understanding and stigmatization. Leveraging machine learning (ML) and natural language processing (NLP) approaches can help bridge this gap by enabling scalable and accessible mental health assessments, offering a data-driven understanding of anxiety from individual and societal perspectives, and shedding light on societal stigmas toward mental health conditions. At the same time, advancing ML and NLP techniques for anxiety research presents unique technical challenges, such as effectively modeling linguistic markers of anxiety and ensuring interpretability in mental health predictions.

This dissertation investigates anxiety from both individual and societal perspectives using artificial intelligence. First, we explore individual manifestations of anxiety through three methodological advancements: (1) integrating contextual and discourse-level embeddings to improve language-based anxiety prediction using Facebook posts and selfreported surveys; (2) enhancing cognitive dissonance detection in Twitter dataset with transfer learning and active learning; and (3) developing longitudinal representation learning approaches that achieve both predictive utility and interpretability of adolescent psychopathology. Finally, we extended our analysis to societal dimension of anxiety by identifying and categorizing social norms expressed in Reddit and Twitter posts and examining their associations with anxiety. By combining data-driven methods with psychological insights, this work studies anxiety from various angles - capturing both individual experiences and societal influences - offering a step toward a more comprehensive understanding of its causes and manifestations.

Speaker: Swanie Juhng

https://stonybrook.zoom.us/j/98905245099?pwd=M7rI7aNfNio281qyebEUdNPBcSiK7Y.1
AI is everywhere and so are the privacy concerns that come with it. At its core, the most common forms of AI we use today are online digital services and thus inherit the usual privacy risks. We'll take a look at indirect prompt injection- a technique that can trick AI tools into revealing or extracting private information as well as techniques being used in academic contexts to manipulate systems and even mislead researchers.

Register here for the online session.
Join CELT on Tuesday, March 31 for a focused, one-hour overview on how to redesign and future-proof assessments in the age of AI! This session will cover three key areas: leveraging AI as a co-pilot for developing effective exam questions, designing authentic assessments, and exploring how AI can strategically support active learning structures like Team-Based Learning (TBL), Project-Based Learning (PBL), and Scenario-Based Learning (SBL).

Register here.

Abstract: How do humans learn the sound patterns of their language? Despite a variety of methods and advances in phonotactic learning, there is still a paucity of computational research, methods and data for languages with tones. In this talk, I will explore this question specifically in light of tone languages, where pitch plays a crucial role in distinguishing words' meaning. I provide an implementation of the Bottom-Up Factor Inference Algorithm over Autosegmental Representations (BUFIA-AR), which learns the rules governing possible tone patterns. Using a dataset of Hausa, a West African tone language, the algorithm successfully identifies patterns that are not permitted in the language. These results (i) confirm long-standing linguistic generalizations, (ii) make more specific predictions about exceptional cases, and (iii) reveal previously unnoticed patterns. The results show how mathematical models of sound structure can be brought into dialogue with both linguistic theory and computational learning, highlighting the broader potential of formal approaches to capture human linguistic knowledge.

Bio: Han Li is a fifth-year Ph.D. student in Linguistics department, specializing in computational linguistics under the supervision of Professor Jeff Heinz. Her research focuses on how sound patterns in language can be formally represented and computationally learned, bridging theoretical linguistics and computer science.

Location: Institute for Advanced Computational Science, Seminar Room

Zoom Meeting: https://stonybrook.zoom.us/j/94043459206?pwd=3ra47h8HghOFRfobRBjZaDMyTwialr.1
Meeting ID: 940 4345 9206
Passcode: 332717


Abstract: Computational pathology has revolutionized cancer diagnosis and research through the analysis of digitized whole slide images (WSIs). However, the giga-pixel size of these images presents profound technical challenges, creating two intertwined bottlenecks: computational inefficiency and label inefficiency. The immense data scale makes standard end-to-end (E2E) training of deep neural networks infeasible due to prohibitive GPU memory requirements, while the reliance on expert pathologists for annotations makes obtaining high-quality labeled data a tedious and expensive process. This proposal confronts these dual challenges by developing a series of novel model architectures, training paradigms, and self-supervised learning methods designed to create a more efficient and effective framework for WSI analysis.

To improve computational efficiency, this proposal first introduces a locally supervised learning paradigm that enables E2E training on entire WSIs by partitioning a network into gradient-isolated modules, circumventing the memory bottleneck of backpropagation. Second, it presents Prompt-MIL, a parameter-efficient fine-tuning framework that reduces the number of trainable parameters, memory consumption, and training time by fine-tuning only few prompts to guide large pre-trained models. Third, this work advances the efficient architecture on WSIs by developing novel State-Space Models (SSMs). It proposes 2DMamba, the first intrinsic Mamba architecture that preserves the crucial 2D spatial structure of images, overcoming the spatial discrepancy inherent in 1D models. Fourth, to address the inefficiency of multi-directional scans in Mamba models, including 2DMamba, it presents Locally Bi-directional Mamba (LBMamba), which introduces a novel, hardware-aware local backward scan that integrates bi-directional scan into a single forward pass, significantly improving throughput performance trade-off. Lastly, it proposes an extension to the LBMamba, warp-level Bi-directional Mamba (WLBMamba) that extends the thread-level bidirectional scan to warp-level bidirectional scan that further improves the throughput performance trade-off.

To improve label efficiency, this proposal proposes a Precise Location-based Matching strategy for self-supervised dense contrastive learning. By allowing a local patch in one augmented view to match multiple overlapping patches in another, creates a more accurate correspondence, leading to superior feature representations for dense prediction tasks like segmentation and detection.

In summary, this proposal presents a holistic investigation into the efficiency bottlenecks in computational pathology. Through these combined contributions in model architecture, training paradigms, and self-supervised learning, this work establishes a more scalable, efficient, and powerful computational framework for analyzing giga-pixel pathology images.

Speaker: Jingwei Zhang

Location: Old Computer Science Room 2114

Zoom: https://stonybrook.zoom.us/j/95187903649?pwd=tV0CNxLu1QKqw7hGmcE1h0rJ2C6n1b.1
Meeting ID: 951 8790 3649 | Passcode: 488916

The University at Albany will host a national gathering of professionals and academics that will focus on the transformative potential of AI while addressing the ethical, technical and institutional challenges posed by AI in education.

The Symposium will feature dynamic keynotes, hands-on workshops and engaging conversations with other participants and subject matter experts.

Topics

  • Teaching, Learning and Workforce Development
  • Research, Creative Arts, and Practice
  • Ethics, Governance and Academic Administration

For event information and registration, visit Events@Albany.

Abstract: Millions of individuals living in disadvantaged communities are burdened by poverty, illegal drug activities, health concerns, and the lack of reliable and affordable access to facilities (e.g., schools, hospitals, and transit stations). To address these societal problems efficiently with broad support, initiatives have called to engage agents (e.g., residents, community leaders, or stakeholders) and consider their preferences on community improvement decisions to make collective community decisions. In this talk, we will focus on our ongoing AI-empowered collective decision-making approaches to improve the accessibility of individuals to facilities by (a) locating facilities to provide essential services and (b) strengthening existing infrastructures via structural modifications (e.g., constructing new roads, bridges, multi-use paths, or shuttle services) subject to individuals' preferences on the locations of the facilities and which communities to improve access, respectively. In particular, we will discuss our (theoretical and algorithmic) studies on modeling these approaches under several settings (e.g., accounting for fairness and agent preferences) and designing fair, transparent, strategy proof, and (approximately) optimal mechanisms to elicit (true) individual preferences and determine collective community decisions in order to improve facility accessibility. Finally, we will discuss other ongoing and future collective decision-making efforts in urban planning and public health (i.e., our recent studies on substance use research) to improve communities.

Bio: Hau Chan is an assistant professor in the School of Computing at the University of Nebraska-Lincoln. He received his Ph.D. in Computer Science from Stony Brook University in 2015 and completed three years of Postdoctoral Fellowships, including at the Laboratory for Innovation Science at Harvard University in 2018. His main research lies in multi-agent aspects of AI for Society and Social Good, focusing on developing modeling and algorithmic foundations for tackling societal problems involving agents and predicting agent behavior in societal contexts, leveraging AI, game theory, mechanism design, and machine learning to better inform policymaking and (collective) decision-making. His team has been addressing societal challenges and fairness issues in various domains, including security (e.g., reducing vulnerability), public health (e.g., reducing substance use and homelessness), and urban planning (e.g., improving accessibility to public facilities), collaborating with domain experts. His research has been supported by NSF, NIH, and USCYBERCOM. He has received several Best Paper Awards at SDM and AAMAS and distinguished/outstanding SPC/PC member recognitions at IJCAI and WSDM. He has given tutorials and talks on computational game theory and mechanism design at venues such as AAMAS and IJCAI, including an Early Career Spotlight at IJCAI 2022. He has served as co-chairs for the AI and Social Good Track, Demonstration Track, Student Activities, Doctoral Consortium, Job Fair, Scholarships, Finance, and Diversity & Inclusion Activities at AAAI, AAMAS, and IJCAI.

Location: Old Computer Science, room 1310