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: 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
Looking to learn about a new topic or skill? Look no further! Gemini's Guided Learning feature acts as your own personal tutor, teaching you about a particular subject through an engaging back and forth conversation. This AI tool helps users develop their knowledge and skills on a wide variety of topics, acting as a patient mentor, breaking down complex topics step-by-step. This session will take place on 2/24 at 11 AM. Please register using the link below!
https://stonybrookuniversity.co1.qualtrics.com/jfe/form/SV_a9PVlBw0E1Bal1A?

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


Abstract:
Deep learning models have achieved remarkable success across a wide range of computer vision tasks, including image classification, semantic segmentation, etc. However, such success highly relies on a large amount of annotated data, which are expensive to obtain. Moreover, their performance often degrades when there exist distribution shifts between training and test data. Domain Adaptation overcomes these issues by transferring knowledge from a label-rich source domain to a related but different target domain. Despite its popularity, domain adaptation is still a challenging task, especially when the data distribution shifts are severe, while the target domain has no or few labeled data.

In this thesis, I develop four efficient domain adaptation approaches to improve model performance on the target domain. Firstly, inspired by the large-scale pretraining of Vision Transformers, I explore Transformer-based domain adaptation for stronger feature representation and design a safe training mechanism to avoid model collapse in the situation of a large domain gap. Secondly, I observe that source models have low confidences on the target data. To address this, I focus on the penultimate activations of target data and propose an adversarial training strategy to enhance model prediction confidences. Thirdly, I study using weak supervision from prior knowledge about target domain label distribution. A novel Knowledge-guided Unsupervised Domain Adaptation paradigm is devised, and a plug-in module is designed to rectify pseudo labels. Lastly, I step into the task of Active Domain Adaptation, where the labels of a small portion of target data can be inquired. I propose a novel active selection criterion based on the local context and devise a progressive augmentation module to better utilize queried target data. The robustness of domain adaptation approaches, in addition to accuracy, is critical yet under-explored. To conclude the thesis, I empirically study set prediction in domain adaptation using the tool of conformal prediction and conformal training.


Location: New Computer Science Bldg., Room 120
Zoom Link: https://stonybrook.zoom.us/j/92736258273?pwd=ipDdh1CTG6dRYmqa3ltUvooei8OfaT.1Meeting ID: 927 3625 8273
Passcode: 466399
Please join us on Zoom for our next event in the Fall 2025 Stony Brook School of Nursing Research Seminar Series presented by our Office of Research and Innovation.

Topic: Responsible Artificial Intelligence: Promoting Health Equity for All

Speaker: Michael P. Cary, Jr., PhD, RN, FAAN.

Dr. Cary is a tenured Associate Professor at the Duke University School of Nursing. Dually trained as a health services researcher and applied health data scientist, Dr. Cary utilizes AI to investigate health disparities in aging populations, thereby promoting health equity and improving healthcare delivery. He co-directs HUMAINE™, an initiative dedicated to equipping nurses and healthcare professionals with the knowledge and skills necessary for the responsible use of AI in clinical practice.

Register: https://web.cvent.com/event/057978a5-a770-4de5-aca5-ad00287e4902/summary

The Vedanta Forum is devoted to one of humanity's oldest and most profound pursuits -- thinking. Thinking about who we truly are: the one that remains constant through childhood and old age, through waking, dream, and deep sleep. Thinking about the source and cause of creation, and its relationship to what inheres in us.

Across history, such thinking, both meditative and scientific, has been aimed at these questions. The ancient Upanishads proclaimed, Tat Tvam Asi -- Thou Art That -- revealing the non-dual identity of the individual and the ultimate reality. Centuries later, modern scientists such as Schrödinger and Bohr echoed similar intuitions about the unity of existence.

Over time, many philosophical approaches, traditions, and interpretive schools have arisen from such inquiry, each offering unique perspectives. The Forum will:

  • Focus on universal approaches and traditions and examine their teachings,

  • Foster comparative studies, and

  • Explore the practical benefits to society from such thinking,

through scholarly studies, dialogue, and debate also promoting accessibility to all qualified seekers. Additionally, the Forum will explore how these reflections can enrich life, education, and even technology.

Location: NCS 120 (New Computer Science), Engineering Dr, Stony Brook, NY 11794.

The program is available at: https://www.vedantaforum.org/events/program

As generative AI tools become increasingly prevalent in education, their impact on collegiate writing raises important questions about creativity, academic integrity, and effective teaching practices. This panel brings together faculty and students to share perspectives on the opportunities and challenges that AI presents in an academic setting. Through an open dialogue, participants will engage in meaningful conversations, allowing for a deeper understanding of each other's viewpoints and fostering collaboration. Students and faculty will explore diverse ways AI can be used in teaching and learning and seek solutions to utilize AI writing tools ethically. This exchange aims to build a community of trust and shared knowledge, ensuring that AI's role in education is both innovative and responsible.

Register here: https://stonybrook.zoom.us/meeting/register/tJAqdOitpjIpHtDGAsGBfEb3ah0YIzhIJolN

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

You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes one short talk 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.

Abstract: The increasing complexity and volume of data from electron microscopy necessitates advanced computational tools for timely and accurate analysis. In this talk, I will present several machine learning (ML) models developed to interpret diverse datasets from transmission electron microscopy (TEM). First, I demonstrate segmentation models for labelling regions of interest from in situ TEM images, such as atomic column positions or reaction sites that allow atomic-level quantitative analysis of data. Second, I introduce a self-supervised CNN model for denoising of low-dose HRTEM images, enabling clearer visualization of atomic features without sacrificing temporal resolution. Finally, a transformer-based model trained to predict copper oxidation states directly from their electron energy loss spectroscopy spectra will be introduced. Together, these projects showcase the power of tailored ML solutions to extract quantitative insights from complex microscopy data.

Biography: Brian Lee is a research associate working for the Electron Microscopy group and Theory and Computation group at the Center for Functional Nanomaterials. Previously, he has received PhD in Mechanical Engineering from Duke University and worked as a postdoc at Purdue University. His research focuses on applying machine learning and simulation techniques for materials science.

Location: CDS, Bldg. 725, Training Room

Join ZoomGov Meeting: https://bnl.zoomgov.com/j/1604383624?pwd=ffQ5cUPNxTI7nzClKQO6cnsNbhF9Vf.1

Meeting ID: 160 438 3624
Passcode: 558449