Abstract:
Artificial Intelligence for Science (AI4Sci) has become a transformative approach in
modeling and understanding complex physical systems, encompassing different scales such as
atomistic systems and continuum systems. In atomistic systems, AI has shown potential in
accelerating simulations, optimizing molecular dynamics, and predicting material and
molecular properties through data-driven approaches, enhancing computational efficiency
while preserving accuracy. For continuum systems, AI provides powerful tools for solving
partial differential equations (PDEs) and learning physical patterns from data, capturing
intricate dynamics that govern physical and engineering processes. This work explores AI
methods--particularly equivariance for neural networks and neural operators--bridging
atomistic and continuum representations. We analyze the implications of incorporating
symmetries to improve model robustness and learning efficiency, providing a cohesive AI- driven framework for advancing scientific discovery. The findings aim to underscore the role
of AI in enhancing accuracy, applicability, scalability, interopretability, and generalization
across scales, from molecular simulations to physical modeling, opening pathways for next- generation applications in computational science.
Biography:
Wenhan Gao is a third-year Ph.D. student in Applied Mathematics at Stony Brook University, where he works under the supervision of Professor Yi Liu. Wenhan's research focuses on
equivariant neural networks, graph neural networks, and AI for partial differential equations. Wenhan's work seeks to leverage the power of symmetries to aid AI models, particularly in
fields such as computer vision (image and video generation), physical simulation (modeling
climate change), and computational chemistry (drug discovery). He has published papers on
the aforementioned topics in leading venues like NeurIPS, Transactions on Machine Learning
Research (TMLR), and Journal of Computational Physics (JCP). He also has several preprints
under review in leading venues like ICLR and CVPR. In addition to his research, Wenhan has
served as a reviewer for top-tier conferences, including ICLR, NeurIPS, ICML, and KDD, and
as a lecturer for undergraduate and graduate courses at Stony Brook University. Wenhan was
awarded the NeurIPS Travel Award and Excellence in Teaching for Fall 2023.
Abstract: Language offers a uniquely powerful lens for understanding the mind: one that can access latent psychological realities often missed by traditional measurement tools. However, as language models expand their ability to capture semantics through context length, expansion into deeper levels of semantics is less explored, especially with respect to understanding cognitive patterns of authors. This dissertation proposes that we can uncover deeper cognitive and affective patterns that reflect more accurate underlying mental states by analyzing language at higher levels of discourse semantics and by modeling latent states.
First, the dissertation focuses on uncovering cognitive styles or thinking patterns manifesting in language. We demonstrate that modeling language at deeper semantic levels such as discourse relations, can unveil latent psychological states and traits, including cognitive styles that influence both mental health and behavior. Introducing a novel blend of transfer and active learning, we efficiently curated a new set of linguistic data on cognitive styles like dissonance. This approach allows for more precise measurement when dealing with rare-classes and low-resource tasks. As a second contribution, effective validation methods are introduced to language-based assessments of the underlying cognitive styles. Controlled behavioral experiments and online studies show that cognitive styles detected through linguistic signals reliably predict real-world behaviors such as decision-making and engagement with extremist communities, both at the individual and community levels, sometimes months in advance
The research further moves beyond traditional measurement tools like questionnaires and expert judgments, which rely on Classical Test Theory, by establishing that language-based assessments more closely approximate true psychological states. The mechanisms by which these assessments outperform standard tools are explained, highlighting their predictive power for behaviors linked to underlying traits. Finally, a more sophisticated approach is explored by modeling psychological outcomes with Item Response Theory (IRT), an improvement over Classical Test Theory. Adaptive language-based assessments are introduced, showing that targeted, adaptive testing based on latent IRT scores can efficiently and accurately capture multiple psychological dimensions.
Taken together, these contributions argue for a shift towards language-based psychological assessments. By integrating deeper discourse-level semantics with measurement theory, this dissertation charts a path towards truer scores of mental states: ones that are more precise, and reflective of the complexity of human cognition and emotions.
Speaker: Vasudha Varadarajan
https://stonybrook.zoom.us/j/
First, the dissertation focuses on uncovering cognitive styles or thinking patterns manifesting in language. We demonstrate that modeling language at deeper semantic levels such as discourse relations, can unveil latent psychological states and traits, including cognitive styles that influence both mental health and behavior. Introducing a novel blend of transfer and active learning, we efficiently curated a new set of linguistic data on cognitive styles like dissonance. This approach allows for more precise measurement when dealing with rare-classes and low-resource tasks. As a second contribution, effective validation methods are introduced to language-based assessments of the underlying cognitive styles. Controlled behavioral experiments and online studies show that cognitive styles detected through linguistic signals reliably predict real-world behaviors such as decision-making and engagement with extremist communities, both at the individual and community levels, sometimes months in advance
The research further moves beyond traditional measurement tools like questionnaires and expert judgments, which rely on Classical Test Theory, by establishing that language-based assessments more closely approximate true psychological states. The mechanisms by which these assessments outperform standard tools are explained, highlighting their predictive power for behaviors linked to underlying traits. Finally, a more sophisticated approach is explored by modeling psychological outcomes with Item Response Theory (IRT), an improvement over Classical Test Theory. Adaptive language-based assessments are introduced, showing that targeted, adaptive testing based on latent IRT scores can efficiently and accurately capture multiple psychological dimensions.
Taken together, these contributions argue for a shift towards language-based psychological assessments. By integrating deeper discourse-level semantics with measurement theory, this dissertation charts a path towards truer scores of mental states: ones that are more precise, and reflective of the complexity of human cognition and emotions.
Speaker: Vasudha Varadarajan
https://stonybrook.zoom.us/j/
All are welcome to attend BMI grand rounds talk by Dr. Le Lu on 04/14.
Le Lu, Ph.D
Executive Director, PAII Inc
Johns Hopkins University
IEEE Fellow, MICCAI Board Member
Time: Wednesday, April 14, 2021 3:00 pm - 4:00 pm
Zoom Meeting
https://stonybrook.zoom.us/j/95617197636?pwd=KytzZ2pVRG9SZGpKZUtpNXJISjNjZz09
Meeting ID: 956 1719 7636 Passcode: 924293
Title:
In Search of Effective and Reproducible Clinical Imaging Biomarkers for Population Health and Oncology Applications of Screening, Diagnosis and Prognosis
Bio:
Le Lu received a PhD in 2007 from Johns Hopkins University. During his first six years at Siemens, he made significant contributions to the company's CT colonography and Lung CAD product lines. From 2013 to 2017, Dr. Lu served as a staff scientist in the Radiology and Imaging Sciences department of the National Institutes of Health Clinical Center. He then went on to found Nvidia's medical image analysis group and he held the position of senior research manager until June 2018. Since then, he has been the Executive Director at PAII Inc., Bethesda Research lab, Maryland, USA which has become one of the leading industrial research labs in medical imaging. He was the main technical leader for two of the most-impactful public radiology image dataset releases (NIH ChestXray14, NIH DeepLesion 2018). He won NIH Clinical Center Director Award in 2017, NIH Mentor of the year award in 2015, and won numerous best paper awards in MICCAI and RSNA from 2016 to 2020 (over 10000 citations). In 2021, He was elected into IEEE Fellow class cited for his contribution to machine learning for cancer detection and diagnosis, and MICCAI society board member (MICCAI-Industry Workgroup Chair). He is currently an Associate Editor for IEEE Trans. Pattern Analysis and Machine Intelligence and IEEE Signal Processing Letters. He has served as an Area Chair for recent MICCAI, AAAI, CVPR, WACV, ICIP and ICHI conferences for 14 times.
Abstract:
This talk will first give an overall on the work of employing deep learning to permit novel clinical workflows in two population health tasks, namely using conventional ultrasound for liver steatosis screening and quantitative reporting; osteoporosis screening via conventional X-ray imaging and AI readers. These two tasks were generally considered as infeasible tasks for human readers, but as proved by our scientific and clinical studies and peer-reviewed publications, they are suitable for AI readers. AI can be a supplementary and useful tool to assist physicians for cheaper and more convenient/precision patient management. Next, the main part of this talk describes a roadmap on three key problems in pancreatic cancer imaging solution: early screening, precision differential diagnosis, and deep prognosis on patient survival prediction. (1) Based on a new self- learning framework, we train the pancreatic ductal adenocarcinoma (PDAC) segmentation model using a larger quantity of patients (≈1,000, four institutions), with a mix of annotated/unannotated venous or multi-phase CT images. Pseudo annotations are generated by combining two teacher models with different PDAC segmentation specialties on unannotated images, and can be further refined by a teaching assistant model that identifies associated vessels around the pancreas. Our approach makes it technically feasible for robust large-scale PDAC screening from multi-institutional multi-phase partially-annotated CT scans. (2) We propose a holistic segmentation-mesh classification network (SMCN) to provide patient-level diagnosis, by fully utilizing the geometry and location information. SMCN learns the pancreas and mass segmentation task and builds an anatomical correspondence-aware organ mesh model by progressively deforming a pancreas prototype on the raw segmentation mask. Our results are comparable to a multimodality clinical test that combines clinical, imaging, and molecular testing for clinical management of patients with cysts. (3) Accurate preoperative prognosis of resectable PDACs for personalized treatment is highly desired in clinical practice. We present a novel deep neural network for the survival prediction of resectable PDAC patients, 3D Contrast-Enhanced Convolutional Long Short-Term Memory network (CE- ConvLSTM), to derive the tumor attenuation signatures from CE-CT imaging studies. Our framework can significantly improve the prediction performances upon existing state-of-the-art survival analysis methods. This deep tumor signature has evidently added values (as a predictive biomarker) to be combined with the existing clinical staging system.
More information can be found at:
https://bmi.stonybrookmedicine.edu/sites/default/files/Lu_le_04_14.pdf
Le Lu, Ph.D
Executive Director, PAII Inc
Johns Hopkins University
IEEE Fellow, MICCAI Board Member
Time: Wednesday, April 14, 2021 3:00 pm - 4:00 pm
Zoom Meeting
https://stonybrook.zoom.us/j/
Meeting ID: 956 1719 7636 Passcode: 924293
Title:
In Search of Effective and Reproducible Clinical Imaging Biomarkers for Population Health and Oncology Applications of Screening, Diagnosis and Prognosis
Bio:
Le Lu received a PhD in 2007 from Johns Hopkins University. During his first six years at Siemens, he made significant contributions to the company's CT colonography and Lung CAD product lines. From 2013 to 2017, Dr. Lu served as a staff scientist in the Radiology and Imaging Sciences department of the National Institutes of Health Clinical Center. He then went on to found Nvidia's medical image analysis group and he held the position of senior research manager until June 2018. Since then, he has been the Executive Director at PAII Inc., Bethesda Research lab, Maryland, USA which has become one of the leading industrial research labs in medical imaging. He was the main technical leader for two of the most-impactful public radiology image dataset releases (NIH ChestXray14, NIH DeepLesion 2018). He won NIH Clinical Center Director Award in 2017, NIH Mentor of the year award in 2015, and won numerous best paper awards in MICCAI and RSNA from 2016 to 2020 (over 10000 citations). In 2021, He was elected into IEEE Fellow class cited for his contribution to machine learning for cancer detection and diagnosis, and MICCAI society board member (MICCAI-Industry Workgroup Chair). He is currently an Associate Editor for IEEE Trans. Pattern Analysis and Machine Intelligence and IEEE Signal Processing Letters. He has served as an Area Chair for recent MICCAI, AAAI, CVPR, WACV, ICIP and ICHI conferences for 14 times.
Abstract:
This talk will first give an overall on the work of employing deep learning to permit novel clinical workflows in two population health tasks, namely using conventional ultrasound for liver steatosis screening and quantitative reporting; osteoporosis screening via conventional X-ray imaging and AI readers. These two tasks were generally considered as infeasible tasks for human readers, but as proved by our scientific and clinical studies and peer-reviewed publications, they are suitable for AI readers. AI can be a supplementary and useful tool to assist physicians for cheaper and more convenient/precision patient management. Next, the main part of this talk describes a roadmap on three key problems in pancreatic cancer imaging solution: early screening, precision differential diagnosis, and deep prognosis on patient survival prediction. (1) Based on a new self- learning framework, we train the pancreatic ductal adenocarcinoma (PDAC) segmentation model using a larger quantity of patients (≈1,000, four institutions), with a mix of annotated/unannotated venous or multi-phase CT images. Pseudo annotations are generated by combining two teacher models with different PDAC segmentation specialties on unannotated images, and can be further refined by a teaching assistant model that identifies associated vessels around the pancreas. Our approach makes it technically feasible for robust large-scale PDAC screening from multi-institutional multi-phase partially-annotated CT scans. (2) We propose a holistic segmentation-mesh classification network (SMCN) to provide patient-level diagnosis, by fully utilizing the geometry and location information. SMCN learns the pancreas and mass segmentation task and builds an anatomical correspondence-aware organ mesh model by progressively deforming a pancreas prototype on the raw segmentation mask. Our results are comparable to a multimodality clinical test that combines clinical, imaging, and molecular testing for clinical management of patients with cysts. (3) Accurate preoperative prognosis of resectable PDACs for personalized treatment is highly desired in clinical practice. We present a novel deep neural network for the survival prediction of resectable PDAC patients, 3D Contrast-Enhanced Convolutional Long Short-Term Memory network (CE- ConvLSTM), to derive the tumor attenuation signatures from CE-CT imaging studies. Our framework can significantly improve the prediction performances upon existing state-of-the-art survival analysis methods. This deep tumor signature has evidently added values (as a predictive biomarker) to be combined with the existing clinical staging system.
More information can be found at:
https://bmi.
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
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
Does This Vehicle Belong to You? Processing the Language of Policing for Improving Police-Community Relations
Dan Jurasky (Stanford)
Engineering Job & Internship Fair hosted by the Career Center
Learn more and RSVP on Handshake.
International Love Data Week is a global event dedicated to celebrating data in all its forms. This year, Stony Brook University is excited to celebrate Love Data Week with a series of 30-minute webinars aimed to promote proficiency with data, showcase innovative data projects, and foster a community of data enthusiasts across campus. Hosted by the Division of Educational & Institutional Effectiveness and facilitated by the Office of Educational Effectiveness, we invite all SBU faculty, staff and students to join in the festivities, learn from colleagues in our campus community, and fall in love with the power of data! Learn more here. |
Abstract: In this talk, we take a step back and argue that many varied and seemingly unrelated attacks on the web are actually symptoms of one deeper problem that has existed since the web's inception. Whether it is attacks due to expired domain names, cloaking done by malicious websites, malvertising, or even our growing distrust of the news can be largely attributed back to the issue of stateless linking. Stateless linking refers to the absence of any integrity guarantees between the time that a link for a remote resource was created, to a future time when this link is resolved by web clients. We draw on 10+ years of research to demonstrate how stateless linking and the resulting lack of content integrity is the true culprit for many of our past, current, and likely future web problems. Successfully tackling this one really challenging problem, has the potential of solving many of our web woes.
Bio: Nick Nikiforakis is affiliated with the National Security Institute. He received his PhD in Computer Science from KU Leuven in Belgium. He received his MSc, in Parallel and Distributed Systems and BSc in Computer Science from the University of Crete, Greece. His research focuses on web security and privacy, software security, and intrusion detection.
Location: NCS 120
Bio: Nick Nikiforakis is affiliated with the National Security Institute. He received his PhD in Computer Science from KU Leuven in Belgium. He received his MSc, in Parallel and Distributed Systems and BSc in Computer Science from the University of Crete, Greece. His research focuses on web security and privacy, software security, and intrusion detection.
Location: NCS 120