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portfolio

A Scalable Probabilistic Model Selection Method for Deep Learning in Gene-Protein Network Inference and Integration

a novel model selection method to automate choice of deep neural network architectures

Human-centered Perceptual and Conceptual Classification of Biomedical Images

Understanding the capabilities of the human visual system with respect to biomedical imaging and in extracting and utilizing tacit knowledge of domain experts

Automated Modeling of Deceptive Intent in Computer Mediated Conversations

Development and validation of a computational system that is able to automatically identify deceptive intent during computer-mediated, face-to-face communication

Novel Methodology for Leveraging Metabolic Simulation to Improve Regulatory Reconstruction

Aggregate gene expressions with context-dependent topological structures of gene regulations to infer new relationships

Utilizing Synergy between Human and Computer Information Processing for Complex Visual Information Organization and Use

Seek innovations in extracting, understanding, and fusing tacit human domain knowledge to advance image semantics interpretation in knowledge rich domains

publications

An Emotional Model for Nonverbal Communication Based on Fuzzy Dynamic Bayesian Network

Published in The 19th Canadian Conference on Electrical and Computer Engineering (CCECE 2006), 2006

Recommended citation: H. Zhang, Rui Li, and J-Z. Sun An Emotional Model for Nonverbal Communication Based on Fuzzy Dynamic Bayesian Network. In: Proceedings of The 19th Canadian Conference on Electrical and Computer Engineering (CCECE 2006), 1534--1537, May 2006. https://ieeexplore.ieee.org/abstract/document/4054552

Emotional Nonverbal Communication Based on Fuzzy Dynamic Bayesian Network

Published in The 9th Intl. Conference on Control, Automation, Robotics and Vision (ICARCV 2006), 2006

Recommended citation: H. Zhang, and Rui Li. Emotional Nonverbal Communication Based on Fuzzy Dynamic Bayesian Network. In: Proceedings of The 9th Intl. Conference on Control, Automation, Robotics and Vision (ICARCV 2006), 1--5, December 2006. https://ieeexplore.ieee.org/abstract/document/4150126

Framework of a Real-Time Adaptive Hypermedia System

Published in The Workshop on Understanding the User of the 32nd Conference of ACM Special Interest Group on Information Retrieval (SIGIR 2009), 2009

Recommended citation: Rui Li, E. Rozanski, and A.R. Haake. Framework of a Real-Time Adaptive Hypermedia System. In: Proceedings of The Workshop on Understanding the User of the 32nd Conference of ACM Special Interest Group on Information Retrieval (SIGIR 2009), 1--5, July 2009. http://ceur-ws.org/Vol-512/paper06.pdf

A User Model to Predict Web Page Viewing Behavior

Published in The 18th Intl. Conference on User Modeling, Adaptation, and Personalization (UMAP 2010), 2010

Recommended citation: Rui Li, E. Rozanski, and A.R. Haake. A User Model to Predict Web Page Viewing Behavior. In: Proceedings of The 18th Intl. Conference on User Modeling, Adaptation, and Personalization (UMAP 2010), 19--21, June 2010.

A Human-Centered Content-Based Image Retrieval System

Published in Annual Symposium of The American Medical Informatics Association (AMIA 2010), 2010

Recommended citation: Rui Li, S.K. Mulpuru, C.F. Calvelli, J.B. Pelz, P-C. Shi, and A.R. Haake. A Human-Centered Content-Based Image Retrieval System. In: 2010 Annual Symposium of The American Medical Informatics Association (AMIA 2010), poster, November 2010.

Human-Centric Approaches to Image Understanding and Retrieval

Published in West New York Image Processing Workshop (WNYIPW 2010), 2010

Recommended citation: Rui Li, P. Vaidyanathan, S.K. Mulpuru, C.F. Calvelli, J.B. Pelz, P-C. Shi, and A.R. Haake. Human-Centric Approaches to Image Understanding and Retrieval. In: Proceedings of 2010 West New York Image Processing Workshop (WNYIPW 2010), 62--65, November 2010. https://ieeexplore.ieee.org/abstract/document/5649743

Exploring Interaction Modes for Image Retrieval

Published in Novel Gaze-Controlled Applications (NGCA 2011), 2011

Recommended citation: C. Engelman, Rui Li, J. Pelz, P-C. Shi and A.R. Haake. Exploring Interaction Modes for Image Retrieval. In: Proceedings of Novel Gaze-Controlled Applications (NGCA 2011), 10--15, May 2011. https://dl.acm.org/doi/abs/10.1145/1983302.1983312

Learning Eye Movement Patterns for Characterization of Perceptual Expertise

Published in The 2012 Symposium on Eye Tracking Research and Applications (ETRA 2012), 2012

Recommended citation: Rui Li, J. Pelz, P-C. Shi, C.O. Alm and A.R. Haake. Learning Eye Movement Patterns for Characterization of Perceptual Expertise. In: Proceedings of The 2012 Symposium on Eye Tracking Research and Applications (ETRA 2012), 393--396, March 2012 https://dl.acm.org/doi/abs/10.1145/2168556.2168645

Annotation Schemes to Encode Domain Knowledge in Medical Narratives

Published in The Workshop VI on Language Annotation of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012), 2012

Recommended citation: W. McCoy, C.O. Alm, C. Calvelli, Rui Li, J.B. Pelz, P-C. Shi, and A.R. Haake. Annotation Schemes to Encode Domain Knowledge in Medical Narratives. In: Proceedings of The Workshop VI on Language Annotation of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012), 95--103, July 2012. https://dl.acm.org/citation.cfm?id=2392761

Learning Image-Derived Eye Movement Patterns to Characterize Perceptual Expertise

Published in The 34th annual meeting of the Cognitive Science Society (CogSci 2012), 2012

Recommended citation: Rui Li, J. Pelz, P-C. Shi and A.R. Haake. Learning Image-Derived Eye Movement Patterns to Characterize Perceptual Expertise. In: Proceedings of The 34th annual meeting of the Cognitive Science Society (CogSci 2012), 190-195, August 2012. https://escholarship.org/content/qt5k67z0n2/qt5k67z0n2.pdf

Image Understanding from Experts’ Eyes by Modeling Perceptual Skills of Diagnostic Reasoning Processes

Published in The 26th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2013), 2013

Recommended citation: Rui Li, P-C. Shi and A.R. Haake. Image Understanding from Experts Eyes by Modeling Perceptual Skills of Diagnostic Reasoning Processes. In: Proceedings of 2013 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2013), 2187--2194, June 2013. https://www.cv-foundation.org/openaccess/content_cvpr_2013/html/Li_Image_Understanding_from_2013_CVPR_paper.html

Infusing Perceptual Expertise and Domain Knowledge into a Human-Centered Image Retrieval System: A Prototype Application

Published in The 2014 Symposium on Eye Tracking Research and Applications (ETRA 2014), 2014

Recommended citation: X. Guo, Rui Li, J. Pelz, P-C. Shi, C.O. Alm and A.R. Haake. Infusing Perceptual Expertise and Domain Knowledge into a Human-Centered Image Retrieval System: A Prototype Application. In: Proceedings of The 2014 Symposium on Eye Tracking Research and Applications (ETRA 2014), 275--278, March 2014. https://dl.acm.org/doi/abs/10.1145/2578153.2578196

Fusing Multimodal Human Expert Data towards Semantic Image Use

Published in The 2014 GazeIn Workshop with the Conference on Multimedia Interaction (ICMI 2014), 2014

Recommended citation: X. Guo, Q. Yu, Rui Li, C.O. Alm and A.R. Haake. Fusing Multimodal Human Expert Data towards Semantic Image Use. In: Proceedings of The Workshop of 2014 Conference on Multimedia Interaction (ICMI 2014), 21--26, November 2014. https://dl.acm.org/doi/abs/10.1145/2666642.2666649

Predicting Computer-Mediated Negotiation Outcomes based on Modeling Facial Expression Synchronization

Published in The 11th IEEE International Conference on Automatic Face and Gesture Recognition (FG 2015), 2015

Recommended citation: Rui Li, J. Curhan and M.E. Hoque. Predicting Computer-Mediated Negotiation Outcomes based on Modeling Facial Expression Synchronization. In: Proceedings of The 11th IEEE International Conference on Automatic Face and Gesture Recognition (FG 2015), 1--6, May 2015. https://ieeexplore.ieee.org/abstract/document/7163102

An Expert-in-the-loop Paradigm for Learning Medical Image Grouping

Published in The 20th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2016), 2016

Recommended citation: X. Guo, Q. Yu, Rui Li, C.O. Alm and A.R. Haake. An Expert-in-the-loop Paradigm for Learning Medical Image Grouping. In: Proceedings of The 20th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2016), 477--488, April 2016. https://link.springer.com/chapter/10.1007/978-3-319-31753-3_38

Automated Malware Detection Using Artifacts in Forensic Memory Images

Published in 2016 IEEE International Symposium on Technologies for Homeland Security (HST 2016), 2016

Recommended citation: R. Mosli, Rui Li, B. Yuan and Y. Pan. Automated Malware Detection Using Artifacts in Forensic Memory Images.In: Proceedings of 2016 IEEE International Symposium on Technologies for Homeland Security (HST 2016), 1-6, May 2016 https://ieeexplore.ieee.org/document/7568881

Intelligent medical image grouping through interactive learning

Published in International Journal of Data Science and Analytics, 2016

Recommended citation: X. Guo, Q. Yu, Rui Li, C.O. Alm, C. Calvelli, P-C. Shi, and A.R. Haake. (2016). "Intelligent medical image grouping through interactive learning." International Journal of Data Science and Analytics. 1(1). https://link.springer.com/article/10.1007/s41060-016-0021-2

Modeling Eye Movement Patterns to Characterize Perceptual Skill in Image-based Diagnostic Reasoning Processes

Published in Computer Vision and Image Understanding, 2016

Recommended citation: Rui Li, P-C. Shi, J. Pelz, C.O. Alm, A.R. Haake. (2016). "Modeling Eye Movement Patterns to Characterize Perceptual Skill in Image-based Diagnostic Reasoning Processes." Computer Vision and Image Understanding. 151(1). https://www.sciencedirect.com/science/article/pii/S1077314216000734

A Behavior-based Approach for Malware Detection

Published in The 13th IFIP WG 11.9 International Conference on Digital Forensics (IFIP WG 11.9 2017), 2017

Recommended citation: R. Mosli, Rui Li, B. Yuan and Y. Pan. A Behavior-based Approach for Malware Detection. Proceedings of The 13th IFIP WG 11.9 International Conference on Digital Forensics (IFIP WG 11.9 2017), 187-201, January 2017. https://link.springer.com/chapter/10.1007/978-3-319-67208-3_11

Modeling Physicians Utterances to Explore Diagnostic Decision-making

Published in The 26th International Joint Conference on Artificial Intelligence (IJCAI 2017), 2017

Recommended citation: X. Guo, Rui Li, Q. Yu and A.R. Haake. Modeling Physicians Utterances to Explore Diagnostic Decision-making. In: Proceedings of The 26th International Joint Conference on Artificial Intelligence (IJCAI 2017), 3700-3706, August 2017. https://www.ijcai.org/Proceedings/2017/517

Understanding Social Interpersonal Interaction via Synchronization Templates of Facial Events

Published in The 32nd AAAI Conference on Artificial Intelligence (AAAI 2018), 2018

Recommended citation: Rui Li, J. Curhan and M.E. Hoque. Understanding Social Interpersonal Interaction via Synchronization Templates of Facial Events. In: Proceedings of The 32nd AAAI Conference on Artificial Intelligence (AAAI 2018), 1579-1586, April 2018. https://www.aaai.org/ocs/index.php/AAAI/AAAI18/paper/viewPaper/17060

Learning Topology-preserving Embedding for Gene Interaction Networks

Published in The 17th European Conference on Computational Biology (ECCB 2018), 2018

Recommended citation: K. KC, Rui Li, F. Cui and A.R. Haake. Learning Topology-preserving Embedding for Gene Interaction Networks. In: The 17th European Conference on Computational Biology (ECCB 2018), September 2018. https://kishankc.com.np/publication/content/publication/kishan-2018-toplology/

GNE: A Deep Learning Framework for Gene Network Inference by Aggregating Biological Information

Published in BMC System Biology, 2019

Recommended citation: K. KC, Rui Li, F. Cui, Q. Yu and A.R. Haake. (2019). "GNE: A Deep Learning Framework for Gene Network Inference by Aggregating Biological Information." BMC System Biology. 13(2). https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-019-0694-y

Bayesian Methods for Radiometric Calibration in Motion Picture Encoding Workflows

Published in SMPTE Motion Imaging Journal, 2019

Recommended citation: R. R. Figueroa, Rui Li. (2019). "Bayesian Methods for Radiometric Calibration in Motion Picture Encoding Workflows." SMPTE Motion Imaging Journal. 128(7). https://ieeexplore.ieee.org/abstract/document/8779779

Multivariate Sparse Coding of Nonstationary Covariances with Gaussian Processes

Published in The 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), 2019

Recommended citation: Rui Li. Multivariate Sparse Coding of Nonstationary Covariances with Gaussian Processes In: Proceedings of The 33rd Conference on Neural Information Processing Systems (NeurIPS 2019). http://papers.nips.cc/paper/8439-multivariate-sparse-coding-of-nonstationary-covariances-with-gaussian-processes

Dynamic Fusion of Eye Movement Data and Verbal Narrations in Knowledge-rich Domains

Published in The 34th Advances in Neural Information Processing Systems (NeurIPS 2020), 2020

Recommended citation: E. Zheng, Q. Yu, Rui Li, P-C Shi, and A.R. Haake. Dynamic Fusion of Eye Movement Data and Verbal Narrations in Knowledge-rich Domains. In: Proceedings of The 34th Advances in Neural Information Processing Systems (NeurIPS 2020). https://proceedings.neurips.cc//paper/2020/file/16837163fee34175358a47e0b51485ff-Paper.pdf

Histopathological distinction of non-invasive and invasive bladder cancers using machine learning approaches

Published in BMC medical informatics and decision making, 2020

Recommended citation: P-N. Yin, K. KC, W-S. Shi, Q. Yu, Rui Li, A.R. Haake, M. Hiroshi, and F. Cui. (2020). "Histopathological distinction of non-invasive and invasive bladder cancers using machine learning approaches." BMC medical informatics and decision making. 20(1). https://link.springer.com/article/10.1186/s12911-020-01185-z

Predicting Biological Interactions with Higher-Order Graph Convolutional Networks

Published in ACM/IEEE Transactions on Computational Biology and Bioinformatics, 2021

Recommended citation: K. KC, Rui Li, F. Cui, and A.R. Haake. (2021). "Predicting Biological Interactions with Higher-Order Graph Convolutional Networks." ACM/IEEE Transactions on Computational Biology and Bioinformatics. 14(8). https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=9354550

Machine learning predicts nucleosome binding modes of transcription factors

Published in BMC Bioinformatics, 2021

Recommended citation: K. KC, S.K. Subramanya, Rui Li, and F. Cui. (2021). "Machine learning predicts nucleosome binding modes of transcription factors." BMC Bioinformatics. 22(1). https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04093-9

A Continual Learning Framework for Uncertainty-Aware Interactive Image Segmentation

Published in The 35th AAAI Conference on Artificial Intelligence (AAAI 2021), 2021

Recommended citation: E. Zheng, Q. Yu, Rui Li, P-C. Shi, and A.R. Haake. A Continual Learning Framework for Uncertainty-Aware Interactive Image Segmentation. In: Proceedings of The 35th AAAI Conference on Artificial Intelligence (AAAI 2021). https://www.aaai.org/AAAI21Papers/AAAI-2989.ZhengE.pdf

TarGAN: Target-Aware Generative Adversarial Networks for Multi-modality Medical Image Translation

Published in The 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021), 2021

Recommended citation: J-X. Chen, J. Wei and Rui Li. TarGAN: Target-Aware Generative Adversarial Networks for Multi-modality Medical Image Translation. In: Proceedings of The 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). https://arxiv.org/pdf/2105.08993

Joint Inference for Neural Network Depth and Dropout Regularization

Published in The 35th Advances in Neural Information Processing Systems (NeurIPS 2021), 2021

Recommended citation: K. KC, Rui Li, and M. Gilany. Joint Inference for Neural Network Depth and Dropout Regularization. In: Proceedings of The 35th Advances in Neural Information Processing Systems (NeurIPS 2021). https://proceedings.neurips.cc/paper/2021/file/dfce06801e1a85d6d06f1fdd4475dacd-Paper.pdf

Dual-Level Adaptive Information Filtering for Interactive Image Segmentation

Published in The 25th International Conference on Artificial Intelligence and Statistics (AISTATS 2022), 2022

Recommended citation: E. Zheng, Q. Yu, Rui Li, P-C. Shi, and A.R. Haake. Dual-Level Adaptive Information Filtering for Interactive Image Segmentation. In: Proceedings of The 25th International Conference on Artificial Intelligence and Statistics (AISTATS 2022). https://proceedings.mlr.press/v151/zheng22b.html

Unsupervised Multi-Modal Medical Image Registration via Discriminator-Free Image-to-Image Translation

Published in The 31st International Joint Conference on Artificial Intelligence (IJCAI 2022), 2022

Recommended citation: Z-K. Chen, J. Wei, and Rui Li. Unsupervised Multi-Modal Medical Image Registration via Discriminator-Free Image-to-Image Translation. In: Proceedings of The 31st International Joint Conference on Artificial Intelligence (IJCAI 2022). https://www.ijcai.org/proceedings/2022/0117.pdf

Slice Imputation: Multiple Intermediate Slices Interpolation for Anisotropic 3D Medical Image Segmentation

Published in Computers in Biology and Medicine, 2022

Recommended citation: Z-T. Wu, J. Wei, J-B. Wang, and Rui Li. (2022). "Slice Imputation: Multiple Intermediate Slices Interpolation for Anisotropic 3D Medical Image Segmentation." Computers in Biology and Medicine. 147. https://pubmed.ncbi.nlm.nih.gov/35696751/

Knowledge Acquisition for Human-In-The-Loop Image Captioning

Published in The 26th International Conference on Artificial Intelligence and Statistics (AISTATS 2023), 2023

Recommended citation: E. Zheng, Q. Yu, Rui Li, P-C. Shi, and A.R. Haake. Knowledge Acquisition for Human-In-The-Loop Image Captioning. In: Proceedings of The 26th International Conference on Artificial Intelligence and Statistics (AISTATS 2023). [https://proceedings.mlr.press/v206/zheng23a.html]

Learning Multi-modal Brain Tumor Segmentation from Privileged Semi-paired MRI Images with Curriculum Disentanglement Learning

Published in Computers in Biology and Medicine, 2023

Recommended citation: Z-C. Liu, J. Wei, Rui Li, and J-L. Zhou. (2023). "Learning Multi-modal Brain Tumor Segmentation from Privileged Semi-paired MRI Images with Curriculum Disentanglement Learning." Computers in Biology and Medicine. 159. https://www.sciencedirect.com/science/article/abs/pii/S001048252300392X

Deep Learning for Histopathological Segmentation of Smooth Muscle in the Urinary Bladder

Published in BMC Medical Informatics and Decision Making, 2023

Recommended citation: S.K. Subramanya, Rui Li, Y. Wang, H. Miyamoto, and F. Cui. (2023). "Deep Learning for Histopathological Segmentation of Smooth Muscle in the Urinary Bladder." BMC Medical Informatics and Decision Making. 23(122). https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-023-02222-3

SFusion: Self-attention based N-to-One Multimodal Fusion Block

Published in The 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023), 2023

Recommended citation: Z. Liu, J. Wei, Rui Li, and J. Zhou. SFusion: Self-attention based N-to-One Multimodal Fusion Block. In: Proceedings of The 26th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2023). https://conferences.miccai.org/2023/papers/596-Paper0388.html

AdaVAE: Bayesian Structural Adaptation for Variational Autoencoder

Published in The 37th Conference on Neural Information Processing Systems (NeurIPS 2023), 2024

Recommended citation: P. Regmi and Rui Li. AdaVAE: Bayesian Structural Adaptation for Variational Autoencoder. In: Proceedings of The 37th Conference on Neural Information Processing Systems (NeurIPS 2023). https://neurips.cc/virtual/2023/poster/70855

talks

MS/BS students

Randy Carlson (MS in CS), Sridevi K. Subramanya (MS in Biology), Nicholas Wilkins (MS in CS), Peng Nien Yin (MS in biology), Japheth Adhavan Abraham (MS in CS), Eduardo Coelho de Lima (MS in IT), Sarvagya Kumar Mishra (MS in IT), Madhumitha Karthikeyan (MS in cybersecurity), Wilson McCoy (MS in CS), Corey Engelman (BS in CS)

PhD students (Co-advising)

Chris Bondy (with Dr. Pengcheng Shi)
Ricardo R. Figueroa (with Dr. Pengcheng Shi)
Ervine Mingxun Zheng (with Dr. Qi Yu)
Rayan H. Mosli (with Dr. Yin Pan)
Xuan Guo (with Dr. Anne R. Haake)

PhD students

Mahendra Singh Thapa (2023-now)
Ruochen (Sicy) Shi (2022-now)
Jeevan Thapa (2022-now)
Paribesh Regmi (2021-now)
Kishan KC (2016-2022, graduated)
Mahdi Gilany (2019-2020)
Chin-Yi Chu (2018-2020)

Rui Li

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