Dong Si - RankMe

58 papers B 1Misc 1Journal 17Unranked 39

Year	Rank	Type	Title / Venue / Authors
2026	—	`conf`	AutismCarebot: Emotion-First, Source-Aware Conversational Support for Autistic Users. CHI Extended Abstracts Shristi Srivastava, Annuska Zolyomi, Dong Si
2025	—	`conf`	Advancing Protein-Ligand Binding Site Prediction with 3D Instance Segmentation Techniques. CAI Esha Rajesh Gavali, Jie Hou, Renzhi Cao, Dong Si
2025	J	`jnl`	AnglesRefine: Refinement of 3D Protein Structures Using Transformer Based on Torsion Angles. IEEE Trans. Comput. Biol. Bioinform. Lei Zhang, JunYong Zhu, Sheng Wang, Jie Hou, Dong Si, Renzhi Cao
2025	J	`jnl`	Beyond current boundaries: Integrating deep learning and AlphaFold for enhanced protein structure prediction from low-resolution cryo-EM maps. Comput. Biol. Chem. Xin Ma, Dong Si
2025	J	`jnl`	GOBoost: leveraging long-tail gene ontology terms for accurate protein function prediction. Bioinform. Lei Zhang, Yang Wang, Xiao Chen, Jie Hou, Dong Si, Rui Ding, Bo Jiang, Hailey Ledenko, Renzhi Cao
2025	—	`conf`	Geometric Deep Learning for Multiple Conformation Generation from Electron Density Images. CAI Saurav Jayakumar, Jie Hou, Renzhi Cao, Dong Si
2024	—	`conf`	Assessing Empathy in Mental Health Caregivers using Conversational AI. ICHI Raghav Naswa, Sugam Jaiswal, Remya Mavila, Weichao Yuwen, Bill Erdly, Dong Si
2024	J	`jnl`	Beyond Current Boundaries: Integrating Deep Learning and AlphaFold for Enhanced Protein Structure Prediction from Low-Resolution Cryo-EM Maps. CoRR Xin Ma, Dong Si
2024	—	`conf`	Building Personality-Adaptive Conversational AI for Mental Health Therapy. BCB Sugam Jaiswal, Joyce Lee, Joe Berria, Raviteja Tanikella, Annuska Zolyomi, Muhammad Aurangzeb Ahmad, Dong Si
2024	J	`jnl`	Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration. Briefings Bioinform. Jason Chen, Ayisha Zia, Albert Luo, Hanze Meng, Fengbin Wang, Jie Hou, Renzhi Cao, Dong Si
2024	—	`conf`	iCare - An AI - Powered Virtual Assistant for Mental Health. ICHI Remya Mavila, Sugam Jaiswal, Raghav Naswa, Weichao Yuwen, Bill Erdly, Dong Si
2023	J	`jnl`	ComplexQA: a deep graph learning approach for protein complex structure assessment. Briefings Bioinform. Lei Zhang, Sheng Wang, Jie Hou, Dong Si, JunYong Zhu, Renzhi Cao
2023	J	`jnl`	Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps. Briefings Bioinform. Andrew Nakamura, Hanze Meng, Minglei Zhao, Fengbin Wang, Jie Hou, Renzhi Cao, Dong Si
2022	—	`conf`	Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments. BCB Mahdi Rahbar, Rahul Kumar Chauhan, Pankil Nimeshbhai Shah, Renzhi Cao, Dong Si, Jie Hou
2022	—	`conf`	DeepTracer-Denoising: Deep Learning for 3D Electron Density Map Denoising. BIBM Haowen Guan, Dong Si
2022	J	`jnl`	Neural representations of cryo-EM maps and a graph-based interpretation. BMC Bioinform. Nathan Ranno, Dong Si
2022	—	`conf`	Psychosis iREACH: Reach for Psychosis Treatment using Artificial Intelligence. BIBM Jonathan Lee, Sarah Kopelovich, Sunny Chieh Cheng, Dong Si
2022	J	`jnl`	ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. Briefings Bioinform. Kyle Hippe, Cade Lilley, Joshua William Berkenpas, Ciri Chandana Pocha, Kiyomi Kishaba, Hui Ding, Jie Hou, Dong Si, Renzhi Cao
2021	J	`jnl`	A Raspberry Pi-Based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram. Sensors Navjodh Singh Dhillon, Agustinus Sutandi, Manoj Vishwanath, Miranda M. Lim, Hung Cao, Dong Si
2021	J	`jnl`	A Raspberry Pi-based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram. CoRR Navjodh Singh Dhillon, Agustinus Sutandi, Manoj Vishwanath, Miranda M. Lim, Hung Cao, Dong Si
2021	J	`jnl`	Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM. CoRR Dong Si, Andrew Nakamura, Runbang Tang, Haowen Guan, Jie Hou, Ammaar Firozi, Renzhi Cao, Kyle Hippe, Minglei Zhao
2021	—	`conf`	Dementia Detection using Transformer-Based Deep Learning and Natural Language Processing Models. ICHI Ploypaphat Saltz, Shih Yin Lin, Sunny Chieh Cheng, Dong Si
2021	J	`jnl`	Self-Attention Generative Adversarial Network for Iterative Reconstruction of CT Images. CoRR Ruiwen Xing, Thomas Humphries, Dong Si
2020	—	`conf`	A Wizard-of-Oz Interface and Persona-based Methodology for Collecting Health Counseling Dialog. CHI Extended Abstracts William R. Kearns, Neha Kaura, Myra Divina, Cuong Vo, Dong Si, Teresa Ward, Weichao Yuwen
2020	J	`jnl`	TopQA: a topological representation for single-model protein quality assessment with machine learning. Int. J. Comput. Biol. Drug Des. John Smith, Matthew Conover, Natalie Stephenson, Jesse Eickholt, Dong Si, Miao Sun, Renzhi Cao
2019	—	`conf`	Automated Threshold Selection for Cryo-EM Density Maps. BCB Jonas Pfab, Dong Si
2019	B	`conf`	Scaling up Prediction of Psychosis by Natural Language Processing. ICTAI Dong Si, Sunny Chieh Cheng, Ruiwen Xing, Chang Liu, Hoi Yan Wu
2019	—	`conf`	Traveler's Next Activity Predication with Location-Based Social Network Data. PredictGIS@SIGSPATIAL Diem To, Dong Si, Ying Chen
2018	J	`jnl`	Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing. J. Comput. Biol. Albert Ng, Dong Si
2018	—	`conf`	Cancer Type Prediction and Classification Based on RNA-sequencing Data. EMBC Yi-Hsin Hsu, Dong Si
2018	—	`conf`	Deep Learning for Resolution Validation of Three Dimensional Cryo-Electron Microscopy Density Maps. BCB Todor K. Avramov, Dong Si
2018	—	`conf`	EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging. BCB Jingjing Yang, Renzhi Cao, Dong Si
2018	—	`conf`	GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps. ISBRA Albert Ng, Adedayo Odesile, Dong Si
2018	J	`jnl`	Machine Learning Classification of Tree Cover Type and Application to Forest Management. Int. J. Multim. Data Eng. Manag. Duncan Macmichael, Dong Si
2018	—	`conf`	Machine Learning of Spatiotemporal Bursting Behavior in Developing Neural Networks. EMBC Jewel Yun-Hsuan Lee, Michael Stiber, Dong Si
2018	—	`conf`	Parkinson's Disease Classification of mPower Walking Activity Participants. EMBC Benjamin Pittman, Reza Hosseini Ghomi, Dong Si
2018	—	`conf`	Who's Next: Evaluating Attrition with Machine Learning Algorithms and Survival Analysis. BigData Congress Jessica Frierson, Dong Si
2017	—	`conf`	A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps. BCB Peter Collins, Dong Si
2017	Misc	`conf`	Addressing Forest Management Challenges by Refining Tree Cover Type Classification with Machine Learning Models. IRI Duncan Macmichael, Dong Si
2017	—	`conf`	Analyze NYC Transportation to Mitigate Speeding and Explore New Business Models Using Machine Learning. ICCDA Joe Ma, Dong Si
2017	—	`conf`	Anomaly Detection from Kepler Satellite Time-Series Data. MLDM Nathaniel Grabaskas, Dong Si
2017	—	`conf`	Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool. BCB Michael Nissenson, Dong Si
2017	—	`conf`	Classification of Brain Activity Using Brainwaves Recorded by Consumer-grade EEG Devices. MDA Elizaveta Kosiachenko, Dong Si
2017	—	`conf`	Comparison of Feature Reduction Methods and Machine Learning Models for Breast Cancer Diagnosis. ICCDA Todor K. Avramov, Dong Si
2017	—	`conf`	Genetic Algorithm Based Beta-Barrel Detection for Medium Resolution Cryo-EM Density Maps. ISBRA Albert Ng, Dong Si
2017	—	`conf`	Prediction of Injuries and Fatalities in Aviation Accidents through Machine Learning. ICCDA R. Alan Burnett, Dong Si
2017	—	`conf`	Prediction of Insurance Claim Severity Loss Using Regression Models. MLDM Ruth M. Ogunnaike, Dong Si
2016	—	`conf`	Automatic Detection of Beta-barrel from Medium Resolution Cryo-EM Density Maps. BCB Dong Si
2016	—	`conf`	Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. BIBM Rongjian Li, Dong Si, Tao Zeng, Shuiwang Ji, Jing He
2015	—	`conf`	Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. ICIG (2) Jing He, Dong Si, Maryam Arab
2014	—	`conf`	Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. EMBC Dong Si, Jing He
2014	—	`conf`	Orientations of beta-strand traces and near maximum twist. BCB Dong Si, Jing He
2013	—	`conf`	A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. BCB Kamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong Si, Jing He
2013	—	`conf`	Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. BCB Dong Si, Jing He
2012	—	`conf`	Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. BCB Kamal Al-Nasr, Lin Chen, Dong Si, Desh Ranjan, Mohammad Zubair, Jing He
2012	—	`conf`	CryoEM skeleton length estimation using a decimated curve. BIBM Workshops Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, Nikos Chrisochoides, Jing He
2012	J	`jnl`	Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. J. Bioinform. Comput. Biol. Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
2011	—	`conf`	A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. BIBM Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He