Dong Si

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 37

Top Topics

Electron Microscopy

Machine Learning

Natural Language Processing

Top Venues

Publications

Andrew Nakamura, Hanze Meng, Minglei Zhao, Fengbin Wang, Jie Hou, Renzhi Cao, Dong Si
Fast and automated protein-DNA/RNA macromolecular complex modeling from cryo-EM maps. Briefings Bioinform. 24 (2) (2023)
Kyle Hippe, Cade Lilley, Joshua William Berkenpas, Ciri Chandana Pocha, Kiyomi Kishaba, Hui Ding, Jie Hou, Dong Si, Renzhi Cao
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features. Briefings Bioinform. 23 (1) (2022)
Nathan Ranno, Dong Si
Neural representations of cryo-EM maps and a graph-based interpretation. BMC Bioinform. (3) (2022)
Mahdi Rahbar, Rahul Kumar Chauhan, Pankil Nimeshbhai Shah, Renzhi Cao, Dong Si, Jie Hou
Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments. BCB (2022)
Haowen Guan, Dong Si
DeepTracer-Denoising: Deep Learning for 3D Electron Density Map Denoising. BIBM (2022)
Jonathan Lee, Sarah Kopelovich, Sunny Chieh Cheng, Dong Si
Psychosis iREACH: Reach for Psychosis Treatment using Artificial Intelligence. BIBM (2022)
Navjodh Singh Dhillon, Agustinus Sutandi, Manoj Vishwanath, Miranda M. Lim, Hung Cao, Dong Si
A Raspberry Pi-based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram. CoRR (2021)
Dong Si, Andrew Nakamura, Runbang Tang, Haowen Guan, Jie Hou, Ammaar Firozi, Renzhi Cao, Kyle Hippe, Minglei Zhao
Artificial Intelligence Advances for De Novo Molecular Structure Modeling in Cryo-EM. CoRR (2021)
Navjodh Singh Dhillon, Agustinus Sutandi, Manoj Vishwanath, Miranda M. Lim, Hung Cao, Dong Si
A Raspberry Pi-Based Traumatic Brain Injury Detection System for Single-Channel Electroencephalogram. Sensors 21 (8) (2021)
Ruiwen Xing, Thomas Humphries, Dong Si
Self-Attention Generative Adversarial Network for Iterative Reconstruction of CT Images. CoRR (2021)
Ploypaphat Saltz, Shih Yin Lin, Sunny Chieh Cheng, Dong Si
Dementia Detection using Transformer-Based Deep Learning and Natural Language Processing Models. ICHI (2021)
William R. Kearns, Neha Kaura, Myra Divina, Cuong Vo, Dong Si, Teresa Ward, Weichao Yuwen
A Wizard-of-Oz Interface and Persona-based Methodology for Collecting Health Counseling Dialog. CHI Extended Abstracts (2020)
John Smith, Matthew Conover, Natalie Stephenson, Jesse Eickholt, Dong Si, Miao Sun, Renzhi Cao
TopQA: a topological representation for single-model protein quality assessment with machine learning. Int. J. Comput. Biol. Drug Des. 13 (1) (2020)
Diem To, Dong Si, Ying Chen
Traveler's Next Activity Predication with Location-Based Social Network Data. PredictGIS@SIGSPATIAL (2019)
Jonas Pfab, Dong Si
Automated Threshold Selection for Cryo-EM Density Maps. BCB (2019)
Dong Si, Sunny Chieh Cheng, Ruiwen Xing, Chang Liu, Hoi Yan Wu
Scaling up Prediction of Psychosis by Natural Language Processing. ICTAI (2019)
Albert Ng, Adedayo Odesile, Dong Si
GPU Accelerated Ray Tracing for the Beta-Barrel Detection from Three-Dimensional Cryo-EM Maps. ISBRA (2018)
Duncan Macmichael, Dong Si
Machine Learning Classification of Tree Cover Type and Application to Forest Management. Int. J. Multim. Data Eng. Manag. 9 (1) (2018)
Todor K. Avramov, Dong Si
Deep Learning for Resolution Validation of Three Dimensional Cryo-Electron Microscopy Density Maps. BCB (2018)
Jewel Yun-Hsuan Lee, Michael Stiber, Dong Si
Machine Learning of Spatiotemporal Bursting Behavior in Developing Neural Networks. EMBC (2018)
Jingjing Yang, Renzhi Cao, Dong Si
EMNets: A Convolutional Autoencoder for Protein Surface Retrieval Based on Cryo-Electron Microscopy Imaging. BCB (2018)
Yi-Hsin Hsu, Dong Si
Cancer Type Prediction and Classification Based on RNA-sequencing Data. EMBC (2018)
Benjamin Pittman, Reza Hosseini Ghomi, Dong Si
Parkinson's Disease Classification of mPower Walking Activity Participants. EMBC (2018)
Albert Ng, Dong Si
Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing. J. Comput. Biol. 25 (3) (2018)
Jessica Frierson, Dong Si
Who's Next: Evaluating Attrition with Machine Learning Algorithms and Survival Analysis. BigData Congress (2018)
Ruth M. Ogunnaike, Dong Si
Prediction of Insurance Claim Severity Loss Using Regression Models. MLDM (2017)
Albert Ng, Dong Si
Genetic Algorithm Based Beta-Barrel Detection for Medium Resolution Cryo-EM Density Maps. ISBRA (2017)
Duncan Macmichael, Dong Si
Addressing Forest Management Challenges by Refining Tree Cover Type Classification with Machine Learning Models. IRI (2017)
Joe Ma, Dong Si
Analyze NYC Transportation to Mitigate Speeding and Explore New Business Models Using Machine Learning. ICCDA (2017)
Michael Nissenson, Dong Si
Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool. BCB (2017)
Peter Collins, Dong Si
A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps. BCB (2017)
R. Alan Burnett, Dong Si
Prediction of Injuries and Fatalities in Aviation Accidents through Machine Learning. ICCDA (2017)
Todor K. Avramov, Dong Si
Comparison of Feature Reduction Methods and Machine Learning Models for Breast Cancer Diagnosis. ICCDA (2017)
Nathaniel Grabaskas, Dong Si
Anomaly Detection from Kepler Satellite Time-Series Data. MLDM (2017)
Elizaveta Kosiachenko, Dong Si
Classification of Brain Activity Using Brainwaves Recorded by Consumer-grade EEG Devices. MDA (2017)
Dong Si
Automatic Detection of Beta-barrel from Medium Resolution Cryo-EM Density Maps. BCB (2016)
Rongjian Li, Dong Si, Tao Zeng, Shuiwang Ji, Jing He
Deep convolutional neural networks for detecting secondary structures in protein density maps from cryo-electron microscopy. BIBM (2016)
Jing He, Dong Si, Maryam Arab
Detection of Secondary Structures from 3D Protein Images of Medium Resolutions and its Challenges. ICIG (2) (2015)
Dong Si, Jing He
Orientations of beta-strand traces and near maximum twist. BCB (2014)
Dong Si, Jing He
Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels. EMBC (2014)
Dong Si, Jing He
Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. BCB (2013)
Kamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong Si, Jing He
A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. BCB (2013)
Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
Improved Efficiency in Cryo-EM Secondary Structure Topology Determination from Inaccurate Data. J. Bioinform. Comput. Biol. 10 (3) (2012)
Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, Nikos Chrisochoides, Jing He
CryoEM skeleton length estimation using a decimated curve. BIBM Workshops (2012)
Kamal Al-Nasr, Lin Chen, Dong Si, Desh Ranjan, Mohammad Zubair, Jing He
Building the initial chain of the proteins through de novo modeling of the cryo-electron microscopy volume data at the medium resolutions. BCB (2012)
Abhishek Biswas, Dong Si, Kamal Al-Nasr, Desh Ranjan, Mohammad Zubair, Jing He
A Constraint Dynamic Graph Approach to Identify the Secondary Structure Topology from cryoEM Density Data in Presence of Errors. BIBM (2011)