Shobeir Fakhraei, Ph.D.

Applied Research Scientist . CTPS Machine Learning Accelerator (MLA) . Amazon

I am a machine learning scientist at Amazon. Prior to Amazon, I have worked at various research institutes including Information Sciences Institute at University of Southern California (USC), Microsoft Research Redmond (MSR), Yahoo! Labs Sunnyvale, University of California Santa Cruz (UCSC), and Henry Ford Health System, and startup companies such as Turi (ex. Graphlab) and The Meet Group (ex. Tagged).
I received my Ph.D. from the Department of Computer Science, University of Maryland College Park (UMD) advised by Lise Getoor, Ph.D.
My research interests include Machine Learning and Data Science especially in areas related to applications of Deep Learning and Probabilistic Graphical Models in Multi-Relational and Heterogeneous Graph Mining, Information Extraction and Integration, Recommender Systems, Spam and Fraud Detection, Statistical Relational Learning, and Biomedical and Health Informatics. I have also received M.Sc. degrees in Bioinformatics and Software Engineering.
I have published papers, been the program committee, and organized workshops at conferences such as KDD, ICML, NIPS, WWW, SDM, ICDM, and WSDM.

Updates

News

2019:

ECML-PKDD'19 Paper: NSEEN: Neural Semantic Embedding for Entity Normalization
ICML-CompBio'19 Paper: Biomedical Named Entity Recognition via Reference-Set Augmented Bootstrapping
VLDB-DMAH'19 Paper: Towards Automated Hypothesis Testing in Neuroscience
VLDB'19 Volunteer Co-Chair
KDD'19 15th International Workshop on Mining and Learning with Graphs (MLG'19) Co-Organizor
PLOS ONE Journal Reviewer
NeurIPS'19 Program Committee
ICML'19 Program Committee
KDD'19 Program Committee
ASONAM'19 Program Committee
USC CSCI 548 and USC CSCI 648 Course Instructor

2018:

NSEEN: Neural Semantic Embedding for Entity Normalization Pre-print with Jose-Luis Ambite
GraphiPy Python package released by an awesome team of my undergrad students. An API wrapper to easily extract social graph data from multiple sources and export them to NetworkX, Gephi, and more
Applied Network Science Special Issue on Machine Learning with Graphs Lead Guest Editor
JMLR and Bioinformatics Journal Reviewer
SDM'19 and WWW'19 Program Committee
USC CSCI 401 Stakeholder / Project Advisor
NSF CISE Panelist
Complex Networks'18 Program Committee
SDM'18 Network Session Chair
KDD'18 14th International Workshop on Mining and Learning with Graphs (MLG'18) Organizor
KDD'18 Program Committee
WSDM'18 First International Workshop on Heterogeneous Networks Analysis and Mining (HeteroNAM'18) Founding Organizor

2017:

SDM'18 Program Committee
WWW'18 and GraML'18 Program Committee
KDD'17 13th International Workshop on Mining and Learning with Graphs (MLG'17) Organizor
Big-Graphs'17 Program Committee
Washington State University (CHAI), Colorado State University, San Francisco State University, University of Idaho, New Mexico State University, University of Maryland (iSchool), University of Maryland Baltimore County Invited talks

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Tweets by @shobeirf

Publications

Journal Articles

A Probabilistic Approach for Collective Similarity-based Drug-Drug Interaction Prediction
Dhanya Sridhar, Shobeir Fakhraei, Lise Getoor
Bioinformatics 2016
[PDF] [BibTeX]
@article{sridhar2016probabilistic,
author = "Sridhar, Dhanya and Fakhraei, Shobeir and Getoor, Lise",
title = "A Probabilistic Approach for Collective Similarity-based Drug-Drug Interaction Prediction",
journal = "Bioinformatics",
year = "2016",
}

Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic
Shobeir Fakhraei, Bert Huang, Louiqa Raschid, Lise Getoor
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 2014
[PDF] [BibTeX] [Data and Code] [Featured on the cover]
@article{fakhraei2014networkbased,
author = "Fakhraei, Shobeir and Huang, Bert and Raschid, Louiqa and Getoor, Lise",
title = "Network-Based Drug-Target Interaction Prediction with Probabilistic Soft Logic",
journal = "IEEE/ACM Transactions on Computational Biology and Bioinformatics",
doi = "10.1109/TCBB.2014.2325031",
year = "2014",
month = "Sept",
volume = "11",
number = "5",
pages = "775-787",
ISSN = "1545-5963",
organization = "IEEE",
note = "Code and data: https://github.com/shobeir/fakhraei_tcbb2014",
}

Bias and Stability of Single Variable Classifiers for Feature Ranking and Selection
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Farshad Fotouhi
Elsevier Expert Systems with Applications (ESWA) 2014
[PDF] [BibTeX]
@article{fakhraei2014bias,
author = "Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Fotouhi, Farshad",
title = "Bias and Stability of Single Variable Classifiers for Feature Ranking and Selection",
doi = "10.1016/j.eswa.2014.05.007",
url = "http://www.sciencedirect.com/science/article/pii/S0957417414002784",
journal = "Expert Systems with Applications",
year = "2014",
volume = "41",
number = "15",
pages = "6945 - 6958",
issn = "0957-4174",
organization = "Elsevier",
}

Conference Proceedings

NSEEN: Neural Semantic Embedding for Entity Normalization
Shobeir Fakhraei, Joel Mathew, Jose Luis Ambite
European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) 2019
[PDF] [BibTeX]
@inproceedings{fakhraei2019NSEEN,
author = {Fakhraei, Shobeir and Mathew, Joel and Ambite, Jose Luis},
title = {NSEEN: Neural Semantic Embedding for Entity Normalization},
booktitle = {European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD)},
year = {2019},
}

HeteroNAM: International Workshop on Heterogeneous Networks Analysis and Mining
Shobeir Fakhraei, Yanen Li, Yizhou Sun, Tim Weninger
ACM International Conference on Web Search and Data Mining (WSDM) 2018
[PDF] [BibTeX]
@inproceedings{fakhraei2019HeteroNAM,
author = {Fakhraei, Shobeir and Li, Yanen and Sun, Yizhou and Weninger, Tim},
title = {HeteroNAM: International Workshop on Heterogeneous Networks Analysis and Mining},
booktitle = {Proceedings of the Eleventh ACM International Conference on Web Search and Data Mining (WSDM)},
year = {2018},
}

Collective Spammer Detection in Evolving Multi-Relational Social Networks
Shobeir Fakhraei, James Foulds, Madhusudana Shashanka, Lise Getoor
ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD) 2015
[PDF] [BibTeX] [Slides] [Poster] [Data and Code] [Dato Conf. Video]
@inproceedings{fakhraei2015collective,
author = {Fakhraei, Shobeir and Foulds, James and Shashanka, Madhusudana and Getoor, Lise},
title = {Collective Spammer Detection in Evolving Multi-Relational Social Networks},
booktitle = {ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)},
year = {2015},
publisher = {ACM Press},
organization = {ACM},
}

HyPER: A Flexible and Extensible Probabilistic Framework for Hybrid Recommender Systems
Pigi Kouki, Shobeir Fakhraei, James Foulds, Magdalini Eirinaki, Lise Getoor
ACM Conference on Recommender Systems (RecSys) 2015
[PDF] [BibTeX] [Code]
@inproceedings{kouki2015HyPER,
author = {Kouki, Pigi and Fakhraei, Shobeir and Foulds, James and Eirinaki, Magdalini and Getoor, Lise},
title = {HyPER: A Flexible and Extensible Probabilistic Framework for Hybrid Recommender Systems},
booktitle = {ACM Conference on Recommender Systems (RecSys)},
year = {2015},
publisher = {ACM Press},
organization = {ACM},
}

Predictable Dual-View Hashing
Mohammad Rastegari, Jonghyun Choi, Shobeir Fakhraei, Hal Daume III, Larry Davis
International Conference on Machine Learning (ICML) 2013
[PDF] [BibTeX] [Slides] [Poster] [Code] [Video]
@inproceedings{rastegari2013predictable,
author = {Mohammad Rastegari and Jonghyun Choi and Shobeir Fakhraei and Hal Daum\'{e} III and Larry S. Davis},
title = {Predictable Dual-View Hashing},
booktitle = {International Conference on Machine Learning (ICML)},
year = {2013}
}

Consensus Feature Ranking in Datasets with Missing Values
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Farshad Fotouhi, Kost Elisevich
IEEE International Conference on Machine Learning and Applications (ICMLA) 2010
[PDF] [BibTeX] [Poster]
@inproceedings{fakhraei2010consensus,
title={Consensus feature ranking in datasets with missing values},
author={Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Fotouhi, Farshad and Elisevich, Kost},
booktitle={Machine Learning and Applications (ICMLA), 2010 Ninth International Conference on},
pages={771--775},
year={2010},
organization={IEEE}
}

Attribute Ranking for Lateralizing Focal Epileptogenicity in Temporal Lobe Epilepsy
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Kost Elisevich, Farshad Fotouhi,
IEEE Iranian Conference of Biomedical Engineering (ICBME) 2010
[PDF] [BibTeX] [Slides]
@inproceedings{fakhraei2010attribute,
title={Attribute ranking for lateralizing focal epileptogenicity in temporal lobe epilepsy},
author={Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Elisevich, Kost and Fotouhi, Farshad},
booktitle={Biomedical Engineering (ICBME), 2010 17th Iranian Conference of},
pages={1--4},
year={2010},
organization={IEEE}
}

Aspect Extraction from Software Design Model
Shobeir Fakhraei, Seyed-Hassan Mirian-Hosseinabadi
International CSI Computer Conference (CSICC) 2007
[PDF] [BibTeX]
@inproceedings{fakhraei2007aspect,
title={Aspect Extraction from Software Design Model},
author={Fakhraei, Shobeir and Mirian-Hosseinabadi,Seyed-Hassan},
booktitle={Proceedings of the 12th International CSI Computer Conference (CSICC)},
pages={1120--1130},
year={2007},
organization={CSICC}
}

Book Chapters

Data Analytics for Pharmaceutical Discoveries
Shobeir Fakhraei, Eberechukwu Onukwugha, Lise Getoor
Healthcare Data Analytics, CRC Press 2015
[PDF] [BibTeX]
@InCollection{fakhraei2015data,
author = "Fakhraei, Shobeir and Onukwugha, Eberechukwu and Getoor, Lise",
title = "Data Analytics for Pharmaceutical Discoveries",
booktitle = "Healthcare Data Analytics",
year = "2015",
publisher = "CRC Press",
pages = "599–623",
}

Workshop Proceedings

Biomedical Named Entity Recognition via Reference-Set Augmented Bootstrapping
Joel Mathew, Shobeir Fakhraei, Jose Luis Ambite
ICML Workshop on Computational Biology 2019
[PDF] [BibTeX]
@InProceedings{mathew2019Biomedical,
author = "Mathew, Joel and Fakhraei, Shobeir and Ambite, Jose Luis",
title = "Biomedical Named Entity Recognition via Reference-Set Augmented Bootstrapping",
booktitle = "ICML Workshop on Computational Biology",
year = "2019",
}

Towards Automated Hypothesis Testing in Neuroscience
Daniel Garijo*, Shobeir Fakhraei*, Varun Ratnakar, Qifan Yang, Hanna Endrias, Yibo Ma, Regina Wang, Michael Bornstein, Joanna Bright, Yolanda Gil, Neda Jahanshad (*equal contribution)
VLDB Workshop on Data Management and Analytics for Medicine and Healthcare 2019
[PDF] [BibTeX]
@InProceedings{fakhraei2019towards,
author = "Garijo*, Daniel, Fakhraei* (*equal contribution), Shobeir and Ratnakar, Varun and Yang, Qifan, and Endrias, Hanna and Ma, Yibo and Wang, Regina and Bornstein, Michael and Bright, Joanna and Gil, Yolanda and Jahanshad, Neda",
title = "Towards Automated Hypothesis Testing in Neuroscience",
booktitle = "VLDB Workshop on Data Management and Analytics for Medicine and Healthcare",
year = "2019",
}

Adaptive Neighborhood Graph Construction for Inference in Multi-Relational Networks
Shobeir Fakhraei, Dhanya Sridhar, Jay Pujara, Lise Getoor
KDD Workshop on Mining and Learning with Graphs (MLG) 2016
[PDF] [BibTeX]
@InProceedings{fakhraei2016adaptive,
author = "Fakhraei, Shobeir and Sridhar, Dhanya and Pujara, Jay Huang and Getoor, Lise",
title = "Adaptive Neighborhood Graph Construction for Inference in Multi-Relational Networks",
booktitle = "KDD Workshop on Mining and Learning with Graphs (MLG)",
year = "2016",
}

Collective Inference and Multi-Relational Learning for Drug-Target Interaction Prediction
Shobeir Fakhraei, Bert Huang, Lise Getoor
NIPS Workshop on Machine Learning in Computational Biology (MLCB) 2013
[PDF] [BibTeX] [Poster] [Journal version]
@InProceedings{fakhraei2013collective,
author = "Fakhraei, Shobeir and Huang, Bert and Getoor, Lise",
title = "Collective Inference and Multi-Relational Learning for Drug-Target Interaction Prediction",
booktitle = "NIPS Workshop on Machine Learning in Computational Biology (MLCB)",
year = "2013",
}

Drug-Target Interaction Prediction for Drug Repurposing with Probabilistic Similarity Logic
Shobeir Fakhraei, Louiqa Raschid, Lise Getoor
ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD) 2013
[PDF] [BibTeX] [Slides] [Journal version]
@InProceedings{fakhraei2013drug,
author = "Fakhraei, Shobeir and Raschid, Louiqa and Getoor, Lise",
title = "Drug-Target Interaction Prediction for Drug Repurposing with Probabilistic Similarity Logic",
booktitle = "ACM SIGKDD 12th International Workshop on Data Mining in Bioinformatics (BIOKDD)",
year = "2013",
publisher = "ACM",
}

Confident Surgical Decision Making in Temporal Lobe Epilepsy by Heterogeneous Classifier Ensembles
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Kost Elisevich, Kourosh Jafari-Khouzani, Farshad Fotouhi
IEEE ICDM Workshop on Biological Data Mining and its Applications in Healthcare (BIODM) 2011
[PDF] [BibTeX] [Slides]
@inproceedings{fakhraei2011confident,
title={Confident surgical decision making in temporal lobe epilepsy by heterogeneous classifier ensembles},
author={Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Jafari-Khouzani, Kourosh and Elisevich, Kost and Fotouhi, Farshad},
booktitle={Data Mining Workshops (ICDMW), 2011 IEEE 11th International Conference on},
pages={1003--1009},
year={2011},
organization={IEEE}
}

Confidence in Medical Decision Making: Application in Temporal Lobe Epilepsy Data Mining
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Farshad Fotouhi, Kost Elisevich
ACM SIGKDD Workshop on Data Mining for Medicine and Healthcare (DMMH) 2011
[PDF] [BibTeX] [Poster]
@inproceedings{fakhraei2011confidence,
title={Confidence in medical decision making: application in temporal lobe epilepsy data mining},
author={Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Fotouhi, Farshad and Elisevich, Kost},
booktitle={Proceedings of the 2011 workshop on Data mining for medicine and healthcare},
pages={60--63},
year={2011},
organization={ACM}
}

Effect of classifiers in consensus feature ranking for biomedical datasets
Shobeir Fakhraei, Hamid Soltanian-Zadeh, Farshad Fotouhi, Kost Elisevich
ACM CIKM Workshop on Data and Text Mining in Biomedical Informatics (DTMBIO) 2010
[PDF] [BibTeX] [Slides]
@inproceedings{fakhraei2010effect,
title={Effect of classifiers in consensus feature ranking for biomedical datasets},
author={Fakhraei, Shobeir and Soltanian-Zadeh, Hamid and Fotouhi, Farshad and Elisevich, Kost},
booktitle={Proceedings of the ACM fourth international workshop on Data and text mining in biomedical informatics},
pages={67--68},
year={2010},
organization={ACM}
}

Professional Experience

Academia

University of Southern California, Los Angeles CA
Research Scientist, (Research: Deep Semantic Embedding and Information Extraction)
University of Maryland, College Park MD
Research Assistant, (Research: Multi-Relational Graph Mining, Statistical Relational Learning)
University of California, Santa Cruz CA
Visiting Research Scholar, (Research: Link Prediction and Recommender Systems, Collective Classification)
Wayne State University, Detroit MI
Instructor, Research Assistant, Teaching Assistant, (Research: Feature Selection, Classification Uncertainty in Medical Applications)

Research Industry

Microsoft Research, Redmond WA
Research Scientist Intern, (Research: Email to Meeting Transfer Patterns)
Yahoo! Research (Labs), Sunnyvale CA
Research Scientist Intern, (Research: Context-aware Recommender Systems)
Turi (Dato) Inc. / Ifwe (Tagged) Inc., Seattle WA / San Francisco CA
Data Science Research Intern, (Research: Heterogeneous Social Networks Spam Detection)
Henry Ford Health System, Detroit MI
Visiting Researcher, (Research: Temporal Lobe Epilepsy Lateralization)

Teaching

University of Southern California, CA

Advanced Information Integration (CSCI 648), Instructor
Information Integration on the Web (CSCI 548), Instructor
Capstone: Design & Construction of Large Software Systems (CSCI 401), Stakeholder / Project Advisor

Wayne State University, MI

Fundamental Structures in Computer Science and Lab (CSC 1500-1501), Instructor
Data Mining Algorithms and Applications (CSC 7810), Teaching Assistant
Graduate Seminar (CSC 8990), Course Coordinator
Introduction to Computer Science (CSC 1000), Lab Instructor

Sharif University of Technology

Software Engineering Lab, Lab Instructor

University of Applied Science and Technology

Introduction to Computer Science, Instructor
Internet Fundamentals and Web Programming, Instructor
Multimedia Systems, Instructor
Computer Networks, Instructor
Database Systems and Lab, Instructor
Data Structures and Algorithms, Instructor
Information Storage and Retrieval, Instructor
Advanced Computer Programming (C++), Instructor
Computer Programming (Introduction to Algorithms), Instructor

Academic Services

Grant Proposal Panelist

National Science Foundation - CISE Review Panel 2018 (Panelist)

Conference and Workshop Organizer and Chair

ACM SIGKDD International Workshop on Mining and Learning with Graphs (MLG): 15th-2019 (Organizer), 14th-2018 (Organizer), 13th-2017 (Organizer), 12th-2016 (Organizer)
ACM WSDM International Workshop on Heterogeneous Networks Analysis and Mining (HeteroNAM): 1st-2018 (Founding Organizer)
International Conference on Very Large Data Bases (VLDB): 2019 (Volunteer Co-Chair)
SIAM International Conference on Data Mining (SDM): 2018 (Session Chair)
Graph Mining Reading Group at Information Science Institute, University of Southern California: 2018 (Founding Organizer)

Journal Editor

Applied Network Science, Machine Learning with Graphs Special Issue: 2018 (Lead Guest Editor)

Journal Reviewer

Journal of Machine Learning Research (JMLR): 2018, 2019
IEEE Transactions on Knowledge & Data Eng. (TKDE): 2013, 2014, 2015, 2016, 2017, 2018
Plos One: 2019
Springer Data Mining & Knowledge Discovery (DAMI): 2018
Bioinformatics (Oxford Academic): 2018
Briefings in Bioinformatics: 2017
IEEE Journal of Biomedical and Health Informatics (JBHI): 2015
Elsevier Journal of Theoretical Biology (JTB): 2015
PeerJ Open Access Biological and Medical Sciences Journal: 2015
Elsevier Expert Systems with Applications (ESWA): 2016, 2017
ACM Transactions on Intelligent Systems and Technology (TIST): 2012

Program Committee

Neural Information Processing Systems (NeurIPS): 2014, 2015, 2019
International Conference on Machine Learning (ICML): 2019
ACM International Conf. on Knowledge Discovery & Data Mining (KDD): 2018, 2019
The Web Conference (WWW): 2018, 2019
SIAM International Conference on Data Mining (SDM): 2018, 2019
Association for the Advancement of Artificial Intelligence Conference (AAAI): 2019
International Joint Conference on Artificial Intelligence (IJCAI): 2016
International Conf. on Advances in Social Networks Analysis & Mining (ASONAM): 2019
Complex Networks: 2018, 2019
IEEE Workshop at the Intersection of Graph Algorithms & Machine Learning (GraML): 2018
IEEE Workshop on High Performance Big Graph Data Analysis, & Mining (BigGraphs): 2017
ACM SIGKDD Workshop on Outlier Definition, Detection & Description (ODD): 2016
International Conf. on Pervasive Computing Technologies for Healthcare (PervasiveHealth): 2013

Contacts

Address:

501 Fairview Ave N.
Seattle, WA 98109

Email:

shobeir@cs.umd.edu