Generative AI Systems

Our Researches

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Highlighted

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128

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2024

Knowledge graph construction in hyperbolic space for automatic image annotation
Knowledge graph construction in hyperbolic space for automatic image annotation
Fariba Lotfi, Mansour Jamzad, Hamid Beigy, Helia Farhood, Quan Z. Sheng, Amin Beheshti
Image and Vision Computing  ·  01 Nov 2024  ·  doi:10.1016/j.imavis.2024.105293

2023

The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, …, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres
Nucleic Acids Research  ·  24 Nov 2023  ·  doi:10.1093/nar/gkad1082
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Integration of 168,000 samples reveals global patterns of the human gut microbiome
Richard J. Abdill, Samantha P. Graham, Vincent Rubinetti, Frank W. Albert, Casey S. Greene, Sean Davis, Ran Blekhman
Cold Spring Harbor Laboratory  ·  11 Oct 2023  ·  doi:10.1101/2023.10.11.560955
Learning Hidden Graphs From Samples
Learning Hidden Graphs From Samples
Ahmad Abniki, Hamid Beigy
IEEE Transactions on Pattern Analysis and Machine Intelligence  ·  01 Oct 2023  ·  doi:10.1109/TPAMI.2023.3283784
Prompted and integrated textual information enhancing aspect-based sentiment analysis
Prompted and integrated textual information enhancing aspect-based sentiment analysis
Xuefeng Shi, Min Hu, Fuji Ren, Piao Shi, Jiawen Deng, Yiming Tang
Journal of Intelligent Information Systems  ·  23 Aug 2023  ·  doi:10.1007/s10844-023-00805-0
Concept drift handling: A domain adaptation perspective
Concept drift handling: A domain adaptation perspective
Mahmood Karimian, Hamid Beigy
Expert Systems with Applications  ·  01 Aug 2023  ·  doi:10.1016/j.eswa.2023.119946
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes
Ricardo Avila, Vincent Rubinetti, Xinghua Zhou, Dongbo Hu, Zhongchao Qian, Marco Alvarado Cano, Everaldo Rodolpho, Ginger Tsueng, Casey Greene, Chunlei Wu
Nucleic Acids Research  ·  18 Apr 2023  ·  doi:10.1093/nar/gkad289
SGCSumm: An extractive multi-document summarization method based on pre-trained language model, submodularity, and graph convolutional neural networks
SGCSumm: An extractive multi-document summarization method based on pre-trained language model, submodularity, and graph convolutional neural networks
Alireza Ghadimi, Hamid Beigy
Expert Systems with Applications  ·  01 Apr 2023  ·  doi:10.1016/j.eswa.2022.119308
Storytelling with Image Data: A Systematic Review and Comparative Analysis of Methods and Tools
Storytelling with Image Data: A Systematic Review and Comparative Analysis of Methods and Tools
Fariba Lotfi, Amin Beheshti, Helia Farhood, Matineh Pooshideh, Mansour Jamzad, Hamid Beigy
Algorithms  ·  02 Mar 2023  ·  doi:10.3390/a16030135
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Hetnet connectivity search provides rapid insights into how two biomedical entities are related
Daniel S. Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J. Heil, …, David N. Nicholson, Yun Hao, Blair D. Sullivan, Michael W. Nagle, Casey S. Greene
Cold Spring Harbor Laboratory  ·  07 Jan 2023  ·  doi:10.1101/2023.01.05.522941

2022

Hetnet connectivity search provides rapid insights into how biomedical entities are related
Hetnet connectivity search provides rapid insights into how biomedical entities are related
Daniel S Himmelstein, Michael Zietz, Vincent Rubinetti, Kyle Kloster, Benjamin J Heil, …, David N Nicholson, Yun Hao, Blair D Sullivan, Michael W Nagle, Casey S Greene
GigaScience  ·  28 Dec 2022  ·  doi:10.1093/gigascience/giad047
Structural virality estimation and maximization in diffusion networks
Structural virality estimation and maximization in diffusion networks
Arman Sepehr, Hamid Beigy
Expert Systems with Applications  ·  01 Nov 2022  ·  doi:10.1016/j.eswa.2022.117657
Attention-based skill translation models for expert finding
Attention-based skill translation models for expert finding
Zohreh Fallahnejad, Hamid Beigy
Expert Systems with Applications  ·  01 May 2022  ·  doi:10.1016/j.eswa.2021.116433
Hybrid multi-document summarization using pre-trained language models
Hybrid multi-document summarization using pre-trained language models
Alireza Ghadimi, Hamid Beigy
Expert Systems with Applications  ·  01 Apr 2022  ·  doi:10.1016/j.eswa.2021.116292
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
Jacob D Krol, Joseph T Burke, Samuel Z Chen, Lo M Sosinski, Faisal S Alquaddoomi, …, Vincent P Rubinetti, Shaddai Amolitos, Kellen M Reason, John B Johnston, Janani Ravi
Cold Spring Harbor Laboratory  ·  22 Feb 2022  ·  doi:10.1101/2022.02.18.461833

2021

Masked Autoencoder for Distribution Estimation on Small Structured Data Sets
Masked Autoencoder for Distribution Estimation on Small Structured Data Sets
Ahmad Khajenezhad, Hatef Madani, Hamid Beigy
IEEE Transactions on Neural Networks and Learning Systems  ·  01 Nov 2021  ·  doi:10.1109/TNNLS.2020.3026572
A distributed density estimation algorithm and its application to naive Bayes classification
A distributed density estimation algorithm and its application to naive Bayes classification
Ahmad Khajenezhad, Mohammad Ali Bashiri, Hamid Beigy
Applied Soft Computing  ·  01 Jan 2021  ·  doi:10.1016/j.asoc.2020.106837
A sampling method based on distributed learning automata for solving stochastic shortest path problem
A sampling method based on distributed learning automata for solving stochastic shortest path problem
Hamid Beigy, Mohammad Reza Meybodi
Knowledge-Based Systems  ·  01 Jan 2021  ·  doi:10.1016/j.knosys.2020.106638

2020

Density peaks clustering based on density backbone and fuzzy neighborhood
Density peaks clustering based on density backbone and fuzzy neighborhood
Abdulrahman Lotfi, Parham Moradi, Hamid Beigy
Pattern Recognition  ·  01 Nov 2020  ·  doi:10.1016/j.patcog.2020.107449
Deep submodular network: An application to multi-document summarization
Deep submodular network: An application to multi-document summarization
Alireza Ghadimi, Hamid Beigy
Expert Systems with Applications  ·  01 Aug 2020  ·  doi:10.1016/j.eswa.2020.113392
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Genome Biology  ·  11 May 2020  ·  doi:10.1186/s13059-020-02021-3
Improved K2 algorithm for Bayesian network structure learning
Improved K2 algorithm for Bayesian network structure learning
Shahab Behjati, Hamid Beigy
Engineering Applications of Artificial Intelligence  ·  01 May 2020  ·  doi:10.1016/j.engappai.2020.103617
The Shapley value for a fair division of group discounts for coordinating cooling loads
The Shapley value for a fair division of group discounts for coordinating cooling loads
Sasan Maleki, Talal Rahwan, Siddhartha Ghosh, Areej Malibari, Daniyal Alghazzawi, Alex Rogers, Hamid Beigy, Nicholas R. Jennings
PLOS ONE  ·  10 Jan 2020  ·  doi:10.1371/journal.pone.0227049
Supervised fuzzy partitioning
Supervised fuzzy partitioning
Pooya Ashtari, Fateme Nateghi Haredasht, Hamid Beigy
Pattern Recognition  ·  01 Jan 2020  ·  doi:10.1016/j.patcog.2019.107013

2019

An iterative stochastic algorithm based on distributed learning automata for finding the stochastic shortest path in stochastic graphs
An iterative stochastic algorithm based on distributed learning automata for finding the stochastic shortest path in stochastic graphs
Hamid Beigy, Mohammad Reza Meybodi
The Journal of Supercomputing  ·  27 Nov 2019  ·  doi:10.1007/s11227-019-03085-0
Sentiment analysis on stock social media for stock price movement prediction
Sentiment analysis on stock social media for stock price movement prediction
Ali Derakhshan, Hamid Beigy
Engineering Applications of Artificial Intelligence  ·  01 Oct 2019  ·  doi:10.1016/j.engappai.2019.07.002
Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128
Learning a metric when clustering data points in the presence of constraints
Learning a metric when clustering data points in the presence of constraints
Ahmad Ali Abin, Mohammad Ali Bashiri, Hamid Beigy
Advances in Data Analysis and Classification  ·  16 May 2019  ·  doi:10.1007/s11634-019-00359-6
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Sequential compression of gene expression across dimensionalities and methods reveals no single best method or dimensionality
Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Cold Spring Harbor Laboratory  ·  11 Mar 2019  ·  doi:10.1101/573782
Viral Cascade Probability Estimation and Maximization in Diffusion Networks
Viral Cascade Probability Estimation and Maximization in Diffusion Networks
Arman Sepehr, Hamid Beigy
IEEE Transactions on Knowledge and Data Engineering  ·  01 Mar 2019  ·  doi:10.1109/TKDE.2018.2840998

2018

Concept-evolution detection in non-stationary data streams: a fuzzy clustering approach
Concept-evolution detection in non-stationary data streams: a fuzzy clustering approach
Poorya ZareMoodi, Sajjad Kamali Siahroudi, Hamid Beigy
Knowledge and Information Systems  ·  16 Oct 2018  ·  doi:10.1007/s10115-018-1266-y
Detection of evolving concepts in non-stationary data streams: A multiple kernel learning approach
Detection of evolving concepts in non-stationary data streams: A multiple kernel learning approach
Sajjad Kamali Siahroudi, Poorya Zare Moodi, Hamid Beigy
Expert Systems with Applications  ·  01 Jan 2018  ·  doi:10.1016/j.eswa.2017.08.033

2017

On dynamicity of expert finding in community question answering
On dynamicity of expert finding in community question answering
Mahmood Neshati, Zohreh Fallahnejad, Hamid Beigy
Information Processing & Management  ·  01 Sep 2017  ·  doi:10.1016/j.ipm.2017.04.002
A graph-theoretic approach toward autonomous skill acquisition in reinforcement learning
A graph-theoretic approach toward autonomous skill acquisition in reinforcement learning
Seed Jalal Kazemitabar, Nasrin Taghizadeh, Hamid Beigy
Evolving Systems  ·  22 Jun 2017  ·  doi:10.1007/s12530-017-9193-9
Associative cellular learning automata and its applications
Associative cellular learning automata and its applications
Meysam Ahangaran, Nasrin Taghizadeh, Hamid Beigy
Applied Soft Computing  ·  01 Apr 2017  ·  doi:10.1016/j.asoc.2016.12.006
Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data
Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data
Zahra Narimani, Hamid Beigy, Ashar Ahmad, Ali Masoudi-Nejad, Holger Fröhlich
PLOS ONE  ·  06 Feb 2017  ·  doi:10.1371/journal.pone.0171240

2016

A novel concept drift detection method in data streams using ensemble classifiers
A novel concept drift detection method in data streams using ensemble classifiers
Mahdie Dehghan, Hamid Beigy, Poorya ZareMoodi
Intelligent Data Analysis  ·  08 Nov 2016  ·  doi:10.3233/IDA-150207
Cascading randomized weighted majority: A new online ensemble learning algorithm
Cascading randomized weighted majority: A new online ensemble learning algorithm
Mohammadzaman Zamani, Hamid Beigy, Amirreza Shaban
Intelligent Data Analysis  ·  15 Jun 2016  ·  doi:10.3233/IDA-160836
Critic learning in multi agent credit assignment problem
Critic learning in multi agent credit assignment problem
Zahra Rahaie, Hamid Beigy
Journal of Intelligent & Fuzzy Systems  ·  30 Apr 2016  ·  doi:10.3233/IFS-162093

2015

Deployment and testing of the sustained petascale Blue Waters system
Deployment and testing of the sustained petascale Blue Waters system
Celso L. Mendes, Brett Bode, Gregory H. Bauer, Jeremy Enos, Cristina Beldica, William T. Kramer
Journal of Computational Science  ·  01 Sep 2015  ·  doi:10.1016/j.jocs.2015.03.007
A dynamic shuffled differential evolution algorithm for data clustering
A dynamic shuffled differential evolution algorithm for data clustering
Wan-li Xiang, Ning Zhu, Shou-feng Ma, Xue-lei Meng, Mei-qing An
Neurocomputing  ·  01 Jun 2015  ·  doi:10.1016/j.neucom.2015.01.058
An ensemble of cluster-based classifiers for semi-supervised classification of non-stationary data streams
An ensemble of cluster-based classifiers for semi-supervised classification of non-stationary data streams
Mohammad Javad Hosseini, Ameneh Gholipour, Hamid Beigy
Knowledge and Information Systems  ·  28 Apr 2015  ·  doi:10.1007/s10115-015-0837-4

2014

A learning automata-based adaptive uniform fractional guard channel algorithm
A learning automata-based adaptive uniform fractional guard channel algorithm
Hamid Beigy, M. R. Meybodi
The Journal of Supercomputing  ·  07 Dec 2014  ·  doi:10.1007/s11227-014-1330-7
Expertness framework in multi-agent systems and its application in credit assignment problem
Expertness framework in multi-agent systems and its application in credit assignment problem
Zahra Rahaie, Hamid Beigy
Intelligent Data Analysis  ·  30 Apr 2014  ·  doi:10.3233/IDA-140654
Pair-copula based mixture models and their application in clustering
Pair-copula based mixture models and their application in clustering
Anandarup Roy, Swapan K. Parui
Pattern Recognition  ·  01 Apr 2014  ·  doi:10.1016/j.patcog.2013.10.004
A localization algorithm for large scale mobile wireless sensor networks: a learning approach
A localization algorithm for large scale mobile wireless sensor networks: a learning approach
Samira Afzal, Hamid Beigy
The Journal of Supercomputing  ·  13 Mar 2014  ·  doi:10.1007/s11227-014-1129-6
Expert group formation using facility location analysis
Expert group formation using facility location analysis
Mahmood Neshati, Hamid Beigy, Djoerd Hiemstra
Information Processing & Management  ·  01 Mar 2014  ·  doi:10.1016/j.ipm.2013.10.001
WISECODE: wise image segmentation based on community detection
WISECODE: wise image segmentation based on community detection
A. A. Abin, F. Mahdisoltani, H. Beigy
The Imaging Science Journal  ·  09 Jan 2014  ·  doi:10.1179/1743131X13Y.0000000069

2013

A new real-coded Bayesian optimization algorithm based on a team of learning automata for continuous optimization
A new real-coded Bayesian optimization algorithm based on a team of learning automata for continuous optimization
Behnaz Moradabadi, Hamid Beigy
Genetic Programming and Evolvable Machines  ·  16 Oct 2013  ·  doi:10.1007/s10710-013-9206-9
Self adaptive routing for dynamic spectrum access in cognitive radio networks
Self adaptive routing for dynamic spectrum access in cognitive radio networks
A. Cagatay Talay, D. Turgay Altilar
Journal of Network and Computer Applications  ·  01 Jul 2013  ·  doi:10.1016/j.jnca.2013.01.007
Integration of scientific and social networks
Integration of scientific and social networks
Mahmood Neshati, Djoerd Hiemstra, Ehsaneddin Asgari, Hamid Beigy
World Wide Web  ·  21 Jun 2013  ·  doi:10.1007/s11280-013-0229-1

2012

A NEW GENETIC ALGORITHM FOR MULTIPLE SEQUENCE ALIGNMENT
A NEW GENETIC ALGORITHM FOR MULTIPLE SEQUENCE ALIGNMENT
ZAHRA NARIMANI, HAMID BEIGY, HASSAN ABOLHASSANI
International Journal of Computational Intelligence and Applications  ·  01 Dec 2012  ·  doi:10.1142/S146902681250023X
Improved direction estimation for Di Zenzo s multichannel image gradient operator
Improved direction estimation for Di Zenzo's multichannel image gradient operator
Lianghai Jin, Hong Liu, Xiangyang Xu, Enmin Song
Pattern Recognition  ·  01 Dec 2012  ·  doi:10.1016/j.patcog.2012.06.003
A GENETIC PROGRAMMING-BASED LEARNING ALGORITHMS FOR PRUNING COST-SENSITIVE CLASSIFIERS
A GENETIC PROGRAMMING-BASED LEARNING ALGORITHMS FOR PRUNING COST-SENSITIVE CLASSIFIERS
ZAHRA NIKDEL, HAMID BEIGY
International Journal of Computational Intelligence and Applications  ·  01 Jun 2012  ·  doi:10.1142/S1469026812500113
A new method of mining data streams using harmony search
A new method of mining data streams using harmony search
Zohre Karimi, Hassan Abolhassani, Hamid Beigy
Journal of Intelligent Information Systems  ·  04 Apr 2012  ·  doi:10.1007/s10844-012-0199-2

2011

Fuzzy identity based signature with applications to biometric authentication
Fuzzy identity based signature with applications to biometric authentication
Piyi Yang, Zhenfu Cao, Xiaolei Dong
Computers & Electrical Engineering  ·  01 Jul 2011  ·  doi:10.1016/j.compeleceng.2011.04.013

2010

Special issue on network-based high performance computing
Special issue on network-based high performance computing
H. Sarbazi-Azad, A. Shahrabi, H. Beigy
The Journal of Supercomputing  ·  19 Mar 2010  ·  doi:10.1007/s11227-010-0423-1

2009

ADAPTIVE LIMITED FRACTIONAL GUARD CHANNEL ALGORITHMS: A LEARNING AUTOMATA APPROACH
ADAPTIVE LIMITED FRACTIONAL GUARD CHANNEL ALGORITHMS: A LEARNING AUTOMATA APPROACH
HAMID BEIGY, M. R. MEYBODI
International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems  ·  01 Dec 2009  ·  doi:10.1142/S0218488509006315
CELLULAR LEARNING AUTOMATA BASED DYNAMIC CHANNEL ASSIGNMENT ALGORITHMS
CELLULAR LEARNING AUTOMATA BASED DYNAMIC CHANNEL ASSIGNMENT ALGORITHMS
HAMID BEIGY, M. R. MEYBODI
International Journal of Computational Intelligence and Applications  ·  01 Sep 2009  ·  doi:10.1142/S1469026809002618
A learning automata-based algorithm for determination of the number of hidden units for three-layer neural networks
A learning automata-based algorithm for determination of the number of hidden units for three-layer neural networks
Hamid Beigy, Mohamad Reza Meybodi
International Journal of Systems Science  ·  01 Jan 2009  ·  doi:10.1080/00207720802145924

2008

Robust control of flexible structures with stable bandpass controllers
Robust control of flexible structures with stable bandpass controllers
Alberto Cavallo, Giuseppe De Maria, Ciro Natale, Salvatore Pirozzi
Automatica  ·  01 May 2008  ·  doi:10.1016/j.automatica.2007.10.020

2007

OPEN SYNCHRONOUS CELLULAR LEARNING AUTOMATA
OPEN SYNCHRONOUS CELLULAR LEARNING AUTOMATA
HAMID BEIGY, M. R. MEYBODI
Advances in Complex Systems  ·  01 Dec 2007  ·  doi:10.1142/S0219525907001264

2006

UTILIZING DISTRIBUTED LEARNING AUTOMATA TO SOLVE STOCHASTIC SHORTEST PATH PROBLEMS
UTILIZING DISTRIBUTED LEARNING AUTOMATA TO SOLVE STOCHASTIC SHORTEST PATH PROBLEMS
HAMID BEIGY, M. R. MEYBODI
International Journal of Uncertainty, Fuzziness and Knowledge-Based Systems  ·  01 Oct 2006  ·  doi:10.1142/S0218488506004217

2005

A nonlinear inverse problem in estimating simultaneously the external forces for a vibration system with displacement-dependent parameters
A nonlinear inverse problem in estimating simultaneously the external forces for a vibration system with displacement-dependent parameters
Cheng-Hung Huang
Journal of the Franklin Institute  ·  01 Nov 2005  ·  doi:10.1016/j.jfranklin.2005.06.006
A general call admission policy for next generation wireless networks
A general call admission policy for next generation wireless networks
Hamid Beigy, M.R. Meybodi
Computer Communications  ·  01 Oct 2005  ·  doi:10.1016/j.comcom.2004.12.009
An adaptive call admission algorithm for cellular networks
An adaptive call admission algorithm for cellular networks
Hamid Beigy, M.R. Meybodi
Computers & Electrical Engineering  ·  01 Mar 2005  ·  doi:10.1016/j.compeleceng.2004.12.002

2004

A MATHEMATICAL FRAMEWORK FOR CELLULAR LEARNING AUTOMATA
A MATHEMATICAL FRAMEWORK FOR CELLULAR LEARNING AUTOMATA
HAMID BEIGY, M. R. MEYBODI
Advances in Complex Systems  ·  01 Sep 2004  ·  doi:10.1142/S0219525904000202

2002

A note on learning automata-based schemes for adaptation of BP parameters
A note on learning automata-based schemes for adaptation of BP parameters
M.R Meybodi, H Beigy
Neurocomputing  ·  01 Oct 2002  ·  doi:10.1016/S0925-2312(01)00686-5
NEW LEARNING AUTOMATA BASED ALGORITHMS FOR ADAPTATION OF BACKPROPAGATION ALGORITHM PARAMETERS
NEW LEARNING AUTOMATA BASED ALGORITHMS FOR ADAPTATION OF BACKPROPAGATION ALGORITHM PARAMETERS
M. R. MEYBODI, H. BEIGY
International Journal of Neural Systems  ·  01 Feb 2002  ·  doi:10.1142/S012906570200090X

2001

BACKPROPAGATION ALGORITHM ADAPTATION PARAMETERS USING LEARNING AUTOMATA
BACKPROPAGATION ALGORITHM ADAPTATION PARAMETERS USING LEARNING AUTOMATA
HAMID BEIGY, MOHAMMAD R. MEYBODI
International Journal of Neural Systems  ·  01 Jun 2001  ·  doi:10.1142/S0129065701000655