Predrag Radivojac

According to our database, Predrag Radivojac authored at least 80 papers between 2002 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Learning Tree-Structured Composition of Data Augmentation.

Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang

Trans. Mach. Learn. Res., 2024

Modeling Multiple Adverse Pregnancy Outcomes: Learning from Diverse Data Sources.

Saurabh Mathur, Veerendra P. Gadekar, Rashika Ramola, Peixin Wang, Ramachandran Thiruvengadam, David M. Haas, Shinjini Bhatnagar, Nitya Wadhwa, Garbhini Study Group, Predrag Radivojac, Himanshu Sinha, Kristian Kersting, Sriraam Natarajan

Proceedings of the Artificial Intelligence in Medicine - 22nd International Conference, 2024

2023

Active feature elicitation: An unified framework.

Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac, Sriraam Natarajan

Frontiers Artif. Intell., February, 2023

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods.

Damiano Piovesan, Davide Zago, Parnal Joshi, M. Clara De Paolis Kaluza, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C. E. Tosatto

CoRR, 2023

Leveraging Structure for Improved Classification of Grouped Biased Data.

Daniel Zeiberg, Shantanu Jain, Predrag Radivojac

Proceedings of the Thirty-Seventh AAAI Conference on Artificial Intelligence, 2023

2022

A roadmap for the functional annotation of protein families: a community perspective.

Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu

Database J. Biol. Databases Curation, 2022

Explaining Deep Tractable Probabilistic Models: The sum-product network case.

Athresh Karanam, Saurabh Mathur, Predrag Radivojac, David M. Haas, Kristian Kersting, Sriraam Natarajan

Proceedings of the International Conference on Probabilistic Graphical Models, 2022

2021

Explaining Deep Tractable Probabilistic Models: The sum-product network case.

Athresh Karanam, Saurabh Mathur, Predrag Radivojac, Kristian Kersting, Sriraam Natarajan

CoRR, 2021

Classification in biological networks with hypergraphlet kernels.

Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac

Bioinform., 2021

A Probabilistic Approach to Extract Qualitative Knowledge for Early Prediction of Gestational Diabetes.

Athresh Karanam, Alexander L. Hayes, Harsha Kokel, David M. Haas, Predrag Radivojac, Sriraam Natarajan

Proceedings of the Artificial Intelligence in Medicine, 2021

2020

The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction.

Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac

Bioinform., 2020

An examination of citation-based impact of the computational biology conferences.

Jayvardan S. Naidu, Justin Delano, Scott Mathews, Predrag Radivojac

Bioinform., 2020

Session Introduction.

Lukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Session Introduction.

Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti

Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting.

Daniel Zeiberg, Shantanu Jain, Predrag Radivojac

Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020

Class Prior Estimation with Biased Positives and Unlabeled Examples.

Shantanu Jain, Justin Delano, Himanshu Sharma, Predrag Radivojac

Proceedings of the Thirty-Fourth AAAI Conference on Artificial Intelligence, 2020

2019

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome.

Kymberleigh A. Pagel, Danny Antaki, Aojie Lian, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

PLoS Comput. Biol., 2019

A new class of metrics for learning on real-valued and structured data.

Ruiyu Yang, Yuxiang Jiang, Scott Mathews, Elizabeth A. Housworth, Matthew W. Hahn, Predrag Radivojac

Data Min. Knowl. Discov., 2019

ISMB/ECCB 2019 Proceedings.

Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac

Bioinform., 2019

Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies.

Rashika Ramola, Shantanu Jain, Predrag Radivojac

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

Session introduction.

Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac

Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

2018

Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data.

Makoto Yamada, Jiliang Tang, Jose Lugo-Martinez, Ermin Hodzic, Raunak Shrestha, Avishek Saha, Hua Ouyang, Dawei Yin, Hiroshi Mamitsuka, Süleyman Cenk Sahinalp, Predrag Radivojac, Filippo Menczer, Yi Chang

IEEE Trans. Knowl. Data Eng., 2018

Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse.

Rodrigo F. Ramalho, Sujun Li, Predrag Radivojac, Matthew W. Hahn

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies.

Yisu Peng, Yuxiang Jiang, Predrag Radivojac

Bioinform., 2018

ISMB 2018 proceedings.

Yana Bromberg, Predrag Radivojac

Bioinform., 2018

On Whom Should I Perform this Lab Test Next? An Active Feature Elicitation Approach.

Sriraam Natarajan, Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac

Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018

2017

Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies.

Yisu Peng, Yuxiang Jiang, Predrag Radivojac

CoRR, 2017

Classification in biological networks with hypergraphlet kernels.

Jose Lugo-Martinez, Predrag Radivojac

CoRR, 2017

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants.

Kymberleigh A. Pagel, Vikas Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

Bioinform., 2017

Session Introduction.

Yana Bromberg, Matthew W. Hahn, Predrag Radivojac

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

Recovering True Classifier Performance in Positive-Unlabeled Learning.

Shantanu Jain, Martha White, Predrag Radivojac

Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence, 2017

2016

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Lonnie R. Welch, Cath Brooksbank, Russell Schwartz, Sarah L. Morgan, Bruno A. Gaëta, Alastair M. Kilpatrick, Daniel Mietchen, Benjamin L. Moore, Nicola J. Mulder, Mark A. Pauley, William R. Pearson, Predrag Radivojac, Naomi Rosenberg, Anne G. Rosenwald, Gabriella Rustici, Tandy J. Warnow

PLoS Comput. Biol., 2016

The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.

Jose Lugo-Martinez, Vikas Pejaver, Kymberleigh A. Pagel, Shantanu Jain, Matthew E. Mort, David N. Cooper, Sean D. Mooney, Predrag Radivojac

PLoS Comput. Biol., 2016

Nonparametric semi-supervised learning of class proportions.

Shantanu Jain, Martha White, Michael W. Trosset, Predrag Radivojac

CoRR, 2016

Estimating the class prior and posterior from noisy positives and unlabeled data.

Shantanu Jain, Martha White, Predrag Radivojac

Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016

2015

A link graph-based approach to identify forum spam.

Youngsang Shin, Steven A. Myers, Minaxi Gupta, Predrag Radivojac

Secur. Commun. Networks, 2015

Ten Simple Rules for a Community Computational Challenge.

Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac

PLoS Comput. Biol., 2015

Training the Next Generation of Quantitative Biologists in the Era of Big Data.

Kristine A. Pattin, Anna C. Greene, Russ B. Altman, Kevin Bretonnel Cohen, Elizabeth Wethington, Carsten Görg, Lawrence E. Hunter, Spencer V. Muse, Predrag Radivojac, Jason H. Moore

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

A maximum-likelihood approach to absolute protein quantification in mass spectrometry.

Chao Ji, Yong Fuga Li, Earl P. Bellinger, Sujun Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.

Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider

PLoS Comput. Biol., 2014

Generalized graphlet kernels for probabilistic inference in sparse graphs.

Jose Lugo-Martinez, Predrag Radivojac

Netw. Sci., 2014

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg

Bioinform., 2014

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac

Bioinform., 2014

Vector Quantization Kernels for the Classification of Protein Sequences and Structures.

Wyatt T. Clark, Predrag Radivojac

Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

2013

ISCB Computational Biology Wikipedia Competition.

Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff MacIntyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost

PLoS Comput. Biol., 2013

Information-theoretic evaluation of predicted ontological annotations.

Wyatt T. Clark, Predrag Radivojac

Bioinform., 2013

Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches.

Sujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors.

Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund

PLoS Comput. Biol., 2012

Computational approaches to protein inference in shotgun proteomics.

Yong Fuga Li, Predrag Radivojac

BMC Bioinform., 2012

Post-translational modifications induce significant yet not extreme changes to protein structure.

Fuxiao Xin, Predrag Radivojac

Bioinform., 2012

2011

Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals.

Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn

PLoS Comput. Biol., 2011

2010

Graphlet Kernels for Prediction of Functional Residues in Protein Structures.

Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac

J. Comput. Biol., 2010

Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.

Fuxiao Xin, Steven A. Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac

BMC Bioinform., 2010

Loss of Post-Translational Modification Sites in Disease.

Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins.

Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac

PLoS Comput. Biol., 2009

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics.

Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang

J. Comput. Biol., 2009

Analysis of AML genes in dysregulated molecular networks.

Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee

BMC Bioinform., 2009

Automated inference of molecular mechanisms of disease from amino acid substitutions.

Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac

Bioinform., 2009

Session Introduction.

Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann

Proceedings of the Biocomputing 2009: Proceedings of the Pacific Symposium, 2009

2008

MutDB: update on development of tools for the biochemical analysis of genetic variation.

Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy W. Heiland, Sean D. Mooney

Nucleic Acids Res., 2008

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

Alaa Abi-Haidar, Jasleen Kaur, Ana Gabriela Maguitman, Predrag Radivojac, Andreas Rechtsteiner, Karin Verspoor, Zhiping Wang, Luis M. Rocha

CoRR, 2008

Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.

Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac

Bioinform., 2008

Session Introduction.

Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann

Proceedings of the Biocomputing 2008, 2008

Gain and loss of phosphorylation sites in human cancer.

Predrag Radivojac, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, Sean D. Mooney

Proceedings of the ECCB'08 Proceedings, 2008

2007

Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability.

Pedro Alves, Randy J. Arnold, Milos V. Novotny, Predrag Radivojac, James P. Reilly, Haixu Tang

Proceedings of the Biocomputing 2007, 2007

2006

Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes.

Chad Haynes, Christopher J. Oldfield, Fei Ji, Niels Klitgord, Michael E. Cusick, Predrag Radivojac, Vladimir N. Uversky, Marc Vidal, Lilia M. Iakoucheva

PLoS Comput. Biol., 2006

Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map.

Sourav Roy, Santiago Schnell, Predrag Radivojac

Comput. Biol. Chem., 2006

Length-dependent prediction of protein intrinsic disorder.

Kang Peng, Predrag Radivojac, Slobodan Vucetic, A. Keith Dunker, Zoran Obradovic

BMC Bioinform., 2006

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

Vladimir Vacic, Lilia M. Iakoucheva, Predrag Radivojac

Bioinform., 2006

Using Compression to Identify Classes of Inauthentic Texts.

Mehmet M. Dalkilic, Wyatt T. Clark, James C. Costello, Predrag Radivojac

Proceedings of the Sixth SIAM International Conference on Data Mining, 2006

Session Introduction.

Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac

Proceedings of the Biocomputing 2006, 2006

A Machine Learning Approach to Predicting Peptide Fragmentation Spectra.

Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, Predrag Radivojac

Proceedings of the Biocomputing 2006, 2006

A computational approach toward label-free protein quantification using predicted peptide detectability.

Haixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer, Milos V. Novotny, James P. Reilly, Predrag Radivojac

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information.

Kang Peng, Slobodan Vucetic, Predrag Radivojac, Celeste J. Brown, A. Keith Dunker, Zoran Obradovic

J. Bioinform. Comput. Biol., 2005

DisProt: a database of protein disorder.

Slobodan Vucetic, Zoran Obradovic, Vladimir Vacic, Predrag Radivojac, Kang Peng, Lilia M. Iakoucheva, Marc S. Cortese, J. David Lawson, Celeste J. Brown, Jason G. Sikes, Crystal D. Newton, A. Keith Dunker

Bioinform., 2005

Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation.

Kenneth Daily, Predrag Radivojac, A. Keith Dunker

Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2005

2004

Classification and knowledge discovery in protein databases.

Predrag Radivojac, Nitesh V. Chawla, A. Keith Dunker, Zoran Obradovic

J. Biomed. Informatics, 2004

Feature Selection Filters Based on the Permutation Test.

Predrag Radivojac, Zoran Obradovic, A. Keith Dunker, Slobodan Vucetic

Proceedings of the Machine Learning: ECML 2004, 2004

2003

Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions.

Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

2002

Improving Sequence Alignments For Intrinsically Disordered Proteins.

Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002