Predrag Radivojac

92 papers A* 5A 1B 2C 2Misc 16Journal 57Unranked 9

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Are Your Fairness Metrics Accurate? A Semi-Supervised Approach to Improving Fairness Estimates Under Sample Selection Bias. KDD (2) M. Clara De Paolis Kaluza, Thulasi Tholeti, Yile Chen, Ricardo Baeza-Yates, Predrag Radivojac, Shantanu Jain
2025	J	`jnl`	Calibration of variant effect predictors for in-frame indels for clinical variant classification. Briefings Bioinform. Haneen Abderrazzaq, Mugdha Singh, Timothy Bergquist, Vikas Pejaver, Anne H. O'Donnell-Luria, Predrag Radivojac
2025	—	`conf`	LLMs for Causal Reasoning in Medicine? A Call for Caution. CODS Saurabh Mathur, Ranveer Singh, Michael A. Skinner, Predrag Radivojac, David M. Haas, Lakshmi Raman, Sriraam Natarajan
2024	J	`jnl`	An algorithm for decoy-free false discovery rate estimation in XL-MS/MS proteomics. Bioinform. Yisu Peng, Shantanu Jain, Predrag Radivojac
2024	J	`jnl`	Learning Tree-Structured Composition of Data Augmentation. CoRR Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang
2024	J	`jnl`	Learning Tree-Structured Composition of Data Augmentation. Trans. Mach. Learn. Res. Dongyue Li, Kailai Chen, Predrag Radivojac, Hongyang R. Zhang
2024	—	`conf`	Modeling Multiple Adverse Pregnancy Outcomes: Learning from Diverse Data Sources. AIME (1) 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
2023	J	`jnl`	Active feature elicitation: An unified framework. Frontiers Artif. Intell. Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac, Sriraam Natarajan
2023	J	`jnl`	CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. CoRR Damiano Piovesan, Davide Zago, Parnal Joshi, M. Clara De Paolis Kaluza, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C. E. Tosatto
2023	A*	`conf`	Leveraging Structure for Improved Classification of Grouped Biased Data. AAAI Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
2022	J	`jnl`	A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 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
2022	—	`conf`	Explaining Deep Tractable Probabilistic Models: The sum-product network case. PGM Athresh Karanam, Saurabh Mathur, Predrag Radivojac, David M. Haas, Kristian Kersting, Sriraam Natarajan
2022	J	`jnl`	Leveraging Structure for Improved Classification of Grouped Biased Data. CoRR Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
2021	B	`conf`	A Probabilistic Approach to Extract Qualitative Knowledge for Early Prediction of Gestational Diabetes. AIME Athresh Karanam, Alexander L. Hayes, Harsha Kokel, David M. Haas, Predrag Radivojac, Sriraam Natarajan
2021	J	`jnl`	Classification in biological networks with hypergraphlet kernels. Bioinform. Jose Lugo-Martinez, Daniel Zeiberg, Thomas Gaudelet, Noël Malod-Dognin, Natasa Przulj, Predrag Radivojac
2021	J	`jnl`	Explaining Deep Tractable Probabilistic Models: The sum-product network case. CoRR Athresh Karanam, Saurabh Mathur, Predrag Radivojac, Kristian Kersting, Sriraam Natarajan
2020	J	`jnl`	An examination of citation-based impact of the computational biology conferences. Bioinform. Jayvardan S. Naidu, Justin Delano, Scott Mathews, Predrag Radivojac
2020	A*	`conf`	Class Prior Estimation with Biased Positives and Unlabeled Examples. AAAI Shantanu Jain, Justin Delano, Himanshu Sharma, Predrag Radivojac
2020	A*	`conf`	Fast Nonparametric Estimation of Class Proportions in the Positive-Unlabeled Classification Setting. AAAI Daniel Zeiberg, Shantanu Jain, Predrag Radivojac
2020	J	`jnl`	New mixture models for decoy-free false discovery rate estimation in mass spectrometry proteomics. Bioinform. Yisu Peng, Shantanu Jain, Yong Fuga Li, Michal Gregus, Alexander R. Ivanov, Olga Vitek, Predrag Radivojac
2020	Misc	`conf`	Session Introduction. PSB Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Alexander A. Morgan, Predrag Radivojac, Nicholas P. Tatonetti
2020	Misc	`conf`	Session Introduction. PSB Lukasz A. Kurgan, Predrag Radivojac, Joel L. Sussman, A. Keith Dunker
2020	J	`jnl`	The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinform. Moses Stamboulian, Rafael F. Guerrero, Matthew W. Hahn, Predrag Radivojac
2019	J	`jnl`	A new class of metrics for learning on real-valued and structured data. Data Min. Knowl. Discov. Ruiyu Yang, Yuxiang Jiang, Scott Mathews, Elizabeth A. Housworth, Matthew W. Hahn, Predrag Radivojac
2019	Misc	`conf`	Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. PSB Rashika Ramola, Shantanu Jain, Predrag Radivojac
2019	J	`jnl`	ISMB/ECCB 2019 Proceedings. Bioinform. Yana Bromberg, Nadia El-Mabrouk, Predrag Radivojac
2019	J	`jnl`	Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput. Biol. Kymberleigh A. Pagel, Danny Antaki, Aojie Lian, Matthew E. Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
2019	Misc	`conf`	Session introduction. PSB Steven E. Brenner, Martha L. Bulyk, Dana C. Crawford, Jill P. Mesirov, Alexander A. Morgan, Predrag Radivojac
2018	J	`jnl`	Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. Bioinform. Yisu Peng, Yuxiang Jiang, Predrag Radivojac
2018	J	`jnl`	ISMB 2018 proceedings. Bioinform. Yana Bromberg, Predrag Radivojac
2018	A*	`conf`	On Whom Should I Perform this Lab Test Next? An Active Feature Elicitation Approach. IJCAI Sriraam Natarajan, Srijita Das, Nandini Ramanan, Gautam Kunapuli, Predrag Radivojac
2018	J	`jnl`	Proteomic Evidence for In-Frame and Out-of-Frame Alternatively Spliced Isoforms in Human and Mouse. IEEE ACM Trans. Comput. Biol. Bioinform. Rodrigo F. Ramalho, Sujun Li, Predrag Radivojac, Matthew W. Hahn
2018	J	`jnl`	Ultra High-Dimensional Nonlinear Feature Selection for Big Biological Data. IEEE Trans. Knowl. Data Eng. 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
2017	J	`jnl`	Classification in biological networks with hypergraphlet kernels. CoRR Jose Lugo-Martinez, Predrag Radivojac
2017	J	`jnl`	Enumerating consistent subgraphs of directed acyclic graphs: an insight into biomedical ontologies. CoRR Yisu Peng, Yuxiang Jiang, Predrag Radivojac
2017	A*	`conf`	Recovering True Classifier Performance in Positive-Unlabeled Learning. AAAI Shantanu Jain, Martha White, Predrag Radivojac
2017	J	`jnl`	Recovering True Classifier Performance in Positive-Unlabeled Learning. CoRR Shantanu Jain, Martha White, Predrag Radivojac
2017	Misc	`conf`	Session Introduction. PSB Yana Bromberg, Matthew W. Hahn, Predrag Radivojac
2017	J	`jnl`	When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinform. 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
2016	J	`jnl`	Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput. Biol. 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
2016	—	`conf`	Estimating the class prior and posterior from noisy positives and unlabeled data. NIPS Shantanu Jain, Martha White, Predrag Radivojac
2016	J	`jnl`	Estimating the class prior and posterior from noisy positives and unlabeled data. CoRR Shantanu Jain, Martha White, Predrag Radivojac
2016	J	`jnl`	Nonparametric semi-supervised learning of class proportions. CoRR Shantanu Jain, Martha White, Michael W. Trosset, Predrag Radivojac
2016	J	`jnl`	The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease. PLoS Comput. Biol. Jose Lugo-Martinez, Vikas Pejaver, Kymberleigh A. Pagel, Shantanu Jain, Matthew E. Mort, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2015	J	`jnl`	A link graph-based approach to identify forum spam. Secur. Commun. Networks Youngsang Shin, Steven A. Myers, Minaxi Gupta, Predrag Radivojac
2015	—	`conf`	A maximum-likelihood approach to absolute protein quantification in mass spectrometry. BCB Chao Ji, Yong Fuga Li, Earl P. Bellinger, Sujun Li, Randy J. Arnold, Predrag Radivojac, Haixu Tang
2015	J	`jnl`	Ten Simple Rules for a Community Computational Challenge. PLoS Comput. Biol. Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
2015	Misc	`conf`	Training the Next Generation of Quantitative Biologists in the Era of Big Data. Pacific Symposium on Biocomputing 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
2014	J	`jnl`	Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLoS Comput. Biol. Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider
2014	J	`jnl`	Generalized graphlet kernels for probabilistic inference in sparse graphs. Netw. Sci. Jose Lugo-Martinez, Predrag Radivojac
2014	J	`jnl`	The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinform. Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg
2014	J	`jnl`	The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinform. Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac
2014	Misc	`conf`	Vector Quantization Kernels for the Classification of Protein Sequences and Structures. Pacific Symposium on Biocomputing Wyatt T. Clark, Predrag Radivojac
2013	J	`jnl`	ISCB Computational Biology Wikipedia Competition. PLoS Comput. Biol. Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff MacIntyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost
2013	—	`conf`	Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. BCB Sujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac
2013	J	`jnl`	Information-theoretic evaluation of predicted ontological annotations. Bioinform. Wyatt T. Clark, Predrag Radivojac
2012	J	`jnl`	An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors. PLoS Comput. Biol. Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund
2012	J	`jnl`	Computational approaches to protein inference in shotgun proteomics. BMC Bioinform. Yong Fuga Li, Predrag Radivojac
2012	J	`jnl`	Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinform. Fuxiao Xin, Predrag Radivojac
2011	J	`jnl`	Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals. PLoS Comput. Biol. Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn
2010	J	`jnl`	Graphlet Kernels for Prediction of Functional Residues in Protein Structures. J. Comput. Biol. Vladimir Vacic, Lilia M. Iakoucheva, Stefano Lonardi, Predrag Radivojac
2010	Misc	`conf`	Loss of Post-Translational Modification Sites in Disease. Pacific Symposium on Biocomputing Shuyan Li, Lilia M. Iakoucheva, Sean D. Mooney, Predrag Radivojac
2010	J	`jnl`	Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. Bioinform. Fuxiao Xin, Steven A. Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2010	J	`jnl`	Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. BMC Bioinform. Fuxiao Xin, Steven A. Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2009	J	`jnl`	A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. J. Comput. Biol. Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang
2009	J	`jnl`	Analysis of AML genes in dysregulated molecular networks. BMC Bioinform. Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee
2009	J	`jnl`	Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinform. Biao Li, Vidhya G. Krishnan, Matthew E. Mort, Fuxiao Xin, Kishore K. Kamati, David N. Cooper, Sean D. Mooney, Predrag Radivojac
2009	J	`jnl`	Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins. PLoS Comput. Biol. Amrita Mohan, Vladimir N. Uversky, Predrag Radivojac
2009	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Atul J. Butte, Maricel G. Kann
2008	B	`conf`	A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. RECOMB Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang
2008	J	`jnl`	Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinform. Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac
2008	C	`conf`	Gain and loss of phosphorylation sites in human cancer. ECCB Predrag Radivojac, Peter H. Baenziger, Maricel G. Kann, Matthew E. Mort, Matthew W. Hahn, Sean D. Mooney
2008	J	`jnl`	MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. Arti Singh, Adebayo Olowoyeye, Peter H. Baenziger, Jessica Dantzer, Maricel G. Kann, Predrag Radivojac, Randy W. Heiland, Sean D. Mooney
2008	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann
2008	J	`jnl`	Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks CoRR Alaa Abi-Haidar, Jasleen Kaur, Ana Gabriela Maguitman, Predrag Radivojac, Andreas Rechtsteiner, Karin Verspoor, Zhiping Wang, Luis M. Rocha
2007	Misc	`conf`	Advancement in Protein Inference from Shotgun Proteomics Using Peptide Detectability. Pacific Symposium on Biocomputing Pedro Alves, Randy J. Arnold, Milos V. Novotny, Predrag Radivojac, James P. Reilly, Haixu Tang
2007	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
2006	Misc	`conf`	A Machine Learning Approach to Predicting Peptide Fragmentation Spectra. Pacific Symposium on Biocomputing Randy J. Arnold, Narmada Jayasankar, Divya Aggarwal, Haixu Tang, Predrag Radivojac
2006	—	`conf`	A computational approach toward label-free protein quantification using predicted peptide detectability. ISMB (Supplement of Bioinformatics) Haixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer, Milos V. Novotny, James P. Reilly, Predrag Radivojac
2006	J	`jnl`	Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes. PLoS Comput. Biol. Chad Haynes, Christopher J. Oldfield, Fei Ji, Niels Klitgord, Michael E. Cusick, Predrag Radivojac, Vladimir N. Uversky, Marc Vidal, Lilia M. Iakoucheva
2006	J	`jnl`	Length-dependent prediction of protein intrinsic disorder. BMC Bioinform. Kang Peng, Predrag Radivojac, Slobodan Vucetic, A. Keith Dunker, Zoran Obradovic
2006	Misc	`conf`	Session Introduction. Pacific Symposium on Biocomputing Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
2006	J	`jnl`	Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinform. Vladimir Vacic, Lilia M. Iakoucheva, Predrag Radivojac
2006	J	`jnl`	Unraveling the nature of the segmentation clock: Intrinsic disorder of clock proteins and their interaction map. Comput. Biol. Chem. Sourav Roy, Santiago Schnell, Predrag Radivojac
2006	A	`conf`	Using Compression to Identify Classes of Inauthentic Texts. SDM Mehmet M. Dalkilic, Wyatt T. Clark, James C. Costello, Predrag Radivojac
2005	J	`jnl`	DisProt: a database of protein disorder. Bioinform. 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
2005	C	`conf`	Intrinsic Disorder and Protein modifications: Building an SVM Predictor for Methylation. CIBCB Kenneth Daily, Predrag Radivojac, A. Keith Dunker
2005	J	`jnl`	Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information. J. Bioinform. Comput. Biol. Kang Peng, Slobodan Vucetic, Predrag Radivojac, Celeste J. Brown, A. Keith Dunker, Zoran Obradovic
2004	J	`jnl`	Classification and knowledge discovery in protein databases. J. Biomed. Informatics Predrag Radivojac, Nitesh V. Chawla, A. Keith Dunker, Zoran Obradovic
2004	—	`conf`	Feature Selection Filters Based on the Permutation Test. ECML Predrag Radivojac, Zoran Obradovic, A. Keith Dunker, Slobodan Vucetic
2003	Misc	`conf`	Prediction of Boundaries Between Intrinsically Ordered and Disordered Protein Regions. Pacific Symposium on Biocomputing Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker
2002	Misc	`conf`	Improving Sequence Alignments For Intrinsically Disordered Proteins. Pacific Symposium on Biocomputing Predrag Radivojac, Zoran Obradovic, Celeste J. Brown, A. Keith Dunker