Predrag Radivojac

This page lists three papers in some of the research areas we are interested in. A complete list of publications is available on the Publications page.

Learning from Biased Data

• Zeiberg D, Jain S, Radivojac P. Leveraging structure for improved classification of grouped biased data. AAAI Conference on Artificial Intelligence, AAAI 2023, pp. 11113-11120, Washington, DC, U.S.A., February 2023. PDF Supp AAAI 
• De Paolis Kaluza MC, Jain S, Radivojac P. An approach to identifying and quantifying bias in biomedical data. Pac. Symp. Biocomput. (2023) 28: 311-322. PDF PubMed 
• Jain S, Delano JD, Sharma H, Radivojac P. Class prior estimation with biased positives and unlabeled examples. AAAI Conference on Artificial Intelligence, AAAI 2020, pp. 4255-4263, New York, New York, U.S.A., February 2020. PDF AAAI

Semi-Supervised Learning

• Zeiberg D, Jain S, Radivojac P. Fast nonparametric estimation of class proportions in the positive-unlabeled classification setting. AAAI Conference on Artificial Intelligence, AAAI 2020, pp. 6729-6736, New York, New York, U.S.A., February 2020. PDF AAAI
• Jain S, White M, Radivojac P. Recovering true classifier performance in positive-unlabeled learning. AAAI Conference on Artificial Intelligence, AAAI 2017, pp. 2066-2072, San Francisco, California, U.S.A., February 2017. PDF Supp AAAI
• Jain S, White M, Radivojac P. Estimating the class prior and posterior from noisy positives and unlabeled data. Advances in Neural Information Processing Systems, NIPS 2016, pp. 2693-2701, Barcelona, Spain, December 2016. PDF

Evaluation of Machine Learning Algorithms

• Ramola R, Jain S, Radivojac P. Estimating classification accuracy in positive-unlabeled learning: characterization and correction strategies. Pac. Symp. Biocomput. (2019) 24: 124-135. PDF PubMed
• Jiang Y, Clark WT, Friedberg I, Radivojac P. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics (2014) 30(17): i609-i616. PDF Supp PubMed
• Clark WT, Radivojac P. Information-theoretic evaluation of predicted ontological annotations. Bioinformatics (2013) 29(13): i53-i61. PDF Supp Code/Data PubMed
• Ian Lawson Van Toch Memorial Award at ISMB/ECCB 2013.

General Machine Learning

• Yang R, Jiang Y, Mathews S, Housworth EA, Hahn MW, Radivojac P. A new class of metrics for learning on real-valued and structured data. Data Min. Knowl. Disc. (2019) 33(4): 995-1016. PDF Supp SupTable
• Natarajan S, Das S, Ramanan N, Kunapuli G, Radivojac P. On whom should I perform this lab test next? An active feature elicitation approach. International Joint Conference on Artificial Intelligence, IJCAI 2018, pp. 3498-3505, Stockholm, Sweden, July 2018. PDF
• Yamada M, Tang J, Lugo-Martinez J, Hodzic E, Shrestha R, Saha A, Ouyang H, Yin D, Mamitsuka H, Sahinalp C, Radivojac P, Menczer F, Chang Y. Ultra high-dimensional nonlinear feature selection for big biological data. IEEE Trans. Knowl. Data Eng. (2018) 30(7): 1352-1365. PDF IEEE-Xplore

Graphs and Hypergraphs

• Lugo-Martinez J, Zeiberg D, Gaudelet T, Malod-Dognin N, Przulj N, Radivojac P. Classification in biological networks with hypergraphlet kernels. Bioinformatics (2021) 37(7): 1000-1007. PDF PubMed
• Peng Y, Jiang Y, Radivojac P. Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies. Bioinformatics (2018) 34(13): i313-i322. PDF Supp Code PubMed  
• Lugo-Martinez J, Radivojac P. Generalized graphlet kernels for probabilistic inference in sparse graphs. Network Science (2014) 2(2): 254-276. PDF

Genome Interpretation

• Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam HJ, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nat. Commun. (2020) 11(1): 5918. PDF PubMed Web
• Pagel KA, Antaki D, Lian A, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. PLoS Comput. Biol. (2019) 15(6): e1007112. PDF PubMed Web
• Pagel KA, Pejaver V, Lin GN, Nam H, Mort M, Cooper DN, Sebat J, Iakoucheva LM, Mooney SD, Radivojac P. When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. Bioinformatics (2017) 33(14): i389-i398. PDF PubMed Web
• Ian Lawson Van Toch Memorial Award at ISMB/ECCB 2017.

Protein Function

• Stamboulian M, Guerrero RF, Hahn MW, Radivojac P. The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinformatics (2020) 36(Supplement_1):i219-i226. PDF PubMed
• Lugo-Martinez J, Pejaver V, Pagel KA, Jain S, Mort M, Cooper DN, Mooney SD, Radivojac P. The loss and gain of functional amino acid residues is a common mechanism causing human inherited disease. PLoS Comput. Biol. (2016) 12(8): e1005091. PDF Supp Data PubMed
• Clark WT, Radivojac P. Vector quantization kernels for the classification of protein sequences and structures. Pac. Symp. Biocomput. (2014) 19: 316-327. PDF PubMed

Mass-Spectrometry Proteomics

• Peng Y, Jain S, Li YF, Gregus M, Ivanov AR, Vitek O, Radivojac P. New mixture models for decoy-free false discovery rate estimation in mass-spectrometry proteomics. Bioinformatics (2020) 36(Supplement_2): i745-i753. PDF PubMed Supp
• Ji C, Li S, Reilly JP, Radivojac P, Tang H. XLSearch: a probabilistic database search algorithm for identifying cross-linked peptides. J. Proteome Res. (2016) 15(6): 1830-1841. PDF Code PubMed
• Li YF, Arnold RJ, Radivojac P, Tang H. Protein identification problem from a Bayesian point of view. Stat. Interface. (2012) 5(1): 21-37. PDF PubMed

Post-Translational Modifications

• Pejaver V, Hsu WL, Xin F, Dunker AK, Uversky VN, Radivojac P. The structural and functional signatures of proteins that undergo multiple events of post-translational modification. Protein Sci. (2014) 23(8): 1077-1093. PDF Supp Web PubMed
• Xin F, Radivojac P. Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinformatics (2012) 28(22): 2905-2913. PDF PubMed
• Radivojac P, Baenziger PH, Kann MG, Mort ME, Hahn MW, Mooney SD. Gain and loss of phosphorylation sites in human cancer. Bioinformatics (2008) 24(16): i241-i247. PDF PubMed

Last update: July 1, 2023