Publications
DECILE research team members indicated in boldface
2025
FairPO: Fair Preference Optimization for Multi-Label Learning
Soumen Kumar Mondal, Akshit Varmora, Prateek Chanda, Ganesh Ramakrishnan
In NeurIPS OPT 2025 Workshop in the Proceedings of The Thirty-ninth Annual Conference on Neural Information Processing Systems (NeurIPS 2025)
Unified Wisdom: Harnessing Collaborative Learning to Improve Efficacy of Knowledge Distillation
Durga S, Atharva Abhijit Tambat, Ganesh Ramakrishnan, Pradeep Shenoy
In Proceedings of The Transactions of Machine Learning Research (TMLR 2025)
Bandit Guided Submodular Curriculum for Adaptive Subset Selection
Prateek Chanda, Prayas Agrawal, Saral Sureka, Lokesh Reddy Polu, Atharv Kshirsagar, Ganesh Ramakrishnan
In Proceedings of The The Thirty-Ninth Annual Conference on Neural Information Processing Systems 2025.
2024
Bayesian Coreset Optimization for Personalized Federated Learning
Prateek Chanda, Shrey Modi, Ganesh Ramakrishnan
International Conference on Learning Representations (ICLR) 2024
SMART: Submodular Data Mixture Strategy for Instruction Tuning
H S V N S Kowndinya Renduchintala, Sumit Bhatia, Ganesh Ramakrishnan
In Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024 - Findings)
DictDis: Dictionary Constrained Disambiguation for Improved NMT
Ayush Maheshwari, Preethi Jyothi, Ganesh Ramakrishnan
In Proceedings of The 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024 - Findings)
Speeding up NAS with Adaptive Subset Selection
Vishak Prasad C, Colin White, Paarth Jain, Sibasis Nayak, Ganesh Ramakrishnan
In Proceedings of The 2024 International Conference on Automated Machine Learning (AutoML 2024)
2023
AUTOMATA: Gradient Based Data Subset Selection for Compute-Efficient Hyper-parameter Tuning
KrishnaTeja Killamsetty, Guttu Sai Abhishek, Aakriti, Ganesh Ramakrishnan, Alexandre V. Evfimievski, Lucian Popa, Rishabh K. Iyer
In Proceedings of the Thirty-sixth Conference on Neural Information Processing Systems (NeurIPS 2022)
INGENIOUS: Using Informative Data Subsets for Efficient Pre-Training of Large Language Models
HSVNS Kowndinya Renduchintala, Krishnateja Killamsetty, Sumit Bhatia, Milan Aggarwal, Ganesh Ramakrishnan, Rishabh Iyer, Balaji Krishnamurthy
Accepted paper at the 2023 Conference on Empirical Methods in Natural Language Processing, EMNLP 2023, (Long paper, Findings Track)
2021
GLISTER: Generalization based Data Subset Selection for Efficient and Robust Learning
Krishnateja Killamsetty, Durga Sivasubramanian, Ganesh Ramakrishnan, Rishabh Iyer
35th AAAI Conference on Artificial Intelligence, AAAI 2021
2020
Data Programming using Continuous and Quality-Guided Labeling Function
Oishik Chatterjee, Ganesh Ramakrishnan, Sunita Sarawagi
In Proceedings of The Thirty-Fourth AAAI Conference on Artificial Intelligence (AAAI 2020), New York, USA.
Coresets for Robust Training of Deep Neural Networks against Noisy Labels
Baharan Mirzasoleiman, Kaidi Cao, Jure Leskovec
In Proc. Advances in Neural Information Processing Systems (NeurIPS), 2020
Coresets for Data-efficient Training of Machine Learning Models
Baharan Mirzasoleiman, Jeff Bilmes, Jure Leskovec
International Conference on Machine Learning (ICML), July 2020
2019
Vishal Kaushal, Rishabh Iyer, Suraj Kothiwade, Rohan Mahadev, Khoshrav Doctor, Ganesh Ramakrishnan
7th IEEE Winter Conference on Applications of Computer Vision (WACV), 2019 Hawaii, USA
2015
Submodularity in data subset selection and active learning
Kai Wei, Rishabh Iyer, Jeff Bilmes
International Conference on Machine Learning (ICML) 2015
2014
Fast multi-stage submodular maximization
Kai Wei, Rishabh K. Iyer, Jeff A. Bilmes
International Conference on Machine Learning (ICML 2014)
Submodular subset selection for large-scale speech training data
Wei, Kai, et al
2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), IEEE, 2014
For a complete list of DECILE publications, please visit:
Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma
Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Blood (2023)
2022
Concerning data inconsistencies in Burkitt lymphoma genome study
Christopher K Rushton, Kostiantyn Dreval, Ryan D Morin. Blood (Epub 2022)
Minimal Information for Reporting a Genomics Experiment
Kostiantyn Dreval, Paul Boutros, Ryan D. Morin. Blood (2022)
Shared and distinct genetic features in human and canine B-cell lymphomas
Krysta M Coyle, Tiana Hillman, Matthew Cheung, Bruno M. Grande, Kevin R. Bushell, Sarah E. Arthur, Miguel Alcaide, Nicole Thomas, Kostiantyn Dreval, Stephanie Wong, Krishanna Campbell, Ryan D. Morin. Blood Advances (2022)
2021
Malgorzata Nowicka, Laura K. Hilton, Margaret Ashton-Key, Chantal E. Hargreaves, Chern Lee, Russell Foxall, Matthew J. Carter, Stephen A. Beers, Kathleen N. Potter, Christopher R. Bolen, Christian Klein, Andrea Knapp, Farheen Mir, Matthew Rose-Zerilli, Cathy Burton, Wolfram Klapper, David W. Scott, Laurie H. Sehn, Umberto Vitolo, Maurizio Martelli, Marek Trneny, Christopher K. Rushton, Graham W. Slack, Pedro Farinha, Jonathan C. Strefford, Mikkel Z. Oestergaard, Ryan D. Morin, Mark S. Cragg. Blood Advances (2021)
Molecular profiling in diffuse large B-cell lymphoma: why so many types of subtypes?
Ryan D. Morin, Sarah E. Arthur and Daniel Hodson. Br J Haem (2021)
Treating lymphoma is now a bit EZ-er
Ryan D. Morin, Sarah E. Arthur and Sarit Assouline. Blood Advances (2021)
Sarah E Arthur, Jie Gao, Shannon Healy, Christopher K Rushton, Nicole Thomas, Laura K Hilton, Kostiantyn Dreval, Jeffrey Tang, Miguel Alcaide, Razvan Cojocaru, Anja Mottok, Adele Telenius, Peter Unrau, Wyndham H Wilson, Louis M Staudt, David W Scott, Daniel J Hodson, Christian Steidl, Ryan D Morin BioRxiv (2021)
2020
Aixiang Jiang , Laura K. Hilton , Jeffrey Tang , Christopher K. Rushton , Bruno M. Grande, David W. Scott, Ryan D. Morin. Blood Cancer Discovery (2020)
Miguel Alcaide, Matthew Cheung, Jack Hillman, S. Rod Rassekh, Rebecca J. Deyell, Gerald Batist, Aly Karsan, Alexander W. Wyatt, Nathalie Johnson, David W. Scott & Ryan D. Morin. Scientific Reports 10, Article number: 12564 (2020).
Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma
Christopher K Rushton, Sarah E Arthur, Miguel Alcaide, Matthew Cheung, Aixiang Jiang, Krysta M Coyle, Kirstie L S Cleary, Nicole Thomas, Laura K Hilton, Neil Michaud, Scott Daigle, Jordan Davidson, Kevin Bushell, Stephen Yu, Ryan N Rys, Michael Jain, Lois Shepherd, Marco A Marra, John Kuruvilla, Michael Crump, Koren Mann, Sarit Assouline, Joseph M Connors, Christian Steidl, Mark S Cragg, David W Scott, Nathalie A Johnson, Ryan D Morin. Blood Adv (2020) 4 (13): 2886–2898.
Coding and non-coding drivers of mantle cell lymphoma identified through exome and genome sequencing
Prasath Pararajalingam, Krysta M. Coyle, Sarah E. Arthur, Nicole Thomas, Miguel Alcaide, Barbara Meissner, Merrill Boyle, Bruno M. Grande, Graham Slack, Andrew J. Mungall, Randy D. Gascoyne, Christian Steidl, Joseph Connors, Diego Villa, Marco A. Marra, Nathalie Johnson, David W. Scott, and Ryan D. Morin. Blood. 2020 Jul 30;136(5):572-584. doi: 10.1182/blood.2019002385.
DLBCL subclassification: divide and conquer?
Ryan D. Morin and David W. Scott. Blood (2020). May 14;135(20):1722-1724. doi: 10.1182/blood.2020005335.
2019
Hilton LK, Tang J, Ben-Neriah S, Alcaide M, Jiang A, Grande BM, Rushton CK, Boyle M, Meissner B, Scott DW, Morin RD. Blood. 2019 Oct 31;134(18):1528-1532.
Miguel Alcaide, Christopher Rushton, Ryan D. Morin. Methods Molecular Biology. 2019;1956:383-435.
Bruno M. Grande*, Daniela S. Gerhard*, Aixiang Jiang, Nicholas B. Griner, Jeremy S. Abramson, Thomas B. Alexander, Hilary Allen, Leona W. Ayers, Jeffrey M. Bethony, Kishor Bhatia, Jay Bowen, Corey Casper, John Kim Choi, Luka Culibrk, Tanja M. Davidsen, Maureen A. Dyer, Julie M. Gastier-Foster, Patee Gesuwan, Timothy C. Greiner, Thomas G. Gross, Benjamin Hanf, Nancy Lee Harris, Yiwen He, John D. Irvin, Elaine S. Jaffe, Steven J.M. Jones, Patrick Kerchan, Nicole Knoetze, Fabio E. Leal, Tara M. Lichtenberg, Yussanne Ma, Jean Paul Martin, Marie-Reine Martin, Sam M. Mbulaiteye, Charles G. Mullighan, Andrew J. Mungall, Constance Namirembe, Karen Novik, Ariela Noy, Martin D. Ogwang, Abraham Omoding, Jackson Orem, Steven J. Reynolds, Christopher K. Rushton, John T. Sandlund, Roland Schmitz, Cynthia Taylor, Wyndham H. Wilson, George W. Wright, Eric Y. Zhao, Marco A. Marra, Ryan D. Morin*, and Louis M. Staudt*. Blood, 133(12):1313–1324, 2019.
A Novel Multiplex droplet digital PCR Assay to Identify and Quantify KRAS Mutations in Clinical Specimens.
Alcaide M*, Cheung M*, Bushell K*, Arthur S, Wong HL, Karasinska J, Renouf D, Schaeffer DF, McNamara S, Couetoux du Tertre M, Batist G, Kennecke HF, Karsan K and Morin RD. Journal of Molecular Diagnostics. J Mol Diagn. 2019 Mar;21(2):214-227.
2018
The Double-Hit Gene Expression Signature Defines a Clinically and Biologically Distinct Subgroup within GCB-DLBCL
Ennishi D*, Jiang A*, Boyle M, Collinge B, Grande BM, Ben-Neriah S, Rushton C, Tang J, Thomas N, Slack GW, Farinha P, Takata K, Miyata-Takata T, Craig J, Mottok A, Meissner B, Saberi S, Bashashati A, Villa D, Savage KJ, Sehn LH, Kridel R, Mungall AJ, Marra MA, Shah SP, Steidl C, Connors JM, Gascoyne RD, Morin RD*, and Scott DW*.
Journal of Clinical Oncology. December 3, 2018.
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.
Arthur SE*, Jiang A*, Grande BM*, Alcaide M, Cojocaru R, Rushton CK, Mottok A, Hilton LK, Lat PK, Zhao EY, Culibrk L, Ennishi D, Jessa S, Chong L, Thomas N, Pararajalingam P, Meissner B, Boyle M, Davidson J, Bushell KR, Lai D, Farinha P, Slack GW, Morin GB, Shah S, Sen D, Jones SJM, Mungall AJ, Gascoyne RD, Audas TE, Unrau P, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD.
Nat Commun. 2018 Oct 1;9(1):4001. doi: 10.1038/s41467-018-06354-3.
Novel Multiplexing Strategies for Quantification of Rare Alleles Using ddPCR.
Alcaide M, Morin RD.
Methods Mol Biol. 2018;1768:275-301. doi: 10.1007/978-1-4939-7778-9_16.
The genomic landscape of two Burkitt lymphoma cases and derived cell lines: comparison between primary and relapse samples.
Wever CM, Geoffrion D, Grande BM, Yu S, Alcaide M, Lemaire M, Riazalhosseini Y, Hébert J, Gavino C, Vinh DC, Petrogiannis-Haliotis T, Dmitrienko S, Mann KK, Morin RD*, Johnson NA*.
Leuk Lymphoma. 2018 Sep;59(9):2159-2174. doi: 10.1080/10428194.2017.1413186.
2017
Targeted Error-Suppressed Detection of Circulating Paternal DNA to Establish a Diagnosis of Gestational Trophoblastic Neoplasm
Jean-Michel Lavoie, Miguel Alcaide, Rosemary A. Fisher, Michael J. Seckl, Ryan Morin, and Anna V. Tinker
JCO Precision Oncology 2017 :1, 1-6
Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits.
Alcaide M, Yu S, Davidson J, Albuquerque M, Bushell K, Fornika D, Arthur S, Grande BM, McNamara S, Tertre MCD, Batist G, Huntsman DG, Cavallone L, Aguilar A, Basik M, Johnson NA, Deyell RJ, Rassekh SR, Morin RD.
Sci Rep. 2017 Sep 5;7(1):10574. doi: 10.1038/s41598-017-10269-2.
Investigating the Genetic Causes of Sudden Unexpected Death in Children Through Targeted Next-Generation Sequencing Analysis.
Dewar LJ*, Alcaide M*, Fornika D, D’Amato L, Shafaatalab S, Stevens CM, Balachandra T, Phillips SM, Sanatani S, Morin RD*, Tibbits GF*.
Circ Cardiovasc Genet. 2017 Aug;10(4). pii: e001738. doi: 10.1161/CIRCGENETICS.116.001738.
Kronos: a workflow assembler for genome analytics and informatics.
Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP.
Gigascience. 2017 Jul 1;6(7):1-10. doi: 10.1093/gigascience/gix042.
Enhancing knowledge discovery from cancer genomics data with Galaxy.
Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD.
Gigascience. 2017 May 1;6(5):1-13. doi: 10.1093/gigascience/gix015.
2016
Multiplex Droplet Digital PCR Quantification of Recurrent Somatic Mutations in Diffuse Large B-Cell and Follicular Lymphoma.
Alcaide M, Yu S, Bushell K, Fornika D, Nielsen JS, Nelson BH, Mann KK, Assouline S, Johnson NA, Morin RD.
Clin Chem. 2016 Sep;62(9):1238-47. doi: 10.1373/clinchem.2016.255315.
Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies.
Volik S, Alcaide M, Morin RD, Collins C.
Mol Cancer Res. 2016 Oct;14(10):898-908.
Phase 2 study of panobinostat with or without rituximab in relapsed diffuse large B-cell lymphoma.
Assouline SE, Nielsen TH, Yu S, Alcaide M, Chong L, MacDonald D, Tosikyan A, Kukreti V, Kezouh A, Petrogiannis-Haliotis T, Albuquerque M, Fornika D, Alamouti S, Froment R, Greenwood CM, Oros KK, Camglioglu E, Sharma A, Christodoulopoulos R, Rousseau C, Johnson N, Crump M, Morin RD*, Mann KK*.
Blood. 2016 Jul 14;128(2):185-94. doi: 10.1182/blood-2016-02-699520.
Genetic Landscapes of Relapsed and Refractory Diffuse Large B-Cell Lymphomas.
Morin RD, Assouline S, Alcaide M, Mohajeri A, Johnston RL, Chong L, Grewal J, Yu S, Fornika D, Bushell K, Nielsen TH, Petrogiannis-Haliotis T, Crump M, Tosikyan A, Grande BM, MacDonald D, Rousseau C, Bayat M, Sesques P, Froment R, Albuquerque M, Monczak Y, Oros KK, Greenwood C, Riazalhosseini Y, Arseneault M, Camlioglu E, Constantin A, Pan-Hammarstrom Q, Peng R, Mann KK, Johnson NA.
Clin Cancer Res. 2016 May 1;22(9):2290-300. doi: 10.1158/1078-0432.CCR-15-2123.
2015
Genetic inactivation of TRAF3 in canine and human B-cell lymphoma.
Bushell KR, Kim Y, Chan FC, Ben-Neriah S, Jenks A, Alcaide M, Fornika D, Grande BM, Arthur S, Gascoyne RD, Steidl C, Morin RD.
Blood. 2015 Feb 5;125(6):999-1005. doi: 10.1182/blood-2014-10-602714.