Homepage of Ilya Safro

ML = Machine Learning/Data Mining, GA = Graph Algorithms/Network Science, NLP = Natural Language Processing/Text Mining, MS = Multiscale Methods, QC = Quantum Computing, CSC = Combinatorial Scientific Computing, BIO = Applications in Computational Biology/Medicine, ENG = Applications in Computational Engineering

(QC) Boris Tsvelikhoskiy, Ilya Safro, Yuri Alexeev "Equivariant QAOA and the Duel of the Mixers", submitted, 2024
(QC,GA) Jose Falla, Quinn Langfitt, Yuri Alexeev, Ilya Safro "Graph Representation Learning for Parameter Transferability in Quantum Approximate Optimization Algorithm", submitted, preprint at https://arxiv.org/abs/2401.06655
(BIO,NLP) Tammy H. Cummings, Joseph Magagnoli, Aliaksandra Sikirzhytskaya, Ilya Tyagin, Ilya Safro, Michael D. Wyatt, Michael Shtutman, S. Scott Sutton "Exposure to angiotensin-converting enzyme inhibitors that cross the blood-brain barrier and the risk of dementia among patients with human immunodeficiency virus", submitted, preprint at https://doi.org/10.1101/2024.01.16.24301275, 2024
(BIO,NLP) Ilya Tyagin, Ilya Safro "Dyport: Dynamic Importance-based Hypothesis Generation Benchmarking Technique", submitted, preprint at https://arxiv.org/pdf/2312.03303.pdf, 2024
(QC) Quinn Langfitt, Jose Falla, Ilya Safro, Yuri Alexeev "Parameter Transferability in QAOA Under Noisy Conditions", IEEE High-Performance and Extreme Computing (HPEC), https://doi.org/10.1109/QCE57702.2023.10252, 2023
(GA) Deepak Ajwani, Rob H. Bisseling, Katrin Casel, Ümit V. Çatalyürek, Cédric Chevalier, Florian Chudigiewitsch, Marcelo Fonseca Faraj, Michael Fellows, Lars Gottesbüren, Tobias Heuer, George Karypis, Kamer Kaya, Jakub Lacki, Johannes Langguth, Xiaoye Sherry Li, Ruben Mayer, Johannes Meintrup, Yosuke Mizutani, François Pellegrini, Fabrizio Petrini, Frances Rosamond, Ilya Safro, Sebastian Schlag, Christian Schulz, Roohani Sharma, Darren Strash, Blair D. Sullivan, Bora Uçar, Albert-Jan Yzelman "Open Problems in (Hyper)Graph Decomposition", technical report, https://arxiv.org/pdf/2310.11812.pdf, 2023
(QC) Boris Tsvelikhoskiy, Ilya Safro, Yuri Alexeev "Of representation theory and quantum approximate optimization algorithm", submitted, preprint at https://arxiv.org/pdf/2309.13787.pdf, 2023
(QC,ML) Ankit Kulshrestha, Danylo Lykov, Ilya Safro, Yuri Alexeev "QArchSearch: A Scalable Quantum Architecture Search Package", accepted in 4th International Workshop on Quantum Computing Software in conjunction with Supercomputing, 2023
(GA,QC) Anthony Angone, Xiaoyuan Liu, Ruslan Shaydulin, Ilya Safro "Hybrid Quantum-Classical Multilevel Approach for Maximum Cuts on Graphs", accepted at IEEE High-Performance and Extreme Computing (HPEC), preprint at https://arxiv.org/pdf/2309.08815.pdf, 2023
(GA) Krish Matta, Xiaoyuan Liu, Ilya Safro "Decomposition Based Refinement for the Network Interdiction Problem", accepted at IEEE High-Performance and Extreme Computing (HPEC), preprint at https://arxiv.org/abs/2307.07577, 2023
(QC) Dylan Herman, Cody Googin, Xiaoyuan Liu, Yue Sun, Alexey Galda, Ilya Safro, Marco Pistoia, Yuri Alexeev "Quantum Computing for Finance", accepted in Nature Reviews Physics, https://www.nature.com/articles/s42254-023-00603-1, 2023
(QC,ML) Ankit Kulshrestha, Xiaoyuan Liu, Hayato Ushijima-Mwesigwa, Bao Bach, Ilya Safro "QAdaPrune: Adaptive Parameter Pruning For Training Variational Quantum Circuit", submitted (will be available soon), 2023
(QC,ML) Ankit Kulshrestha, Xiaoyuan Liu, Hayato Ushijima-Mwesigwa, Ilya Safro "Learning To Optimize Quantum Neural Network Without Gradients", accepted at IEEE Quantum Computing and Engineering (QCE), preprint at https://arxiv.org/pdf/2304.07442.pdf, 2023
(QC,GA) Alexey Galda, Eesh Gupta, Jose Falla, Xiaoyuan Liu, Danylo Lykov, Yuri Alexeev, Ilya Safro "Similarity-Based Parameter Transferability in the Quantum Approximate Optimization Algorithm", accepted in Frontiers in Quantum Science and Technology (section Quantum Information Theory), DOI: 10.3389/frqst.2023.1200975, 2023
(GA,ENG) Ahmad Momeni, Varsha Chauhan, Abdulrahman Bin Mahmoud, Kalyan Piratla, Ilya Safro "Generation of Synthetic Water Distribution Data Using a Multi-Scale Generator-Optimizer", Journal of Pipeline Systems Engineering and Practice, vol. 14(1), https://ascelibrary.org/doi/full/10.1061/JPSEA2.PSENG-1358, 2023
(NLP,ENG) David Marasco, Ilya Tyagin, Justin Sybrandt, James H. Spencer, Ilya Safro "Literature-based Discovery for Landscape Planning", Technical Report arXiv:2306.02588 [cs.AI], https://arxiv.org/abs/2306.02588, 2023
(QC,GA) Cameron Ibrahim, Danylo Lykov, Zichang He, Yuri Alexeev, Ilya Safro "Constructing Optimal Contraction Trees for Tensor Network Quantum Circuit Simulation", IEEE High Performance Extreme Computing (HPEC) 2022 (best student paper award), pp. 1-8, preprint at https://arxiv.org/abs/2209.02895
(QC,GA,ML) Xiaoyuan Liu, Ilya Tyagin, Hayato Ushijima-Mwesigwa, Indradeep Ghosh, Ilya Safro "Towards Practical Explainability with Cluster Descriptors", Workshop on Optimization Based Techniques for Emerging Data Mining Problems (OEDM'22, ICDM workshop), preprint at https://arxiv.org/pdf/2210.10662.pdf, 2022
(QC,GA) Xiaoyuan Liu, Ruslan Shaydulin, Ilya Safro "Quantum Approximate Optimization Algorithm with Sparsified Phase Operator", IEEE Quantum Computing and Engineering (QCE), pp. 197-203, preprint at https://arxiv.org/abs/2205.00118, 2022
(ML,QC) Ankit Kulshrestha, Ilya Safro "BEINIT: Avoiding Barren Plateaus in Variational Quantum Algorithms", IEEE Quantum Computing and Engineering (QCE), pp. 197-203, preprint at https://arxiv.org/abs/2204.13751, 2022
(QC,GA) Xiaoyuan Liu, Hayato Ushijima-Mwesigwa, Indradeep Ghosh, Ilya Safro "Partitioning Dense Graphs with Hardware Accelerators", International Conference on Computational Science (ICCS), pp. 476-483, preprint at https://arxiv.org/abs/2202.09420, 2022
(QC) Dylan Herman, Cody Googin, Xiaoyuan Liu, Alexey Galda, Ilya Safro, Yue Sun, Marco Pistoia, Yuri Alexeev "A Survey of Quantum Computing for Finance", 2022, technical report preprint at https://arxiv.org/pdf/2201.02773.pdf
(NLP) Farah Alshanik, Amy Apon, Yuheng Du, Alexander Herzog, Ilya Safro "Proactive Query Expansion for Streaming Data Using External Source", IEEE International Conference on Big Data (BIGDATA), 2022 preprint at https://arxiv.org/pdf/2201.06592.pdf
(QC) Alexey Galda, Xiaoyuan Liu, Danylo Lykov, Yuri Alexeev, Ilya Safro "Transferability of optimal QAOA parameters between random graphs", IEEE International Conference on Quantum Computing and Engineering (QCE), Quantum Algorithms and Applications track, preprint at https://arxiv.org/pdf/2106.07531.pdf, 2021
(NLP,ML) Ilya Tyagin, Ankit Kulshrestha, Justin Sybrandt, Krish Matta, Michael Shtutman, Ilya Safro "Accelerating COVID-19 research with graph mining and transformer-based learning", Innovative Applications of Artificial Intelligence (AAAI/IAAI), Vol. 36(11), pp. 12673-12679, https://www.biorxiv.org/content/10.1101/2021.02.11.430789v1, 2022
(ML) Ankit Kulshrestha, Ilya Safro "CONFAIR: Configurable and Interpretable Algorithmic Fairness", submitted, preprint at https://arxiv.org/abs/2111.08878, 2021
(QC) Xiaoyuan Liu, Anthony Angone, Ruslan Shaydulin, Ilya Safro, Yuri Alexeev, Lukasz Cincio "Layer VQE: A Variational Approach for Combinatorial Optimization on Noisy Quantum Computers", IEEE Transactions on Quantum Engineering, Vol. 3, pp. 1-20, preprint at https://arxiv.org/abs/2102.05566, 2021
(QC) Ruslan Shaydulin, Stuart Hadfield, Tad Hogg, Ilya Safro "Classical symmetries and QAOA", Quantum Information Processing, Vol. 20, Num. 11, pp. 1-28, preprint at https://arxiv.org/pdf/2012.04713.pdf, 2021
(NLP, BIO) Ilya Tyagin, Ilya Safro "Interpretable Visualization of Scientific Hypotheses in Literature-based Discovery", BioCretive Workshop VII, preprint at https://www.biorxiv.org/content/10.1101/2021.10.29.466471v12021
(QC,GA) Xiaoyuan Liu, Hayato Ushijima-Mwesigwa, Avradip Mandal, Sarvagya Upadhyay, Ilya Safro, Arnab Roy "Leveraging Special-Purpose Hardware for Local Search Heuristics", Computational Optimization and Applications, vol. 82, pp. 1-29, 2022, DOI https://doi.org/10.1007/s10589-022-00354-2, preprint at https://arxiv.org/pdf/1911.09810.pdf
(NLP) Justin Sybrandt, Ilya Safro "CBAG: Conditional Biomedical Abstract Generation", PLOS One, DOI https://doi.org/10.1371/journal.pone.0253905, preprint at http://arxiv.org/pdf/2002.05637.pdf, 2021
(GA) Zirou Qiu, Ruslan Shaydulin, Xiaoyuan Liu, Yuri Alexeev, Christopher S. Henry, Ilya Safro "ELRUNA: Elimination Rule-based Network Alignment", ACM Journal of Experimental Algorithmics, vol. 26, pp. 1-32, DOI https://doi.org/10.1145/3450703, preprint at https://arxiv.org/abs/1911.05486, 2021
(GA,CSC) Hayato Ushijima-Mwesigwa, Jeffrey D. Hyman, Aric Hagberg, Ilya Safro, Satish Karra, Carl W. Gable, Gowri Srinivasan "Multilevel Graph Partitioning for Three-Dimensional Discrete Fracture Network Flow Simulations", Mathematical Geosciences, vol. 53, pp. 1699â€“1724, preprint at https://arxiv.org/abs/1902.08029, 2020
(NLP) Farah Alshanik, Amy Apon, Alexander Herzog, Ilya Safro, Justin Sybrandt "Accelerating Text Mining Using Domain-Specific Stop Word Lists", International Worshop on Big Data Reduction, IEEE Big Data 2020, preprint at https://arxiv.org/pdf/2012.02294.pdf, 2020
(ML,MS) Ehsan Sadrfaridpour, Korey Palmer, Ilya Safro "AML-SVM: Adaptive Multilevel Learning with Support Vector Machines", IEEE International Conference on Big Data (BIGDATA), pp. 788-797, preprint at https://arxiv.org/pdf/2011.02592.pdf, 2020
(QC,MS) Hayato Ushijima-Mwesigwa, Ruslan Shaydulin, Susan Mniszewski, Christian Negre, Yuri Alexeev, Ilya Safro "Multilevel Combinatorial Optimization Across Quantum Architectures", ACM Transactions on Quantum Computing, Vol. 2(1), pp. 1-29, 2021, preprint at https://arxiv.org/abs/1910.09985
(GA,ML) Fei Ding, Xiaohong Zhang, Justin Sybrandt, Ilya Safro "Unsupervised Hierarchical Graph Representation Learning by Mutual Information Maximization", ACM KDD 2020 Workshop on Mining and Learning with Graphs, preprint at https://arxiv.org/pdf/2003.08420.pdf, 2020
(GA,ML) Justin Sybrandt, Ilya Safro "FOBE and HOBE: First- and High-Order Bipartite Embeddings", ACM KDD 2020 Workshop on Mining and Learning with Graphs, preprint at https://arxiv.org/abs/1905.10953, 2020
(GA) Manuel Penschuck, Ulrik Brandes, Michael Hamann, Sebastian Lamm, Ulrich Meyer, Ilya Safro, Peter Sanders, Christian Schulz "Recent Advances in Scalable Network Generation", 2022, a chapter in "Massive graphs analytics", David Bader ed., preprint at https://arxiv.org/abs/2003.00736
(NLP,ML) Justin Sybrandt, Ilya Tyagin, Michael Shtutman, Ilya Safro "AGATHA: Automatic Graph-mining and Transformer based Hypothesis Generation Approach", 29TH ACM International Conference on Information and Knowledge Management (CIKM'20), pp. 2757-2764, preprint at http://arxiv.org/pdf/2002.05635.pdf, 2020
(ML,GA) Justin Sybrandt, Ruslan Shaydulin, Ilya Safro "Hypergraph Partitioning with Embeddings", IEEE Transactions on Knowledge and Data Engineering (TKDE), Vol. 34(6), pp. 2771-2782, DOI: 10.1109/TKDE.2020.3017120, 2020, preprint at https://arxiv.org/pdf/1909.04016.pdf
(QC,GA) Ruslan Shaydulin, Ilya Safro, Jeffrey Larson "Multistart Methods for Quantum Approximate Optimization", IEEE High Performance Extreme Computing Conference (HPEC) 2019 (best student paper award), preprint at https://arxiv.org/abs/1905.08768
(QC,GA) Ruslan Shaydulin, Hayato Ushijima-Mwesigwa, Christian F.A. Negre, Ilya Safro, Susan M. Mniszewski, Yuri Alexeev "Hybrid Approach for Solving Optimization Problems on Small Quantum Computers", IEEE Computer, vol. 52(6), pp. 18-26, download, 2019
(ML,MS) Ehsan Sadrfaridpour, Talayeh Razzaghi, Ilya Safro "Engineering fast multilevel support vector machines", Machine Learning, Vol. 108, Issue 11, 1879-1917, 2019, Springer, https://doi.org/10.1007/s10994-019-05800-7, preprint at https://arxiv.org/abs/1707.07657
(GA,MS) Varsha Chauhan, Alexander Gutfraind, Ilya Safro "Multiscale Planar Graph Generation", Applied Network Science, vol. 4, issue 1, 2019, preprint at arXiv:1802.09617
(NLP,BIO) Marina Aksenova, Justin Sybrandt, Biyun Cui, Vitali Sikirzhytski, Hao Ji, Diana Odhiambo, Mathew Lucius, Jill R. Turner, Eugenia Broude, Edsel Pea, Sofia Lizzaraga, Jun Zhu, Ilya Safro, Michael D Wyatt, Michael Shtutman "Inhibition of the DDX3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation", Journal of Neuroimmune Pharmacology, Vol. 15, Issue 2, pp. 209-223, preprint at bioRxiv https://doi.org/10.1101/591438, 2019
(GA) Hayato Ushijima-Mwesigwa, MD Zadid Khan, Mashrur A Chowdhury, Ilya Safro "Centralities for Networks with Consumable Resources", Network Science, Vol. 7, Issue 3, pp. 376-401, https://doi.org/10.1017/nws.2019.7, preprint at arXiv:1903.00642, 2019
(ML,NLP) Chris Gropp, Alexander Herzog, Ilya Safro, Paul Wilson, Amy Apon "Clustered Latent Dirichlet Allocation for Scientific Discovery", Workshop on Big Data Tools, Methods, and Use Cases for Innovative Scientific Discovery (BTSD), IEEE BigData 2019, previous version "Scalable Dynamic Topic Modeling with Clustered Latent Dirichlet Allocation (CLDA)", download, 2019
(ML,ENG) Zadid Khan, Sakib Khan, Mashrur Chowdhury, Ilya Safro, Hayato Ushijima-Mwesigwa "Wireless Charging Utility Maximization and Intersection Control Delay Minimization Framework for Electric Vehicles", Computer-Aided Civil and Infrastructure Engineering, DOI link https://doi.org/10.1111/mice.12439, download, 2019
(ML,ENG) William Locke, Justin Sybrandt, Ilya Safro, Sez Atamturktur "Using Drive-by Health Monitoring to Detect Bridge Damage Considering Environmental and Operational Effects", Journal of Sound and Vibration, Vol. 468, download preprint, 2020
(QC,GA) Ruslan Shaydulin, Haayto Ushijima-Mwesigwa, Ilya Safro, Susan Mniszewski, Yuri Alexeev "Network Community Detection On Small Quantum Computers", Advanced Quantum Technologies, vol. 2, issue 9, https://doi.org/10.1002/qute.201900029, preprint at download, 2019
(GA,CSC,MS) Ruslan Shaydulin, Jie Chen, Ilya Safro "Relaxation-Based Coarsening for Multilevel Hypergraph Partitioning", SIAM Multiscale Modeling and Simulations, vol. 17, issue 1, pp. 482-506, 2019, download
(GA,ENG) Hayato Ushijima-Mwesigwa, MD Zadid Khan, Mashrur A Chowdhury, Ilya Safro "Optimal Installation for Electric Vehicle Wireless Charging Lanes", Journal of Industrial and Management Optimization, vol. 17, issue 3, pp. 1315-1341, 2021, download preprint
(QC,GA) Ruslan Shaydulin, Haayto Ushijima-Mwesigwa, Ilya Safro, Susan Mniszewski, Yuri Alexeev "Community Detection Across Emerging Quantum Architectures", in proceedings of the 3rd International Workshop on Post Moore's Era Supercomputing (PMES 2018), Supercomputing , preprint at arXiv:1810.07765, 2018
(ML) Saroj K. Dash, I. Safro, Ravisutha S. Srinivasamurthy "Spatio-temproal prediction of crimes using network analytic approach", IEEE International Conference on Big Data 2018 (BIGDATA), pp. 1912-1917, preprint at arXiv:1808.06241, 2018
(NLP) Justin Sybrandt, Angelo Carrabba, Alexander Herzog, Ilya Safro "Are Abstracts Enough for Hypothesis Generation?", IEEE International Conference on Big Data 2018 (BIGDATA), pp. 1504-1513, 2018, preprint at arXiv:1804.05942
(GA,CSC,MS) Ruslan Shaydulin, Ilya Safro "Aggregative Coarsening for Multilevel Hypergraph Partitioning", Symposium on Experimental Algorithms (SEA), Vol. 103, pp. 2:1-2:15, 10.4230/LIPIcs.SEA.2018.2, 2018, preprint at arXiv:1802.09610
(NLP) Justin Sybrandt, Michael Shtutman, Ilya Safro "Large-Scale Validation of Hypothesis Generation Systems via Candidate Ranking", IEEE International Conference on Big Data 2018 (BIGDATA), pp. 1494-1503, 2018, preprint at arXiv:1802.03793
(GA,CSC,MS) William Hager, James Hungerford, Ilya Safro "A Multilevel Bilinear Programming Algorithm for the Vertex Separator Problem", Computational Optimization and Applications, vol. 69, issue 1, pp. 189-223, 2018, download
(ML,BIO) Talayeh Razzaghi, Ilya Safro, Joseph Ewing, Ehsan Sadrfaridpour, John Scott "Predictive Models for Bariatric Surgery Risks with Imbalanced Medical Datasets", Annals of Operations Research, https://doi.org/10.1007/s10479-019-03156-8, 2019, download preprint
(GA) Christian Staudt, Michael Hamann, Alexander Gutfraind, Ilya Safro, Henning Meyerhenke "Generating realistic scaled complex networks", Applied Network Science, vol 2(1), 36p, 2017, download
(NLP) Justin Sybrandt, Michael Shtutman, Ilya Safro "MOLIERE: Automatic Biomedical Hypothesis Generation System", Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (oral presentation, in top 8%), pp. 1633-1642, 2017, download
(ML,ENG) MD Zadid Khan, Mashrur A Chowdhury, Sakib M. Khan, Ilya Safro, Hayato Ushijima-Mwesigwa "Utility Maximization Framework for Opportunistic Wireless Electric Vehicle Charging", Transportation Research Board, Paper no. 18-06481, download, 2017
(ML) Parth Bhavsar, Ilya Safro, Nidhal Bouayanaya, Robi Polikar, Dimah Dera "Chapter 12: Machine learning in transportation data analytics", in Data analytics for intelligent transportation systems, Apon, Chowdhury, Dey eds., 2017
(NLP) Yuliya Bolotova, Jie Lou, Ilya Safro "Detecting and monitoring foodborne illness outbreaks: Twitter communications and the 2015 U.S. Salmonella outbreak linked to imported cucumbers", Technical report, 2017, TigerPrints Publications. 1, http://tigerprints.clemson.edu/ag_envsci_pub/1, download
(NLP) Neela Avudaiappan, Alexander Herzog, Sneha Kadam, Yuheng Du, Jason Thatcher, Ilya Safro "Detecting and Summarizing Emergent Events in Microblogs and Social Media Streams by Dynamic Centralities", In Proceedings of IEEE International Conference on Big Data (BIGDATA), pp. 1627-1634, 2017, download conference version, download long version at arXiv:1610.06431
(ML,MS) Ehsan Sadrfaridpour, Sandeep Jeereddy, Ken Kennedy, Andre Luckow, Talayeh Razzaghi, Ilya Safro "Algebraic multigrid support vector machines", European Symposium on Artificial Neural Networks (ESANN), 2017, (long version arXiv:1611.05487), download, 2017
(GA) Christian Staudt, Michael Hamann, Ilya Safro, Alexander Gutfraind, and Henning Meyerhenke "Generating Scaled Replicas of Real-World Networks", In Cherifi H., Gaito S., Quattrociocchi W., Sala A. (eds) Complex Networks & Their Applications V. COMPLENET 2016. Studies in Computational Intelligence, vol 693. Springer
(ML,MS,BIO) Talayeh Razzaghi, Oleg Roderick, Ilya Safro, Nicholas Marko "Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values", PLOS One 11(5), 2016 download
(GA,MS) Emmanuel John, Ilya Safro "Single- and Multi-level Network Sparsification by Algebraic Distance", Journal of Complex Networks, Vol. 3(5), pp. 352-388, 2016 download
(GA) Aydin Buluc, Henning Meyerhenke, Ilya Safro, Peter Sanders, Christian Schulz "Recent Advances in Graph Partitioning", Algorithm Engineering: Selected Results and Surveys 9220, pp. 117-158, Preprint arXiv:1311.3144, 2016, download
(GA) Noam Goldberg, Sven Leyffer, Ilya Safro "Optimal Response to Epidemics and Cyber Attacks in Networks", Networks, Volume 66(2), pages 145-158, 2015, download
(GA,MS) Alexander Gutfraind, Ilya Safro, Lauren Meyers "Multiscale Network Generation", In Proceedings of IEEE 18th International Conference on Information Fusion (FUSION), pages 158-165, 2015, download (earlier preprint ANL/MCS-P3009-0712, download)
(ML,MS,BIO) Talayeh Razzaghi, Oleg Roderick, Ilya Safro, Nicholas Marko "Fast Imbalanced Classification of Healthcare Data with Missing Values", In Proceedings of IEEE 18th International Conference on Information Fusion (Fusion), pages 774-781, 2015, download
(ML,MS) Talayeh Razzaghi, Ilya Safro, "Scalable Multilevel Support Vector Machines", International Conference on Computational Science (ICCS) 2015, Procedia Computer Science, Volume 51, 2015, pp. 2683-2687, ISSN 1877-0509, download (long version at ArXiv:1410.3348, download)
(GA,CSC,MS) William Hager, James Hungerford, Ilya Safro "A Continuous Refinement Strategy for the Multilevel Computation of Vertex Separators", In Proceedings of International Conference on Learning and Intelligent Optimization (LION 8), pp. 77-81, Springer International Publishing, 2014, download
(GA,MS) Sven Leyffer, Ilya Safro "Fast Response to Infection Spread and Cyber Attacks on Large-Scale Networks", vol 1(2), pp. 183--199, Journal of Complex Networks, 2013, download
(GA,MS,CSC) Ilya Safro, Peter Sanders, Christian Schulz "Advanced Coarsening Schemes for Graph Partitioning", ACM Journal of Experimental Algorithmics, Vol. 19, pp. 2.2:1--2.2:24, 2015, download
(GA,CSC) Jie Chen, Ilya Safro "A Measure of the Connection Strengths between Graph Vertices with Applications", International Conference on Computational Science, Procedia CS, vol. 4, pp. 196-205, 2011, download
(GA,CSC,MS) Ilya Safro, Peter Sanders, Christian Schulz, "Advanced Coarsening Schemes for Graph Partitioning", Symposium on Experimental Algorithms (SEA), LNCS Vol. 7276, pp. 369-380, 2012
(GA,MS,CSC) Dorit Ron, Ilya Safro, Achi Brandt, "Relaxation-based coarsening and multiscale graph organization", SIAM Multiscale Modeling and Simulations, Vol. 9, No. 1, pp. 407-423, 2011, download
(GA,MS,CSC) Ilya Safro, Boris Temkin, "Multiscale approach for the network compression-friendly ordering", Journal of Discrete Algorithms, Vol. 9, pp. 190-202, 2011, download
(CSC,MS) Dorit Ron, Ilya Safro, Achi Brandt, "A fast multigrid algorithm for energy minimization under planar density constraints", SIAM Multiscale Modeling and Simulations, Vol. 8, No. 5, pp. 1599-1620, 2010, download
(CSC) Andrew Lyons, Ilya Safro, Jan Utke, "Randomized Heuristics for Exploiting Jacobian Scarcity", Optimization Methods and Software, Vol. 27, No. 2, pp. 311-322, 2012, download
(GA,CSC) Jie Chen, Ilya Safro, "Algebraic Distance on Graphs", SIAM Journal on Scientific Computing, Vol. 33, No. 6, pp. 3468-3490, 2011, download
(ML) Oleg Roderick, Ilya Safro, "Learning Highly-Filtered Data by Nonlinear Spectral Methods", Learning and Intelligent Optimization, Springer LNCS, vol. 6073, pp. 154-168, 2010, download
(GA,CSC) Erik Boman, Umit Catalyurek, Cedric Chevalier, Karen Devine, Ilya Safro, Michael Wolf, "Advances in Parallel Partitioning, Load Balancing, and Matrix Ordering", Journal of Physics: Conference Series, vol. 180, 2009, download
(GA,CSC,MS) Ilya Safro, Paul Hovland, Jaewook Shin, Michelle Strout, "Improving random walk performance", in Proceedings of the International Conference on Scientific Computing (CSC), pp. 108-112, 2009, download
(GA,CSC,MS) Cedric Chevalier, Ilya Safro, "Comparison of coarsening schemes for multilevel graph partitioning", Learning and Intelligent Optimization, LNCS 5851, pp. 191-205. Springer, 2009, download
(GA,CSC,MS) Ilya Safro, Dorit Ron, Achi Brandt, "Multilevel Algorithms for Linear Ordering Problems", ACM Journal of Experimental Algorithmics, vol. 13, pp. 1.4-1.20, 2008, download
(GA,CSC,MS) Ilya Safro, "Multilevel Algorithms for Combinatorial Optimization Problems", Ph.D. Thesis, The Weizmann Institute of Science, 2007, download
(BIO) Liron Klipcan, Ilya Safro, Boris Temkin, Mark Safro, "Optimal growth temperature of prokaryotes correlates with class II amino acid composition", FEBS Letters (Federation of European Biochemical Societies), vol. 580/6, pp. 1672-1676, 2006, download
(GA,CSC,MS) Ilya Safro, Dorit Ron, Achi Brandt, "A Multilevel Algorithm for the Minimum 2-sum Problem", Journal of Graph Algorithms and Applications, vol. 10/2, 2006, download
(GA,CSC,MS) Ilya Safro, Dorit Ron, Achi Brandt, "Graph Minimum Linear Arrangement by Multilevel Weighted Edge Contractions", Journal of Algorithms, vol. 60/1, pp. 24-41, 2006, download
(GA,CSC,MS) Ilya Safro, "The minimum linear arrangement problem", M.Sc. Thesis, Weizmann Institute of Science,2002.
(BIO) Ilya Safro, Lee Segel, "Collective stochastic versions of playable games as metaphors for complex biosystems: Team Collect Four", Complexity 8 (2003), 46-55, download

Patents

Alexander Gutfraind, Ilya Safro "Use of Algorithms for Realistic Network Generation", CURF Reference 2015-058, 2016, direct link

Book chapters

P. Bhavsar, Ilya Safro, N. Bouayanaya, R. Polikar, D. Dera "Machine Learning in Transportation Data Analytics", a chapter in "Data Analytics for Intelligent Transportation Systems" M. Chowdhury, A. Apon, and K. Dey eds., in press, 2016
Ilya Safro, Dorit Ron, Achi Brandt, "Fast Multilevel Algorithms for Linear Ordering Problems", in Computational Optimization: New Research Developments, Nova Science Publishers, ISBN: 978-1-60692-671-0, 2010, download

ArXiv/Technical Reports

Ilya Safro, "Discovery of new hypotheses about the relation of biological objects using MEDLINE information", 2000.

Ilya Safro, "The minimum linear arrangement problem on proper interval graphs", arXiv, cs.DM/0608008, 2002, download.
Sergey Benditkis, Ilya Safro, "Generalizations of the Hanoi Towers problem", arXiv, cs.DM/0612070, 1998, download.
Oleg Roderick, Ilya Safro, "Polynomial Interpolation for Predicting Decisions and Recovering Missing Data", Preprint ANL/MCS-P1586-0209, Argonne National Laboratory, 2009.

Selected extended abstracts

Leonid Brodsky, Michael Kositsky, Andrei Leontovich, Y. Kalaidzidis, Ilya Safro, Michael Shtutman, Elena Feinstein, "Gene Expression Analysis Tools", Annual Israeli Bioinformatics Symposium, 2002.
Ilya Safro, Dorit Ron, Achi Brandt, "Multilevel Algorithms for Linear Ordering Problems", SIAM Workshop on Combinatorial Scientific Computing, 2005, download.
Andrew Lyons, Ilya Safro, "Randomized Heuristics for Exploiting Jacobian Scarcity", Dagstuhl Seminar on Combinatorial Scientific Computing, 2009, download.
Dorit Ron, Ilya Safro, Achi Brandt, "Fast Multilevel Solver for Quadratic Optimization under Planar Density Constraints", European Conference on Operational Research, 2009.
Ilya Safro, "Algebraic Distance and Its Applications to Combinatorial Scientific Computing Problems", SIAM Workshop on Combinatorial Scientific Computing, 2009.
Ilya Safro, B.Temkin, "Multiscale approach for network compression-friendly ordering", SIAM Workshop on Combinatorial Scientific Computing, 2011.
Ilya Safro, "Multiscale Algorithms for Analysis and Optimization Problems on Large Networks", Complex Networks, 2012.
James Hungerford, William Hager, Ilya Safro "A Multilevel Vertex Separator Alogrithm Based on the Solution of Bilinear Programs", SIAM Workshop on Combinatorial Scientific Computing, 2016
Susan M Mniszewski, Hayato Montezuma Ushijima-Mwesigwa, Christian Francisco Andres Negre, Ilya Safro "Multilevel Quantum Annealing for Graph Partitioning", Tech. Report LA-UR-18-27179, Quantum Computing Workshop, Argonne National Lab, download, 2018
Marina Aksenova, Justin Sybrandt, Biyun Cui, Mathew Lucius, Hao Ji, Michael D Wyatt, Ilya Safro, Jun Zhu, Michael Shtutman "Inhibition of the DEAD Box RNA Helicase 3 prevents HIV-1 Tat- and cocaine-induced neurotoxicity by targeting microglai activation", NIDA Genetic Consortium Meeting, 2019
Xiaoyuan Liu, Anthony Angone, Ruslan Shaydulin, Ilya Safro, Yuri Alexeev, Lukasz Cincio "An Approach for Combinatorial Optimization on Noisy Quantum Computers", Bulletin of the American Physical Society, APS, 2021