Monographs
[M2] I. Shomorony and R. Heckel, Information-Theoretic Foundations of DNA Data Storage, Foundations and Trends® in Communications and Information Theory: Vol. 19: No. 1, pp 1-106, Feb. 2022. doi: 10.1561/0100000117.
[M1] I. Shomorony and A. S. Avestimehr, Multihop Wireless Networks: A Unified Approach to Relaying and Interference Management, Foundations and Trends in Networking, vol. 8, no. 3, pp. 149-280, Dec. 2014. doi: 10.1561/1300000044.
Journal Papers
[J25] A. N. Ravi and I. Shomorony, Prioritized Federated Learning: Leveraging Non-Priority Clients for Targeted Model Improvement, Transactions on Machine Learning Research, 2024.
[J24] K. Mazooji and I. Shomorony, Substring Density Estimation from Traces, IEEE Transactions on Information Theory, 2024.
[J23] A. N. Ravi, A. Vahid, and I. Shomorony, An Information Theory for Out-of-Order Media With Applications in DNA Data Storage, IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, Special Issue, 2024.
[J22] N. Weinberger and I. Shomorony, Fundamental Limits of Reference-Based Sequence Reordering, IEEE Transactions on Information Theory, 2024.
[J21] G. Greenberg, A. Ravi, and I. Shomorony, The Metagenomic Binning Problem: Clustering Markov Sequences, IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, November 2023.
[J20] G. Greenberg, A. Ravi, and I. Shomorony, LexicHash: sequence similarity estimation via lexicographic comparison of hashes, Bioinformatics, November 2023.
[J19] S. Nassirpour, I. Shomorony, and A. Vahid, DNA Merge-Sort: A Family of Nested Varshamov-Tenengolts Reassembly Codes for Out-of-Order Media, IEEE Transactions on Communications, November, 2023.
[J18] I. Shomorony, Data-driven precision medicine through the analysis of biological functional modules, Cell Reports Medicine, Volume 3, Issue 12, December 2022.
[J17] G. Greenberg and I. Shomorony, Improving bacterial genome assembly using a test of strand orientation, Bioinformatics, September 2022.
[J16] M. Goyal, G. Serrano, J. Argemi, I. Shomorony, M. Hernaez, I. Ochoa, JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation, Bioinformatics, 2022.
[J15] A. Ravi, A. Vahid and I. Shomorony, Coded Shotgun Sequencing, IEEE Journal on Selected Areas in Information Theory, 2022.
[J14] I. Shomorony and A. Vahid, Torn-Paper Coding, IEEE Transactions on Information Theory, Vol 67, No 12, December 2021.
[J13] I. Shomorony and R. Heckel, DNA-Based Storage: Models and Fundamental Limits, IEEE Transactions on Information Theory, Vol 67, No 6, June 2021.
[J12] A. Yekkehkhany, E. Arian, R. Nagi and I. Shomorony, A Cost-Based Analysis for Risk-Averse Explore-Then-Commit Finite-Time Bandits, IISE Transactions, 2021.
[J11] T. Baharav, G. Kamath, D. Tse, and I. Shomorony, Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments, Patterns, Vol 1, No 6, July 2020.
[J10] I. Shomorony*, E. Cirulli*, et al., Unsupervised integration of multimodal dataset identifies novel signatures of health and disease, Genome Medicine, 2020. (*equal contributions)
[J9] G. Kamath*, I. Shomorony*, F. Xia*, T. Courtade, D. Tse, HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution, Genome Research, 2017. (*equal contributions)
[J8] I. Shomorony, T. Courtade, S. Kim, and D.Tse, Information-optimal Genome Assembly via Sparse Read-Overlap Graphs, Bioinformatics, Vol 37, No 17, 2016
[J7] I. Shomorony, T. Courtade, D. Tse, Fundamental Limits of Genome Assembly under an Adversarial Erasure Model. IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, Vol 2, No 2, Dec. 2016., 2016.
[J6] I. Shomorony and A. S. Avestimehr, Degrees of Freedom of Two-Hop Wireless Networks: Everyone Gets the Entire Cake, IEEE Transactions on Information Theory, Vol 60, No 5, May 2014.
[J5] R. Etkin, F. Parvaresh, I. Shomorony and A. S. Avestimehr, "Computing Half-Duplex Schedules in Gaussian Relay Networks via Min-Cut Approximations", IEEE Transactions on Information Theory, Vol 60, No 11, Nov 2014.
[J4] H. Asnani, I. Shomorony, A. S. Avestimehr and T. Weissman, "Network Compression: Worst-Case Analysis", IEEE Transactions on Information Theory, Vol 61, No 7, July 2015.
[J3] I. Shomorony, R. Etkin, F. Parvaresh and A. S. Avestimehr, "Diamond Networks with Bursty Traffic: Bounds on the Minimum Energy-Per-Bit", IEEE Transactions on Information Theory, Vol 60, No 1, January 2014.
[J2] I. Shomorony and A. S. Avestimehr, "Worst-Case Additive Noise in Wireless Networks", IEEE Transactions on Information Theory, Vol 59, No 6, June 2013.
[J1] I. Shomorony and A. S. Avestimehr, "Two-Unicast Wireless Networks: Characterizing the Degrees of Freedom", IEEE Transactions on Information Theory, Vol 59, No 1, January 2013.
Conference Papers
[C41] Y. Gerzon, I. Shomorony, N. Weinberger, "Capacity of Frequency-based Channels: Encoding Information in Molecular Concentrations," ISIT 2024.
[C40] K. Mazooji and I. Shomorony, "An Instance-Based Approach to the Trace Reconstruction Problem," 58th Annual Conference on Information Sciences and Systems (CISS), 2024.
[C39] S. Shin, I. Shomorony and H. Zhao, "Efficient Learning of Linear Graph Neural Networks via Node Subsampling," NeurIPS 2023.
[C38] M. Tiwari, R. Kang, D. Lee, S. Thrun, I. Shomorony and M. Zhang, "BanditPAM++: Faster k-medoids Clustering," NeurIPS 2023.
[C37] K. Levick and I. Shomorony, "Fundamental Limits of Multiple Sequence Reconstruction from Substrings," ISIT 2023.
[C36] K. Mazooji and I. Shomorony, "Substring Density Estimation from Traces," ISIT 2023.
[C35] Y.-H. Li, R. Gabrys, I. Shomorony, and O. Milenkovic, "Finding a Burst of Positives via Nonadaptive Semiquantitative Group Testing," ISIT 2023.
[C34] J. Sima, Y.-H. Li, I. Shomorony, and O. Milenkovic, "On Constant-Weight Binary B2-Sequences," ISIT 2023.
[C33] N. Weinberger and I. Shomorony, "Fundamental Limits of Reference-Based Sequence Reordering," ISIT 2023.
[C32] S. Shin, H. Zhao, and I. Shomorony, "Adaptive power method: Eigenvector estimation from sampled data," conference on Algorithmic Learning Theory (ALT), 2023.
[C31] T. Liu, G. Greenberg, and I. Shomorony, "CVQVAE: A representation learning method for multiomics single cell data integration," Machine Learning in Computational Biology (MLCB), 2022.
[C30] M. Tiwari, R. Kang, J.-Y. Lee, S. Thrun, C. Piech, I. Shomorony, and M. Zhang, "MABSplit: Faster Forest Training Using Multi-Armed Bandits," Conference on Neural Information Processing Systems (NeurIPS) 2022
[C29] A. Ravi, A. Vahid and I. Shomorony, "Capacity of the Shotgun Sequencing Channel," ISIT 2022.
[C28] K. Mazooji, S. Kannan, W. S. Noble and I. Shomorony, "Fundamental Limits of Multi-Sample Flow Graph Decomposition", ISIT 2022.
[C27] M. Abolfathi, I. Shomorony, A. Vahid, and J. H. Jafarian, "A Game-Theoretically Optimal Defense Paradigm against Traffic Analysis Attacks using Multipath Routing and Deception," 27th ACM on Symposium on Access Control Models and Technologies (SACMAT), 2022.
[C26] K. Levick, R. Heckel and I. Shomorony, "Achieving the Capacity of a DNA Storage Channel with Linear Coding Schemes", Conference on Information Sciences and Systems (CISS), 2022.
[C25] A. Ravi, A. Vahid and I. Shomorony, "Capacity of the Torn Paper Channel with Lost Pieces," ISIT 2021.
[C24] I. Shomorony and G. Kamath, "Sketching and Sequence Alignment: A Rate-Distortion Perspective," ISIT 2021.
[C23] K. Mazooji, R. Dong, and I. Shomorony, "Private DNA Sequencing: Hiding Information in Discrete Noise," Proceedings of IEEE Information Theory Workshop, 2021.
[C22] M. Tiwari, M. Zhang, J. Mayclin, S. Thrun, C. Piech, and I. Shomorony, "BanditPAM: Almost Linear Time k-Medoids Clustering via Multi-Armed Bandits," Conference on Neural Information Processing Systems (NeurIPS) 2020
[C21] G. Kamath, T. Baharav, and I. Shomorony, "Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment," Conference on Neural Information Processing Systems (NeurIPS) 2020
[C20] I. Shomorony and A. Vahid, "Communicating over the Torn-Paper Channel," IEEE Global Communications Conference (IEEE GLOBECOM), 2020
[C19] T. Baharav, G. Kamath, D. Tse, and I. Shomorony, "Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments", RECOMB 2020.
[C18] S. Shin, R. Heckel and I. Shomorony, "Capacity of the Erasure Shuffling Channel", ICASSP 2020.
[C17] G. Greenberg and I. Shomorony, "The Metagenomic Binning Problem: Clustering Markov Sequences", ITW 2019.
[C16] I. Shomorony and R. Heckel, "Capacity Results for the Noisy Shuffling Channel", ISIT 2019.
[C15] R. Heckel*, I. Shomorony*, K. Ramchandran and D. Tse, "Fundamental Limits of DNA Storage Systems", ISIT 2017. (*equal contributions)
[C14] J. Hui, I. Shomorony, K. Ramchandran and T. Courtade, "Overlap-Based Genome Assembly from Variable-Length Reads", ISIT 2016.
[C13] I. Shomorony, G. Kamath, F. Xia, T. Courtade and D. Tse, "Partial DNA Assembly: A Rate-Distortion Perspective", ISIT 2016.
[C12] A. Vahid, I. Shomorony and R. Calderbank, "Informational Bottlenecks in Two-Unicast Wireless Networks with Delayed CSIT", Allerton 2015.
[C11] I. Shomorony, T. Courtade and D. Tse, "Do Read Errors Matter for Genome Assembly?", ISIT 2015.
[C10] I. Shomorony and A. S. Avestimehr, "Sampling Large Data on Graphs", IEEE GlobalSIP, 2014.
[C9] I. Shomorony and A. S. Avestimehr, "A Generalized Cut-Set Bound for Deterministic Multi-Flow Networks and its Applications", ISIT 2014.
[C8] R. Etkin, F. Parvaresh, I. Shomorony and A. S. Avestimehr, "On Efficient Min-Cut Approximations in Half-Duplex Relay Networks", ISIT 2013.
[C7] H. Asnani, I. Shomorony, A. S. Avestimehr and T. Weissman, "Network Compression: Worst-Case Analysis"</a>, ISIT 2013.
[C6] I. Shomorony and A. S. Avestimehr, "Degrees of Freedom of Two-Hop Wireless Networks: Everybody Gets the Entire Cake", Allerton 2012. (Slides)
[C5] I. Shomorony and A. S. Avestimehr, "On the Role of Deterministic Models in K x K x K Wireless Networks", ITW 2012.
[C4] I. Shomorony, A. S. Avestimehr, H. Asnani and T. Weissman, "Worst-Case Source for Distributed Compression with Quadratic Distortion", ITW 2012.
[C3] I. Shomorony and A. S. Avestimehr, "Is Gaussian Noise the Worst-Case Additive Noise in Wireless Networks?", ISIT 2012.
[C2] I. Shomorony, R. Etkin, F. Parvaresh and A. S. Avestimehr, "Bounds on the Minimum Energy-Per-Bit for Bursty Traffic in Diamond Networks", ISIT 2012.
[C1] I. Shomorony and A. S. Avestimehr, "Sum Degrees-of-Freedom of Two-Unicast Wireless Networks", ISIT 2011. (Student Paper Award Finalist)