Ilan Shomorony

Electrical and Computer Engineering, UIUC

I am an assistant professor in the ECE department at the University of Illinois at Urbana-Champaign. My main research interests are in information theory, machine learning, and computational biology. Prior to joining UIUC, I spent a year as a data scientist at Human Longevity.

news

Sept 20, 2024

Paper "Prioritized Federated Learning: Leveraging Non-Priority Clients for Targeted Model Improvement" with my student Aditya Ravi accepted to the Transactions on Machine Learning Research

June 6, 2024

Paper "Substring Density Estimation from Traces" with my student Kayvon Mazooji accepted to the IEEE Transactions on Information Theory

May 21, 2024

Paper "An Information Theory for Out-of-Order Media With Applications in DNA Data Storage" with Aditya Ravi and Alireza Vahid published in a special issue of the IEEE Transactions on Molecular, Biological, and Multi-Scale Communications

May 1, 2024

Paper "Faster Maximum Inner Product Search in High Dimensions" with my Mo Tiwari et al. accepted to ICML 2024

Apr 2, 2024

Paper "Fast Multiple Sequence Alignment via Multi-Armed Bandits" with my student Kayvon Mazooji accepted to ISMB 2024

Mar 29, 2024

Paper "Fundamental Limits of Reference-Based Sequence Reordering" with Nir Weinberger published at IEEE Transactions on Information Theory

Nov 15, 2023

My student Grant Greenberg successfully defended his PhD thesis. Congrats, Grant!

Nov 15, 2023

Paper "The Metagenomic Binning Problem: Clustering Markov Sequences" with my student Grant Greenberg published at the IEEE Transactions on Molecular, Biological, and Multi-Scale Communications

Nov 15, 2023

Paper "DNA Merge-Sort: A Family of Nested Varshamov-Tenengolts Reassembly Codes for Out-of-Order Media" with Sajjad Nassirpour and Alireza Vahid published at IEEE Transactions on Communications

Oct 25, 2023

Paper "LexicHash: sequence similarity estimation via lexicographic comparison of hashes" with my students Grant Greenberg and Aditya Ravi published in Bioinformatics

Sep 21, 2023

Two papers accepted to NeurIPS 2023:

Efficient Learning of Linear Graph Neural Networks via Node Subsampling with Seiyun Shin and Han Zhao
BanditPAM++: Faster k-medoids Clustering with Mo Tiwari, Ryan Kang, Donghyun Lee, Sebastian Thrun and Martin Zhang

April 20, 2023

Two of my students, Seiyun Shin and Kel Levick, selected as Mavis Future Faculty Fellows!

April 14, 2023

Five papers accepted to ISIT 2023:

Fundamental Limits of Multiple Sequence Reconstruction from Substrings with Kel Levick
Substring Density Estimation from Traces with Kayvon Mazooji
Finding a Burst of Positives via Nonadaptive Semiquantitative Group Testing with Yun-Han Li, Ryan Gabrys, Jin Sima, and Olgica Milenkovic
On Constant-Weight Binary B2-Sequences with Jin Sima, Yun-Han Li, and Olgica Milenkovic
Fundamental Limits of Reference-Based Sequence Reordering with Nir Weinberger

April 5, 2023

I am one of the organizers of the 6th Health Data Analytics Summit. It is a fully online event and you can register for free here!

Mar 16, 2023

I gave a talk at the Stanford ISL Colloquium on "An Information Theory for Out-of-Order Information" (Slides)

Feb 14, 2023

I gave an invited talk at ITA on the adaptive power method. (Slides)

Dec 21, 2022

Paper "Adaptive power method: Eigenvector estimation from sampled data" with Han Zhao and our student Seiyun Shin accepted to the conference on Algorithmic Learning Theory (ALT)

Dec 20, 2022

I wrote a preview article on "Data-driven precision medicine through the analysis of biological functional modules" for Cell Reports Medicine.

Nov 2, 2022

Paper "CVQVAE: A representation learning method for multiomics single cell data integration" with students Tianyu Liu and Grant Greenberg accepted as a spotlight in the Machine Learning in Computational Biology (MLCB) meeting

Sep 14, 2022

Paper "MABSplit: Faster Forest Training Using Multi-Armed Bandits" with Mo Tiwari et al. accepted to to NeurIPS 2022

June 7, 2022

Paper “Improving Bacterial Genome Assembly Using a Test of Strand Orientation” with my student Grant Greenberg accepted to ECCB 2022

May 17, 2022

Two papers accepted to ISIT 2022:

"Capacity of the Shotgun Sequencing Channel" with Aditya Ravi and Alireza Vahid
Fundamental Limits of Multi-Sample Flow Graph Decomposition with Kayvon Mazooji, Sreeram Kannan and Bill Noble

April 19, 2022

Paper A Game-Theoretically Optimal Defense Paradigm against Traffic Analysis Attacks using MultiPath Routing and Deception with Masoumeh Abolfathi et al. accepted to SACMAT 2022

Mar 1, 2022

Paper “JIND: Joint Integration and Discrimination for Automated Single-Cell Annotation” with Mohit Goyal et al. published at Bioinformatics

Feb 24, 2022

Our Foundations and Trends monograph "Information-Theoretic Foundations of DNA Data Storage" is out!

Feb 18, 2022

Paper "Coded Shotgun Sequencing" with my student Aditya Ravi published at the IEEE Journal on Selected Areas in Information Theory

Jan 18, 2022

I'm teaching a new course ECE598IS: Fundamental Limits in Data Science

Jan 11, 2022

Paper "Achieving the Capacity of a DNA Storage Channel with Linear Coding Schemes" with my student Kel Levick accepted to CISS 2022

Sept 23, 2021

Paper "Torn-Paper Coding" with Alireza Vahid accepted to IEEE Transactions on Information Theory

April 30, 2021

Two papers accepted to ISIT 2021:

"Capacity of the Torn Paper Channel with Lost Pieces" with Aditya Ravi and Alireza Vahid
"Sketching and Sequence Alignment: A Rate-Distortion Perspective" with Govinda Kamath

Jan 26, 2021

Paper “DNA-Based Storage: Models and Fundamental Limits” with Reinhard Heckel accepted to IEEE Transactions on Information Theory

Jan 4, 2021

I was awarded the NSF CAREER Award!

Dec 22, 2020

Paper “Private DNA Sequencing: Hiding Information in Discrete Noise” with my student Kayvon Mazooji and collaborator Roy Dong accepted to ITW 2020 (preprint).

Sep 25, 2020

Two papers accepted to NeurIPS 2020:

Aug 16, 2020

Paper “Communicating over the Torn-Paper Channel” with Alireza Vahid accepted to Globecom 2020. A longer version of the paper is available here.

Jul 31, 2020

Paper “Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments” published at Cell Patterns (open access).

May 6, 2020

Paper “Capacity of the Erasure Shuffling Channel” with my student Seiyun Shin was presented at ICASSP 2020 as part of a special session on “Signal Processing and Coding for Macromolecular Storage and Computing”.

Feb 4, 2020

I gave an invited talk at the ITA Workshop on “Pairwise alignment of DNA sequences via spectral Jaccard similarity” (Manuscript)

Jan 10, 2020

Paper “An unsupervised learning approach to identify novel signatures of health and disease from multimodal data” with collaborators from Human Longevity is now published on Genome Medicine.

Dec 23, 2019

Paper “Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments” accepted to RECOMB 2020 (bioRxiv preprint).

Jun 13, 2019

Paper “The Metagenomic Binning Problem: Clustering Markov Sequences” with my student Grant Greenberg to be presented at ITW 2019 (Manuscript).

May 22, 2019

Paper “Capacity Results for the Noisy Shuffling Channel” with Reinhard Heckel to be presented at ISIT 2019 (Manuscript).

Mar 21, 2019

I organized a session on “Computational Methods for Genomics and Biological Data” at CISS 2019.