Publications

Journals

• Optimal Codes Correcting a Substring Edit
  Y. Li, Y. Tang, H. Lou, R. Gabrys, and F. Farnoud, IEEE Trans. Information Theory, Apr. 2025.
• Correcting a Substring Edit Error of Bounded Length
  Y. Tang, S. Motamen, H. Lou, K. Whritenour, S. Wang, R. Gabrys, and F. Farnoud, IEEE Trans. Communications, Jan. 2025.
• Non-binary Codes for Correcting a Burst of at Most t Deletions
  S. Wang, Y. Tang, J. Sima, R. Gabrys, and F. Farnoud, IEEE Trans. Information Theory, Feb. 2024.
• Low-Redundancy Codes for Correcting Multiple Short-Duplication and Edit Errors [IEEE]
  Y. Tang, S. Wang, H. Lou, R. Gabrys, and F. Farnoud, IEEE Trans. Information Theory, May 2023.
• Data Deduplication with Random Substitutions [IEEE]
  H. Lou and F. Farnoud, IEEE Trans. Information Theory, May 2022.
• Error-Correcting Codes for Short Tandem Duplication and Edit Errors [IEEE]
  Y. Tang and F. Farnoud, IEEE Trans. Information Theory, Feb. 2022.
• Multidimensional Clinical Surveillance of Pseudomonas aeruginosa Reveals Complex Relationships between Isolate Source, Morphology, and Antimicrobial Resistance
  L.J. Dunphy, G.L. Kolling, M.L. Jenior, J. Carroll, A.E. Attai, F. Farnoud, A.J. Mathers, M.A. Hughes, and J.A. Papin, mSphere, July 2021.
• Error-correcting Codes for Noisy Duplication Channels [IEEE]
  Y. Tang and F. Farnoud, IEEE Trans. Information Theory, Feb. 2021.
• Single-Error Detection and Correction for Duplication and Substitution Channels
  Y. Tang, Y. Yehezkeally, M. Schwartz, and F. Farnoud, “IEEE Trans. Information Theory, Nov. 2020.
• Evolution of k-mer Frequencies and Entropy in Duplication and Substitution Mutation Systems
  H. Lou, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 66, May 2020.
• The Entropy Rate of Some Polya String Models
  O. Elishco, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 65, Dec. 2019.
• Reconciling Similar Sets of Data
  R. Gabrys, F. Farnoud, IEEE Trans. Communications, vol 67, Aug. 2019.
• Estimation of Duplication History under a Stochastic Model for Tandem Repeats [Code]
  F. Farnoud, M. Schwartz, and J. Bruck, BMC Bioinformatics, Feb. 2019.
• Duplication Distance to the Root for Binary Sequences [IEEE]
  N. Alon, J. Bruck, F. Farnoud, and S. Jain, IEEE Trans. Information Theory, vol. 63, Dec. 2017.
• Capacity and Expressiveness of Genomic Tandem Duplication [IEEE]
  S. Jain, F. Farnoud, and J. Bruck, IEEE Trans. Information Theory, vol. 63, Oct. 2017.
• Computing Similarity Distances Between Rankings [ScienceDirect]
  F. Farnoud, G. J. Puleo, O. Milenkovic, and L. Su, Discrete Applied Mathematics, Available online Sep. 2017.
• Duplication-correcting codes for data storage in the DNA of living organisms [IEEE]
  S. Jain, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 63, Mar. 2017.
• MetaCRAM: An Integrated Pipeline for Metagenomic Data Processing and Compression [BMC Bioinformatics]
  M. Kim, X. Zhang, J.G. Ligo, F. Farnoud, V.V. Veeravalli, and O. Milenkovic, BMC Bioinformatics, Feb. 2016.
• The Capacity of String-Duplication Systems [IEEE]
  F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 62, Feb. 2016.
• Bounds for Permutation Rate-Distortion [IEEE]
  F. Farnoud, M. Schwartz, and J. Bruck, IEEE Trans. Information Theory, vol. 62, Feb. 2016.
• HyDRA: Gene Prioritization via Hybrid Distance-Score Rank Aggregation [Bioinformatics] [Supplementary Data]
  M. Kim, F. Farnoud, and O. Milenkovic, Bioinformatics, 31(7), 2015.
• Codes Correcting Erasures and Deletions for Rank Modulation [IEEE]
  R. Gabrys, E. Yaakobi, F. Farnoud, F. Sala, J. Bruck, and L. Dolecek, IEEE Trans. Information Theory, vol. 62, Jan. 2016.
• Approximate Sorting of Data Streams with Limited Storage [Springer]
  F. Farnoud, E. Yaakobi, and J. Bruck, J. Combinatorial Optimization. Aug. 2015.
• An Axiomatic Approach to Constructing Distances for Rank Comparison and Aggregation [IEEE] [Slides]
  F. Farnoud, and O. Milenkovic, IEEE Trans. Information Theory, vol. 60, Oct. 2014.
• Multipermutation Codes in the Ulam Metric for Non-volatile Memories [IEEE]
  F. Farnoud and O. Milenkovic, IEEE J. Selected Areas in Communications, vol. 32, May 2014.
• Error-Correction in Flash Memories via Codes in the Ulam Metric [IEEE]
  F. Farnoud, V. Skachek, and O. Milenkovic, IEEE Trans. Information Theory, vol. 59, pp. 3003-3020, May 2013.
• Sorting of Permutations by Cost-Constrained Transpositions [IEEE]
  F. Farnoud and O. Milenkovic, IEEE Trans. Information Theory, vol. 58, Jan. 2012.
• On the Multimessage Capacity Region for Undirected Ring Networks [IEEE]
  S.M.S.T. Yazdi, S.A. Savari, G. Kramer, K. Carlson, and F. Farnoud, IEEE Trans. Information Theory, vol. 56, Apr. 2010.
• A Packet-Based Photonic Label Switching Router for a Multirate All-Optical CDMA-Based GMPLS Switch [IEEE]
  F. Farnoud, M. Ibrahimi, and J. Salehi, IEEE J. Sel. Topics Quantum Electron., vol. 13, May 2007.

Selected Conference Publications

• Ranking with Multiple Oracles: From Weak to Strong Stochastic Transitivity
  T. Jin, Y. Wu, Q. Gu, F. Farnoud, International Conference on Machine Learning (ICML), July 2025, Acc. rate: 26.9%.
• Borda Regret Minimization for Generalized Linear Dueling Bandits
  Y. Wu, T. Jin, Q. Di, H. Lou, F. Farnoud, Q. Gu, International Conference on Machine Learning (ICML), July 2024, Acc. rate: 27.5%.
• Variance-aware Regret Bounds for Stochastic Contextual Dueling Bandits
  Q. Di, T. Jin, Y. Wu, H. Zhao, F. Farnoud, Q. Gu, International Conference on Learning Representations (ICLR), May 2024, Acc. rate: 31%.
• Active Ranking without Strong Stochastic Transitivity
  H. Lou, T. Jin, Y. Wu, P. Xu, Q. Gu, F. Farnoud, Conference on Neural Information Processing Systems (NeurIPS), New Orleans, Louisiana, Nov. 2022, Acc. rate: 25.6%.
• Adaptive Sampling for Heterogeneous Rank Aggregation from Noisy Pairwise Comparisons
  Y. Wu, T. Jin, H. Lou, P. Xu, F. Farnoud, Q. Gu, Artificial Intelligence and Statistics (AISTATS), Virtual, Mar. 2022, Acc. rate: 29.2%.
• Efficient Search of Circular Repeats and MicroDNA Reintegration in DNA Sequences
  Y. Wang, H. Lou, P. Kumar, A. Dutta and F. Farnoud, IEEE 20th Int. Conf. Bioinformatics and Bioengineering (BIBE), Oct. 2020, Acc. rate: 32%.
• Rank Aggregation via Heterogeneous Thurstone Preference Models
  T. Jin, P. Xu, Q. Gu, F. Farnoud, AAAI Conference on Artificial Intelligence, New York, NY, Feb. 2020, Acc. rate: 20.6%, Oral 4.5%.
• Reliable Broadcast of Safety Messages in Vehicular Ad Hoc Networks
  F. Farnoud and S. Valaee, In Proc. IEEE INFOCOM, Rio de Janeiro, Brazil, Apr. 2009, Acc. rate: 19.7%.

Complete List of Peer-Reviewed Conference Publications

• (*) Improving Smoothness in Huffman Coding: Canonical and Pre-allocated Variations
  H. Luo, F. Farnoud, Submittted to IEEE Information Theory Workshop, 2025.
• Ranking with Multiple Oracles: From Weak to Strong Stochastic Transitivity
  T. Jin, Y. Wu, Q. Gu, F. Farnoud, International Conference on Machine Learning (ICML), July 2025, Acc. rate: 26.9%.
• Borda Regret Minimization for Generalized Linear Dueling Bandits
  Y. Wu, T. Jin, Q. Di, H. Lou, F. Farnoud, Q. Gu, International Conference on Machine Learning (ICML), July 2024, Acc. rate: 27.5%.
• Asymptotically Optimal Codes Correcting One Substring Edit
  Y. Li, Y. Tang, H. Lou, R. Gabrys, F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Athens, Greece, July 2024.
• Variance-aware Regret Bounds for Stochastic Contextual Dueling Bandits
  Q. Di, T. Jin, Y. Wu, H. Zhao, F. Farnoud, Q. Gu, Int. Conf. Learning Representations (ICLR), Vienna, Austria, May 2024, Acc. rate: 31%.
• Correcting a Substring Edit Error of Bounded Length
  Y. Tang, S. Motamen, H. Lou, K. Whritenour, S. Wang, R. Gabrys, F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Taipei, Taiwan, June 2023.
• Linial's Algorithm and Systematic Deletion-Correcting Codes
  Y. Li, F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Taipei, Taiwan, June 2023.
• Active Ranking without Strong Stochastic Transitivity
  H. Lou, T. Jin, Y. Wu, P. Xu, Q. Gu, F. Farnoud, Conference on Neural Information Processing Systems (NeurIPS), New Orleans, Louisiana, Nov. 2022, Acc. rate: 25.6%.
• Permutation Codes for Correcting a Burst of at Most t Deletions
  S. Wang, Y. Tang, R. Gabrys, F. Farnoud, 58th Allerton Conf.\ Communication, Control, and Computing, Monticello, Illinois, Sep. 2022.
• Universal Compression of Large Alphabets With Constrained Compressors
  H. Lou, F. FarnoudIEEE Int. Symp. Information Theory (ISIT), Espoo, Finland, June 2022.
• Correcting Multiple Short Duplication and Substitution Errors
  Y. Tang, S. Wang, R. Gabrys, F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Espoo, Finland, June 2022.
• Adaptive Sampling for Heterogeneous Rank Aggregation from Noisy Pairwise Comparisons
  Y. Wu, T. Jin, H. Lou, P. Xu, F. Farnoud, Q. Gu, Artificial Intelligence and Statistics (AISTATS), Virtual, Mar. 2022, Acc. rate: 29.2%.
• Correcting deletion errors in DNA data storage with enzymatic synthesis
  Y. Tang and F. Farnoud, IEEE Information Theory Workshop (ITW), Kanazawa, Japan, Oct. 2021.
• Asymptotic Analysis of Data Deduplication with a Constant Number of Substitutions [arXiv]
  H. Lou and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Melbourne, Australia, July 2021.
• Error-correcting codes for short tandem duplications and at most p substitutions
  Y. Tang and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Melbourne, Australia, July 2021.
• Non-binary Codes for Correcting a Burst of at Most 2 Deletions
  S. Wang, J. Sima and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Melbourne, Australia, July 2021.
• Efficient Search of Circular Repeats and MicroDNA Reintegration in DNA Sequences
  Y. Wang, H. Lou, P. Kumar, A. Dutta and F. Farnoud, IEEE 20th Int. Conf. Bioinformatics and Bioengineering (BIBE), Cincinnati, OH, Oct. 2020.
• Error-correcting Codes for Short Tandem Duplication and Substitution Errors
  Y. Tang and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Los Angeles, CA, June 2020.
• Data Deduplication with Random Substitutions
  H. Lou and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Los Angeles, CA, June 2020.
• Coding for Optimized Writing Rate in DNA Storage
  S. Jain, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Los Angeles, CA, June 2020.
• Rank Aggregation via Heterogeneous Thurstone Preference Models
  T. Jin, P. Xu, Q. Gu, F. Farnoud, AAAI Conference on Artificial Intelligence, New York, NY, Feb. 2020, Acc. rate: 20.6%, Oral 4.5%.
• Finite-Time Behavior of k-mer Frequencies and Waiting Times in Noisy-Duplication Systems
  H. Lou, F. Farnoud, Asilomar Conference on Signals, Systems, and Computers, Monterey, CA, Nov. 2019.
• Error-correcting Codes for Noisy Duplication Channels
  Y. Tang, F. Farnoud, Allerton Conference on Communication, Control, and Computing, Monticello, IL, Sep. 2019.
• Single-Error Detection and Correction for Duplication and Substitution Channels
  Y. Tang, Y. Yehezkeally, M. Schwartz, and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Paris, France, June 2019.
• Evolution of N-Gram Frequencies Under Duplication and Substitution Mutations [IEEE]
  H. Lou, M. Schwartz, F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Vail, Colorado, June 2018.
• Reconciling Similar Sets
  R. Gabrys, and F. Farnoud, 55th Annu. Allerton Conf. Communication, Control, and Computing, Monticello, IL, Oct. 2017.
• Noise and Uncertainty in String-duplication Systems [IEEE]
  S. Jain, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Aachen, Germany, June 2017.
• On the Duplication Distance of Binary Strings [IEEE]
  N. Alon, J. Bruck, F. Farnoud, and S. Jain, IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.
• Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms [IEEE]
  S. Jain, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.
• The Capacity of Some Polya String Models [IEEE]
  O. Elishco, F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Barcelona, Spain, July 2016.
• A Stochastic Model for Genomic Interspersed Duplication
  F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.
• Capacity and Expressiveness of Genomic Tandem Duplication 
  S. Jain, F. Farnoud, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.
• Reconciling Similar Sets of Data
  R. Gabrys, and F. Farnoud, IEEE Int. Symp. Information Theory (ISIT), Hong Kong, China, June 2015.
• Approximate Sorting of Data Streams with Limited Storage [Slides]
  F. Farnoud, E. Yaakobi, and J. Bruck, Computing and Combinatorics Conf. (COCOON), Atlanta, GA, Aug. 2014.
• The Capacity of String-Duplication Systems [Slides]
  F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Bounds for Permutation Rate-Distortion
  F. Farnoud, M. Schwartz, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Multipermutation Codes in the Ulam Metric [Slides]
  F. Farnoud and O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Similarity Distances between Permutations
  L. Su, F. Farnoud, and O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Single-Deletion-Correcting Codes over Permutations
  R. Gabrys, E. Yaakobi, F. Farnoud, F. Sala, J. Bruck, and L. Dolecek, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Codes Correcting Erasures and Deletions for Rank Modulation
  R. Gabrys, E. Yaakobi, F. Farnoud, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Honolulu, HI, June 2014.
• Gene Prioritization via Weighted Kendall Rank Aggregation
  M. Kim, F. Raisali, F. Farnoud, O. Milenkovic, IEEE Int. Workshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP), Saint Martin Island, Dec. 2013.
• MetaPar: Metagenomic Sequence Assembly via Iterative Reclassification
  M. Kim, J.G. Ligo, A. Emad, F. Farnoud, O. Milenkovic, and V.V. Veeravalli, In Proc. IEEE Global Conf. Signal and Information Processing (GlobalSIP), Dec. 2013.
• Aggregating Rankings with Positional Constraints
  F. Farnoud, O. Milenkovic, IEEE Information Theory Workshop (ITW), Seville, Spain, Sep. 2013.
• Building Consensus via Iterative Voting
  F. Farnoud, E. Yaakobi, O. Milenkovic, and J. Bruck, IEEE Int. Symp. Information Theory (ISIT), Istanbul, Turkey, Jul. 2013.
• Weighted Rank Aggregation via Relaxed Integer Programming
  F. Raisali, F. Farnoud, O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Istanbul, Turkey, Jul. 2013.
• A General Framework for Distributed Vote Aggregation
  B. Touri, F. Farnoud, A. Nedich, O. Milenkovic, American Control Conf. (ACC), Washington, DC, Jun. 2013.
• Alternating Markov Chains for Distribution Estimation in the Presence of Errors
  F. Farnoud, N.P. Santhanam, and O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Boston, MA, Jul. 2012.
• Rank Modulation for Translocation Error Correction [Slides]
  F. Farnoud, V. Skachek, and O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Boston, MA, Jul. 2012.
• Nonuniform Vote Aggregation Algorithms
  F. Farnoud, B. Touri, and O. Milenkovic, IEEE Int. Conf. Signal Processing and Communications (SPCOM), Bangalore, India, Jul. 2012.
• Decomposing Permutations via Cost-Constrained Transpositions
  F. Farnoud and O. Milenkovic, IEEE Int. Symp. Information Theory (ISIT), Saint Petersburg, Russia, Jul./Aug. 2011.
• A Graphical Model for Computing the Minimum Cost Transposition Distance
  F. Farnoud, C.-Y. Chen, O. Milenkovic, and N. Kashyap, IEEE Information Theory Workshop (ITW), Dublin, Ireland, Aug./Sep. 2010.
• Small-Sample Distribution Estimation over Sticky Channels
  F. Farnoud, O. Milenkovic, and N.P. Santhanam, IEEE Int. Symp. Information Theory (ISIT), Jun./Jul. 2009.
• Reliable Broadcast of Safety Messages in Vehicular Ad Hoc Networks
  F. Farnoud and S. Valaee, In Proc. IEEE INFOCOM, Rio de Janeiro, Brazil, Apr. 2009, Acc. rate: 19.7%.
• Repetition-Based Broadcast in Vehicular Ad Hoc Networks in Rician Channel with Capture
  F. Farnoud and S. Valaee, IEEE INFOCOM Workshops, Phoenix, AZ, Apr. 2008.
• Message Broadcast Using Optical Orthogonal Codes in Vehicular Communication Systems
  F. Farnoud, B. Hassanabadi, and S. Valaee, 1st ACM Int. Workshop on Wireless Networking for Intelligent Transportation Systems, Vancouver, BC, Aug. 2007.
• A Multimessage Capacity Region for Undirected Ring Networks
  S. Yazdi, S. Savari, F. Farnoud, and G. Kramer, IEEE Int. Symp. Information Theory (ISIT), Nice, France, June 2007.

Theses

• Distances on Rankings: from Social Choice to Flash Memories
  Ph.D. Thesis, University of Illinois at Urbana-Champaign, Urbana, IL, May 2013
• Reliable Broadcast of Safety Messages in Vehicular Ad hoc Networks
  M.Sc. Thesis, University of Toronto, Toronto, ON, August 2008