Publications

2023

Saad Mneimneh, Three Points Make a Right Triangle. MoMATH conference on Mathematics Of Various Entertaining Subjects MOVES, August 2023.

Alexey Nikolaev and Saad Mneimneh, Modeling and Analysis of Affiliation Networks with Preferential Attachment and Subsumption. Phys. Rev. E 108, 014310, July 2023.

2022

Saad Mneimneh, A Binomial Sum of Harmonic Numbers. Elsevier Journal of Discrete Mathematics, 346(1), accepted September 2022.

Saad Mneimneh, Living on a Random Torus. MoMATH conference on Mathematics Of Various Entertaining Subjects MOVES, August 2022.

2021

Lia Di, Saymon Akther, Edgaras Bezrucenkovas, Larisa Ivanova, Brian Sulkow, Bing Wu, Saad Mneimneh, Maria Gomes-Solecki, and Weigang Qiu. "Maximum antigen diversification in a lyme baterial population and evolutionary strategies to overcome pathoden diversity." The ISME Journal pp. 1-18, August 2021.

2020

Saad Mneimneh. "Simple Variations on The Tower of Hanoi: A Study of Recurrences and Proofs by Induction." Teaching Mathematics and Computer Science 17(2), 131-158. (there is a calculation mistake in the speed section, 544x10^3 should be 1089x10^3 and 146 should be 136) PDF

2019

Syed Ali Ahmed, Saad Mneimneh. "Gibbs/MCMC Sampling for Multiple RNA Interaction with Suboptimal Solutions." IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10.1109/TCBB.2018.2890519.

2018

Syed Ali Ahmed, Saman Farhat, and Saad Mneimneh. "Making Multiple RNA Interaction Practical." Proceedings of the International Conference on Combinatorial Optimization and Applications COCOA 2018, December 2018, Atlanta Georgia.

2017

Saad Mneimneh and Syed Ali Ahmed. "Combinatorial and Probabilistic Aspects of the Multiple RNA Interaction Problem." Poster for RECOMB 2017, May 2017 Hong Kong.

Saad Mneimneh and Alexey Nikolaev. "Counting with Code." ACM Journal of Computing Sciences in Colleges, April 2017 (also presented at CCSCNE 2017). PDF

Saad Mneimneh, Suman Bhunia, Felisa Vazquez-Abad, Shamik Sengupta. "A Game-Theoretic and Stochastic Survivability Mechanism against Induced-Attacks in Cognitive Radio Networks." Journal of Pervasive and Mobile Computing, April 2017. PDF

Alexey Nikolaev, Saad Mneimneh, Amotz Bar-Noy, Ram Ramanathan. "Controlled Growth of Simplicial Complex Networks." In 2017 IEEE Conference on Computer Communications Workshops INFOCOM WKSHPS (also presented at NetSciX 2017).

2016

Radford, Jason, Amotz Barnoy, Alexey Nikolaev, Saad Mneimneh, David Lazer, and Ram Ramanathan. "Testing Higher-Order Network Structures in an Online Experiment." In Proceedings of the 19th ACM Conference on Computer Supported Cooperative Work and Social Computing Companion, pp. 377-380. ACM, 2016. PDF

Mneimneh, Saad, and Syed Ali Ahmed. "Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-optimal Solutions." In International Conference on Algorithms for Computational Biology, pp. 78-90. Springer International Publishing, 2016. PDF

Mneimneh, Saad, and Syed Ali Ahmed. "A sampling approach for multiple RNA interaction: Finding sub-optimal solutions fast." In International Conference on Bioinformatics Models, Methods, and Algorithms, 2016.

2015

Mneimneh, Saad, and Saman Farhat. "The Offline Carpool Problem Revisited." In International Symposium on Mathematical Foundations of Computer Science, pp. 483-492. Springer Berlin Heidelberg, 2015. PDF

Mneimneh, Saad, and Farhat Saman. "The offline carpool problem." In the Cologne-Twente Workshop on Graphs and Combinatorial Optimization, Turkey, May 2015.

Mneimneh, Saad, and Syed Ali Ahmed. "Multiple RNA interaction: beyond two." IEEE transactions on nanobioscience 14, no. 2 (2015): 210-219. PDF

Mneimneh, Saad. "Fibonacci in The Curriculum: Not Just a Bad Recurrence." Proceedings of the 46th ACM Technical Symposium on Computer Science Education. ACM, 2015. PDF

Assarpour, Ali, Saman Farhat, Ou Liu, Alexey Nikolaev, Amotz Bar-Noy, Prithwish Basu, Saad Mneimneh, and Ram Ramanathan. "Measuring the strength of networks of teams: Metrics and properties." In 2015 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS), pp. 414-419. IEEE, 2015. PDF

2014

Ahmed, Syed Ali, and Saad Mneimneh. "Multiple RNA interaction with sub-optimal solutions." In International Symposium on Bioinformatics Research and Applications, pp. 149-162. Springer International Publishing, 2014. PDF

2013

Nikolaev, Alexey, and Saad Mneimneh. "A mathematical model for secondary structure in proteins." In Bioinformatics and Bioengineering (BIBE), 2013 IEEE 13th International Conference on, pp. 1-6. IEEE, 2013. PDF

Mneimneh, Saad, Syed Ali Ahmed, and Nancy L. Greenbaum. "Multiple RNA Interaction-Formulations, Approximations, and Heuristics." In BIOINFORMATICS, pp. 242-249. 2013.

Ahmed, Syed Ali, Saad Mneimneh, and Nancy L. Greenbaum. "A combinatorial approach for multiple RNA interaction: formulations, approximations, and heuristics." In International Computing and Combinatorics Conference, pp. 421-433. Springer Berlin Heidelberg, 2013. PDF

Nikolaev, Alexey, and Mneimneh, Saad. "From sequence to structure: A percolation theory approach." In Informs Computing Society, January 2013.

Nikolaev, Alexey, and Mneimneh, Saad. "A model of clusters in binary and ternary strings applied to protein secondary structure prediction." In Applied Mathematics Modeling and Computational Sciences meeting AMMCS 2013, Canada.

2012

Mneimneh, Saad. "Crossing Over… Markov Meets Mendel." PLoS Comput Biol 8, no. 5 (2012): e1002462. PDF

2011

Mneimneh, Saad. "Crossing Over: Markov Meets Mendel." RECOMB-BE satellite conference on Bioinformatics Education, 2011, Vienna.

2009

Mneimneh, Saad. "On the approximation of optimal structures for RNA-RNA interaction." IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 6.4 (2009): 682-688. PDF

Xianfa Xie, Juan Coronado, Saad Mneimneh, Susan Epstein, Weigang Qiu, and Peter Lipke. "On the evolution of fungal cell walls." In IV international Conference on Molecular Mechanisms of Fungal Cell Wall Biogenesis, Warsaw 2009.

2008

Mneimneh, Saad. "Matching from the first iteration: An iterative switching algorithm for an input queued switch." IEEE/ACM Transactions on Networking (TON) 16, no. 1 (2008): 206-217. PDF

2007

Coronado, Juan E., Saad Mneimneh, Susan L. Epstein, Wei-Gang Qiu, and Peter N. Lipke. "Conserved processes and lineage-specific proteins in fungal cell wall evolution." Eukaryotic cell 6, no. 12 (2007): 2269-2277. PDF

Mneimneh, Saad. "How to waste 2/3 of the throughput of a switch: a tight characterization of load balancing algorithms that do not split." In 2007 Workshop on High Performance Switching and Routing, pp. 1-5. IEEE, 2007. PDF

2006

Mneimneh, Saad, and Franck Quessette. "Linear complexity algorithms for maximum advance deflection routing in some networks." In 2006 Workshop on High Performance Switching and Routing, pp. 127-133. IEEE, 2006. PDF

Mneimneh, Saad. "Load balancing in a switch without buffers." In 2006 Workshop on High Performance Switching and Routing, pp. 193-200. IEEE, 2006. PDF

Mneimneh, Saad. "On The Approximation of Optimal Structures for RNA-RNA Interaction." In LSS Computational Systems Bioinformatics CSB 2006, Stanford University.

2004

Mneimneh, Saad. "RNA-RNA interaction is NP-complete and some approximation algorithms." SMU technical report 04-CSE-03, July 2004.

Mneimneh, Saad. "An iterative switching algorithm with (possibly) one iteration." In Network Computing and Applications, 2004.(NCA 2004). Proceedings. Third IEEE International Symposium on, pp. 223-231. IEEE, 2004.

2003

Mneimneh, Saad, and Kai-Yeung Siu. "On achieving throughput in an input-queued switch." IEEE/ACM Transactions on Networking (TON) 11, no. 5 (2003): 858-867. PDF

2002

Mneimneh, Saad, Vishal Sharma, and Kai-Yeung Siu. "Switching using parallel input-output queued switches with no speedup." IEEE/ACM Transactions on Networking 10, no. 5 (2002): 653-665. PDF

Mneimneh, Saad, and Kai-Yeung Siu. "Scheduling unsplittable flows using parallel switches." In Communications, 2002. ICC 2002. IEEE International Conference on, vol. 4, pp. 2410-2415. IEEE, 2002. PDF

Mneimneh Saad. "Algorithmic Aspects of High Speed Switching." MIT Thesis, 2002.

1999

Rabih Zbib, Saad Mneimneh et al. "The Trierarch Trigger Architecture." In Proceedings of the Advanced Telecommunication and Information Distribution Research Program ATIRP (DoD/ARL), February 1999.

1998

Judson Harward, Albert Bailey, Issam Bazzi, Saad Mneimneh et al. "An Improved Hierarchical Caching Architecture for Low Bandwidth Networks." In Proceedings of the Advanced Telecommunication and Information Distribution Research Program ATIRP (DoD/ARL), February 1998.

1997

Mneimneh Saad et al. "A Generalized Data Stream Interface." In Proceedings of the Advanced Telecommunication and Information Distribution Research Program ATIRP (DoD/ARL), January 1997.