Milenkovic Coding/Algorithms/Bioinformatics Group

 

Publications

Book Chapters

  • Structured LDPC codes
    B.Vasic, E.Kurtas, A.Kuznetsov, and O.Milenkovic, CRC Coding and Signal Processing for Magnetic Recording Systems
  • Coding and Detection for Multitrack Systems
    B.Vasic and O.Milenkovic, CRC Coding and Signal Processing for Magnetic Recording Systems.
  • The Three Faces of DNA/RNA Sequence Hybridization
    O. Milenkovic, Systems Bioinformatics: An Engineering Case-Based Approach, pp. 285-313, Artech House, 2007.
  • Data Processing and Storage in Cells: An Information-Theoretic Viewpoint
    O. Milenkovic, Advances in Information Recording, Editors P. Siegel, E. Soljanin, A. van Wijngaarden, and B. Vasic, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, vol. 73, pp. 105-147, 2008.

Journal Papers (Published/Accepted/Submitted)

  1. J. Dingel and O. Milenkovic, List-Decoding Methods for Inferring Gene Networks, submitted, August 2008.

  2. A. McGregor and O. Milenkovic, On the Hardness of Approximating Stopping and Trapping Sets, submitted to IEEE Trans. on Inform. Theory, August 2008.

  3. W. Dai, M. Sheikh, O. Milenkovic, and R. Baraniuk, Compressive Sensing DNA Microarrays, submitted, July 2008.

  4. W. Dai and O. Milenkovic, Weighted Superimposed Codes and Integer Compressive Sensing, submitted to IEEE Trans. on Inform. Theory, June 2008.

  5. W. Dai and O. Milenkovic, Subspace Pursuit for Compressive Sensing: Closing the Gap Between Performance and Complexity, submitted, March 2008.

  6. T. Hehn, J. Huber, O. Milenkovic, and S. Laendner , Multiple-Bases Belief-Propagation for Decoding of Short Block Codes, submitted August 2007, in revision.

  7. S. Laendner, T, Hehn, O. Milenkovic, and J. Huber, Two methods for reducing the error floor of LDPC codes (title changed to The Trapping Redundancy of Block codes), accepted conditioned on minor revisions, 2008.

  8. T. Hehn, O. Milenkovic, Laendner, and J. Huber, The Stopping Redundancy Hierarchy and Automorphism Group Decoding of Cyclic Codes, accepted for publication, IEEE Trans. on Inform. Theory, 2008.

  9. V. Nagarajan, S. Laendner, N. Jayakumar, O. Milenkovic and S. Khatri, High-Throughput VLSI Implementations of Iterative Decoders and Related Code Construction Problems,  The Journal of VLSI Signal Processing, Vol. 49, No. 1, pp. 185-206, Springer Verlag, May 2007.

  10. O. Milenkovic, E. Soljanin, and P. Whiting, Asymptotic Spectra of Trapping Sets in Regular and Irregular LDPC Code Ensembles,
    IEEE Trans. on Info. Theory, vol. 53, no. 1, pp. 39-55, January 2007.

  11. S. Laendner and O. Milenkovic, Codes Based on Latin Squares: Stopping Set, Trapping Set, and Cycle-Length Distribution Analysis, IEEE Trans. on Communication Theory, Vol. 55, No. 2, pp. 303-312, February 2007.

  12. O. Milenkovic, D.Leyba, and N. Kashyap, Shortened Array Codes of Large Girth,
    IEEE Trans. on Info. Theory, Vol. 5, No. 8, pp. 3707-3722, August 2006.

  13. O. Milenkovic and N. Kashyap, On the Design of Codes for DNA Computing,
    Lecture Notes in Computer Science 3969, pp. 100-119, Springer Verlag, Berlin-Heidelberg, 2006.

  14. V. Kumar and O. Milenkovic, On Unequal Error Protection LDPC Codes Based on Plotkin-type Constructions, IEEE Transactions on Communications, vol. 54, no. 6, pp. 994-1005, June 2006.

  15. V. Kumar and O. Milenkovic, On Graphical Representations of Algebraic Codes Suitable for Iterative Decoding, IEEE Communication Letters, Vol. 9, No. 8, pp. 729-731, August 2005.

  16. O.Milenkovic and K. Compton, Average Case Analysis of Gosper's Algorithm for a Class of Urn Model Inputs, Algorithmica, Vol. 43, No. 3, pp. 211-244, September 2005.

  17. I. Djordjevic, O. Milenkovic, and B. Vasic, Generalized LDPC Codes for Long-Haul Optical Communication Systems, IEEE Journal of Lightwave Technology, Vol. 23, No. 5, pp. 1939-1946, May 2005.

  18. O. Milenkovic, Higher Weight and Coset Weight Enumerators of Formally Self-Dual codes,
    Designs, Codes and Cryptography, Vol. 35, pp. 81-109, April 2005.

  19. O. Milenkovic, I. Djordjevic, and B. Vasic, Block-Circulant Low-Density Parity-Check Codes for Optical Communication Systems, IEEE Journal of Selected Topics in Quantum Electronics, Vol. 10, No. 2, pp. 294-299, April 2004.

  20. B. Vasic, O. Milenkovic, Combinatorial Constructions of Low-Density Parity-Check Codes for Iterative Decoding, IEEE Transactions on Information Theory, Vol. 50, No.6, pp 1156-1176, June 2004.

  21. O. Milenkovic, K. Compton, Probabilistic Transforms and Combinatorial Urn Models,
    Combinatorics, Probability and Computing, pp. 645-675, Vol. 13 No. 4-5, July-September 2004.

  22. O. Milenkovic, S. Coffey, K. Compton, The Third Support Weight Enumerators of the [32,16,8] Doubly-Even, Self-Dual Codes, IEEE Transactions on Information Theory, Vol. 49, No. 3, March 2003.

  23. O. Milenkovic, and B. Vasic, Permutation (d,k) Codes: Efficient Enumerative Coding and Phrase Length Distribution Shaping, IEEE Transactions on Information Theory, Vol. 46, No.7, pp. 2671-2675, Nov. 2000.

  24. B. Vasic, S.McLaughlin, and O. Milenkovic, Shannon Capacity of M-ary Redundant Multitrack Runlength Limited Codes, IEEE Transactions on Information Theory, Vol. 44, No. 2, pp. 766-774, March 1998.

  25. B. Vasic, and O. Milenkovic, Power Spectral Density of Multitrack (0,G/I) Codes,
    IEEE Electronics Letters, Vol. 33, No. 9, pp.784-786, April 1997.

  26. O. Milenkovic, S. McLaughlin, B.Vasic, Scrambling for Unequiprobable Signaling, IEEE Electronics Letters, Vol. 32, No. 17, pp. 1551-1552, Aug. 1996.

Journal Papers (In Preparation)

  1. O. Milenkovic, Constrained Coding via Context-Free Grammars with Applications in Bioinformatics, May 2008.

Selected Conference Publications

  1. Information and Coding Theory in Bioinformatics

    2. J. Dingel and O. Milenkovic, “A List-Decoding Approach for Inferring the Dynamics of Gene Regulatory Networks,” accepted for presentation at ISIT’08, Toronto , Canada , 2008.

    M. Sheikh, O. Milenkovic, and R. Baraniuk, “Designing compressive sensing DNA microarrays,”Proceedings of the IEEEWorkshop on Computational Advances in Multi-Sensor Adaptive Processing (CAMSAP), St. Thomas, U.S. Virgin Islands, December 2007.

    M. Sheikh, S. Sarvotham, Olgica Milenkovic, and R. Baraniuk, “DNA array decoding from nonlinear measurements by belief propagation,” Proceedings of the IEEE Workshop on Statistical SignalProcessing (SSP), Madison , Wisconsin , August 2007.

    D. Huang and O. Milenkovic, “Superimposed coding for iterative detection of DNA microarray spot failures,” accepted for presentation at IEEE Genetic Signal Processing and Statistics (GENSIPS) conference, 2008.

    J. Dingel and O. Milenkovic, “Decoding the dynamics of gene regulatory networks under a dynamical model,” accepted for presentation at the Fifth International Workshop on Computational Systems Biology, Leipzig, Germany, 2008 (voted one of top three papers at the conference).

    O. Milenkovic, “Constrained Coding via Context-Free Grammars with Applications to RNA Sequence Analysis,” Proceedings of the ISIT’2007.

    O. Milenkovic and N. Kashyap, “Construction of DNA Codes which Avoid Secondary Structures,” Proceedings of the IEEE International Symposium on Information Theory 2005 (5 pages), Adelaide , Australia , September 2005.

    O. Milenkovic, N. Kashyap, and B. Vasic, “Coding for DNA Computers Controlling Gene Expression Levels,” Invited paper, IEEE Conference on Decision and Control, CDC’2005, (6 pages) Seville , Spain , December 2005.

    S. Chilappagari, O. Milenkovic, and B. Vasic, “Compression of DNA Sequences using Fractal Grammars and Integer Wavelet Transforms,” Proceedings of the Genetic Signal Processing Symposium (GENSIPS), (2 pages) Rhode Island.

    O. Milenkovic and N. Kashyap, “Constructions of Codes for DNA Computing,” Proceedings of the Workshop on Coding and Cryptography, WCC’05, pp. 204-214, Bergen , Norway , March 2005.

    O. Milenkovic and B. Vasic, “Information Theory Problems in Genetics,” Proceedings of the IEEE Information Theory Workshop, ITW’2004, pp. 60-64, San Antonio, October 2004.

  2. LDPC Codes and Iterative Decoding

    3. W. Dai and O. Milenkovic, “Iterative Subspace Pursuit Decoding of Euclidean SuperimposedCodes,” TURBO CODING 2008 Symposium, Lausanne , September 2008.

    A. McGregor and O. Milenkovic, “On the Hardness of Approximating Stopping and TrappingSets,” Proceedings of the ITW’08, Lake Tahoe , 2007.

    T. Hehn, S. Laendner, O. Milenkovic, and J. Huber, “The Stopping Redundancy Hierarchy of Cyclic Codes”, presented at the 44th Allerton Conference 2006 (regular paper), September 2006.

    S. Laendner, T. Hehn, O. Milenkovic, and J. Huber, “When Does one Parity-Check Equation Matter?,” Proceedings of the Globecom 2006, San Fracisco, 2006.

    O. Milenkovic, E. Soljanin , and P. Whiting, “Stopping and Trapping Sets in Generalized Covering Arrays,” Proceedings of the CISS’2006, March 2006.

    O. Milenkovic, E. Soljanin, and P. Whiting, “Trapping Sets in Irregular LDPC Code Ensembles,” Proceedings of the ICC’2006, (6 pages), December 2005 (the paper received honorable mentioning as the runner up for the best paper award).

    O. Milenkovic, E. Soljanin and P. Whiting, “Asymptotic Distributions of Combinatorial Configurations in Random Regular LDPC Code Ensembles,” presented at the 43rd Allerton Conference on Communications, Control and Computing (long paper), September-October 2005.

    S. Laendner and O. Milenkovic, “Algorithmic and Combinatorial Analysis of Trapping Sets in Structured LDPC Codes,” Proceedings of the 2005 International Conference on Wireless Networks, Communications and Mobile Computing,WirelessCom 2005, (6 pages) Maui, Hawaii, June 2005.

    V. Kumar and O. Milenkovic, “On Representations of Algebraic Codes Suitable for Iterative Decoding,”Proceedings of the 39th Conference on Information Sciences and Systems, CISS’2005, pp. 41, Baltimore, March 2005.

    I. B. Djordjevic, O. Milenkovic, and B. Vasic, “Generalized Low-Density Parity-Check Codes for Long-Haul High-Speed Optical Communication,” Proceedings of the Optical Fiber Communication Conference and Exposition and The National Fiber Optic Engineers Conference, OFC’2005, OThW6, (2 pages), Washington D.C., March 2005.

    V. Kumar and O. Milenkovic, “Unequal Error Protection LDPC Codes Based on Plotkin-Type Constructions,” Proceedings of the IEEE Global Telecommunications Conference, Globecom 2004, CT15-2, pp. 493-497, Dallas , Texas , December 2004.

    D. Leyba, O. Milenkovic, D. Bennet, and N. Kashyap, “New Partition Regular Sequences and Generalized Array Codes of Large Girth,” Proceedings of the 42nd Annual Conference on Communications, Control and Computing, pp. 240-249, Allerton, IL, October 2004.

    V. Kumar, O. Milenkovic, and B. Vasic, “Structured LDPC Codes over GF(2m) and Companion Matrix Based Decoding,” Proceedings of the IEEE International Symposium on Information Theory, ISIT’2004, p. 226, Chicago, June-July 2004.

    O. Milenkovic, V. Kumar, and B. Vasic, “Companion Matrix Based Decoding” presented at IEEE CTW’2004, Capri (no Proceedings published).

    O. Milenkovic and S. Laendner, “Analysis of the Cycle Structure of LDPC Codes Based on Latin Squares,” Proceedings of the IEEE International Conference on Communications ICC’2004, CT15-5, pp. 777-781, Paris , France , June 2004.

    O. Milenkovic, K. Prakash, and B. Vasic, “Regular and Irregular LDPC Codes Based on Cycle-Invariant Difference Sets,” Proceedings of the 41st Annual Allerton Conference on Communication, Control and Computing, pp. 1700-1701, October 2003.

  3. Algebraic Error-Control Coding

    4. W. Dai and O. Milenkovic, “Weighted `1 Superimposed Codes,” accepted for presentation, CodingTheory Days in Saint Petersburg , October 2008.

    C. Lott, O. Milenkovic, and E. Soljanin, “Hybrid ARQ: theory, state of the art and future directions,” Proceedings of the ITW’07, Bergen , Norway , 2007.

    T. Hehn, O. Milenkovic, S. Laendner, and J. Huber, “Iterative Permutation Decoding and the Stopping Redundancy Hierarchy of Codes,” Proceedings of the ISIT, Nice, France , 2007.

    T. Hehn, S. Laendner, J. Huber, and O. Milenkovic, “Multiple Bases Decoding of Algebraic Codes,” Proceedings of the ISIT, Nice, France , 2007.  

    V. Kumar and O. Milenkovic, “Improved Distance Bounds for Recursive Decoding of Reed-Muller Codes,” Proceedings of the Eighth International IEEE Symposium on Communication Theory and Applications 2005, pp. 326-331, St. Martin’s College, Ambleside, UK, July 2005.

    O. Milenkovic and B. Vasic, “Asymptotic Analysis of A* Maximum Likelihood Decoding with Reliability Reordering,” Proceedings of the Information Theory Workshop, ITW’2003, pp. 316-319, Sorbone, Paris , April 2003.

    O. Milenkovic and K. Compton, “A Method for Reducing the Number of Unknown Coefficients of Generalized Hamming Weight Enumerators,” Proceedings of the 2002 IEEE International Symposium on Information Theory, p. 234, Lauzanne, Switzerland, July 2002.

    O. Milenkovic, “On the Generalized Hamming Weight Enumerators and Coset Weight Distributions of Even, Isodual Codes ,” Proceedings of the 2001 IEEE International Symposium on InformationTheory, p. 62, Washington D.C. , USA , June 2001.

  4. Constrained Coding

    5. O. Milenkovic and B. Vasic “Power spectral density of multitrack (O,G/I) codes,” Proceedings of theIEEE Information Theory Symposium, Ulm , Germany , p. 142, July 1997.

    B. Vasic and O. Milenkovic, “Cyclic Two-dimensional IT Reducing Codes,” Proceedings of the IEEE \Information Theory Symposium, Ulm , Germany , p. 414, July 1997.

    S. McLaughlin, O. Milenkovic, and B. Vasic, “Channel Capacity of M-ary Multitrack Runlength Limited Channels ,” Proceedings of the IEEE Information Theory Symposium, Ulm, Germany, p. 139, July 1997.

    O. Milenkovic, B. Vasic, and S. Denic, “Novel M-ary (d,k) Codes,” accepted for publication in the Proceedings of the Canadian Workshop on Information Theory, Toronto , Canada , June 1997.

    B. Vasic, O. Milenkovic, D.Vasic, “Channel Capacities and Spectra of Maxentropic (O,G/I) Matched-Spectral-Null Sequences,” Proceedings of the IEEE IT Workshop, (1 page) Rydzyna , Poland , 1995.

  5. Information Theory

    6. B. Vasic and O. Milenkovic, “Cyclic Two-dimensional IT Reducing Codes,” Proceedings of the IEEE \Information Theory Symposium, Ulm , Germany , p. 414, July 1997.

    S. Denic, C. Charalambous, S. Djouadi, and O. Milenkovic, “Capacity of MIMO Gaussian Channelswith H1 Normed Channel Uncertainties,” Proceedings of the Canadian Workshop on Information Theory, pp. 315-318, Montreal, Canada, 2005.

    O. Milenkovic and S. Denic, “Characterization of Generalized Tsallis Entropies,” Proceedings of the Canadian Workshop on Information Theory, pp. 20-23, Montreal , Canada 2005.

    V. Nagarajan and O. Milenkovic, “Structured LDPC Codes over Polya Urn Model Channels,” Proceedings of the IEEE Canadian Conference on Electrical and Computer Engineering, IEEE CCECE’2004,V1-0541, pp. 543-546, Niagara Falls, May 2004.

  6. Compressive Sampling

    7. W. Dai and O. Milenkovic, “Sparse Weighted Euclidean Superimposed Coding for Integer CompressedSensing” Proceedings of the CISS, Princeton , 2008.

    W. Dai and O. Milenkovic, “Weighted Euclidean Superimposed Codes for Integer Compressed Sensing,” accepted for presentation at ITW’08, Porto , Portugal , 2008.

  7. Theoretical Computer Science

    8. O. Milenkovic, “Analysis of Combinatorial Bin Models with Application in Coding Theory,” Proceedings of the IEEE International Symposium on Information Theory, ISIT’2004, p. 273, Chicago, July 2004.

  8. VLSI Implementations

    9. V. Nagarajan, N. Jayakumar, S. Khatri and O. Milenkovic, “High Throughput VLSI Implementations of Iterative Decoders and Related Code Construction Problems,” Proceedings of the IEEE Global Telecommunications Conference, Globecom 2004, CT11-8 (5 pages), Dallas , Texas , December 2004.

     

Invited Conference Papers

    W. Dai and O. Milenkovic, “Low Complexity Comressive Sensing Reconstruction Algorithms,” Special Session “Algorithmic Probability and Combinatorics,” American Mathematical Society (AMS) Meeting, October 4-5, Vancouver , Canada .

    O. Milenkovic, “Group Testing for DNA Microarray Designs,” Schloss Dagstuhl Seminar on Group Testing in the Life Sciences, July 2008.

    J. Dingel, O. Milenkovic, and A. Ashikhmin, “List Decoding of Reed-Muller Codes with Applications in Bioinformatics,” Mathematical Theory of Networks and Systems, July 2008.

    J. Dingel and O. Milenkovic, ”Reverse Engineering of Gene Regulatory Networks via Iterative List Decoding,” Proceedings of the ITW’08, Porto , Portugal , 2008.

    W. Dai, N. Kiyavash, and O. Milenkovic, “Spherical Codes for Sparse Digital Fingerprinting,” Spring Central Meeting of the American Mathematical Society, AMS’08, Special Session on Algebraic Aspects of Coding Theory, Bloomington, IN, April 2008.

    W. Dai and O. Milenkovic, “Constrained Compressed Sensing via Superimposed Coding,” presented at the Third Information Theory and Applications Workshop, ITA’08, San Diego , CA , 2008.  

    J. Dingel and O. Milenkovic, ”Reverse Engineering of Gene Regulatory Networks via Iterative List Decoding,” presented at the Third Information Theory and Applications Worksho, ITA’08, San Diego, CA, 2008.

    W. Dai and O. Milenkovic, “Coding-Theoretic Problems in Genetics: Superimposed Codes for Compressed Sensing DNA Microarrays,” OberwolfachWorkshop on Coding Theory, December 2007.

    O. Milenkovic, E. Soljanin, and P. Whiting, “Asymptotic Enumeration of Trapping Sets in Rando Tanner Graph Ensembles,” Regional American Mathematical Society Meeting, Special Session on Algorithmic Probability and Combinatorics, AMS’07, Chicago, October 2007.

    O. Milenkovic, R. Baraniuk, T. Simunic-Rosing, “Compressed Sensing Meets Bioinformatics: A New DNA Microarray Architecture,” Information Theory and Applications Workshop, San Diego , January, 2007.

    O. Milenkovic, “On the Generalized Reversal Distance,” American Mathematical Society Meeting, New Orleans , January 2007.

    O. Milenkovic and E. Soljanin, “Enumerating RNA Secondary Structures: A Constrained Coding Approach,” Asilomar Conference on Signals, Systems and Communication, October 2006.

    O. Milenkovic, “Enumerating RNA Motifs,” Allerton Conference on Communication, Control and Computing,September 2006.

    O. Milenkovic, “Error and Quality Control Coding for DNA Microarrays,” Information TheoryWorkshoporganized as part of the Inauguration Ceremony of the Jacobs School of Engineering Center for Information Theory and its Applications, San Diego, February 2006.

    O. Milenkovic, “Constrained and Error-Control Coding for DNA Computers,” Workshop on Statistical Physics and Coding, Santa Fe , January 2005 (joint work with N. Kashyap).

    O. Milenkovic, “Problems in Combinatorial and Number Theory Arising in the Construction of LDPC Codes,” American Mathematical Society Meeting, Evanston , Illinois , October 2004.

    O. Milenkovic and B. Vasic, “How DNA Stores Information and Efficient DNA Storage,” DIMACS Workshop on Theoretical Advances In Information Recording, March 2004.

    O. Milenkovic and K. Compton, “Average Case Analysis of Gosper’s Algorithm,” American Mathematical Society Meeting, Bloomington , Indiana , April 2003.

    K. Compton and O. Milenkovic, “Probabilistic transforms in the analysis of algorithms,” Eight Seminar on Analysis of Algorithms, Strobl , Austria , June 2002.

    K. Compton and O. Milenkovic, “An Analysis Inspired by Gosper’s Algorithm,” Seventh Seminar on Analysis of Algorithms, Tatihou , France , July 2001.

    BANFF , Special Session on Applications of Matroid Theory to Coding, 2009.