Siddharth Jain

That's me 

Siddharth Jain
PhD Candidate
Advisor: Professor Jehoshua (Shuki) Bruck
Electrical Engineering Department
Caltech
Email: sidjain at caltech dot edu
Phone: +1-6266521958
Photo Credits: Prachi Parihar
Erdős Number: 2

Research Interests

Information and Coding Theory, Bioinformatics, Data Compression, Machine Learning.

Current Research

String Duplication Systems

Motivated by the phenomenon of tandem duplications observed in DNA, we investigate the diversity of sequences that can be generated by a series of tandem duplications applied on a seed. This diversity is characterized by mathematical measures of capacity and expressiveness. Given a sequence, we calculate upper and lower bounds on the number of steps required to reduce the sequence by omitting tandem repeats to its seed. We also develop algorithms that perform near optimal reduction.
  • Siddharth Jain, F. Farnoud, Jehoshua Bruck
    Capacity and Expressiveness of Genomic Tandem Duplication [pdf]
    IEEE Transactions on Information Theory, vol 63, no. 10, pp. 6129-6138, October 2017.
    shorter version in Proceedings of 2015 IEEE International Symposium on Information Theory (ISIT), pp. 1946-1950, Hong Kong.

  • Noga Alon, Jehoshua Bruck, F. Farnoud, Siddharth Jain
    On the Duplication Distance of Binary Strings[pdf]
    in Proceedings of 2016 IEEE International Symposium on Information Theory (ISIT), pp. 260-264 , Barcelona, Spain.

Codes for DNA Storage

Design error correcting codes for storage under duplication and substitution errors.
  • Siddharth Jain, F. Farnoud, M. Schwartz, Jehoshua Bruck
    Noise and Uncertainty in String-Duplication Systems
    in Proceedings of 2017 IEEE International Symposium on Information Theory (ISIT), pp. 3130-3134, Aachen, Germany.

  • Siddharth Jain, F. Farnoud, M. Schwartz, Jehoshua Bruck
    Duplication-Correcting Codes for Data Storage in the DNA of a Living Organism[pdf]
    IEEE Transactions on Information Theory, vol 63, no. 8, pp. 4996-5010, August 2017.
    shorter version in Proceedings of 2016 IEEE International Symposium on Information Theory (ISIT), pp. 1028-1032, Barcelona, Spain.

Past Research

Match Lengths, Zero Entropy and Large Deviations

We investigate the match length expression in the context of Sliding Window Lempel-Ziv Algorithm for zero entropy sequences. We also prove large deviation property for recurrence times and propose entropy estimator based on them under certain mixing conditions.
  • Siddharth Jain, R. K. Bansal
    On Match Lengths, Zero Entropy and Large Deviations - with Application to Sliding Window Lempel-Ziv Algorithm[Link][pdf]
    IEEE Transactions on Information Theory, vol. 61, no. 1, pp. 120-132, January 2015.

  • Siddharth Jain, R. K. Bansal
    On Large Deviation Property of Recurrence Times[Link] [pdf]
    Proceedings of IEEE Intenational Symposium on Information Theory (ISIT) 2013, pp. 2880-2884, Istanbul, Turkey.

  • Siddharth Jain, R. K. Bansal
    On Match Lengths and Asymptotic Behavior of Sliding Window Lempel-Ziv Algorithm for Zero Entropy Sequences[Link][pdf]
    Proceedings of IEEE International Syposium on Information Theory (ISIT) 2013, pp. 2885-2889, Istanbul, Turkey.

Fractional Calculus based approaches in Control

We propose a fractal optimal controller for heart rate control through pacemaker. The dynamics of the the heart rate are modeled by fractional differential equation. We also use a similar approach to perform power management for multi-voltage and frequency islands multiprocesser platforms.
  • Paul Bogdan, Siddharth Jain, Kartikeya Goyal, Radu Marculescu
    Implantable Pacemakers Control and Optimization via Fractional Calculus Approach: A Cyber Physical Systems (CPS) Perspective[Link] [pdf]
    International Conference on Cyber Physical Systems (ICCPS), pp. 23-32, CPS Week 2012, Beijing, China.

  • Paul Bogdan, Siddharth Jain, Radu Marculescu
    Pacemaker Control of Heart Rate Variability: A CPS Perspective[Link][pdf]
    ACM Transactions on Embedded and Computing Systems (TECS), vol. 12, no. 1s, Article 50, March 2013.

  • Paul Bogdan, Radu Marculescu, Siddharth Jain
    Dynamic Power Management for Multi-domain Processor Systems-on-Chip Platforms: An Optimal Control Approach[Link][pdf]
    ACM Transactions on Design Automation of Electronic Systems (TODAES), vol. 18, no. 4, Article 46, October 2013.

  • Paul Bogdan, Radu Marculescu, Siddharth Jain and Rafael Tornero Gavila,
    An Optimal Control Approach to Power Management for Multi-Voltage and Frequency Islands Multi Processor platforms under highly variable workloads[Best Paper Award][Link] [pdf]
    International Syposium on Networks-On-Chip (NOCS) 2012, pp. 35-42, Lyngby, Denmark.

Talks

  • Decoding the Past.
    Molecular Programming Project (MPP) Workshop, Boston, Massachusetts, December 9-11, 2016.

  • Biological Information Channel.
    IPAM Computational Genomics Summer Institute (CGSI), UCLA, July 2016.

  • Duplication Correcting Codes for DNA Storage.
    Molecular Programming Project (MPP) Workshop, Seattle, Washington, January 15-18, 2016.

Posters

  • Siddharth Jain, F. Farnoud, M. Schwartz, Jehoshua Bruck
    Capacity and Diversity of Tandem Duplication.
    Invited Poster in Molecular Programming Project (MPP) Workshop, San Francisco, California, January 9-11, 2015.