Siddharth Jain

Current Research

Data Quality and Value

Netanel Raviv , Siddharth Jain, Jehoshua Bruck
Data Equals Money, But How Much? On Mathematical Methods of Data Pricing
CodML Workshop, ICML 2019

Disease Risk Estimation

The evolution channel of the human genome is controlled by hereditary, environmental and stochastic factors. Repeat regions in the genome can be traced back in time algorithmically to make inference about the effect of the aforementioned factors on the mutation rate of the genome. By inferring the evolutionary history of the tandem repeat regions, we show how this knowledge can be used to make predictions about the risk of incurring a mutation based disease, specifically cancer.

Siddharth Jain, B. Mazaheri, N. Raviv, Jehoshua Bruck
Mutation Profile and related labeled Genomic Components, Methods and Systems
Patent application filed, 2019.

Siddharth Jain, B. Mazaheri, N. Raviv, Jehoshua Bruck
Cancer Classification from Healthy DNA using Machine Learning
bioRxiv [Link]

Siddharth Jain, B. Mazaheri, N. Raviv, Jehoshua Bruck
Short Tandem Repeats Information in TCGA is Statistically Biased by Amplification
bioRxiv [Link]

Balanced Sequences

Many genomes including our own human genome share a property termed as 2nd Chargaff Rule. According to this rule the number of occurences of a k-mer is almost equal to the number of occurences of it's reverse complement. For example, #A = #T, #C = #G, #AC = #GT and so on. This property is observed to hold upto a certain k known as K-Limit which depends on the length of genome. For human genome, the K-Limit is 10. In this project, we investigate models based on reversed tandem and interspered duplications for sequence generation that can give sequences satisfying the 2nd Chargaff Rule. We find fundamental limit onthe number of generations required to generate such balanced sequences for a given K-Limit. We compare the sequences generated by these models with real genome sequences and find results that give valubale insights into the evolution of genomes.
  • Siddharth Jain, N. Raviv, Jehoshua Bruck
    Attaining the 2nd Chargaff Rule by Tandem Duplications[pdf]
    accepted in 2018 IEEE International Symposium on Information Theory (ISIT)

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
    Duplication Distance to the Root for Binary Sequences[pdf]
    IEEE Transactions on Information Theory, vol 63, no. 12, pp. 7793-7803, December 2017.

  • 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 live-DNA Storage

The advances in CRISPR have led to the realization of storing information inside the DNA of a living organism. As the cell replicates, this information can become erroneous due to mutation errors. Recovery of the stored information requires design of error correcting schemes that can correct these evolutionary errors. We investigated an evolution channel with unbounded duplication errors and came up with the error correcting codes. We also investigated errors caused by substitution mutations alongside duplications to come up with sphere packing bounds.
  • Siddharth Jain, F. Farnoud, M. Schwartz, Jehoshua Bruck
    Noise and Uncertainty in String-Duplication Systems[pdf]
    in Proceedings of 2017 IEEE International Symposium on Information Theory (ISIT), pp. 3120-3124, 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.