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This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…
Magnetic resonance imaging (MRI) reconstruction is an active inverse problem which can be addressed by conventional compressed sensing (CS) MRI algorithms that exploit the sparse nature of MRI in an iterative optimization-based manner.…
Let G be a finite strongly connected aperiodic directed graph in which each edge carries a label from a finite alphabet A. Then G induces a trellis coded quantizer for encoding an alphabet A memoryless source. A source sequence of long…
We consider the reconstruction of a codeword from multiple noisy copies that are independently corrupted by insertions, deletions, and substitutions. This problem arises, for example, in DNA data storage. A common code construction uses a…
Tree search methods have demonstrated impressive performance in code generation. Previous methods combine tree search with reflection that summarizes past mistakes to achieve iterative improvement. However, these methods face significant…
In the framework of multidimensional Compressed Sensing (CS), we introduce an analytical reconstruction formula that allows one to recover an $N$th-order $(I_1\times I_2\times \cdots \times I_N)$ data tensor $\underline{\mathbf{X}}$ from a…
In a distributed storage systems (DSS), regenerating codes are used to optimize bandwidth in the repair process of a failed node. To optimize other DSS parameters such as computation and disk I/O, Distributed Replication-based Simple…
Channeled spectropolarimetry measures the spectrally resolved Stokes parameters. A key aspect of this technique is to accurately reconstruct the Stokes parameters from a modulated measurement of the channeled spectropolarimeter. The…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
There are applications that may require removing the trace of a sample from the system, e.g., a user requests their data to be deleted, or corrupted data is discovered. Simply removing a sample from storage units does not necessarily remove…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…
The population recovery problem asks one to recover an unknown distribution over $n$-bit strings given access to independent noisy samples of strings drawn from the distribution. Recently, Ban et al. [BCF+19] studied the problem where the…
To achieve ultra-high storage capacity, the data tracks are squeezed more and more on the magnetic recording disks, causing severe intertrack interference (ITI). The multihead multitrack (MHMT) detector is proposed to better combat ITI.…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
The diffusion models including Denoising Diffusion Probabilistic Models (DDPM) and score-based generative models have demonstrated excellent performance in speech synthesis tasks. However, its effectiveness comes at the cost of numerous…
Software Defined Networks (SDN) face many security challenges today. A great deal of research has been done within the field of Intrusion Detection Systems (IDS) in these networks. Yet, numerous approaches still rely on deep learning…
Compressive sensing (CS) has been studied and applied in structural health monitoring for wireless data acquisition and transmission, structural modal identification, and spare damage identification. The key issue in CS is finding the…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…