Related papers: The Random Variables of the DNA Coverage Depth Pro…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
Unsupervised dimensionality reduction is one of the commonly used techniques in the field of high dimensional data recognition problems. The deep autoencoder network which constrains the weights to be non-negative, can learn a low…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and…
While most current high-throughput DNA sequencing technologies generate short reads with low error rates, emerging sequencing technologies generate long reads with high error rates. A basic question of interest is the tradeoff between read…
Density reconstruction from X-ray projections is an important problem in radiography with key applications in scientific and industrial X-ray computed tomography (CT). Often, such projections are corrupted by unknown sources of noise and…
We address the problem of securing distributed storage systems against eavesdropping and adversarial attacks. An important aspect of these systems is node failures over time, necessitating, thus, a repair mechanism in order to maintain a…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
The explosion in the volumes of data being stored online has resulted in distributed storage systems transitioning to erasure coding based schemes. Yet, the codes being deployed in practice are fairly short. In this work, we address what we…
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
We investigate the problem of maintaining an encoded distributed storage system when some nodes contain adversarial errors. Using the error-correction capabilities that are built into the existing redundancy of the system, we propose a…
We address the problem of securing distributed storage systems against passive eavesdroppers that can observe a limited number of storage nodes. An important aspect of these systems is node failures over time, which demand a repair…
Deep neural networks (DNN) have been a de facto standard for nowadays biometric recognition solutions. A serious, but still overlooked problem in these DNN-based recognition systems is their vulnerability against adversarial attacks.…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
Deoxyribonucleic Acid (DNA) as a storage medium with high density and long-term preservation properties can satisfy the requirement of archival storage for rapidly increased digital volume. The read and write processes of DNA storage are…
Deep neural networks (DNNs) play a crucial role in the field of artificial intelligence, and their security-related testing has been a prominent research focus. By inputting test cases, the behavior of models is examined for anomalies, and…
Many emerging Web services, such as email, photo sharing, and web site archives, need to preserve large amounts of quickly-accessible data indefinitely into the future. In this paper, we make the case that these applications' demands on…