Related papers: Reconstruction from Substrings with Partial Overla…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
Weak superimposed codes are combinatorial structures related closely to generalized cover-free families, superimposed codes, and disjunct matrices in that they are only required to satisfy similar but less stringent conditions. This class…
Over the long history of machine learning, which dates back several decades, recurrent neural networks (RNNs) have been used mainly for sequential data and time series and generally with 1D information. Even in some rare studies on 2D…
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…
Computed tomography is widely used to examine internal structures in a non-destructive manner. To obtain high-quality reconstructions, one typically has to acquire a densely sampled trajectory to avoid angular undersampling. However, many…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…
A new algorithm is proposed for a) unsupervised learning of sparse representations from subsampled measurements and b) estimating the parameters required for linearly reconstructing signals from the sparse codes. We verify that the new…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
We consider the problem of updating the information about multiple longest common sub-sequences. This kind of sub-sequences is used to highlight information that is shared across several information sequences, therefore it is extensively…
The linkage construction and its generalization is one of the most powerful constructions for constant dimension code, accounting for approximately 50\% of all the listed parameters. We show how to improve the linkage construction of…
Complex nonlinear dynamics are ubiquitous in many fields. Moreover, we rarely have access to all of the relevant state variables governing the dynamics. Delay embedding allows us, in principle, to account for unobserved state variables.…
The non-uniform sampling is a powerful approach to enable fast acquisition but requires sophisticated reconstruction algorithms. Faithful reconstruction from partial sampled exponentials is highly expected in general signal processing and…