Related papers: A new DNA alignment method based on inverted index
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
Registration is the process that computes the transformation that aligns sets of data. Commonly, a registration process can be divided into four main steps: target selection, feature extraction, feature matching, and transform computation…
In this paper, we propose DeepAlign, a novel approach to multi-perspective process anomaly correction, based on recurrent neural networks and bidirectional beam search. At the core of the DeepAlign algorithm are two recurrent neural…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Order-preserving pattern matching was introduced recently but it has already attracted much attention. Given a reference sequence and a pattern, we want to locate all substrings of the reference sequence whose elements have the same…
In many classification problems, we want a classifier that is robust to a range of non-semantic transformations. For example, a human can identify a dog in a picture regardless of the orientation and pose in which it appears. There is…
Omics technologies enable unbiased investigation of biological systems through massively parallel sequence acquisition or molecular measurements, bringing the life sciences into the era of Big Data. A central challenge posed by such omics…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
Convolutional Neural Network (CNN) has gained state-of-the-art results in many pattern recognition and computer vision tasks. However, most of the CNN structures are manually designed by experienced researchers. Therefore, auto- matically…
Parts of DNA sequences known as exons and introns play very different role in coding and storage of genetic information. Here we show that their conducting properties are also very different. Taking into account long-range correlations…
The aim of this paper is to propose a new method to identify main paths in a technological domain using patent citations. Previous approaches for using main path analysis have greatly improved our understanding of actual technological…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
Genome sequencing technology has improved significantly in few last years and resulted in abundance genetic data. Artificial intelligence has been employed to analyze genetic data in response to its sheer size and variability. Gene…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…