Related papers: One, Two, Three and N Dimensional String Search Al…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
Template matching is a basic method in image analysis to extract useful information from images. In this paper, we suggest a new method for pattern matching. Our method transform the template image from two dimensional image into one…
We study an indexing architecture to store and search in a database of high-dimensional vectors from the perspective of statistical signal processing and decision theory. This architecture is composed of several memory units, each of which…
The paper considers various formalisms based on Automata, Temporal Logic and Regular Expressions for specifying queries over sequences. Unlike traditional binary semantics, the paper presents a similarity based semantics for thse…
Orthogonal arrays play a fundamental role in many applications. However, constructing orthogonal arrays with the required parameters for an application usually is extremely difficult and, sometimes, even impossible. Hence there is an…
This work generalizes the binary search problem to a $d$-dimensional domain $S_1\times\cdots\times S_d$, where $S_i=\{0, 1, \ldots,n_i-1\}$ and $d\geq 1$, in the following way. Given $(t_1,\ldots,t_d)$, the target element to be found, the…
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Data series are a special type of multidimensional data present in numerous domains, where similarity search is a key operation that has been extensively studied in the data series literature. In parallel, the multidimensional community has…
Similarity query is the family of queries based on some similarity metrics. Unlike the traditional database queries which are mostly based on value equality, similarity queries aim to find targets "similar enough to" the given data objects,…
We give a dimensionality reduction procedure to approximate the sum of distances of a given set of $n$ points in $R^d$ to any "shape" that lies in a $k$-dimensional subspace. Here, by "shape" we mean any set of points in $R^d$. Our…
The symmetry classification method is applied to the string-like scalar fields in two-dimensional space-time. When the configurational space is three-dimensional and reducible we present the complete list of the systems admiting higher…
In this paper we present novel algorithms for several multidimensional data processing problems. We consider problems related to the computation of restricted clusters and of the diameter of a set of points using a new distance function. We…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
Developing an MR sequence is challenging and remains largely constrained by human intuition. Recently, AI-driven approaches have been proposed; however, most require an initial sequence for parameter optimization or extensive training…