Original String Research Articles

Reconstruction algorithms for DNA-storage systems

Motivated by DNA storage systems, this work presents the DNA reconstruction problem, in which a length-n string, is passing through the DNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are called traces. A DNA reconstruction algorithm is a mapping which receives t traces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm’s estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for the shortest common supersequence and the longest common subsequence problems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.

Performance and Improvement of Linguistic Data Analysis on Different Languages Using Deep Learnedness Techniques

India is an assorted country with various kinds of societies in each edge of the country. This is an organization of 30 states and 8 association regions with various dialects and particular social legacy. Thus, there have been many discussions on the beginning of the constitution, and the worry of the public language. It is said about the language of India, "The language expressed in India changes very much like the flavour of water changes in India each couple of kilometres". Nonetheless, India does not have a public language as there is an impressive contrast between an authority language and a public language. infusion synopsis of message archives generally comprises of positioning the record string of words and separating the highest-level string of words subject to the rundown dimension requirements. We investigate and commitment of different directed acquisition calculations to the string of words positioning assignment. That is the reason, we present an original string of words positioning philosophy in view of the similitude score between an up-and-comer string of words and touchstone rundowns. The famous direct relapse framework accomplished the high-grade outcomes in undeniably assessed datasets. Moreover, the direct relapse framework, which included Part-of-Speech supported highlights, beat the same with factual elements as it were. The proposed framework beat than the current framework with boundaries/measurements as precision (81.43%), blunder rate (0.13), val_loss (0.41), val_accuracy (0.50), size of dataset utilized in research (1.30 GB), No. of ages (50), Time-intricacy (O(n2)) and execution time (1012 ms).

Incremental association rules update algorithm based on the sort compression matrix

Association rule algorithm has always been a research hotspot in the field of data mining, in the context of today’s big data era, in order to efficiently obtain association rules and effectively update them, based on the original fast update pruning (FUP) algorithm, an association rule incremental update algorithm (FBSCM) based on sorting compression matrix is proposed to solve the shortcomings of frequent scanning of transaction datasets. Firstly, The algorithm maps the transaction dataset as a Boolean matrix, and changes the storage mode of the matrix(that is, adding two columns and a row vector); Secondly, the matrix is compressed many times during the generation of frequent k-itemset; After that, the items in the matrix are sorted incrementally according to the support degree of the itemset; Finally, the original string comparison operation is replaced by the vector product of each column of the matrix. Experimental results and analysis show that the FBSCM algorithm has higher temporal performance than the traditional FUP algorithm in different incremental dataset sizes, different minimum support thresholds and different feature datasets, especially when the incremental transaction volume is large or the minimum support degree is small.

Base41: A proposal for printable encoding of bit strings

AbstractThis article presents the proposal of a novel encoding method for representing binary data in printable format. The encoding procedure reversibly transforms binary strings into printable letter sequences using a mapping from bit strings to an alphabet of 41 symbols taken from a subset of the English uppercase and lowercase letters. The decoding process reversibly recovers an original bit string from the encoded printable string. The encoding and decoding algorithms along with the properties of this coding are examined and discussed. In particular, the use of only URL‐safe and clearly visually distinguishable characters is emphasized.

W algebra and eigenvalues of the low-order string constraint operators for the discrete KP hierarchy

Firstly, for any p ∈ N , the string constraint operators without the redundant variables are calculated, which are imposed by the string equation on the τ -function of the p -reduced discrete Kadomtsev–Petviashvili (dKP) hierarchy. Furthermore, the commutators of the string constraint operators without the redundant variables are calculated. It is found that although the string constraint operators without the redundant variables are different from the original string constraint operators with the redundant variables, they also form a Virasoro algebra and a W algebra after a transformation. Moreover, using the algebraic structure, eigenvalues of the low-order string equation constraint operators are calculated. Based on the obtained eigenvalues, it is also proved that the τ -function of the p -reduced dKP hierarchy constrained by the string equation is a vacuum vector for a Witt algebra. When p = 2 , it is coincident with the classical fact that the τ -function of the Korteweg–de Vries hierarchy constrained by the string equation is a vacuum vector for a Virasoro algebra.

On the Longest Common Cartesian Substring Problem

AbstractA Cartesian tree is associated with a string of numbers and is structured as a heap from which the original string can be recovered. Although Cartesian trees have been introduced 40 years ago, the Cartesian tree matching problem appeared very recently. It consists in finding all substrings of given text, which have the same Cartesian tree as that of a given pattern. In this paper, we address the problem of computing the longest common Cartesian substrings of two strings and present three methods for such problem. Our first method is based on a classical suffix tree construction and solves the problem in randomized linear time and linear space, although the space overhead is quite prohibitive in the case of large strings. Our second solution is based on classical dynamic programming, and our third solution is based on a constructive approach. Both of them run in quadratic worst case time but are more space economical in practice. From our experimental results, it turns out that our second solution runs faster than the standard suffix tree solution for short strings, whereas our third solution is more suitable for large strings, when storing a full suffix tree becomes prohibitive.

Попередні дослідження пасивного струнного решета

The article presents the results of research into the operation of the model of the original string sieve. The sieve is equipped with synthetic strings made of ultra-small diameter Dyneema braided cord. The purpose of this study is to evaluate the performance and identify the main indicators of the technological efficiency of the proposed fixed sieve installed at an angle to the horizon. Preliminary studies of the sowing sieve model were carried out by implementing the plan of a full factorial experiment. The experiments were carried out on a model of a seed sieve with holes of 2 mm. In the course of experiments, a post-harvest heap of winter wheat with natural clogging was used. The criterion for evaluating the efficiency of separation is the mass of seeding, and the specific feed and the angle of inclination of the sieve are the operating factors. The operational efficiency was established and the main performance indicators of the model were identified. The statistical mathematical model of the process allows us to assert the linear dependence of the criterion on the operating factors and to obtain a quantitative assessment of their influence on the process of cleaning the grain mixture. The surface of the response of the mass of the selected seeding from the specific loading of a unit of the sieve area and the angle of its inclination is constructed. An analysis of the regression equation and the response surface was carried out, during which design flaws were identified and tasks for further research were formulated. The factor that was found to be influential in the course of the previous experiments – the angle of inclination at the minimum value does not fully ensure guaranteed performance, since during the experiments clogging and accumulation of piles on the separating surface were periodically observed. An increase in the mass of the selected seeding is achieved by reducing the angle of the passive sieve to 17º and increasing the specific supply to 160 kg/dm2 ּh. A decrease in feed worsens the sieving process, especially at a small angle of inclination of the sieve, however, according to the Student's test, it is not significant. The resulting non-classical dependence may indicate the imperfection of the layout, the influence of unforeseen factors, etc., and requires further research.

K-Approximate Quasiperiodicity Under Hamming and Edit Distance

Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text T is a string whose occurrences in T cover all positions of T. A seed of text T is a cover of a superstring of T. In various applications exact quasiperiodicity is still not sufficient due to the presence of errors. We consider approximate notions of quasiperiodicity, for which we allow approximate occurrences in T with a small Hamming, Levenshtein or weighted edit distance. In previous work Sim et al. (J Korea Inf Sci Soc 29(1):16–21, 2002) and Christodoulakis et al. (J Autom Lang Comb 10(5/6), 609–626, 2005) showed that computing approximate covers and seeds, respectively, under weighted edit distance is NP-hard. They, therefore, considered restricted approximate covers and seeds which need to be factors of the original string T and presented polynomial-time algorithms for computing them. Further algorithms, considering approximate occurrences with Hamming distance bounded by k, were given in several contributions by Guth et al. They also studied relaxed approximate quasiperiods. We present more efficient algorithms for computing restricted approximate covers and seeds. In particular, we improve upon the complexities of many of the aforementioned algorithms, also for relaxed quasiperiods. Our solutions are especially efficient if the number (or total cost) of allowed errors is small. We also show conditional lower bounds for computing restricted approximate covers and prove NP-hardness of computing non-restricted approximate covers and seeds under the Hamming distance.

Automatic Search-and-Replace From Examples With Coevolutionary Genetic Programming.

We describe the design and implementation of a system for executing search-and-replace text processing tasks automatically, based only on examples of the desired behavior. The examples consist of pairs describing the original string and the desired modified string. Their construction, thus, does not require any specific technical skill. The system constructs a solution to the specified task that can be used unchanged on popular existing software for text processing. The solution consists of a search pattern coupled with a replacement expression: the former is a regular expression which describes both the strings to be replaced and their portions to be reused in the latter, which describes how to build the modified strings. Our proposed system is internally based on genetic programming and implements a form of cooperative coevolution in which two separate populations are evolved independently, one for search patterns and the other for replacement expressions. We assess our proposal on six tasks of realistic complexity obtaining very good results, both in terms of absolute quality of the solutions and with respect to the challenging baselines considered.

An Experimental Performance Analysis on Robotics Process Automation (RPA) With Open Source OCR Engines: Microsoft Ocr And Google Tesseract OCR

Robotic Process Automation (RPA) plays an important role in the solution for automating human digital interaction in various software domains like IT, Business Strategy and so on. Optical Character Recognition(OCR) superimposes subtitled characters on an image.Here we use two Open source OCR engines, Google Tesseract OCR - It literally makes use of the open source Tesseract OCR Engine[1]. Microsoft OCR - This is another open source OCR engine accessible in the Robotics Process Automation tool, UiPath[1]. The technique of optical character recognition (OCR) has been used to transform printed text into editable text. In various applications, OCR is a very useful and common technique. OCR precision can be dependent on algorithms for text preprocessing and segmentation. Often because of different scale, design, orientation, complex picture context, etc., it is difficult to retrieve text from the image. We begin this paper with an introduction to the Optical Character Recognition (OCR) process, in this paper, we propose a research analysis to estimate the accuracy of two open source OCR engines with Robotics Process Automation(RPA). These RPA processes are created using the UiPath tool and our results compare the OCR engines performance during the execution with the workflow and save the results to our local storage or on cloud storage if cloud support enabled and here we used local storage for purpose, and the result analysis and error analysis was evaluated by manual process which also included excel formulas to calculate the accuracy of the extracted string with the original string.

MD5( ) Bypassing Through SQL Injection

Web-based application attacks are growing dramatically in number and severity. They found that web applications that are poorly validated and verified are susceptible to attacks by the attacker. network related SQL attacks. The MD5 (message digest algorithm) hashing method is a one-way cryptographic function that accepts any text field as input and produces a fixed-length digest value that may be used to identify the original message as output. Most security experts advise replacing the MD hash algorithm with a much more secure message digest. ”Because of these collisions, a hacker or malicious user may construct files with almost the same exact hash as another, making it difficult to be certain that the file has not been interfered with. As a result, it should not be utilised for anything. Developers should instead use a Solid Cryptographic Hash function or a Symmetric Cryptographic Algorithm. this research paper demonstrates how md5 function in php can be bypassed when its parameter is set to ”TRUE” ie.,[ md5( ’x’, TRUE)], this makes the hashing value(x) to be raw bytes than hexa-coded value which is much more easier to inject a SQL Statement and retrieve the original String. The above is demonstrated using SQL Fiddle in which a sample php code value fields are hashed and when its md5() is set to TRUE ,how SQLI bypasses md5().The best approach for solving above problem is to use symmetric hash function like Sha1() , sha2(),CRC which does multiple layer of hashing and when using md5() not to set its parameter to” TRUE”.

Combinatorial Algorithms for String Sanitization

String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge (e.g., trips to mental health clinics from a string representing a user’s location history). In this article, we consider the problem of sanitizing a string by concealing the occurrences of sensitive patterns, while maintaining data utility, in two settings that are relevant to many common string processing tasks. In the first setting, we aim to generate the minimal-length string that preserves the order of appearance and frequency of all non-sensitive patterns. Such a string allows accurately performing tasks based on the sequential nature and pattern frequencies of the string. To construct such a string, we propose a time-optimal algorithm, TFS-ALGO. We also propose another time-optimal algorithm, PFS-ALGO, which preserves a partial order of appearance of non-sensitive patterns but produces a much shorter string that can be analyzed more efficiently. The strings produced by either of these algorithms are constructed by concatenating non-sensitive parts of the input string. However, it is possible to detect the sensitive patterns by “reversing” the concatenation operations. In response, we propose a heuristic, MCSR-ALGO, which replaces letters in the strings output by the algorithms with carefully selected letters, so that sensitive patterns are not reinstated, implausible patterns are not introduced, and occurrences of spurious patterns are prevented. In the second setting, we aim to generate a string that is at minimal edit distance from the original string, in addition to preserving the order of appearance and frequency of all non-sensitive patterns. To construct such a string, we propose an algorithm, ETFS-ALGO, based on solving specific instances of approximate regular expression matching. We implemented our sanitization approach that applies TFS-ALGO, PFS-ALGO, and then MCSR-ALGO, and experimentally show that it is effective and efficient. We also show that TFS-ALGO is nearly as effective at minimizing the edit distance as ETFS-ALGO, while being substantially more efficient than ETFS-ALGO.

Integration of large‐scale molecular networks and exomic data can identify Alzheimer's disease genes

AbstractBackgroundWe introduce a new approach to identify gene variants linked to common complex diseases. This method combines whole exome sequencing and large‐scale molecular network analysis. For proof of principle, we studied the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Alzheimer’s Disease Sequencing Project (ADSP) cohorts. In each, we evaluated the coding variants of 16,087 genes in the context of their ∼6,471,000 gene‐gene interactions, and prioritized genes that sorted cases from controls.MethodThe deleterious functional effect of every coding variant was quantified based on an Evolutionary Action (EA) model for the impact of similar variants across evolutionary history. For each gene, this impact was averaged over every individual from the ADNI (or the ADSP) cohort, and this average was used to modulate the edge weights of the STRING network of protein‐protein interactions. This process was carried out in cases and separately in controls, to yield two modified copies of the original STRING network, one representing the mutational perturbation from individuals affected with Alzheimer’s and, the other, representing those found in healthy individuals. We systematically compared these two graphs in order to identify, region by region and gene by gene, which parts of the network was significantly mutationally perturbed.ResultAmong the 100 top‐ranked in ADSP and, separately, in ADNI, a quarter are identical. This overlap indicates a robustness surpassing Genome‐wide association studies. One such gene, for example, is TOMM40, which is known to be relevant to AD. More broadly, these top‐ranked genes also significantly overlap, are significantly enriched for, or significantly diffuse to known gold standard AD genes and AD‐related diseases and pathways. These criteria for success show the top‐ranked genes are not random and are relevant to AD.ConclusionThis approach to integrate sequencing data with network information promises to be a useful new tool to elucidate disease genes in AD and other complex, common diseases.

Data Hiding in Symmetric Circular String Art

Creative digital artwork is usually the outcome of a long period of intellectual creation and labor of an artist. Similarly, computer-created digital artwork is an outcome of a large amount of machine time and computational resources. However, such intellectual properties can be easily copied by illegal users. Copyright protection of digital art is increasingly more important than before. Recently, using a computational approach to generate string art tends to be popular and attractive. To protect the illegal usage of the digital form of string art, we propose a data hiding algorithm specifically designed for string art. A digital string art image consists of a sequence of string lines, each specified by two nails fixed at the two ends of that line. The encrypted secret data (the watermark) is embedded into the list of line segments by odd–even modulation, where a bit ‘1’ is embedded by forcing the next node to be an odd node, and a bit ‘0’ is embedded by forcing the next node to be an even node. To minimize the impact of data embedding on the quality of the original string art image, a local optimization algorithm is developed to select the nodes that produce minimal distortion. To quantify the embedding distortion, we introduce a smoothing filter model for the human vision system (HVS) specifically tailored to string art image. Experimental results show that using the proposed algorithm, the distortion between the original string art image and the watermarked string art image is unnoticeable. The modified string art image is statistically indistinguishable from the original string art, and hence is secure under steganalysis. To our best knowledge, this is the first work towards data hiding and copyright protection of digital string art.

Implementation of Digital Watermarking Technique to Secure IPR of Web Application Code

Theft of software code is rapidly increasing with the growth of internet all over the world. That becomes the serious issue for the creator of the software code, as they invest their time and money to develop software code. Code for the Web based application can be accessed easily, as they are available as open source. These software codes can be tempered and can be misused any time. The protection of such web application code is essential. For the security of such codes from unauthorized accessibility, number of protection methods have been designed and developed. A model was proposed by Himanshu et al [4] for the protection of copyright of software code. In which few extra character stings were embedded in the encrypted original string. In this model concept of cryptography was implemented. This research paper is presented as the implementation procedure of the Digital Watermarking Technique to secure Intellectual Property Right of the web application code developed in ASP.NET using Visual C# programming language.

Encoding High-Cardinality String Categorical Variables

Statistical models usually require vector representations of categorical variables, using for instance one-hot encoding. This strategy breaks down when the number of categories grows, as it creates high-dimensional feature vectors. Additionally, for string entries, one-hot encoding does not capture information in their representation.Here, we seek low-dimensional encoding of high-cardinality string categorical variables. Ideally, these should be: scalable to many categories; interpretable to end users; and facilitate statistical analysis. We introduce two encoding approaches for string categories: a Gamma-Poisson matrix factorization on substring counts, and the min-hash encoder, for fast approximation of string similarities. We show that min-hash turns set inclusions into inequality relations that are easier to learn. Both approaches are scalable and streamable. Experiments on real and simulated data show that these methods improve supervised learning with high-cardinality categorical variables. We recommend the following: if scalability is central, the min-hash encoder is the best option as it does not require any data fit; if interpretability is important, the Gamma-Poisson factorization is the best alternative, as it can be interpreted as one-hot encoding on inferred categories with informative feature names. Both models enable autoML on the original string entries as they remove the need for feature engineering or data cleaning.

Study Explores Mechanisms of Surface Damage on Coiled Tubing

This article, written by JPT Technology Editor Chris Carpenter, contains highlights of paper SPE 194254, “Study on Mechanism of Coiled Tubing Surface Damage in Injector Heads,” by Zhihong Zhou, Guofeng Zhang, Fayong Yuan, Tang Wang, Yunwei Gao, and Weijia Wang, Jianghan Shale Gas Development Technical Service Company, prepared for the 2019 SPE/ICoTA Well Intervention Conference and Exhibition, The Woodlands, Texas, USA, 26–27 March. The paper has not been peer reviewed. Although several kinds of mechanical damage cause coiled tubing (CT) failure, longitudinal plowing marks (LPMs) account for a large portion of such damage. Understanding the mechanisms of LPM damage on CT surfaces will help reduce the occurrence of this type of damage. In this paper, the authors study the stress status of CT string held by gripper blocks, the axial force distribution of gripper blocks, and the longitudinal resonance of CT strings in vertical wells. Introduction The overwhelming majority (greater than 80%) of CT failures have been classified into four categories: corrosion, mechanical damage, string-manufacturing issues, and human error. Of these, failures caused by mechanical damage constitute almost 30% of all CT failures. Further study of these types of mechanical damage reached the following two important conclusions: LPMs, which are injector-related, account for 46% of mechanical damage observed on CT strings from 2006 to 2017. Recent periods that have seen dramatic increases in mechanical damage coincide with plug milling and higher-grade-CT operations. The authors propose that the pressure in the CT string plays a role in mechanical damage. Contact Status Between CT and Gripper Blocks The gripper blocks carried by chains are used to hold CT strings in place. The gripper blocks are divided into single-pitch and two-pitch categories. The engagements between the CT string and the gripper blocks are sometimes suboptimal. The contact area between the gripper and CT string is only at the end-point of the arc, and the contact stress is much higher there than at the point at which the gripper blocks grip the original CT string. According to the von Mises yield criterion, if the von Mises stress is larger than the yield stress at any point, the material at that point will yield and plastic strain will be produced. Distribution of Gripper-Block Lifting Forces in the Injector Commonly, several pairs of gripper blocks engage the CT string to provide the friction forces needed for deployment and retrieval of the tubing into and out of the wellbore. How the axial loads of these pairs of gripper blocks are distributed is essential to safe operation and avoidance of CT damage. To obtain the axial load distribution of all pairs of gripper blocks, a mechanical model is created by the authors and discussed in the complete paper.

Batch codes from Hamming and Reed-Muller codes

Batch codes, introduced by Ishai et al., encode a string $x \in \Sigma^{k}$ into an $m$-tuple of strings, called buckets. In this paper we consider multiset batch codes wherein a set of $t$-users wish to access one bit of information each from the original string. We introduce a concept of optimal batch codes. We first show that binary Hamming codes are optimal batch codes. The main body of this work provides batch properties of Reed-Muller codes. We look at locality and availability properties of first order Reed-Muller codes over any finite field. We then show that binary first order Reed-Muller codes are optimal batch codes when the number of users is 4 and generalize our study to the family of binary Reed-Muller codes which have order less than half their length.

Finger Search in Grammar-Compressed Strings

Grammar-based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. Given a grammar, the random access problem is to compactly represent the grammar while supporting random access, that is, given a position in the original uncompressed string report the character at that position. In this paper we study the random access problem with the finger search property, that is, the time for a random access query should depend on the distance between a specified index f, called the finger, and the query index i. We consider both a static variant, where we first place a finger and subsequently access indices near the finger efficiently, and a dynamic variant where also moving the finger such that the time depends on the distance moved is supported. Let n be the size the grammar, and let N be the size of the string. For the static variant we give a linear space representation that supports placing the finger in O(log N) time and subsequently accessing in O(log D) time, where D is the distance between the finger and the accessed index. For the dynamic variant we give a linear space representation that supports placing the finger in O(log N) time and accessing and moving the finger in O(log D + log log N) time. Compared to the best linear space solution to random access, we improve a O(log N) query bound to O(log D) for the static variant and to O(log D + log log N) for the dynamic variant, while maintaining linear space. As an application of our results we obtain an improved solution to the longest common extension problem in grammar compressed strings. To obtain our results, we introduce several new techniques of independent interest, including a novel van Emde Boas style decomposition of grammars.

Protocol for a systematic review: Interventions addressing men, masculinities and gender equality in sexual and reproductive health: An evidence and gap map and systematic review of reviews.

Protocol for a systematic review: Interventions addressing men, masculinities and gender equality in sexual and reproductive health: An evidence and gap map and systematic review of reviews.