Code String Research Articles

Our DNA family reunion

As we begin to personalize our life to the string of four-letter code (GATC) that holds the secrets to our phenotypic differences based on our genetic variation, I believe the success of public health genomics will stem from our ability to be mindful of how connected we are to each other. 99.9% of our genomes are identical, and it is that which defines our humanity. I do not doubt that genomics will help us to live longer, healthier, and perhaps better than we did during the preHuman Genome Project era. The speed of sequencing technology will continue to improve as we expedite genomic information processing, the cost of the sequencing will be as low as a few hundred dollars, and the wealth of genomic data will increase to fuse new genome-wide association studies (GWAS) with possible implications for better medicine and health. Using GWAS we could personalize our diet based on our genes and epigenetic factors that influence the ‘on and off switch’ of our genes along with our behaviour. The potential use of genomics in health and medicine to prevent disease, reduce disease severity, delay diseasemanifestation and even avoid death may all be within our reach. When I teach my undergraduate course ‘Genomics in Public Health’, I ponder the take-home messages I want my students to remember after completing my course. Will they learn the history of the Human Genome Project? Will they understand the complexity of genomic information?Will they

Detection and elimination of similar Web pages based on text structure and string of feature code

In order to reduce the interference of the duplicated Web pages,and improve the efficiency of detection and elimination of similar Web pages,a new kind of large-scale Web page detection algorithm was proposed.Firstly,adopting the Web label values,the algorithm created the text structure trees to realize the fingerprint similarity calculation layer by layer.Secondly,the head and tail words of a certain sentence,in which high frequency punctuations occur,were extracted out as the feature code.Lastly,the fingerprint similarity of Web page features was discriminated with Bloom filter algorithm.The experimental results show that the algorithm can improve the recall rate up to more than 90%,and reduce the time complexity to O(n).

A New String Matching Algorithm and its Application in Hand-Written Digits Recognition

In this paper a new algorithm is introduced for syntactic pattern recognition and string matching by using linked listdata structure which later could be used for hand written digits recognition.At first,handwritten digits are changed to string as input pattern by using chaincodethen the achieved string is recognized by using refer algorithm being implemented by linked list. This refer algorithm is able to compute the distance between the chain code strings shown in the implementation. The suggested algorithm reduces time complexity ofleven shtein's algorithm from second-order to linear-orderand in addition is able to decrease the consumption memory and increase accuracy of handwritten digits recognition as well. Our proposed implemented algorithm has 94.8% accuracy over 3000 handwritten digits samples.

LDPC and SHA based iris recognition for image authentication

We introduce a novel way to authenticate an image using Low Density Parity Check (LDPC) and Secure Hash Algorithm (SHA) based iris recognition method with reversible watermarking scheme, which is based on Integer Wavelet Transform (IWT) and threshold embedding technique. The parity checks and parity matrix of LDPC encoding and cancellable biometrics i.e., hash string of unique iris code from SHA-512 are embedded into an image for authentication purpose using reversible watermarking scheme based on IWT and threshold embedding technique. Simply by reversing the embedding process, the original image, parity checks, parity matrix and SHA-512 hash are extracted back from watermarked-image. For authentication, the new hash string produced by employing SHA-512 on error corrected iris code from live person is compared with hash string extracted from watermarked-image. The LDPC code reduces the hamming distance for genuine comparisons by a larger amount than for the impostor comparisons. This results in better separation between genuine and impostor users which improves the authentication performance. Security of this scheme is very high due to the security complexity of SHA-512, which is 2256 under birthday attack. Experimental results show that this approach can assure more accurate authentication with a low false rejection or false acceptance rate and outperforms the prior arts in terms of PSNR.

8-OR

Aim A ‘Silver Standard’ for HLA data collection and reporting has been described at ImmPort (immport.niaid.nih.gov, “Proposal for HLA Data Validation”) to address ambiguity resolution in the recording and reporting of HLA typing results. While standards are critical for HLA data interoperability, they are not meaningful until useful tools are developed and made available for community use. We are developing distributable tools that implement this silver standard. Here we describe the development a web service to create, update, and retrieve HLA typing data in standardized formats without the need for NMDP allele codes and the corresponding inherent introduction of new ambiguities. Methods ReST web services with HTTP negotiation are being developed employing a Java library that manages HLA typing data using standardized formats. These formats include the XML based Histoimmunogenetics Markup Language (HML) and a simple character-delimited string format (GL String) able to encode ambiguity within HLA typing. Resources are identified with a simple Uniform Resource Identifier (URI). Results The services build on a foundation of an open access database schema for IMGT/HLA reference sequence data (updated quarterly), and objects such as alleles, lists of alleles, haplotypes, genotypes, lists of genotypes and multi-locus unphased genotypes. Public services include creating, updating, and retrieving these objects. Content negotiation allows data retrieval in a variety of formats including GL String, HML, HTML, JSON, and QR Code. Conclusions The tools being developed here provide the HLA researcher, clinician and lab technician a common resource for managing HLA data in a standardized way. We envision these tools to augment workflows through creating new instances of HLA typing objects when needed, and retrieval of those objects and their associated metadata when called upon.

Plagiarism Detection among Source Codes using Adaptive Methods

We propose an adaptive method for detecting plagiarized pairs from a large set of source code. This method is adaptive in that it uses an adaptive algorithm and it provides an adaptive threshold for determining plagiarism. Conventional algorithms are based on greedy string tiling or on local alignments of two code strings. However, most of them are not adaptive; they do not consider the characteristics of the program set, thereby causing a problem for a program set in which all the programs are inherently similar. We propose adaptive local alignment? variant of local alignment that uses an adaptive similarity matrix. Each entry of this matrix is the logarithm of the probabilities of the keywords based on their frequency in a given program set. We also propose an adaptive threshold based on the local outlier factor (LOF), which represents the likelihood of an entity being an outlier. Experimental results indicate that our method is more sensitive than JPlag, which uses greedy string tiling for detecting plagiarism-suspected code pairs. Further, the adaptive threshold based on the LOF is shown to be effective, and the detection performance shows high sensitivity with negligible loss of specificity, compared with that using a fixed threshold.

The historical biogeography of Mammalia

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.

The Research on Pan-Genes of an Object Boundary

The aim of this paper is to give some researches and instructions of relations between the special shapes of an object boundary and their 8-adjacency chain code strings, characteristics of these chain code strings, internal relations among these chain code strings. These characteristics can be used to identify the region of an object boundary, when necessary, to generate this regional boundary. But this is irrelevant to various operations on image. This function of a chain code string is similar to the roles of genes in biology, is called pan-genes. An object boundary on binary image is considered by many tiny line segments connected with each other. The research on characteristics of chain code strings of line segments is an important segment of recognition and generation of an object boundary. This paper gives characteristics of chain code strings of pan-genes corresponding line segments, relations among these chain code strings, chain code string organization forms of chain code string units of line segments (these units are abbreviated with UL), the effective ways and methods on recognition and generation of line segments. Thus, this paper studies the chain code features of corners and circles. This paper gives a variety forms and features of ULs, shows the effects and methods on recognition and generation of an object boundary, gets basic properties of chain code strings about corners and circles.

Regular expression containment

We present a new sound and complete axiomatization of regular expression containment. It consists of the conventional axiomatization of concatenation, alternation, empty set and (the singleton set containing) the empty string as an idempotent semiring, the fixed- point rule E * = 1 + E × E * for Kleene-star, and a general coinduction rule as the only additional rule. Our axiomatization gives rise to a natural computational interpretation of regular expressions as simple types that represent parse trees, and of containment proofs as coercions . This gives the axiom- atization a Curry-Howard-style constructive interpretation: Containment proofs do not only certify a language-theoretic contain- ment, but, under our computational interpretation, constructively transform a membership proof of a string in one regular expression into a membership proof of the same string in another regular expression. We show how to encode regular expression equivalence proofs in Salomaa's, Kozen's and Grabmayer's axiomatizations into our containment system, which equips their axiomatizations with a computational interpretation and implies completeness of our axiomatization. To ensure its soundness, we require that the computational interpretation of the coinduction rule be a hereditarily total function. Hereditary totality can be considered the mother of syn- tactic side conditions: it "explains" their soundness, yet cannot be used as a conventional side condition in its own right since it turns out to be undecidable. We discuss application of regular expressions as types to bit coding of strings and hint at other applications to the wide-spread use of regular expressions for substring matching, where classical automata-theoretic techniques are a priori inapplicable. Neither regular expressions as types nor subtyping interpreted coercively are novel per se . Somewhat surprisingly, this seems to be the first investigation of a general proof-theoretic framework for the latter in the context of the former, however.

A dual-route perspective on brain activation in response to visual words: Evidence for a length by lexicality interaction in the visual word form area (VWFA)

Based on our previous work, we expected the Visual Word Form Area (VWFA) in the left ventral visual pathway to be engaged by both whole-word recognition and by serial sublexical coding of letter strings. To examine this double function, a phonological lexical decision task (i.e., “Does xxx sound like an existing word?”) presented short and long letter strings of words, pseudohomophones, and pseudowords (e.g., Taxi, Taksi and Tazi). Main findings were that the length effect for words was limited to occipital regions and absent in the VWFA. In contrast, a marked length effect for pseudowords was found throughout the ventral visual pathway including the VWFA, as well as in regions presumably engaged by visual attention and silent-articulatory processes. The length by lexicality interaction on brain activation corresponds to well-established behavioral findings of a length by lexicality interaction on naming latencies and speaks for the engagement of the VWFA by both lexical and sublexical processes.

Explicit Encoding of Multimodal Percepts by Single Neurons in the Human Brain

Different pictures of Marilyn Monroe can evoke the same percept, even if greatly modified as in Andy Warhol's famous portraits. But how does the brain recognize highly variable pictures as the same percept? Various studies have provided insights into how visual information is processed along the "ventral pathway," via both single-cell recordings in monkeys and functional imaging in humans. Interestingly, in humans, the same "concept" of Marilyn Monroe can be evoked with other stimulus modalities, for instance by hearing or reading her name. Brain imaging studies have identified cortical areas selective to voices and visual word forms. However, how visual, text, and sound information can elicit a unique percept is still largely unknown. By using presentations of pictures and of spoken and written names, we show that (1) single neurons in the human medial temporal lobe (MTL) respond selectively to representations of the same individual across different sensory modalities; (2) the degree of multimodal invariance increases along the hierarchical structure within the MTL; and (3) such neuronal representations can be generated within less than a day or two. These results demonstrate that single neurons can encode percepts in an explicit, selective, and invariant manner, even if evoked by different sensory modalities.

Improved sequential MAP estimation of CABAC encoded data with objective adjustment of the complexity/efficiency tradeoff

This paper presents an improved sequential MAP estimator to be used as a joint source-channel decoding technique for CABAC encoded data. The decoding process is compatible with realistic implementations of CABAC in standards like H.264, i.e, handling adaptive probabilities, context modeling and integer arithmetic coding. Soft-input decoding is obtained using an improved sequential decoding technique, which allows to obtain a tradeoff between complexity and efficiency. The algorithms are simulated in a context reminiscent of H264. Error detection is realized by exploiting on one side the properties of the binarization scheme and on the other side the redundancy left in the code string. As a result, the CABAC compression efficiency is preserved and no additional redundancy is introduced in the bit stream. Simulation results outline the efficiency of the proposed techniques for encoded data sent over AWGN and UMTS-OFDM channels.

Prospective Payment to Encourage System Wide Quality Improvement

Casemix-based inpatient prospective payment systems allocate payments for acute care based on what is done within an episode of care without regard for the outcome. To date, they have provided little incentive to improve quality. The Centers for Medicare & Medicaid Services have recently excluded 8 avoidable complications from their payment system. This study models an inpatient prospective payment system that comprehensively excludes not-present-on-admission and other complication diagnoses from the entire funding process, effectively adding a diagnosis-related group (DRG)-specific average complication payment across all discharges. Complication-averaged cost weights were estimated using the same patient level cost dataset used for estimating the relative resource weights for Victorian public hospitals in 2006-07. All codes with a "C" prefix (secondary diagnoses that are coded as having arisen after admission) and codes that define a condition that prima facie represent a specific complication of care were excluded from the code string. The episodes were then regrouped to DRGs and new complication-averaged cost weights were developed. When complication codes were excluded across 1.2 million discharges, 1.37% became ungroupable, 14.86% included at least one complication diagnosis code, and 1.56% grouped to another DRG. Modeled funding for individual metropolitan hospitals in Victoria, Australia, was redistributed by -2.5% to 1.8%. The cost weights reflect the average cost of preventable and unpreventable complications and have the potential to drive improvements in clinical care. This study is in contrast to previous studies estimating the funding impact of preventing all complications.

A Systematic Nomenclature for Codifying Engineered Nanostructures

Nanotechnology's growing applications are fueled by the synthesis and engineering of a myriad nanostructures, yet there is no systematic naming or classification scheme for such materials. This lack of a coherent nomenclature is confusing the interpretation of data sets and threatens to hamper the pace of progress and risk assessment. A systematic nomenclature that encodes the overall composition, size, shape, core and ligand chemistry, and solubility of nanostructures is presented. A typographic string of minimalist field codes facilitates digital archiving and searches for desired properties. This nomenclature system could also be used for nanomaterial hazard labeling.

Acoustic signal encoding method and apparatus, acoustic signal decoding method and apparatus and recording medium

In an acoustic signal encoding apparatus (100), a tone/noise judgment block (110) judges whether an entered acoustic time sequential signal is a tone or a noise. In case of a tone, a tone component signal is extracted by a tone component extraction block (121) and the tone component parameter is normalized and quantized by a normalization/quantization block (122). Moreover, the residual time sequential signal of the acoustic time sequential signal subtracted by the tone component signal is converted into spectrum information by a spectrum conversion block (131) and the spectrum information is normalized and quantized by a normalization/quantization block (132). A code string generation block (140) generates a code string by the quantized tone component parameter and quantized residual component spectrum information.

A passport recognition and face verification using enhanced fuzzy ART based RBF network and PCA algorithm

In this paper, passport recognition and face verification methods which can automatically recognize passport codes and discriminate forgery passports to improve efficiency and systematic control of immigration management are proposed. Adjusting the slant is very important for recognition of characters and face verification since slanted passport images can bring various unwanted effects to the recognition of individual codes and faces. Therefore, after smearing the passport image, the longest extracted string of characters is selected. The angle adjustment can be conducted by using the slant of the straight and horizontal line that connects the center of thickness between left and right parts of the string. Extracting passport codes is done by Sobel operator, horizontal smearing, and 8-neighborhood contour tracking algorithm. The string of codes can be transformed into binary format by applying repeating binary method to the area of the extracted passport code strings. The proposed radial basis function (RBF) network is applied to the middle layer of RBF network by using the fuzzy logic connection operator and proposing the enhanced fuzzy adaptive resonance theory (ART) algorithm that dynamically controls the vigilance parameter. After several tests using a forged passport and the passport with slanted images, the proposed method was proven to be effective in recognizing passport codes and verifying facial images.

An Evaluation of the Quality of Obstetric Morbidity Coding Using an Objective Assessment Tool, the Performance Indicators for Coding Quality (PICQ)

The Performance Indicators for Coding Quality (PICQ) is a data quality assessment tool developed by Australia's National Centre for Classification in Health (NCCH). PICQ consists of a number of indicators covering all ICD-10-AM disease chapters, some procedure chapters from the Australian Classification of Health Intervention (ACHI) and some Australian Coding Standards (ACS). The indicators can be used to assess the coding quality of hospital morbidity data by monitoring compliance of coding conventions and ACS; this enables the identification of particular records that may be incorrectly coded, thus providing a measure of data quality. There are 31 obstetric indicators available for the ICD-10-AM Fourth Edition. Twenty of these 31 indicators were classified as Fatal, nine as Warning and two Relative. These indicators were used to examine coding quality of obstetric records in the 2004-2005 financial year Australian national hospital morbidity dataset. Records with obstetric disease or procedure codes listed anywhere in the code string were extracted and exported from the SPSS source file. Data were then imported into a Microsoft Access database table as per PICQ instructions, and run against all Fatal and Warning and Relative (N=31) obstetric PICQ 2006 Fourth Edition Indicators v.5 for the ICD-10- AM Fourth Edition. There were 689,905 gynaecological and obstetric records in the 2004-2005 financial year, of which 1.14% were found to have triggered Fatal degree errors, 3.78% Warning degree errors and 8.35% Relative degree errors. The types of errors include completeness, redundancy, specificity and sequencing problems. It was found that PICQ is a useful initial screening tool for the assessment of ICD-10-AM/ACHI coding quality. The overall quality of codes assigned to obstetric records in the 2004- 2005 Australian national morbidity dataset is of fair quality.

New Attack Tricks Antivirus Software

Traditionally, antivirus products stop malicious software by recognizing code signatures unique to different types of malware. When the applications encounter a file with a code string that matches one in their database for a known virus, they block its access to the intended victim's computer. However, with the advent of Web 2.0, in which Web sites make it easy for users to add content, hackers have found a new way to spread malicious code and short-circuit the pattern-matching antivirus approach. DCO employs algorithms to change and disguise JavaScript-based malware code without making it less harmful, thereby keeping pattern-matching antivirus software from recognizing exploits.

Research on GA-ANN Integration and Its Applications to Cold Extrusion Process Design

Based on the research of the functions of ANN-based cold extrusion process design system, genetic algorithm (GA) is proposed to optimize the topology and parameters of artificial neural networks (ANN), in order to improve the running efficiency of the networks. The binary encoding approach is implemented to represent the GA chromosome. The code string or the chromosome was divided into three parts: the first part is the binary code of the cold extruded part; the second part is the binary code of the topology and parameters of ANN; the last is the binary code of the semi-cold-extruded-part or the billet. The 1/F(X) function is selected as the fitness function in GA, where, X represents the binary code of the cold extruded part, F(X) represents the error between the real outputs of ANN and the desired results; the biased roulette wheel selection method is used for selecting operation in this paper; two-point crossover and one-point mutation are selected for these two types of genetic operations. Finally, the typical cold extruded part is used for verification as an example by using the optimized ANN, the result shows that ANN optimized by GA has efficiency and validity in the cold extrusion process design system.

Court Stenography-To-Text ("STT") in Hong Kong: A Jurilinguistic Engineering Effort

Implementation of legal bilingualism in Hong Kong after 1997 has necessitated the production of voluminous and extensive court proceedings and judgments in both Chinese and English. For the Chinese records, Cantonese, a dialect of Chinese, is the home language of more than 90% of the population in Hong Kong and is thus officially used in the courts. For the court proceedings, Cantonese speech would have to be recorded, and a Cantonese Computer-Aided Transcription system has been developed. The transcription system converts stenographic codes into Chinese text, i.e. from phonetic to orthographic representation of the language. The main challenge lies in the resolution of the severe ambiguity resulting from homocode problems in the conversion process. Cantonese Chinese is typified by problematic homonymy, which presents serious challenges. The N-gram statistical model is employed to estimate the most probable character string of the input transcription codes. Domain-specific corpora have been compiled to support the statistical computation. To improve accuracy, scalable techniques such as domain-specific transcription and special encoding are used. Put together, these techniques deliver 96% transcription accuracy.