65 results about "Suffix array" patented technology

The invention discloses a method for rapidly screening positions from a position database. The method relates to the position database, a position index generator, a position search server and a Web client. The position index generator is interconnected with the position database by an open database. The position index generator generates an index file according to the position data in the position database in an index structure based on a suffix array and distributes the generated index file to the position search server. The position search server is connected with the Web client through a socket. The Web client sends an inquiry request to the position search server through the socket. The position search server searches the index file and returns search results to the Web client for display through the socket. According to the method, all positions in the position database can be searched rapidly and effectively, and the search speed is greatly improved at the premise of guaranteeing the search accuracy.

A system and method of identifying repeat subsequences having at least a value of x for threshold of different left contexts and a value of y for a threshold of different right contexts for an input sequence are disclosed. The method may include generating a lexicographically sorted suffix array for the input sequence and a longest common prefix array. The suffix array is traversed in lexicographic order comparing the longest common prefix values between consecutive suffixes. Suffixes with the same longest common prefix are representative of occurrence of the same repeat, a higher longest common prefix indicates a new occurrence of a longer repeat, and a lower longest common prefix indicates the last occurrence of a repeat.

The invention is applicable to the field of information extraction and provides an extracting method and a device of a complex named entity. The method comprises the steps of filtering text data of a text, connecting substrings separated by punctuations in the filtered text data into a long string through specified connectors, recording a home position of a Chinese character or an English character of the long string, storing the recorded home position of the Chinese character or the English character into an established suffix data set to determine an ordered sequence of suffixes in the suffix data set, determining a longest common prefix of the adjacent suffixes according to the ordered sequence of the suffixes, taking the determined longest common prefix of the adjacent suffixes as a repeated string of the text, and extracting the complex named entity of the text according to at least two out of the frequency of the repeated string of the text, mutual information of the repeated string and the independence of the repeated string. With the adoption of the method and the device, the more accurate complex named entity can be obtained, and the extracting accuracy of the complex named entity is improved.

The invention provides a rapid character string matching method based on a suffix array. The method includes two stages, the first stage includes that the appearing position of a pattern string in a text string is limited in a possible interval of the suffix array taking a first character of the pattern string as a beginning character by binary search, and the second stage includes that search conditions are further limited on the interval, suffixes with the length smaller than that of the pattern string and with last characters different from those of the pattern string are excluded, the comparison frequency of the characters is decreased, character string matching range is narrowed, and the appearing position of the pattern string in the text string is rapidly acquired.

The invention belongs to the computer technology field, and provides a classification method, device and system based on a platelet differentially expressed gene marker. The method comprises the steps that a sequencing reading sequence of a target sample platelet transcriptome is acquired; a comparison result between the sequencing reading sequence and a human genome is acquired according to a suffix array search algorithm and a sequence splitting/searching/extending strategy; a gene expression estimation value is determined according to a maximum likelihood method; a gene expression difference of a positive sample set and a negative sample set is acquired through a linear statistical method; a hyperplane expression is constructed according to the positive sample set and the negative sample set; an entity gene expression estimation values are classified according to the hyperplane expression, the entity gene expression estimation values and a support vector machine principle. According to the classification method, device and system based on the platelet differentially expressed gene marker, the differentially expressed gene marker can be quickly and accurately identified, and the classification precision of corresponding individuals of a group is improved.

The invention discloses a method for multi-thread parallel construction of a suffix array and a system. The method comprises the following steps: scanning a character string X, calculating the types of characters and suffixes by using an L/S type recognition method, and recording in an array t; scanning the array t, finding out the positions where LMS characters appear, obtaining first character pointers of LMS substrings and recording the pointers of the LMS substrings with an array P1; performing parallel induction and sorting on all LMS substrings in the X by the P1, a B and an SA and saving in an SA1; according to the sorting result, performing multi-thread parallel renaming on the LMS substrings in the X to form an X1; checking whether each character in the X1 is unique, if yes, directly sorting suffixes of the X1 to calculate a suffix array of the X1 and saving in the SA1; and finally calculating a suffix array of the X and saving in the SA according to the suffix array of the X1 saved in the SA1. The invention has high running speed, can be matched with the memory of a multi-core computer, and is suitable for constructing a suffix array of a large-scale string.

A system and method are disclosed for inexact search acceleration using reference data. A representative system includes one or more memory circuits storing a plurality of queries and a FM-index of the reference data; and one or more FPGAs configured to select a query; select a substring of the selected query; read a section of the FM-index and calculate a plurality of suffix array intervals for the substring with a corresponding plurality of prepended characters in a first or next position; read a first or next character in the first or next position of the query and select a suffix array interval for the read first character; determine whether the suffix array interval is valid and whether a beginning of the query has been reached; returning a first search result when the suffix array interval is valid and the beginning of the query has been reached; and returning a second search result that no match of the query with the reference data was found when the suffix array interval is not valid.

A data structure of index information for retrieving pair character strings on a computer at high speed is provided. A method of retrieving a pair character strings appearing in close proximity of each other in a document using the index information at high speed is also provided. Bits of a suffix array of reference document data are rearranged, thereby creating index information LSA localizable, or usable as an index for a subregion of the document. Through use of this, a process of dichotomizing a region, where the entire document is designated as an initial region, is repeated and positions of index information for a query character string in the reference document data are gradually detailed. The distance between the pair is evaluated and candidates are narrowed down. Finally, positions where the pair character strings occur in close proximity of each other are identified.

The invention discloses a gene sequence alignment method and system. The method comprises the following steps: storing a reference genome sequence and a query genome sequence in a distributed storage system; under a Spark heterogeneous distributed computing platform framework, segmenting a reference genome sequence according to row offset, and preprocessing to obtain a plurality of preprocessed reference data sets; establishing an index for each preprocessing reference data set by adopting a suffix array algorithm, and combining all the preprocessing reference data sets after the index is established to obtain a reference sequence index file; carrying out CUDA fine-grained sequence comparison on each fragment in the query genome sequence and a reference sequence index file by adopting a seed extension algorithm, and determining position information of each fragment in the reference sequence index file; and combining the position information of all the fragments in the reference sequence index file to obtain a gene sequence comparison result. According to the invention, the calculation speed and precision of a large-scale sequence alignment algorithm are improved.

The invention discloses a suffix array indexing method for a real-time data stream. The method comprises the following steps: a server receives the real-time data stream, extracts source data, and pretreats the source data into documents; parsing the document, distributing the document according to the domain, receiving the source data in each domain, and starting an independent thread to index and store the data; a domain consists of a plurality of segments. After receiving the source data, the domain object writes the source data directly into the segments and sets the segment source data update signal to return the response. If all domains of the document return a response, the response information is returned to the client; the suffix array construction tool listens for the segment source data update signal in the background, automatically constructs the suffix array for the segment source data, and generates the segment suffix array; a segment source data, a segment suffix array,and a segment information are linked into a full suffix array index, and the source data is indexed successfully. The invention can index heterogeneous data in real time without word segmentation, andadopts asynchronous mode to generate index to accelerate response time. The invention is suitable for data indexing field.

The invention provides a parallel data difference method. The parallel data difference method comprises the steps that 1, files are preprocessed, wherein a source file and a target file are initialized, a suffix array of the source file is generated, and a patch file is created and initialized; 2, the target file is segmented, wherein the target file is segmented according to the thread number, and one thread is added for each part of segmented target file to perform independent processing; 3, the thread processing process is performed, the segmented target file is initialized in each thread, patch files are created, the source file and the target file are compared through the suffix array to generate differential data, and the differential data is written into the patch file; 4, host processes are merged and process, wherein the patch files with the written differential data of the threads are written into the patch files together. By adopting a multi-thread paralleling technology, the patch generating speed is improved.

The invention relates to a short message search method based on suffix arrays. The method comprises the steps that S1, a suffix array is constructed for each short message in a short message list, and then all suffix array items in all the suffix arrays obtained through construction are ordered; S2, when a keyword for searching for a short message is received, all characters in the received keyword are sequentially used as indexes for binary search according to a character receiving order; S3, the i(th) character in the keyword is used as an index to perform binary search in all the suffix array items which are ordered, and the suffix array corresponding to the suffix array items with the first character being the index is used as an i(th) search result; S4, it is assumed that i=i+1, the i(th) character in the keyword is used as an index to perform binary search in the suffix array items contained in an (i-1)th search result, and then the suffix array corresponding to the suffix array items with the first character being the index is used as the i(th) search result; and S5, the step S4 is executed repeatedly till i is greater than n, and at the moment the short message corresponding to the i(th) search result is used as a short message search result to be output, wherein n is the number of characters contained in the keyword.