Deafness mutation mining using regular expression based pattern matching.
Ontology highlight
ABSTRACT: Background
While keyword based queries of databases such as Pubmed are frequently of great utility, the ability to use regular expressions in place of a keyword can often improve the results output by such databases. Regular expressions can allow for the identification of element types that cannot be readily specified by a single keyword and can allow for different words with similar character sequences to be distinguished.Results
A Perl based utility was developed to allow the use of regular expressions in Pubmed searches, thereby improving the accuracy of the searches.Conclusion
This utility was then utilized to create a comprehensive listing of all DFN deafness mutations discussed in Pubmed records containing the keywords "human ear".
SUBMITTER: Frenz CM
PROVIDER: S-EPMC2180167 | biostudies-literature | 2007 Oct
REPOSITORIES: biostudies-literature
Publications
Deafness mutation mining using regular expression based pattern matching.
BMC medical informatics and decision making 20071025
<h4>Background</h4>While keyword based queries of databases such as Pubmed are frequently of great utility, the ability to use regular expressions in place of a keyword can often improve the results output by such databases. Regular expressions can allow for the identification of element types that cannot be readily specified by a single keyword and can allow for different words with similar character sequences to be distinguished.<h4>Results</h4>A Perl based utility was developed to allow the u ...[more]
Similar Datasets
Project description:As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.
| S-EPMC540068 | biostudies-literature
Project description:BackgroundRegular expression matching (REM) is widely employed as the major tool for deep packet inspection (DPI) applications. For automatic processing, the regular expression patterns need to be converted to a deterministic finite automata (DFA). However, with the ever-increasing scale and complexity of pattern sets, state explosion problem has brought a great challenge to the DFA based regular expression matching. Rule grouping is a direct method to solve the state explosion problem. The original rule set is divided into multiple disjoint groups, and each group is compiled to a separate DFA, thus to significantly restrain the severe state explosion problem when compiling all the rules to a single DFA.ObjectiveFor practical implementation, the total number of DFA states should be as few as possible, thus the data structures of these DFAs can be deployed on fast on-chip memories for rapid access. In addition, to support fast pattern update in some applications, the time cost for grouping should be as small as possible. In this study, we aimed to propose an efficient grouping method, which generates as few states as possible with as little time overhead as possible.MethodsWhen compiling multiple patterns into a single DFA, the number of DFA states is usually greater than the total number of states when compiling each pattern to a separate DFA. This is mainly caused by the semantic overlaps among different rules. By quantifying the interaction values for each pair of rules, the rule grouping problem can be reduced to the maximum k-cut graph partitioning problem. Then, we propose a heuristic algorithm called the one-step greedy (OSG) algorithm to solve this NP-hard problem. What's more, a subroutine named the heuristic initialization (HI) algorithm is devised to further optimize the grouping algorithms.ResultsWe employed three practical rule sets for the experimental evaluation. Results show that the OSG algorithm outperforms the state-of-the-art grouping solutions regarding both the total number of DFA states and time cost for grouping. The HI subroutine also demonstrates its significant optimization effect on the grouping algorithms.ConclusionsThe DFA state explosion problem has became the most challenging issue in the regular expression matching applications. Rule grouping is a practical direction by dividing the original rule sets into multiple disjoint groups. In this paper, we investigate the current grouping solutions, and propose a compact and efficient grouping algorithm. Experiments conducted on practical rule sets demonstrate the superiority of our proposal.
| S-EPMC6200238 | biostudies-literature
Project description:BackgroundMore so than face-to-face counseling, users of online text-based services might drop out from a session before establishing a clear closure or expressing the intention to leave. Such premature departure may be indicative of heightened risk or dissatisfaction with the service or counselor. However, there is no systematic way to identify this understudied phenomenon.PurposeThis study has two objectives. First, we developed a set of rules and used logic-based pattern matching techniques to systematically identify premature departures in an online text-based counseling service. Second, we validated the importance of premature departure by examining its association with user satisfaction. We hypothesized that the users who rated the session as less helpful were more likely to have departed prematurely.MethodWe developed and tested a classification model using a sample of 575 human-annotated sessions from an online text-based counseling platform. We used 80% of the dataset to train and develop the model and 20% of the dataset to evaluate the model performance. We further applied the model to the full dataset (34,821 sessions). We compared user satisfaction between premature departure and completed sessions based on data from a post-session survey.ResultsThe resulting model achieved 97% and 92% F1 score in detecting premature departure cases in the training and test sets, respectively, suggesting it is highly consistent with the judgment of human coders. When applied to the full dataset, the model classified 15,150 (43.5%) sessions as premature departure and the remaining 19,671 (56.5%) as completed sessions. Completed cases (15.2%) were more likely to fill the post-chat survey than premature departure cases (4.0%). Premature departure was significantly associated with lower perceived helpfulness and effectiveness in distress reduction.ConclusionsThe model is the first that systematically and accurately identifies premature departure in online text-based counseling. It can be readily modified and transferred to other contexts for the purpose of risk mitigation and service evaluation and improvement.
| S-EPMC8632835 | biostudies-literature
Project description:Palm-print based individual identification is regarded as an effectual method for identifying persons with high confidence. Palm-print with larger inner surface of hand contains many features such as principle lines, ridges, minutiae points, singular points, and textures. Feature based pattern matching has faced the challenge that the spatial positional variations occur between the training and test samples. To perform effective palm-print features matching, Rabin-Karp Palm-Print Pattern Matching (RPPM) method is proposed in this paper. With the objective of improving the accuracy of pattern matching, double hashing is employed in RPPM method. Multiple patterns of features are matched using the Aho-Corasick Multiple Feature matching procedure by locating the position of the features with finite set of bit values as an input text, improving the cumulative accuracy on hashing. Finally, a time efficient bit parallel ordering presents an efficient variation on matching the palm-print features of test and training samples with minimal time. Experiment is conducted on the factors such as pattern matching efficiency rate, time taken on multiple palm-print feature matching efficiency, and cumulative accuracy on hashing.
| S-EPMC4678081 | biostudies-other
Project description:Since the coronavirus disease (COVID-19) outbreak in December 2019, studies have been addressing diverse aspects in relation to COVID-19 and Variant of Concern 202012/01 (VOC 202012/01) such as potential symptoms and predictive tools. However, limited work has been performed towards the modelling of complex associations between the combined demographic attributes and varying nature of the COVID-19 infections across the globe. This study presents an intelligent approach to investigate the multi-dimensional associations between demographic attributes and COVID-19 global variations. We gather multiple demographic attributes and COVID-19 infection data (by 8 January 2021) from reliable sources, which are then processed by intelligent algorithms to identify the significant associations and patterns within the data. Statistical results and experts' reports indicate strong associations between COVID-19 severity levels across the globe and certain demographic attributes, e.g. female smokers, when combined together with other attributes. The outcomes will aid the understanding of the dynamics of disease spread and its progression, which in turn may support policy makers, medical specialists and society, in better understanding and effective management of the disease.
| S-EPMC7890495 | biostudies-literature
Project description:A method for improving crystallographic phases is presented that is based on the preferential occurrence of certain local patterns of electron density in macromolecular electron-density maps. The method focuses on the relationship between the value of electron density at a point in the map and the pattern of density surrounding this point. Patterns of density that can be superimposed by rotation about the central point are considered equivalent. Standard templates are created from experimental or model electron-density maps by clustering and averaging local patterns of electron density. The clustering is based on correlation coefficients after rotation to maximize the correlation. Experimental or model maps are also used to create histograms relating the value of electron density at the central point to the correlation coefficient of the density surrounding this point with each member of the set of standard patterns. These histograms are then used to estimate the electron density at each point in a new experimental electron-density map using the pattern of electron density at points surrounding that point and the correlation coefficient of this density to each of the set of standard templates, again after rotation to maximize the correlation. The method is strengthened by excluding any information from the point in question from both the templates and the local pattern of density in the calculation. A function based on the origin of the Patterson function is used to remove information about the electron density at the point in question from nearby electron density. This allows an estimation of the electron density at each point in a map, using only information from other points in the process. The resulting estimates of electron density are shown to have errors that are nearly independent of the errors in the original map using model data and templates calculated at a resolution of 2.6 A. Owing to this independence of errors, information from the new map can be combined in a simple fashion with information from the original map to create an improved map. An iterative phase-improvement process using this approach and other applications of the image-reconstruction method are described and applied to experimental data at resolutions ranging from 2.4 to 2.8 A.
| S-EPMC2745877 | biostudies-literature
Project description:Due to the limited resources of wireless sensor network, low efficiency of real-time communication scheduling, poor safety defects, and so forth, a queuing performance evaluation approach based on regular expression match is proposed, which is a method that consists of matching preprocessing phase, validation phase, and queuing model of performance evaluation phase. Firstly, the subset of related sequence is generated in preprocessing phase, guiding the validation phase distributed matching. Secondly, in the validation phase, the subset of features clustering, the compressed matching table is more convenient for distributed parallel matching. Finally, based on the queuing model, the sensor networks of task scheduling dynamic performance are evaluated. Experiments show that our approach ensures accurate matching and computational efficiency of more than 70%; it not only effectively detects data packets and access control, but also uses queuing method to determine the parameters of task scheduling in wireless sensor networks. The method for medium scale or large scale distributed wireless node has a good applicability.
| S-EPMC4226180 | biostudies-other
Project description:A motion trajectory is an intuitive representation form in time-space domain for a micromotion behavior of moving target. Trajectory analysis is an important approach to recognize abnormal behaviors of moving targets. Against the complexity of vehicle trajectories, this paper first proposed a trajectory pattern learning method based on dynamic time warping (DTW) and spectral clustering. It introduced the DTW distance to measure the distances between vehicle trajectories and determined the number of clusters automatically by a spectral clustering algorithm based on the distance matrix. Then, it clusters sample data points into different clusters. After the spatial patterns and direction patterns learned from the clusters, a recognition method for detecting vehicle abnormal behaviors based on mixed pattern matching was proposed. The experimental results show that the proposed technical scheme can recognize main types of traffic abnormal behaviors effectively and has good robustness. The real-world application verified its feasibility and the validity.
| S-EPMC3926328 | biostudies-other
Project description:Perceptual systems often force systematically biased interpretations upon sensory input. These interpretations are obligatory, inaccessible to conscious control, and prevent observers from perceiving alternative percepts. Here we report a similarly impenetrable phenomenon in the domain of language, where the syntactic system prevents listeners from detecting a simple perceptual pattern. Healthy human adults listened to three-word sequences conforming to patterns readily learned even by honeybees, rats, and sleeping human neonates. Specifically, sequences either started or ended with two words from the same syntactic category (e.g., noun-noun-verb or verb-verb-noun). Although participants readily processed the categories and learned repetition patterns over nonsyntactic categories (e.g., animal-animal-clothes), they failed to learn the repetition pattern over syntactic categories, even when explicitly instructed to look for it. Further experiments revealed that participants successfully learned the repetition patterns only when they were consistent with syntactically possible structures, irrespective of whether these structures were attested in English or in other languages unknown to the participants. When the repetition patterns did not match such syntactically possible structures, participants failed to learn them. Our results suggest that when human adults hear a string of nouns and verbs, their syntactic system obligatorily attempts an interpretation (e.g., in terms of subjects, objects, and predicates). As a result, subjects fail to perceive the simpler pattern of repetitions--a form of syntax-induced pattern deafness that is reminiscent of how other perceptual systems force specific interpretations upon sensory input.
| S-EPMC2791640 | biostudies-literature
Project description:The biomedical text mining community has focused on developing techniques to automatically extract important relations between biological components and semantic events involving genes or proteins from literature. In this paper, we propose a novel approach for mining relations and events in the biomedical literature using approximate subgraph matching. Extraction of such knowledge is performed by searching for an approximate subgraph isomorphism between key contextual dependencies and input sentence graphs. Our approach significantly increases the chance of retrieving relations or events encoded within complex dependency contexts by introducing error tolerance into the graph matching process, while maintaining the extraction precision at a high level. When evaluated on practical tasks, it achieves a 51.12% F-score in extracting nine types of biological events on the GE task of the BioNLP-ST 2011 and an 84.22% F-score in detecting protein-residue associations. The performance is comparable to the reported systems across these tasks, and thus demonstrates the generalizability of our proposed approach.
| S-EPMC3629260 | biostudies-literature