Pub Date : 2019-02-15DOI: 10.7287/peerj.preprints.27540v1
J. Fanelli, John Waxler
Hundreds of thousands of home users are victimized by cyber-attacks every year. Most experts agree that average home users are not doing enough to protect their computers and their information from cyber-attacks. Improperly managed home computers can lead to individuals losing data, systems performing slowly, loss of identity, and ransom payments; en masse attacks can act in concert to infect personal computers in business and government. Currently, home users receive conflicting guidance for a complicated terrain, often in the form of anecdotal 'Top 10' lists, that is not appropriate for their specific needs, and in many instances, users ignore all guidance. Often, these popular ‘Top 10’ lists appear to be based solely on opinion. Ultimately, we asked ourselves the following: how can we provide home users with better guidance for determining and applying appropriate security controls that meet their needs and can be verified by the cyber security community? In this paper, we propose a methodology for determining and prioritizing the most appropriate security controls for home computing. Using Multi Criteria Decision Making (MCDM) and subject matter expertise, we identify, analyze and prioritize security controls used by government and industry to determine which controls can substantively improve home computing security. We apply our methodology using examples to demonstrate its benefits.
{"title":"Prioritizing computer security controls for home users","authors":"J. Fanelli, John Waxler","doi":"10.7287/peerj.preprints.27540v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27540v1","url":null,"abstract":"Hundreds of thousands of home users are victimized by cyber-attacks every year. Most experts agree that average home users are not doing enough to protect their computers and their information from cyber-attacks. Improperly managed home computers can lead to individuals losing data, systems performing slowly, loss of identity, and ransom payments; en masse attacks can act in concert to infect personal computers in business and government. Currently, home users receive conflicting guidance for a complicated terrain, often in the form of anecdotal 'Top 10' lists, that is not appropriate for their specific needs, and in many instances, users ignore all guidance. Often, these popular ‘Top 10’ lists appear to be based solely on opinion. Ultimately, we asked ourselves the following: how can we provide home users with better guidance for determining and applying appropriate security controls that meet their needs and can be verified by the cyber security community? In this paper, we propose a methodology for determining and prioritizing the most appropriate security controls for home computing. Using Multi Criteria Decision Making (MCDM) and subject matter expertise, we identify, analyze and prioritize security controls used by government and industry to determine which controls can substantively improve home computing security. We apply our methodology using examples to demonstrate its benefits.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"38 1","pages":"e27540"},"PeriodicalIF":0.0,"publicationDate":"2019-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87416354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-02-13DOI: 10.7287/peerj.preprints.27534v1
P. Corti, F. Bartoli, Alessio Fabiani, C. Giovando, Athanasios Tom Kralidis, A. Tzotsos
GeoNode is an open source framework designed to build geospatial content management systems (GeoCMS) and spatial data infrastructure (SDI) nodes. Its development was initiated by the Global Facility for Disaster Reduction and Recovery (GFDRR) in 2009 and adopted by a large number of organizations in the following years. Using an open source stack based on mature and robust frameworks and software like Django, OpenLayers, PostGIS, GeoServer and pycsw, an organization can build on top of GeoNode its SDI or geospatial open data portal. GeoNode provides a large number of user friendly capabilities, broad interoperability using Open Geospatial Consortium (OGC) standards, and a powerful authentication/authorization mechanism. Supported by a vast, diverse and global open source community, GeoNode is an official project of the Open Source Geospatial Foundation (OSGeo).
{"title":"GeoNode: an open source framework to build spatial data infrastructures","authors":"P. Corti, F. Bartoli, Alessio Fabiani, C. Giovando, Athanasios Tom Kralidis, A. Tzotsos","doi":"10.7287/peerj.preprints.27534v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27534v1","url":null,"abstract":"GeoNode is an open source framework designed to build geospatial content management systems (GeoCMS) and spatial data infrastructure (SDI) nodes. Its development was initiated by the Global Facility for Disaster Reduction and Recovery (GFDRR) in 2009 and adopted by a large number of organizations in the following years. Using an open source stack based on mature and robust frameworks and software like Django, OpenLayers, PostGIS, GeoServer and pycsw, an organization can build on top of GeoNode its SDI or geospatial open data portal. GeoNode provides a large number of user friendly capabilities, broad interoperability using Open Geospatial Consortium (OGC) standards, and a powerful authentication/authorization mechanism. Supported by a vast, diverse and global open source community, GeoNode is an official project of the Open Source Geospatial Foundation (OSGeo).","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"44 1","pages":"e27534"},"PeriodicalIF":0.0,"publicationDate":"2019-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73747957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-02-11DOI: 10.7287/peerj.preprints.27529v1
S. Perera, F. Leymann, Paul Fremantle
This paper presents an assessment of blockchain technology based on the Emerging Technology Analysis Canvas (ETAC) to evaluate the drivers and potential outcomes. The ETAC is a framework to critically analyze emerging technologies. The assessment finds that blockchain can fundamentally transform the world. It is ready for specific applications in use cases such as digital currency, lightweight financial systems, ledgers, provenance, and disintermediation. However, Blockchain faces significant technical gaps in other use cases and needs at least 5-10 years to come to full fruition in those spaces. Sustaining the current level of effort (e.g. startups, research) for this period of time may be challenging. We also find that the need and merits of decentralized infrastructures compared to centralized and semi-centralized alternatives is not always clear. Given the risk involved and significant potential returns, we recommend a cautiously optimistic approach to blockchain with the focus on concrete use cases. The primary contributions of this paper are a use case centric categorization of the blockchain, a detailed discussion on challenges faced by those categories, and an assessment of their future.
{"title":"A use case centric survey of Blockchain: status quo and future directions","authors":"S. Perera, F. Leymann, Paul Fremantle","doi":"10.7287/peerj.preprints.27529v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27529v1","url":null,"abstract":"This paper presents an assessment of blockchain technology based on the Emerging Technology Analysis Canvas (ETAC) to evaluate the drivers and potential outcomes. The ETAC is a framework to critically analyze emerging technologies.\u0000 The assessment finds that blockchain can fundamentally transform the world. It is ready for specific applications in use cases such as digital currency, lightweight financial systems, ledgers, provenance, and disintermediation.\u0000 However, Blockchain faces significant technical gaps in other use cases and needs at least 5-10 years to come to full fruition in those spaces. Sustaining the current level of effort (e.g. startups, research) for this period of time may be challenging. We also find that the need and merits of decentralized infrastructures compared to centralized and semi-centralized alternatives is not always clear. Given the risk involved and significant potential returns, we recommend a cautiously optimistic approach to blockchain with the focus on concrete use cases.\u0000 The primary contributions of this paper are a use case centric categorization of the blockchain, a detailed discussion on challenges faced by those categories, and an assessment of their future.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"5 1","pages":"e27529"},"PeriodicalIF":0.0,"publicationDate":"2019-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84615785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-02-08DOI: 10.7287/peerj.preprints.27524v1
T. Kamnardsiri, W. Janchai, P. Khuwuthyakorn, Wacharee Rittiwat
This study aimed to propose the method of implementation of the Knowledge-Based System (KBS) in the case of approach-run phase. The proposed method was implemented for improving the long jump performance of athletes in the approach-run phase. Moreover, this study aimed to examine KBS concurrent validity in distinguishing between professional and amateur populations and then KBS convergent validity against a Tracker video analysis tool. Seven running professionals aged 19 to 42 years and five amateurs aged 18 to 38 years had captured with ten conditions of different movements (C1 to C10) using a standard video camera (60 fps, 10 mm lens). The camera was fixed on the tripod. The results showing an age-related difference in a speed measurement of ten conditions were evidently using the KBS. Good associations were found between KBS and Tracker 4.94 video analysis tool across various conditions of three variables that were the starting position (r=0.926 and 0.963), the maximum velocity (r=0.972 and 0.995) and the location of maximum velocity (r=0.574 and 0.919). In conclusion, the proposed method is a reliable tool for measuring the starting position, maximum speed and position of maximum speed. Furthermore, the proposed method can also distinguish speed performance between professional and amateur across multiple movement conditions.
{"title":"Implementation and validity of the long jump knowledge-based system: Case of the approach run phase","authors":"T. Kamnardsiri, W. Janchai, P. Khuwuthyakorn, Wacharee Rittiwat","doi":"10.7287/peerj.preprints.27524v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27524v1","url":null,"abstract":"This study aimed to propose the method of implementation of the Knowledge-Based System (KBS) in the case of approach-run phase. The proposed method was implemented for improving the long jump performance of athletes in the approach-run phase. Moreover, this study aimed to examine KBS concurrent validity in distinguishing between professional and amateur populations and then KBS convergent validity against a Tracker video analysis tool. Seven running professionals aged 19 to 42 years and five amateurs aged 18 to 38 years had captured with ten conditions of different movements (C1 to C10) using a standard video camera (60 fps, 10 mm lens). The camera was fixed on the tripod. The results showing an age-related difference in a speed measurement of ten conditions were evidently using the KBS. Good associations were found between KBS and Tracker 4.94 video analysis tool across various conditions of three variables that were the starting position (r=0.926 and 0.963), the maximum velocity (r=0.972 and 0.995) and the location of maximum velocity (r=0.574 and 0.919). In conclusion, the proposed method is a reliable tool for measuring the starting position, maximum speed and position of maximum speed. Furthermore, the proposed method can also distinguish speed performance between professional and amateur across multiple movement conditions.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"6 1","pages":"e27524"},"PeriodicalIF":0.0,"publicationDate":"2019-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78080447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-02-03DOI: 10.7287/peerj.preprints.27516v1
Fahmina Taranum, S. Mahin
With the enhancement in technical field of communication, efforts are made by the researchers to provide security. Security is dispensing protection and privacy to the system for the channeled data against any unwarranted access and refinements. MANET is a variant of wireless network used essentially by the dynamic devices with high motility and vulnerability. The distinctions like dynamic layout and curbed resources make them susceptible to miscellaneous kinds of threats. One such attack is wormhole which sneak and peep data with malicious intensions and operates either in coordinated or uncoordinated fashion. In its coordinated version, the malicious nodes coordinate their operations whereas in the uncoordinated version; they operate solitarily with the aim to decline the network performance. In this work, we aim to propose an algorithm for deployment of wormhole attack communicating with its peer through a tunnel. Planting of this attack in the network lays the foundation for developing successful strategies to mitigate their effects on the system.
{"title":"Deployment of coordinated worm-hole peer in MANETs","authors":"Fahmina Taranum, S. Mahin","doi":"10.7287/peerj.preprints.27516v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27516v1","url":null,"abstract":"With the enhancement in technical field of communication, efforts are made by the researchers to provide security. Security is dispensing protection and privacy to the system for the channeled data against any unwarranted access and refinements. MANET is a variant of wireless network used essentially by the dynamic devices with high motility and vulnerability. The distinctions like dynamic layout and curbed resources make them susceptible to miscellaneous kinds of threats. One such attack is wormhole which sneak and peep data with malicious intensions and operates either in coordinated or uncoordinated fashion. In its coordinated version, the malicious nodes coordinate their operations whereas in the uncoordinated version; they operate solitarily with the aim to decline the network performance. In this work, we aim to propose an algorithm for deployment of wormhole attack communicating with its peer through a tunnel. Planting of this attack in the network lays the foundation for developing successful strategies to mitigate their effects on the system.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"1 1","pages":"e27516"},"PeriodicalIF":0.0,"publicationDate":"2019-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83084571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Electronic health records (EHRs) are notorious for reducing the face-to-face time with patients while increasing the screen-time for clinicians leading to burnout. This is especially problematic for psychiatry care in which maintaining consistent eye-contact and non-verbal cues are just as important as the spoken words. In this ongoing work, we explore the feasibility of automatically generating psychiatric EHR case notes from digital transcripts of doctor-patient conversation using a two-step approach: (1) predicting semantic topics for segments of transcripts using supervised machine learning, and (2) generating formal text of those segments using natural language processing. Through a series of preliminary experimental results obtained through a collection of synthetic and real-life transcripts, we demonstrate the viability of this approach.
{"title":"Automatically Generating Psychiatric Case Notes From Digital Transcripts of Doctor-Patient Conversations","authors":"Nazmul Kazi, Indika Kahanda","doi":"10.18653/v1/W19-1918","DOIUrl":"https://doi.org/10.18653/v1/W19-1918","url":null,"abstract":"Electronic health records (EHRs) are notorious for reducing the face-to-face time with patients while increasing the screen-time for clinicians leading to burnout. This is especially problematic for psychiatry care in which maintaining consistent eye-contact and non-verbal cues are just as important as the spoken words. In this ongoing work, we explore the feasibility of automatically generating psychiatric EHR case notes from digital transcripts of doctor-patient conversation using a two-step approach: (1) predicting semantic topics for segments of transcripts using supervised machine learning, and (2) generating formal text of those segments using natural language processing. Through a series of preliminary experimental results obtained through a collection of synthetic and real-life transcripts, we demonstrate the viability of this approach.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"46 1 1","pages":"e27497"},"PeriodicalIF":0.0,"publicationDate":"2019-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78370082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-11DOI: 10.7287/peerj.preprints.27477v1
M. El-Dosuky, G. El-adl
E-government provides access to services anytime anywhere. There are many e-Government frameworks already exist to integrate e-government services, but efficient full interoperability still a challenge. Interoperability per se can be modeled via four maturity stages, in which the interoperability zone is the holy grail of full interoperability to be reached ultimately with strategy alignment. As e-government services shift in the same way as e-commerce with value chain, this implicitly implies the possibility of benefiting from blockchain with e-government. Blockchain is a nascent promising architecture, whose transactions are permanent, verifiable, and recorded in a distributed ledger. This research article suggests applying blockchain in achieving e- government interoperability. Forms are juxtaposed on the outer borders of the system. These forms adopt those used by UK government, because they are standard as well as they are available for Python developers. Once a form has been completed, PySOA calls the requested service, before storing the data in Ontology Blockchain. After the service is performed, the policies are analyzed in batch processing using quantgov. A report is submitted to the central government periodically. Ontology Blockchain has a dual effect. On the one hand, it works as a secure data storage. On the other hand, it cooperates with PySOA in supporting both technology and semantic interoperability . The most important feature of the proposed method is the presence of (Government Interoperability Zone Alignment; GIZA), which acts as a backbone that coherently connects the internal subcomponents. This linkage is possible, because each form has an title, that corresponds to the appropriate service name. Each service in turn has a counterpart in the wallets stored in Ontology blockchain. To measure interoperability empirically, there is a need for metrics. This study adopts and quantizes a standard interoperability matrix along three dimensions of interoperability of Conceptual (Syntax& Semantics), Organizational (Responsibilities& Organization per se), and Technology (Platform& Communication). While concerns are : data, business, service, and process. Any deviation from the standard could contributes to the interoperability score (counting mismatches) or interoperability grade (counting absolute differences). An estimation is performed, for 1000 total random cases. It is estimated that the probability of getting a conceptual/technical interoperability score as large as the standard strategy score is (713 /1000 = 0.713 (2 in 3). It is estimated too that the probability of getting a organizational interoperability score as large as the standard strategy score is (712 /1000 = 0.712 (2 in 3). Then, Markov model is proposed to provide an accurate representation of the evolution of the strategies over time.
{"title":"GIZAChain: e-Government Interoperability Zone Alignment, based on blockchain technology","authors":"M. El-Dosuky, G. El-adl","doi":"10.7287/peerj.preprints.27477v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27477v1","url":null,"abstract":"E-government provides access to services anytime anywhere. There are many e-Government frameworks already exist to integrate e-government services, but efficient full interoperability still a challenge.\u0000 Interoperability per se can be modeled via four maturity stages, in which the interoperability zone is the holy grail of full interoperability to be reached ultimately with strategy alignment. As e-government services shift in the same way as e-commerce with value chain, this implicitly implies the possibility of benefiting from blockchain with e-government. Blockchain is a nascent promising architecture, whose transactions are permanent, verifiable, and recorded in a distributed ledger.\u0000 This research article suggests applying blockchain in achieving e- government interoperability. Forms are juxtaposed on the outer borders of the system. These forms adopt those used by UK government, because they are standard as well as they are available for Python developers. Once a form has been completed, PySOA calls the requested service, before storing the data in Ontology Blockchain. After the service is performed, the policies are analyzed in batch processing using quantgov. A report is submitted to the central government periodically. Ontology Blockchain has a dual effect. On the one hand, it works as a secure data storage. On the other hand, it cooperates with PySOA in supporting both technology and semantic interoperability . The most important feature of the proposed method is the presence of (Government Interoperability Zone Alignment; GIZA), which acts as a backbone that coherently connects the internal subcomponents. This linkage is possible, because each form has an title, that corresponds to the appropriate service name. Each service in turn has a counterpart in the wallets stored in Ontology blockchain.\u0000 To measure interoperability empirically, there is a need for metrics. This study adopts and quantizes a standard interoperability matrix along three dimensions of interoperability of Conceptual (Syntax& Semantics), Organizational (Responsibilities& Organization per se), and Technology (Platform& Communication). While concerns are : data, business, service, and process. Any deviation from the standard could contributes to the interoperability score (counting mismatches) or interoperability grade (counting absolute differences). An estimation is performed, for 1000 total random cases. It is estimated that the probability of getting a conceptual/technical interoperability score as large as the standard strategy score is (713 /1000 = 0.713 (2 in 3). It is estimated too that the probability of getting a organizational interoperability score as large as the standard strategy score is (712 /1000 = 0.712 (2 in 3). Then, Markov model is proposed to provide an accurate representation of the evolution of the strategies over time.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"9 1","pages":"e27477"},"PeriodicalIF":0.0,"publicationDate":"2019-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83202054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-05DOI: 10.7287/peerj.preprints.27465v2
Nick Papoulias
Background. Context-free grammars (CFGs) and Parsing-expression Grammars (PEGs) are the two main formalisms used by formal specifications and parsing frameworks to describe programming languages. They mainly differ in the definition of the choice operator, describing language alternatives. CFGs support the use of non-deterministic choice (i.e., unordered choice), where all alternatives are equally explored. PEGs support a deterministic choice (i.e., ordered choice), where alternatives are explored in strict succession. In practice the two formalisms, are used through concrete classes of parsing algorithms (such as Left-to-right, rightmost derivation (LR) for CFGs and Packrat parsing for PEGs), that follow the semantics of the formal operators. Problem Statement. Neither the two formalisms, nor the accompanying algorithms are sufficient for a complete description of common cases arising in language design. In order to properly handle ambiguity, recursion, precedence or associativity, parsing frameworks either introduce implementation specific directives or ask users to refactor their grammars to fit the needs of the framework/algorithm/formalism combo. This introduces significant complexity even in simple cases and results in incompatible grammar specifications. Our Proposal. We introduce Multi-Ordered Grammars (MOGs) as an alternative to the CFG and PEG formalisms. MOGs aim for a better exploration of ambiguity, ordering, recursion and associativity during language design. This is achieved by (a) allowing both deterministic and non-deterministic choices to co-exist, and (b) introducing a form of recursive and scoped ordering. The formalism is accompanied by a new parsing algorithm (Gray) that extends chart parsing (normally used for Natural Language Processing) with the proposed MOG operators. Results. We conduct two case-studies to assess the expressiveness of MOGs, compared to CFGs and PEGs. The first consists of two idealized examples from literature (an expression grammar and a simple procedural language). The second examines a real-world case (the entire Smalltalk grammar and eleven new Smalltalk extensions) probing the complexities of practical needs. We show that in comparison, MOGs are able to reduce complexity and naturally express language constructs, without resorting to implementation specific directives. Conclusion. We conclude that combining deterministic and non-deterministic choices in a single grammar specification is indeed not only possible but also beneficial. Moreover, augmented by operators for recursive and scoped ordering the resulting multi-ordered formalism presents a viable alternative to both CFGs and PEGs. Concrete implementations of MOGs can be constructed by extending chart parsing with MOG operators for recursive and scoped ordering.
{"title":"Parsing multi-ordered grammars with the Gray algorithm","authors":"Nick Papoulias","doi":"10.7287/peerj.preprints.27465v2","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27465v2","url":null,"abstract":"Background. Context-free grammars (CFGs) and Parsing-expression Grammars (PEGs) are the two main formalisms used by formal specifications and parsing frameworks to describe programming languages. They mainly differ in the definition of the choice operator, describing language alternatives. CFGs support the use of non-deterministic choice (i.e., unordered choice), where all alternatives are equally explored. PEGs support a deterministic choice (i.e., ordered choice), where alternatives are explored in strict succession. In practice the two formalisms, are used through concrete classes of parsing algorithms (such as Left-to-right, rightmost derivation (LR) for CFGs and Packrat parsing for PEGs), that follow the semantics of the formal operators. Problem Statement. Neither the two formalisms, nor the accompanying algorithms are sufficient for a complete description of common cases arising in language design. In order to properly handle ambiguity, recursion, precedence or associativity, parsing frameworks either introduce implementation specific directives or ask users to refactor their grammars to fit the needs of the framework/algorithm/formalism combo. This introduces significant complexity even in simple cases and results in incompatible grammar specifications. Our Proposal. We introduce Multi-Ordered Grammars (MOGs) as an alternative to the CFG and PEG formalisms. MOGs aim for a better exploration of ambiguity, ordering, recursion and associativity during language design. This is achieved by (a) allowing both deterministic and non-deterministic choices to co-exist, and (b) introducing a form of recursive and scoped ordering. The formalism is accompanied by a new parsing algorithm (Gray) that extends chart parsing (normally used for Natural Language Processing) with the proposed MOG operators. Results. We conduct two case-studies to assess the expressiveness of MOGs, compared to CFGs and PEGs. The first consists of two idealized examples from literature (an expression grammar and a simple procedural language). The second examines a real-world case (the entire Smalltalk grammar and eleven new Smalltalk extensions) probing the complexities of practical needs. We show that in comparison, MOGs are able to reduce complexity and naturally express language constructs, without resorting to implementation specific directives. Conclusion. We conclude that combining deterministic and non-deterministic choices in a single grammar specification is indeed not only possible but also beneficial. Moreover, augmented by operators for recursive and scoped ordering the resulting multi-ordered formalism presents a viable alternative to both CFGs and PEGs. Concrete implementations of MOGs can be constructed by extending chart parsing with MOG operators for recursive and scoped ordering.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"30 1","pages":"e27465"},"PeriodicalIF":0.0,"publicationDate":"2019-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84643768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.7287/peerj.preprints.27608v1
C. Lortie
There is extensive support and choice in R to support meta-analyses. Two common packages in the natural sciences include meta and metafor. Here, a brief contrast of the strengths of each is described for the synthesis scientist. Meta is a direct, intuitive choice for rapid implementation of general meta-analytical statistics. Metafor is a comprehensive package for analyses if the fit models are more complex. Both packages provide estimates of heterogeneity, excellent visualization tools, and functions to explore publication bias. Preference and critical outcomes can facilitate choice between these two specific options. Nonetheless, metafor has a steeper learning curve but greater rewards.
{"title":"A contrast of meta and metafor packages for meta-analyses in R","authors":"C. Lortie","doi":"10.7287/peerj.preprints.27608v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27608v1","url":null,"abstract":"There is extensive support and choice in R to support meta-analyses. Two common packages in the natural sciences include meta and metafor. Here, a brief contrast of the strengths of each is described for the synthesis scientist. Meta is a direct, intuitive choice for rapid implementation of general meta-analytical statistics. Metafor is a comprehensive package for analyses if the fit models are more complex. Both packages provide estimates of heterogeneity, excellent visualization tools, and functions to explore publication bias. Preference and critical outcomes can facilitate choice between these two specific options. Nonetheless, metafor has a steeper learning curve but greater rewards.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"9 1","pages":"e27608"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89984378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-01-01DOI: 10.7287/peerj.preprints.27479v1
Morteza Pourreza Shahri, Indika Kahanda
Identifying protein-phenotype relations is of paramount importance for applications such as uncovering rare and complex diseases. One of the best resources that captures the protein-phenotype relationships is the biomedical literature. In this work, we introduce ProPheno, a comprehensive online dataset composed of human protein/phenotype mentions extracted from the complete corpora of Medline and PubMed. Moreover, it includes co-occurrences of protein-phenotype pairs within different spans of text such as sentences and paragraphs. We use ProPheno for completely characterizing the human protein-phenotype landscape in biomedical literature. ProPheno, the reported findings and the gained insight has implications for (1) biocurators for expediting their curation efforts, (2) researches for quickly finding relevant articles, and (3) text mining tool developers for training their predictive models. The RESTful API of ProPheno is freely available at http://propheno.cs.montana.edu.
{"title":"ProPheno: An online dataset for completely characterizing the human protein-phenotype landscape in biomedical literature","authors":"Morteza Pourreza Shahri, Indika Kahanda","doi":"10.7287/peerj.preprints.27479v1","DOIUrl":"https://doi.org/10.7287/peerj.preprints.27479v1","url":null,"abstract":"Identifying protein-phenotype relations is of paramount importance for applications such as uncovering rare and complex diseases. One of the best resources that captures the protein-phenotype relationships is the biomedical literature. In this work, we introduce ProPheno, a comprehensive online dataset composed of human protein/phenotype mentions extracted from the complete corpora of Medline and PubMed. Moreover, it includes co-occurrences of protein-phenotype pairs within different spans of text such as sentences and paragraphs. We use ProPheno for completely characterizing the human protein-phenotype landscape in biomedical literature. ProPheno, the reported findings and the gained insight has implications for (1) biocurators for expediting their curation efforts, (2) researches for quickly finding relevant articles, and (3) text mining tool developers for training their predictive models. The RESTful API of ProPheno is freely available at http://propheno.cs.montana.edu.","PeriodicalId":93040,"journal":{"name":"PeerJ preprints","volume":"35 1","pages":"e27479"},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89391783","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：