Formal Representation Model Research Articles

RCM-extractor: an automated NLP-based approach for extracting a semi formal representation model from natural language requirements

RCM-extractor: an automated NLP-based approach for extracting a semi formal representation model from natural language requirements

BELTracker: evidence sentence retrieval for BEL statements.

Biological expression language (BEL) is one of the main formal representation models of biological networks. The primary source of information for curating biological networks in BEL representation has been literature. It remains a challenge to identify relevant articles and the corresponding evidence statements for curating and validating BEL statements. In this paper, we describe BELTracker, a tool used to retrieve and rank evidence sentences from PubMed abstracts and full-text articles for a given BEL statement (per the 2015 task requirements of BioCreative V BEL Task). The system is comprised of three main components, (i) translation of a given BEL statement to an information retrieval (IR) query, (ii) retrieval of relevant PubMed citations and (iii) finding and ranking the evidence sentences in those citations. BELTracker uses a combination of multiple approaches based on traditional IR, machine learning, and heuristics to accomplish the task. The system identified and ranked at least one fully relevant evidence sentence in the top 10 retrieved sentences for 72 out of 97 BEL statements in the test set. BELTracker achieved a precision of 0.392, 0.532 and 0.615 when evaluated with three criteria, namely full, relaxed and context criteria, respectively, by the task organizers. Our team at Mayo Clinic was the only participant in this task. BELTracker is available as a RESTful API and is available for public use.Database URL: http://www.openbionlp.org:8080/BelTracker/finder/Given_BEL_Statement

Sharable computer-based clinical practice guidelines: rationale, obstacles, approaches, and prospects.

Clinical practice guideline automation at the point of care is of growing interest, yet most guidelines are authored in unstructured narrative form. Computer-based execution depends on a formal structured representation, and also faces a number of other challenges at all stages of the guideline lifecycle: modeling, authoring, dissemination, implementation, and update. This is because of the multiplicity of conceptual models, authoring tools, authoring approaches, intended applications, implementation platforms, and local interface requirements and operational constraints. Complexity and time required for development and structure are also huge obstacles. These factors argue for convergence on a common shared model for representation that can be the basis of dissemination. A common model would facilitate direct interpretation or mapping to multiple implementation environments. GLIF (GuideLine Interchange Format) is a formal representation model for guidelines, created by the InterMed Collaboratory as a proposed basis for a shared representation. GLIF currently addresses the process of authoring and dissemination; the InterMed team's major focus now is on tools to facilitate these tasks and the mapping to clinical information system environments. Because of limitations in what can be done by a single team with finite resources, however, and the variety of additional perspectives that need to be accommodated, the InterMed team has determined that further development of a shared representation would be best served as an open process in which the world community is engaged. Under the auspices of the HL7 Decision Support Technical Committee, a GLIF Special Interest Group has been established, which is intended to be a forum for collaborative refinement and extension of a standard representation that can support the needs of the guideline lifecycle. Significant areas for future work will need to include demonstrations of effective means for incorporating guide-lines at point of care, reconciliation of functional requirements of different models and identification of those most important for supporting practical implementation, im-proved means for authoring and management of complexity, and methods for automatically analyzing and validating syntax, semantics, and logical consistency of guidelines.

A New Approach for Representing and Querying Textual Attributes in Databases

In this paper, a new approach to deal with textual attributes in databases is presented. The basic idea is to give a new representation for these attributes, so that it allows us to treat them together with and in the same way than the other database attributes in querying, data warehousing, data mining processes, etc. Additionally, the transformation process of the textual attribute implies the obtaining of a global representation, which includes a great part of the attribute meaning. Moreover, this representation can be improved by using an ontology during the querying process, which enables the semantic queries. The formal representation model is presented in the paper, as well as the mathematical bases for dealing with it. The whole implementation process is also described by using a medical database to show the experimental results. Finally, a set of semantic query examples are offered to explain the advantages of this new approach.

Conceptual graph-based knowledge representation for supporting reasoning in African traditional medicine

Although African patients use both conventional or modern and traditional healthcare simultaneously, it has been proven that 80% of people rely on African traditional medicine (ATM). ATM includes medical activities stemming from practices, customs and traditions which were integral to the distinctive African cultures. It is based mainly on the oral transfer of knowledge, with the risk of losing critical knowledge. Moreover, practices differ according to the regions and the availability of medicinal plants. Therefore, it is necessary to compile tacit, disseminated and complex knowledge from various Tradi-Practitioners (TP) in order to determine interesting patterns for treating a given disease. Knowledge engineering methods for traditional medicine are useful to model suitably complex information needs, formalize knowledge of domain experts and highlight the effective practices for their integration to conventional medicine. The work described in this paper presents an approach which addresses two issues. First it aims at proposing a formal representation model of ATM knowledge and practices to facilitate their sharing and reusing. Then, it aims at providing a visual reasoning mechanism for selecting best available procedures and medicinal plants to treat diseases. The approach is based on the use of the Delphi method for capturing knowledge from various experts which necessitate reaching a consensus. Conceptual graph formalism is used to model ATM knowledge with visual reasoning capabilities and processes. The nested conceptual graphs are used to visually express the semantic meaning of Computational Tree Logic (CTL) constructs that are useful for formal specification of temporal properties of ATM domain knowledge. Our approach presents the advantage of mitigating knowledge loss with conceptual development assistance to improve the quality of ATM care (medical diagnosis and therapeutics), but also patient safety (drug monitoring).

Indeterminate direction relation model based on fuzzy description framework

The indetermination of direction relation is a hot topic for fuzzy GIS researchers. The existing models only study the effects of indetermination of spatial objects, but ignore the uncertainty of direction reference framework. In this paper, first a formalized representation model of indeterminate spatial objects is designed based on quadruple (x, y, A, μ), then a fuzzy direction reference framework is constructed by revising the cone method, in which the partitions of direction tiles are smooth and continuous, and two neighboring sections are overlapped in the transitional zones with fuzzy method. Grounded on these, a fuzzy description model for indeterminate direction relation is proposed in which the uncertainty of all three parts (source object, reference object and reference frame) is taken into account simultaneously. In the end, case studies are implemented to test the rationality and validity of the model.

A Formal Model for Representation and Querying of Structured Documents

Most documents have a hierarchical structure, which can be made explicit by markup languages such as SGML. In this paper we propose a formal model for representation of hierarchically structured documents, to be used as the basis for document query languages. The model uses a redundant representation of the document elements to simplify the expression of common queries. As an illustration of the power of the model we show how queries might be expressed, both as set-theoretic expressions and in a simple algebra, and outline how queries might be evaluated in a practical system.

Automated transformation of algorithms into register-transfer level implementations

This paper describes a high-level synthesis system, called CAMAD, for transforming algorithms into hardware implementation structures at register-transfer level. The algorithms are used to specify the behaviors of the hardware to be designed. They are first translated into a formal representation model which is based on timed Petri nets and consists of separate but related descriptions of control and data path. The formal model is used as an intermediate design representation and supports an iterative transformation approach to high-level synthesis. The basic idea is that once the behavioral specification is translated into the initial design representation, it can be viewed as a primitive implementation. Correctness-preserving transformations are then used to successively transform the initial design into an efficient implementation. Selection of transformations is guided by an optimization strategy which makes design decisions concerning operation scheduling, data path allocation, and control allocation simultaneously. The integration of these several synthesis subtasks has resulted in a better chance to reach the globally optimal solution. Experimental results show that our approach produces improved register-transfer designs, especially in the cases when the designed hardware consists of data paths and control logics that are tightly coupled.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Modelling and verification of end-to-end transport protocols

End-to-end transport protocols are a fundamental concept in networking. Its situation within the protocol hierarchy as well as its main functions are first reviewed. A formal representation model, particularly well adapted to this kind of protocols, but useful also for other protocol types, is then introduced. The separation of the protocol automation in two distinct finite state automata and the splitting of the state set of one of these automata in a set of user partial states and a set of network partial states are main features of this model. A modelling methodology allowing a straightforward application of the model to any end-to-end transport protocol is also described. A second part of the paper is concerned with the validation of the control functions of protocols. A method for detection of deadlock situations is presented. This method consists of determining all possible deadlock situations and then of testing whether these situations may be reached by the protocol. Some results of the verification of the Cyclades transport protocol are also reproduced.