Q-Map: Clinical Concept Mining from Clinical Documents
Over the past decade, there has been a steep rise in
the data-driven analysis in major areas of medicine, such as clinical
decision support system, survival analysis, patient similarity analysis,
image analytics etc. Most of the data in the field are well-structured
and available in numerical or categorical formats which can be used
for experiments directly. But on the opposite end of the spectrum,
there exists a wide expanse of data that is intractable for direct
analysis owing to its unstructured nature which can be found in the
form of discharge summaries, clinical notes, procedural notes which
are in human written narrative format and neither have any relational
model nor any standard grammatical structure. An important step
in the utilization of these texts for such studies is to transform
and process the data to retrieve structured information from the
haystack of irrelevant data using information retrieval and data mining
techniques. To address this problem, the authors present Q-Map in
this paper, which is a simple yet robust system that can sift through
massive datasets with unregulated formats to retrieve structured
information aggressively and efficiently. It is backed by an effective
mining technique which is based on a string matching algorithm
that is indexed on curated knowledge sources, that is both fast
and configurable. The authors also briefly examine its comparative
performance with MetaMap, one of the most reputed tools for medical
concepts retrieval and present the advantages the former displays over
Definition of a Computing Independent Model and Rules for Transformation Focused on the Model-View-Controller Architecture
This paper presents a model-oriented development approach to software development in the Model-View-Controller (MVC) architectural standard. This approach aims to expose a process of extractions of information from the models, in which through rules and syntax defined in this work, assists in the design of the initial model and its future conversions. The proposed paper presents a syntax based on the natural language, according to the rules agreed in the classic grammar of the Portuguese language, added to the rules of conversions generating models that follow the norms of the Object Management Group (OMG) and the Meta-Object Facility MOF.
Domain Driven Design vs Soft Domain Driven Design Frameworks
This paper presents and compares the SSDDD “Systematic Soft Domain Driven Design Framework” to DDD “Domain Driven Design Framework” as a soft system approach of information systems development. The framework use SSM as a guiding methodology within which we have embedded a sequence of design tasks based on the UML leading to the implementation of a software system using the Naked Objects framework. This framework has been used in action research projects that have involved the investigation and modelling of business processes using object-oriented domain models and the implementation of software systems based on those domain models. Within this framework, Soft Systems Methodology (SSM) is used as a guiding methodology to explore the problem situation and to develop the domain model using UML for the given business domain. The framework is proposed and evaluated in our previous works, a comparison between SSDDD and DDD is presented in this paper, to show how SSDDD improved DDD as an approach to modelling and implementing business domain perspectives for Information Systems Development. The comparison process, the results, and the improvements are presented in the following sections of this paper.
A Generic Approach to Reuse Unified Modeling Language Components Following an Agile Process
Unified Modeling Language (UML) is considered as one of the widespread modeling language standardized by the Object Management Group (OMG). Therefore, the model driving engineering (MDE) community attempts to provide reuse of UML diagrams, and do not construct it from scratch. The UML model appears according to a specific software development process. The existing method generation models focused on the different techniques of transformation without considering the development process. Our work aims to construct an UML component from fragments of UML diagram basing on an agile method. We define UML fragment as a portion of a UML diagram, which express a business target. To guide the generation of fragments of UML models using an agile process, we need a flexible approach, which adapts to the agile changes and covers all its activities. We use the software product line (SPL) to derive a fragment of process agile method. This paper explains our approach, named RECUP, to generate UML fragments following an agile process, and overviews the different aspects. In this paper, we present the approach and we define the different phases and artifacts.
A Study of Quality Assurance and Unit Verification Methods in Safety Critical Environment
In the present case study we examined the development and testing methods of systems that contain safety-critical elements in different industrial fields. Consequentially, we observed the classical object-oriented development and testing environment, as both medical technology and automobile industry approaches the development of safety critical elements that way. Subsequently, we examined model-based development. We introduce the quality parameters that define development and testing. While taking modern agile methodology (scrum) into consideration, we examined whether and to what extent the methodologies we found fit into this environment.
, quality management
, unit verification
, model base testing
, agile methods
, object-oriented programming
, field specific modelling
, user story
, UML Standard.
Business Domain Modelling Using an Integrated Framework
This paper presents an application of a “Systematic
Soft Domain Driven Design Framework” as a soft systems approach
to domain-driven design of information systems development. The
framework use SSM as a guiding methodology within which we have
embedded a sequence of design tasks based on the UML leading to
the implementation of a software system using the Naked Objects
framework. This framework have been used in action research
projects that have involved the investigation and modelling of
business processes using object-oriented domain models and the
implementation of software systems based on those domain models.
Within this framework, Soft Systems Methodology (SSM) is used as
a guiding methodology to explore the problem situation and to
develop the domain model using UML for the given business
domain. The framework is proposed and evaluated in our previous
works, and a real case study “Information Retrieval System for
academic research” is used, in this paper, to show further practice and
evaluation of the framework in different business domain. We argue
that there are advantages from combining and using techniques from
different methodologies in this way for business domain modelling.
The framework is overviewed and justified as multimethodology
using Mingers multimethodology ideas.
Towards an E-Learning Platform Multi-Agent Based On the E-Tutoring for Collaborative Work
This article presents our prototype MASET (Multi
Agents System for E-Tutoring Learners engaged in online
collaborative work). MASET that we propose is a system which
basically aims to help tutors in monitoring the collaborative work of
students and their various interactions. The evaluation of such
interactions by the tutor is based on the results provided by the
automatic analysis of the interaction indicators. This system is
predicated upon the middleware JADE (Java Agent Development
Framework) and e-learning Moodle platform. The MASET
environment is modeled by AUML which allows structuring the
different interactions between agents for the fulfillment and
performance of online collaborative work. This multi-agent system
has been the subject of a practical experimentation based on the
interactions data between Master Computer Engineering and System
Unified Structured Process for Health Analytics
Health analytics (HA) is used in healthcare systems
for effective decision making, management and planning of
healthcare and related activities. However, user resistances, unique
position of medical data content and structure (including
heterogeneous and unstructured data) and impromptu HA projects
have held up the progress in HA applications. Notably, the accuracy
of outcomes depends on the skills and the domain knowledge of the
data analyst working on the healthcare data. Success of HA depends
on having a sound process model, effective project management and
availability of supporting tools. Thus, to overcome these challenges
through an effective process model, we propose a HA process model
with features from rational unified process (RUP) model and agile
Some Considerations on UML Class Diagram Formalisation Approaches
Unified Modelling Language (UML) is a software modelling language that is widely used and accepted. One significant drawback, of which, is that the language lacks formality. This makes carrying out any type of rigorous analysis difficult process. Many researchers attempt to introduce their approaches to formalise UML diagrams. However, it is always hard to decide what language and/or approach to use. Therefore, in this paper, we highlight some of the advantages and disadvantages of number of those approaches. We also try to compare different counterpart approaches. In addition, we draw some guidelines to help in choosing the suitable approach. Special concern is given to the formalisation of the static aspects of UML shown is class diagrams.
UML Model for Double-Loop Control Self-Adaptive Braking System
In this paper, we present an activity diagram model for double-loop control self-adaptive braking system. Since activity diagram helps to improve visibility of self-adaption. We can easily find where improvement is needed on double-loop control. Double-loop control is adopted since the design conditions and actual conditions can be different. The system is reconfigured in runtime by using double-loop control. We simulated to verify and validate our model by using MATLAB. We compared single-loop control model with double-loop control model. Simulation results show that double-loop control provides more consistent brake power control than single-loop control.
Knowledge Based Concept Analysis Method using Concept Maps and UML: Security Notion Case
One of the most ancient humankind concerns is knowledge formalization i.e. what a concept is. Concept Analysis, a branch of analytical philosophy, relies on the purpose of decompose the elements, relations and meanings of a concept. This paper aims at presenting a method to make a concept analysis obtaining a knowledge representation suitable to be processed by a computer system using either object-oriented or ontology technologies. Security notion is, usually, known as a set of different concepts related to “some kind of protection". Our method concludes that a more general framework for the concept, despite it is dynamic, is possible and any particular definition (instantiation) depends on the elements used by its construction instead of the concept itself.
Augmenting Use Case View for Modeling
Mathematical, graphical and intuitive models are often
constructed in the development process of computational systems.
The Unified Modeling Language (UML) is one of the most popular
modeling languages used by practicing software engineers. This
paper critically examines UML models and suggests an augmented
use case view with the addition of new constructs for modeling
software. It also shows how a use case diagram can be enhanced. The
improved modeling constructs are presented with examples for
clarifying important design and implementation issues.
Automatic Generation of OWL Ontologies from UML Class Diagrams Based on Meta- Modelling and Graph Grammars
Models are placed by modeling paradigm at the center of development process. These models are represented by languages, like UML the language standardized by the OMG which became necessary for development. Moreover the ontology engineering paradigm places ontologies at the center of development process; in this paradigm we find OWL the principal language for knowledge representation. Building ontologies from scratch is generally a difficult task. The bridging between UML and OWL appeared on several regards such as the classes and associations. In this paper, we have to profit from convergence between UML and OWL to propose an approach based on Meta-Modelling and Graph Grammars and registered in the MDA architecture for the automatic generation of OWL ontologies from UML class diagrams. The transformation is based on transformation rules; the level of abstraction in these rules is close to the application in order to have usable ontologies. We illustrate this approach by an example.
System-Level Energy Estimation for SoC based on the Dynamic Behavior of Embedded Software
This paper describes a system-level SoC energy
consumption estimation method based on a dynamic behavior of
embedded software in the early stages of the SoC development. A
major problem of SOC development is development rework caused by
unreliable energy consumption estimation at the early stages. The
energy consumption of an SoC used in embedded systems is strongly
affected by the dynamic behavior of the software. At the early stages
of SoC development, modeling with a high level of abstraction is
required for both the dynamic behavior of the software, and the
behavior of the SoC. We estimate the energy consumption by a UML
model-based simulation. The proposed method is applied for an actual
embedded system in an MFP. The energy consumption estimation of
the SoC is more accurate than conventional methods and this proposed
method is promising to reduce the chance of development rework in
the SoC development. ∈
Symbolic Model Checking of Interactions in Sequence Diagrams with Combined Fragments by SMV
In this paper, we proposed a method for detecting consistency violation between state machine diagrams and a sequence diagram defined in UML 2.0 using SMV. We extended a method expressing these diagrams defined in UML 1.0 with boolean formulas so that it can express a sequence diagram with combined fragments introduced in UML 2.0. This extension made it possible to represent three types of combined fragment: alternative, option and parallel. As a result of experiment, we confirmed that the proposed method could detect consistency violation correctly with SMV.
Model Checking Consistency of UML Diagrams Using Alloy
In this paper, we proposed a method for detecting consistency violation between UML state machine diagrams and communication diagrams using Alloy. Using input language of Alloy, the proposed method expresses system behaviors described by state machine diagrams, message sequences described by communication diagrams, and a consistency property. As a result of application for an example system, we confirmed that consistency violation could be detected using Alloy correctly.
Effect of Electromagnetic Fields on Structure and Pollen Grains Development in Chenopodium album L
The role of the pollen grain, with to the reproductive
process of higher plants, is to deliver the spermatic cells to the
embryo sac for egg fertilization. The aim of this project was study
the effect of electromagnetic fields on structure and pollen grains
development in Chenopodium album. Anthers of Chenopodium
album L. were collected at different stages of development from
control (without electromagnetic field) and plants grown at 10m from
the field sources. Structure and development of pollen grains were
studied and compared. The studying pollen structure by Light and
Scanning electron microscopy showed that electromagnetic fields
reduction of pollen grains number and male sterility, thus , in some
anthers, pollen grains were attached together and deformed compared
to control ones. The data presented suggest that prolonged exposures
of plants to magnetic field may cause different biological effects at
the cellular tissue and organ levels.
Microbial Production of Levan using Date Syrup and Investigation of Its Properties
Levan, an exopolysaccharide, was produced by
Microbacterium laevaniformans and its yield was characterized as a
function of concentrations of date syrup, sucrose and the fermentation
time. The optimum condition for levan production from sucrose was
at concentration of 20% sucrose for 48 h and for date syrup was 25%
for 48 h. The results show that an increase in fermentation time
caused a decrease in the levan production at all concentrations of date
syrup tested. Under these conditions after 48 h in sucrose medium,
levan production reached 48.9 g/L and for date syrup reached 10.48
g/L . The effect of pH on the yield of the purified levan was examined
and the optimum pH for levan production was determined to be 6.0.
Levan was composed mainly of fructose residues when analyzed by
TLC and FT-IR spectroscopy. Date syrup is a cheap substrate widely
available in Iran and has potential for levan production. The thermal
stability of levan was assessed by Thermo Gravimetric Analysis
(TGA) that revealed the onset of decomposition near to 49°C for the
levan produced from sucrose and 51°C for the levan from date syrup.
DSC results showed a single Tg at 98°C for levan produced from
sucrose and 206 °C for levan from date syrup.
The Survey and the Comparison of Maximum Likelihood, Mahalanobis Distance and Minimum Distance Methods in Preparing Landuse Map in the Western Part of Isfahan Province
In this research three methods of Maximum Likelihood, Mahalanobis Distance and Minimum Distance were analyzed in the Western part of Isfahan province in the Iran country. For this purpose, the IRS satellite images and various land preparation uses in region including rangelands, irrigation farming, dry farming, gardens and urban areas were separated and identified. In these methods, matrix error and Kappa index were calculated and accuracy of each method, based on percentages: 53.13, 56.64 and 48.44, were obtained respectively. Considering the low accuracy of these methods to separate land uses due to spread of the land uses, it-s suggested the visual interpretation of the map, to preparing the land use map in this region. The map prepared by visual interpretation is in high accuracy if it will be accompany with the visit of the region.
Extensions to Some AOSE Methodologies
This paper looks into areas not covered by prominent
Agent-Oriented Software Engineering (AOSE) methodologies.
Extensive paper review led to the identification of two issues, first
most of these methodologies almost neglect semantic web and
ontology. Second, as expected, each one has its strength and
weakness and may focus on some phases of the development
lifecycle but not all of the phases. The work presented here builds
extensions to a highly regarded AOSE methodology (MaSE) in order
to cover the areas that this methodology does not concentrate on. The
extensions include introducing an ontology stage for semantic
representation and integrating early requirement specification from a
methodology which mainly focuses on that. The integration involved
developing transformation rules (with the necessary handling of nonmatching
notions) between the two sets of representations and
building the software which automates the transformation. The
application of this integration on a case study is also presented in the
paper. The main flow of MaSE stages was changed to smoothly
accommodate the new additions.
A Model Driven Based Method for Scheduling Analysis and HW/SW Partitioning
Unified Modeling Language (UML) extensions for real time embedded systems (RTES) co-design, are taking a growing interest by a great number of industrial and research communities. The extension mechanism is provided by UML profiles for RTES. It aims at improving an easily-understood method of system design for non-experts. On the other hand, one of the key items of the co- design methods is the Hardware/Software partitioning and scheduling tasks. Indeed, it is mandatory to define where and when tasks are implemented and run. Unfortunately the main goals of co-design are not included in the usual practice of UML profiles. So, there exists a need for mapping used models to an execution platform for both schedulability test and HW/SW partitioning. In the present work, test schedulability and design space exploration are performed at an early stage. The proposed approach adopts Model Driven Engineering MDE. It starts from UML specification annotated with the recent profile for the Modeling and Analysis of Real Time Embedded systems MARTE. Following refinement strategy, transformation rules allow to find a feasible schedule that satisfies timing constraints and to define where tasks will be implemented. The overall approach is experimented for the design of a football player robot application.
Application of a Systemic Soft Domain-Driven Design Framework
This paper proposes a “soft systems" approach to
domain-driven design of computer-based information systems. We
propose a systemic framework combining techniques from Soft
Systems Methodology (SSM), the Unified Modelling Language
(UML), and an implementation pattern known as “Naked Objects".
We have used this framework in action research projects that have
involved the investigation and modelling of business processes using
object-oriented domain models and the implementation of software
systems based on those domain models. Within the proposed
framework, Soft Systems Methodology (SSM) is used as a guiding
methodology to explore the problem situation and to generate a
ubiquitous language (soft language) which can be used as the basis
for developing an object-oriented domain model. The domain model
is further developed using techniques based on the UML and is
implemented in software following the “Naked Objects"
implementation pattern. We argue that there are advantages from
combining and using techniques from different methodologies in this
The proposed systemic framework is overviewed and justified as
multimethodologyusing Mingers multimethodology ideas.
This multimethodology approach is being evaluated through a
series of action research projects based on real-world case studies. A
Peer-Tutoring case study is presented here as a sample of the
framework evaluation process
Stepwise Refinement in Executable-UML for Embedded System Design: A Preliminary Study
The fast growth in complexity coupled with requests for shorter development periods for embedded systems are bringing demands towards a more effective, i.e. higher-abstract, design process for hardaware/software integrated design. In Software Engineering area, Model Driven Architecture (MDA) and Executable UML (xUML) has been accepted to bring further improvement in software design. This paper constructs MDA and xUML stepwise transformations from an abstract specification model to a more concrete implementation model using the refactoring technique for hardaware/software integrated design. This approach provides clear and structured models which enables quick exploration and synthesis, and early stage verification.
A Tool for Checking Conformance of UML Specification
Unified Modeling Language (UML) is a standard
language for modeling of a system. UML is used to visually specify
the structure and behavior of a system. The system requirements are
captured and then converted into UML specification. UML
specification uses a set of rules and notations, and diagrams to
specify the system requirements. In this paper, we present a tool for
developing the UML specification. The tool will ease the use of the
notations and diagrams for UML specification as well as increase the
understanding and familiarity of the UML specification. The tool will
also be able to check the conformance of the diagrams against each
other for basic compliance of UML specification.
Cosastudio: A Software Architecture Modeling Tool
A key aspect of the design of any software system is
its architecture. An architecture description provides a formal model
of the architecture in terms of components and connectors and how
they are composed together. COSA (Component-Object based
Software Structures), is based on object-oriented modeling and
component-based modeling. The model improves the reusability by
increasing extensibility, evolvability, and compositionality of the
software systems. This paper presents the COSA modelling tool
which help architects the possibility to verify the structural coherence
of a given system and to validate its semantics with COSA approach.
Evaluation of Risk Attributes Driven by Periodically Changing System Functionality
Modeling of the distributed systems allows us to
represent the whole its functionality. The working system instance
rarely fulfils the whole functionality represented by model; usually
some parts of this functionality should be accessible periodically.
The reporting system based on the Data Warehouse concept seams to
be an intuitive example of the system that some of its functionality is
required only from time to time. Analyzing an enterprise risk
associated with the periodical change of the system functionality, we
should consider not only the inaccessibility of the components
(object) but also their functions (methods), and the impact of such a
situation on the system functionality from the business point of view.
In the paper we suggest that the risk attributes should be estimated
from risk attributes specified at the requirements level (Use Case in
the UML model) on the base of the information about the structure of
the model (presented at other levels of the UML model). We argue
that it is desirable to consider the influence of periodical changes in
requirements on the enterprise risk estimation. Finally, the
proposition of such a solution basing on the UML system model is
An UML Statechart Diagram-Based MM-Path Generation Approach for Object-Oriented Integration Testing
MM-Path, an acronym for Method/Message Path, describes the dynamic interactions between methods in object-oriented systems. This paper discusses the classifications of MM-Path, based on the characteristics of object-oriented software. We categorize it according to the generation reasons, the effect scope and the composition of MM-Path. A formalized representation of MM-Path is also proposed, which has considered the influence of state on response method sequences of messages. .Moreover, an automatic MM-Path generation approach based on UML Statechart diagram has been presented, and the difficulties in identifying and generating MM-Path can be solved. . As a result, it provides a solid foundation for further research on test cases generation based on MM-Path.
Formal Modeling and Verification of Software Models
Graph transformation has recently become more and
more popular as a general visual modeling language to formally state
the dynamic semantics of the designed models. Especially, it is a
very natural formalism for languages which basically are graph (e.g.
UML). Using this technique, we present a highly understandable yet
precise approach to formally model and analyze the behavioral
semantics of UML 2.0 Activity diagrams. In our proposal, AGG is
used to design Activities, then using our previous approach to model
checking graph transformation systems, designers can verify and
analyze designed Activity diagrams by checking the interesting
properties as combination of graph rules and LTL (Linear Temporal
Logic) formulas on the Activities.
UML Modeling for Instruction Pipeline Design
Unified Modeling language (UML) is one of the
important modeling languages used for the visual representation of
the research problem. In the present paper, UML model is designed
for the Instruction pipeline which is used for the evaluation of the
instructions of software programs. The class and sequence diagrams
are designed & performance is evaluated for instructions of a sample
program through a case study.
A Novel Method for Behavior Modeling in Uncertain Information Systems
None of the processing models in the software
development has explained the software systems performance
evaluation and modeling; likewise, there exist uncertainty in the
information systems because of the natural essence of requirements,
and this may cause other challenges in the processing of software
development. By definition an extended version of UML (Fuzzy-
UML), the functional requirements of the software defined
uncertainly would be supported. In this study, the behavioral
description of uncertain information systems by the aid of fuzzy-state
diagram is crucial; moreover, the introduction of behavioral diagrams
role in F-UML is investigated in software performance modeling
process. To get the aim, a fuzzy sub-profile is used.