dataesr/scientific-paragraphs-categorization huggingface dataset:
In addition to these DFD techniques, the DARTS method uses other notations that we will present in the section related to ADARTS. 7) Strengths and weaknesses For these three methods, the main advantage is the use of a high level of structured analysis of data. They are easy to take in hand, because they use fairly well known diagrams (data flow diagram and control flow diagram). They present some limitations: 1) They are unsuitable for prototyping. 2) The steps must be carried out sequentially for a successful implementation. 3) It is difficult to control the time required for the full implementation of the system. In addition to these limits, CODARTS presents few others: it is designed primarily for the ADA language, the notations used are not easy to understand, it is complex to use and offers a limited number of views in the system design.
MASCOT is based on processes or activities in a system and has for goal to design interactive and complex real-time applications, in a highly structured approach. It focuses on the communication between the different components of the system and requires that the specification be complete at each level. 2) Usability MASCOT is based on a form of functional and structural decomposition, which is particularly suitable for use in the development of large distributed real-time embedded systems for data processing. The emphasis is on the word "large": a large number of people involved in the development, a large amount of code to write, a large number of requirements to be taken into account at the same time, a wide variety or quantity of hardware resources, a project whose development extends over a long period.
Of course, all these measures of sizes are relative. The method provides a design language and a graphical notation, and a process of conceptual derivation. MASCOT models are stated in terms of a set of text modules and diagrams that support the principles of data flow on which the method is founded. These diagrams are used to show the decomposition of a system into subsystems consisting of concurrent tasks. The interfaces between the tasks are in the form of channels (message queues) and pools (information hiding modules). There is a textual language to describe the graphic representation. The main steps of this method are: 1) Fully describe the internal functions of the system, and its relations with the outside. This is done through the network diagram. 2) The first network is decomposed into components of lower level, 3) the components are encoded in terms of algorithms and data structures.
In terms of tools, we have the development environment of MASCOT version 3. 1, which was defined in terms of a set of functions to control the progressive capture of a design. 3) Compositionality Modular as its name suggests, the cornerstone of the method is a particular formalism by which a complex software can be broken down into a number of smaller components that interact with each other, and this decomposition process can be repeated at any depth required to produce a manageable development task. 4) Existence of Notations Dedicated to Real-Time MASCOT provides the ability to use certain communication protocols  [22]. These protocols allow asynchronous communication, which prevents implicitly the interlocked timing relationships into the synchronous communication. 5) Dependability MASCOT does not define any technique of dependability, if we refer only to the elements chosen in this work to characterize this criterion.
6) Illustration example MASCOT is characterized by two types of elementary basic components: activity (a single thread of execution), which is an active element, and IDA (intercommunication data area) which is a passive element. IDAs are interconnected to form a data flow diagram. Connection to physical entities (represented by a grey rectangle) is made by dashed lines, which indicate what software unit is responsible of which hardware. MASCOT uses a number of concepts and notations for systems modelling, including: -Activity: A rectangle with rounded edges and often a circle -IDA: A rectangle or a rectangle with rounded side. -Window: A small full rectangle. This is a IDA point, marking the passive end of a connection of data flow. -The port: A small full circle, this is a point in the activity that marks the active end of a connection of data flows.
7) Strengths and weaknesses One of the strengths of MASCOT is that it relies on the Ada language and as such, it benefits of its advantages in terms of design of large systems, of high level of abstraction, etc. The fact to be based on a form of functional and structural decomposition makes it well suited to the development of large distributed real-time embedded systems for data processing. MASCOT has some limits, among which: it does not directly support the requirements analysis (needs) and goes directly into building models; there are not many tools supporting it; it is not suitable for prototyping or for rapid application development; its use greatly increases development costs.
2) Usability ADARTS provides a graphical representation and textual notations for modelling real-time systems. The stage of the structured design in DARTS is replaced by the one of modules structuring, with concealment of information provided by Ada. It can be considered as similar to DARTS, but with some improvements such as abstraction and decomposition. Another version of DARTS also exists and is intended for the design of distributed real-time applications: this is DARTS/DA. It proposes an approach based on five steps: development of an environmental and behavioural model (development of a context diagram, of a states-transition diagram, of data flows and control flows diagrams, of a data dictionary and production of a mini specification), structuring the system in concurrent tasks (production of a tasks architecture diagram and specification of the behaviour of each task), structuring of system as information's abstraction modules (construction of the system architecture schema), development of a design based on Ada architecture (only required for the implementation in Ada), definition of Ada components interfaces (only required for the implementation in Ada, here a specification of Ada packages is produced).
This method is supported by tools such as IBM Rational Rhapsody published by IBM, which is a model-driven development environment, very interesting for systems engineers and software developers of real time and embedded systems; it allows to create many Ada compatible diagrams and to generate the corresponding Ada code, but also C, C++, Java and C# code. 3) Compositionality Decomposition is one of the improvements brought by ADARTS to DARTS  [25]. Indeed, in addition to supporting the mapping to Ada, one of the goals of this extension of DARTS, is to provide more maintainable and reusable designs, adopting greater use of information abstraction than DARTS. This concern for maintainability and reusability leads to the decomposition of the system into subsystems that provide a range of services supported by objects and functions.
STOOD offers many features: it makes it possible to ensure an update of traceability between the system and the software models and the initial requirements, which may be imported from text files or other tools; It provides a graphical editor for building of architecture models of the software and its environment (libraries, runtime platform, …); it also allows detailed design, checking a design, integrating analysis tools, automatic code generation in Ada, C and C++, and generating design documentation. 3) Compositionality As mentioned above, the HOOD method is based on system decomposition into a components hierarchy describing the system. Thus the objects are identified, and for each object, its children objects are identified, and so on. It guarantees a low coupling between modules (components) of a system, which is a necessary factor for system components reusability and maintainability.
Unified Modelling Language (UML) 1) Presentation UML  [31] -  [35]  can be considered as a combination of the notations that exist in methods such as ROOM, HOOD, YSM MASCOT, etc. The word "unified" implies a unification of different models. Several diagrams it uses are adapted from other methods. It contains notations that are lacking in other methodologies and it tries to improve and standardise them. It is very well supported by a variety of tools compared to other methods, and its use requires no formal knowledge. 2) Usability UML is not a method (i. e. a normative description of the modelling steps), but a graphical language for representing various aspects of a system. It provides a set of graphical notations grouped into charts specific to each aspect of a system. Each graphical notation has an associated text which explains its content.
Unified Modelling Language-Real Time (UML-RT) 1) Presentation UML-RT  [2]  [38]  [39]  is an extension of UML for modelling embedded reactive and real time software systems. It is a UML profile proposed as modelling language of such systems. It particularly focuses on the description of the system at the architectural level, the definition of the overall system structure. It defines new concepts for modelling systems such as capsules, and uses these concepts in UML collaboration diagrams to obtain a description of the architecture. UML-RT implements some ideas of HOOD, ROOM and MASCOT, and adds them to the classical (traditional) UML notations. We can cite for example the capsule diagram that incorporates children objects, similarly to the "Parent-child" object relationship of the HOOD method, as well as passive and active ports that already existed in ROOM.
Architectures definition is based on the components and the interactions between them. There exists several tools  [42] [43]  supporting the AADL standard at different levels (modelling, analysis, scheduling). We can mention free tools such as Osate, Cheddar, Ocarina, Topcased, and commercialised tools such as: Stood, AADL inspector, Taste. Osate provides AADL support for Eclipse. In the first version, Osate supports the first release of AADL. The second version is available since august 2011 and it supports AADL r2. Cheddar is a tool for real-time scheduling analysis which works typically with STOOD and AADL Inspector. Ocarina is able to load an AADL r1 or r2 project, to run analysis and to generate code from the model. Topcased is an environment for eclipse including a generator of graphical editor.
SysML 1) Presentation SysML  [46]  [47] is a graphical modelling language developed by OMG (Object Management Group) in response (of industry) to the RFP (Request For Proposal) of UML for systems engineering. It is a UML profile representing a subset of that modelling language with some extensions. It supports the specification, analysis, design, verification and validation of systems that include hardware, software, data, personnel and procedures. It is a visual modelling language that provides semantics (meaning) and notation (representation of meaning). 2) Usability SysML replaces UML classes by blocks for a vocabulary more suitable to Systems Engineering. A block encompasses any concept of software, hardware, data, process, and even of human resources management. SysML reuses a part of UML2, and also provides its own definitions.
Therefore, it does not use the thirteen diagrams of UML2, but provides a set of diagrams suitable for Systems Engineering. SysML supports the exchange of data For modelling a system, SysML provides a set of diagrams divided into 3 categories relative to the views of systems: -Structural diagrams that describe the components of the product and its environment. Among these we have in particular the parametric diagram, which is a SysML extension for analysis of critical parameters of systems; -Dynamic diagrams that model the behaviour of the system in response to its environment; -The requirements diagram, which is a SysML extension. The order of presentation of these diagrams does not define the methodology for modelling a system with SysML. The SysML language is incorporated in some commercial software like Sparx Systems Enterprise Architect (SysML plugin), IBM Rational Software Modeler, MagicDraw (SysML plugin required) and open source software as TopCased (Eclipse), Papyrus, and OpenEmbeDD TTools.
7) Strengths and weaknesses SysML offers the advantage of being accessible to software developers that will find many similarities with    -This ensures consistency of data as SysML rules give each model element a single definition, built by gathering information from its different representations, and forbid them to contradict. This also reduces the risk of errors; -It facilitates the use of simulation as a SysML model can assemble all the information needed to model the system, to simulate its behaviour and to compare the results with the requirements in order to validate (or not) solutions. SysML has weaknesses: The genericity of some concepts, such as block is a source of misunderstanding and needs to be quickly clarified when modelling. SysML can be seen as a high-level language for the analysis and design of complex systems to some granularity, but that is not sufficient for the complete development of a system.
It includes, as sub profiles, CoreElement, NFP, GRM and Alloc profiles; -The package MARTE design model bringing together sub-profiles dedicated to the design, namely GCM, HLAM and DRM; -The package MARTE analysis model combining the sub-profiles dedicated to the analysis which are GQAM, SAM and PAM; -The package MARTE Annexes gathering the utilities or transverse sub-profiles and template library. MARTE is a relatively young standard, and therefore the number of tools supporting it remains low, but is intended to increase rapidly in the coming years. There are UML modelers that currently support profile MARTE: -Papyrus: it is free and is part of the Eclipse project. 3) Compositionality The design of the whole system is modular. Based on his needs, the user can select a particular subset of the 14 sub-profiles of MARTE.
Software architecture of the speed control system with MARTE. the application, one can assign different weights to the criteria in order to take into account the relative importance of each criterion. Table  6  gives the overall score of the studied languages and methods across all considered criteria comparison. We note that according to these criteria, recent languages such as UML-MARTE, AADL and SysML are best classified; but also the HOOD method. Note, however, that in considering the criteria individually, rankings change. Thus, some methods such as DARTS, ADARTS, CODARTS and MASCOT are less easy to use than languages like UML, UML-RT, SysML; but are well provided with respect to elements linked to real time. We also note that only some (YSM, HOOD, AADL, MARTE) of these approaches allow the co-design.
The combination has been done with the assignment of identical weights to different criteria. However, the adoption of different weights is possible to take into account the relative importance of each criterion. In this work are also presented the notations and concepts offered by the approaches to model a system and illustrated their use through an example, in order to enable readers to assess the degree of coverage of each criterion for each approach and to understand the score given for each criterion. This work shows that in general, methods and languages do not cover all the phases (and aspects) of the development of embedded and real time systems. This is reflected in the comparison tables, by the variation of marks obtained by each approach according to the criterion. Special mention is made, to languages such as UML, SysML, UML-MARTE and AADL, which offer notations and diagrams for most of the phases of the RTES development cycle, and also to the HOOD composite structure CruiseStructure «messagePort» +eCom:I_En  [1]  «messagePort» +bpCom:I_BP  [1]  «messagePort» +uiCom:I_UI  [1]  «messagePort» +wrCom:I_WR  [1]  «messagePort» +taCom:I_TA  [1]  CruiseControlSystem «messagePort» +eCom:I_En  [1]  «messagePort» +bpCom:I_BP  [1]  «messagePort» +uiCom:I_UI  [1]  «messagePort» +wrCom:I_WR  [1]  «messagePort» +taCom:I_TA  [1]  «flowPort» out_ok_to_run: Integer  [1]  CruiseControlSystem:: +in_c:InControl  [1]  «flowPort» out_ok_to_run: Integer  [1]  «flowPort» out_velocity: Interger  [1]  CruiseControlSystem:: +c:ComputeVelocity  [1]  «flowPort» out_velocity: Interger  [1]  «flowPort» in_pre_vel: Integer  [1]  «flowPort» in_velocity: Integer  [1]  «flowPort» outDesiredSpeed: Integer  [1]  CruiseControlSystem::+cds: ComputeDesiredSpeed  [1]  «flowPort» in_pre_vel: Integer  [1]  «flowPort» in_velocity: Integer  [1]  «flowPort» outDesiredSpeed: Integer  [1]  ts:I_TA  [1]  CruiseControlSystem:: +ct:ComputeThrottle    method which, in addition to being object-oriented, defines a fairly standard development life cycle.
5) Dependability AVATAR language [48]  can be used to enrich the design diagrams of SysML, especially to provide them with a formal semantics. This language is supported by TTool, which is interfaced with the UPPAAL [48]  tool, with the aim of checking the logic and the temporality of SysML design models. Thus, a SysML model can be used for simulations and requirements analysis. 6) Example of illustration.
e. , EBOLA virus) but absent from its host (i. e. , human). This inspires us to use RAW to compute the distance between two species in our study. Here we have used their software called EAGLE to compute the set of RAWs considering each species in turn as the reference and the remaining species as targets. To elaborate, recall that we were given a set, S = {s 1 , s 2 ,. , s k } of k sequences. For a particular pair of sequence s i , s j ∈ S, we first compute RAW s i ,s j (RAW s j ,s i ), i. e. , the set of RAWs considering s i (s j ) as the reference and s j (s i ) as the target sequence. Then we compute the Length Weighted Index (LWI) (discussed above) of both RAW s i ,s j and RAW s j ,s i. This gives us two distance values for a particular pair of species. We then take the average of these two distance measures.
Results and discussion We have used the same datasets used in  [18]  and  [1]. In particular, we have conducted our experiments (5) GCC � (x, y) = NUM G MAW x �MAW y + NUM C MAW x �MAW y NUM � MAW x �MAW y (6) GCC (x, y) = 1 - NUM G MAW x MAW y + NUM C MAW x MAW y NUM � MAW x MAW y (7) R k (x, y) = W k (x) W k (y) (8) M k (x, y) = {α ∈ R k (x, y) : W k-1 (α) M k-1 (x, y) = ∅} on the first exon sequences of β-globin genes from 11 species, namely, Human, Goat, Gallus, Opossum, Lemur, Mouse, Rabbit, Rat, Bovine, Gorilla, and Chimpanzee. Because the gene family of β-globin has a significant biological role in oxygen transport in organisms, it is used to analyze DNA and the first exon of the β-globin gene is an example for many DNA studies instead of computing similarity/dissimilarity of the whole genomes.
Inspired by the experimental setup of Garcia and Pinho  [2] , we consider two scenarios: the original sequence itself and the original sequence concatenated with its reversed complement (artificial words across the boundary between both sequences are ignored). The former will be referred to as the noRC setting and the latter as the RC setting. The motivation for using the reverse complement is to take into consideration words that might occur in the reverse complement strand but that might be absent from the direct strand. We have used the algorithm of  [11]  to compute the MAW sets using their implementation, which is available at: http://github. com/solonas13/maw. We have used EAGLE software of  [20]  to compute the RAW sets; EAGLE is available at: http://bioinformatics. ua. pt/ software/eagle/.
The code to compute the distance matrices and analyze the results were written in C++ language and can be found at: https://github. com/srautonu/AWorDS. We have also implemented a related web-based tool with limited capacity here: http://www. ekngine. com/AWorDS. It is planned that this web-tool will be improved with more functionalities in near future. We have considered five distance measures described in "Distance measures" section based on the MAW sets. Additionally, we have considered LWI and GC content distance measures involving RAW sets. With noRC and RC settings, this gives us a total of 14 distance matrices. For the sake of brevity we do no provide all the distance matrices in this paper. However, these can be found here: https://github. com/srautonu/AWorDS and also in the Additional files 1, 2, 3 and 4.
Phylogenetic tree reconstruction Phylogenetic tree of a group of species (taxa) describes the evolutionary relationship among the species. In sequence-based Phylogenetic reconstruction, the input is a set of homologous sequences from different species and these methods construct quite accurate trees on small to moderate sized datasets. Distance based phylogeny reconstruction methods start by computing a matrix that gives us the pairwise distances between the sequences under consideration. This distance matrix is then used to estimate the tree using standard clustering methods or specially tailored methods to reconstruct the phylogeny from the distance matrix. The distance measures analyzed in this paper have also been used to reconstruct phylogenetic trees using two well-known methods, namely, unweighted pair group method with arithmetic mean (UPGMA)  [21]  and Neighbor Joining (NJ)  [22].
Acknowledgements This research work has been partially supported by an  INSPIRE Strategic Partnership Award , administered by the  British Council ,  Bangladesh  for the project titled " Advances in algorithms for next generation biological sequences". Tanver Athar  is supported by an  EPSRC  grant ( Doctoral Training Grant  # EP/ L504798/1 ). The authors acknowledge the critiques of the anonymous reviewers and the comments from Editors that helped improve the manuscript. Part of this research work was done when M. Sohel Rahman  was on a Sabbatical Leave from  BUET  and was visiting  King's College, London.
Availability of supporting data The data used in our experiments, the code to compute the distance matrices and analyze the results can be found here: https://github. com/srautonu/AWorDS. The implementation of the algorithm of  [11]  is available here: http://github. com/solonas13/maw. The EAGLE software of  [20]  to compute the RAW sets is available here: http:// bioinformatics. ua. pt/software/eagle/. We have also setup a preliminary version of a web-based tool here: http:// www. ekngine. com/AWorDS.
We present the data processing pipeline to generate calibrated data products from the Spectral and Photometric Imaging Receiver (SPIRE) imaging Fourier Transform Spectrometer on the Herschel Space Observatory. The pipeline processes telemetry from SPIRE observations and produces calibrated spectra for all resolution modes. The spectrometer pipeline shares some elements with the SPIRE photometer pipeline, including the conversion of telemetry packets into data timelines and calculation of bolometer voltages. We present the following fundamental processing steps unique to the spectrometer: temporal and spatial interpolation of the scan mechanism and detector data to create interferograms; Fourier transformation; apodization; and creation of a data cube. We also describe the corrections for various instrumental effects including first-and second-level glitch identification and removal, correction of the effects due to emission from the Herschel telescope and from within the spectrometer instrument, interferogram baseline correction, temporal and spatial phase correction, non-linear response of the bolometers, and variation of instrument performance across the focal plane arrays.