Anderson Amorim - Academia.edu (original) (raw)

Papers by Anderson Amorim

Research paper thumbnail of Metaheuristics for multiple sequence alignment: A systematic review

Computational Biology and Chemistry, 2021

The Multiple Sequence Alignment (MSA) is a key task in bioinformatics, because it is used in diff... more The Multiple Sequence Alignment (MSA) is a key task in bioinformatics, because it is used in different important biological analysis, such as function and structure prediction of unknown proteins. There are several approaches to perform MSA and the use of metaheuristics stands out because of the search ability of these methods, which generally leads to good results in a reasonable amount of time. This paper presents a Systematic Literature Review (SLR) on metaheuristics for MSA, compiling relevant works published between 2014 and 2019. The results of our SLR show the constant interest in this subject, due to the several recent publications that use different metaheuristics to obtain more accurate alignments. Moreover, the final results of our SLR show a multi-objective and hybrid approaches trends, which generally leads these methods to achieve even better results. Thus, we show in this work how the use of metaheuristics to perform MSA still remains an important and promising open research field.

Research paper thumbnail of Project Scope Management: A Strategy Oriented to the Requirements Engineering

Proceedings of the 19th International Conference on Enterprise Information Systems, 2017

Scope management is an area of project management defined by PMBoK, which has processes to regist... more Scope management is an area of project management defined by PMBoK, which has processes to register and control everything that belongs to the project boundaries. Although the relevance of this area to the success of projects, its application is still a challenge, which is potentialized by the lack of computational tools to support project management that integrate the scope management totality. In addition, the lack of understanding of project requirements is another factor that hinders the execution of this area, because often the stakeholders do not have full knowledge of their needs at the beginning of the project, resulting in changes throughout the project lifecycle, which increases the costs and deadlines. In this sense, the objective of this work is to propose the integration of the scope management with the requirements engineering, in order to better identify the requirements of a project and to understand what needs to be done, contributing to the success of projects. For the evaluation of the results obtained, a requirements engineering module was developed and integrated with a previously developed computational tool for project management and it aims to assist the application of the project management following the guidelines and good practices proposed on PMBoK.

Research paper thumbnail of A Hybrid Approach using Progressive and Genetic Algorithms for Improvements in Multiple Sequence Alignments

The multiple sequence alignment is one of the main tasks in bioinformatics. It is used in differe... more The multiple sequence alignment is one of the main tasks in bioinformatics. It is used in different important biological analysis, such as function and structure prediction of unknown proteins. There are several approaches to perform multiple sequence alignment and the use of heuristics and meta-heuristics stands out because of the search ability of these methods, which generally leads to good results in a reasonable amount of time. The progressive alignment and genetic algorithm are among the most used heuristics and meta-heuristics to perform multiple sequence alignment. However, both methods have disadvantages, such as error propagation in the case of progressive alignment and local optima results in the case of genetics algorithm. Thus, this work proposes a new hybrid refinement phase using a progressive approach to locally realign the multiple sequence alignment produced by genetic algorithm based tools. Our results show that our method is able to improve the quality of the ali...

Research paper thumbnail of Guidelines for the development of educational games to motivate the learning of theoretical concepts in Engineering and Computing courses

Computer Applications in Engineering Education, 2021

Educational software, especially gaming, have been the target of research in different areas due ... more Educational software, especially gaming, have been the target of research in different areas due to their potential benefits in promoting more dynamic, interactive, and motivating learning. The use of educational games for teaching in Engineering and Computing courses, such as Electrical Engineering, Computer Engineering, Software Engineering, and Computer Science, given the familiarity of these students with computers, can promote greater engagement in the study of theoretical concepts. However, existing educational games still lack the good motivational quality considered essential to ensure real learning. In this context, this paper defines guidelines that address the development of educational games focusing on motivational quality. To support the definition of these guidelines, different motivational methods, together with the attributes that can be improved in a student such as autonomy, effort, and overcoming, were analyzed. These guidelines were applied in the development of an educational game prototype as proof of concept to confirm its effective applicability and its contributions to motivate students. The prototype was assessed by 118 students of the higher education in Computing for 15 days. The majority of participants in the assessment process attested that the prototype meets the motivational quality subcriteria, promoting fun (55%), challenge (68%), social interaction (59%), and feeling of satisfaction (74%). It was then possible to verify its attendance to the desired motivational quality and attest to the potential of the established guidelines.

Research paper thumbnail of Performance Improvement of SNP Search Using Multithread Programming

Journal of Computer Science, 2018

Pattern recognition is an important field in Bioinformatics and a well-known task is the search f... more Pattern recognition is an important field in Bioinformatics and a well-known task is the search for Single Nucleotide Polymorphism (SNP). It is possible to search for a known SNP position and analyze it using patterns of DNA bases, called masks. Nonetheless, this process becomes computationally expensive as the amount of available genomic data increases. Thus, in this study, we have developed a parallelization scheme, based on multithread programming, to SNP analysis using masks. In our tests, we noticed that the proposed scheme improved the execution time in 98.05 times when compared with the sequential approach.

Research paper thumbnail of An approach for COFFEE objective function to global DNA multiple sequence alignment

Computational biology and chemistry, 2018

Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can... more Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can be used to prediction of structures or functions of unknown proteins and to phylogenetic tree reconstruction. There are many heuristics to perform multiple sequence alignment, as Progressive Alignment, Ant Colony, Genetic Algorithms, among others. Along the years, some tools were proposed to perform MSA and MSA-GA is one of them. The MSA-GA is a tool based on Genetic Algorithm to perform multiple sequence alignment and its results are generally better than other well-known tools in bioinformatics, as Clustal W. The COFFEE objective function was implemented in the MSA-GA in order to allow it to produce better alignments to less similar sequence sets of proteins. Nonetheless, the COFFEE objective function is not suited do perform multiple sequence alignment of nucleotides. Thus, we have modified the COFFEE objective function, previously implemented in the MSA-GA, to allow it to obtain bet...

Research paper thumbnail of Improving risk identification process in project management

Proceedings of the 28th International Conference on Software Engineering and Knowledge Engineering, 2016

Nowadays there are many information systems which aim the decision-making, automating the process... more Nowadays there are many information systems which aim the decision-making, automating the processes of project management. However, many times these systems limit the specific functions related to risk management processes and do not allow the control and effective treatment of uncertain events that may affect the project goals. Thus, this paper proposes the integrated use of the Delphi Technique and Risk Breakdown Structure-RBS in order to contribute to the identification of risks, considering the opportunities and threats in a project, to enhance the beneficial effects of the opportunities and avoid the harmful effects of threats. For the evaluation of the results, it was performed the improvement of a system called System to Aid Project Managing-SAPM, in order to support the automated execution of risk management with an emphasis on risk identification process, since this is a crucial stage for risk management in projects. As a result of this work, it is observed that the combined use of the Delphi Technique and RBS allows the risk identification process can be performed fast and safely through the anonymity of those involved and global visualization of the project.

Research paper thumbnail of A parallel approach of COFFEE objective function to multiple sequence alignment

Journal of Physics: Conference Series, 2015

The computational tools to assist genomic analyzes show even more necessary due to fast increasin... more The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Research paper thumbnail of Improvements in the sensibility of MSA-GA tool using COFFEE objective function

Journal of Physics: Conference Series, 2015

The sequence alignment is one of the most important tasks in Bioinformatics, playing an important... more The sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis. There are many strategies to perform sequence alignment, since those use deterministic algorithms, as dynamic programming, until those ones, which use heuristic algorithms, as Progressive, Ant Colony (ACO), Genetic Algorithms (GA), Simulated Annealing (SA), among others. In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results. In the tests, we were able to verify the approach using COFFEE function achieved better results in 81% of the lower similarity alignments when compared with WSP approach. Moreover, even in the tests with more similar sets, the approach using COFFEE was better in 43% of the times.

Research paper thumbnail of Metaheuristics for multiple sequence alignment: A systematic review

Computational Biology and Chemistry, 2021

The Multiple Sequence Alignment (MSA) is a key task in bioinformatics, because it is used in diff... more The Multiple Sequence Alignment (MSA) is a key task in bioinformatics, because it is used in different important biological analysis, such as function and structure prediction of unknown proteins. There are several approaches to perform MSA and the use of metaheuristics stands out because of the search ability of these methods, which generally leads to good results in a reasonable amount of time. This paper presents a Systematic Literature Review (SLR) on metaheuristics for MSA, compiling relevant works published between 2014 and 2019. The results of our SLR show the constant interest in this subject, due to the several recent publications that use different metaheuristics to obtain more accurate alignments. Moreover, the final results of our SLR show a multi-objective and hybrid approaches trends, which generally leads these methods to achieve even better results. Thus, we show in this work how the use of metaheuristics to perform MSA still remains an important and promising open research field.

Research paper thumbnail of Project Scope Management: A Strategy Oriented to the Requirements Engineering

Proceedings of the 19th International Conference on Enterprise Information Systems, 2017

Scope management is an area of project management defined by PMBoK, which has processes to regist... more Scope management is an area of project management defined by PMBoK, which has processes to register and control everything that belongs to the project boundaries. Although the relevance of this area to the success of projects, its application is still a challenge, which is potentialized by the lack of computational tools to support project management that integrate the scope management totality. In addition, the lack of understanding of project requirements is another factor that hinders the execution of this area, because often the stakeholders do not have full knowledge of their needs at the beginning of the project, resulting in changes throughout the project lifecycle, which increases the costs and deadlines. In this sense, the objective of this work is to propose the integration of the scope management with the requirements engineering, in order to better identify the requirements of a project and to understand what needs to be done, contributing to the success of projects. For the evaluation of the results obtained, a requirements engineering module was developed and integrated with a previously developed computational tool for project management and it aims to assist the application of the project management following the guidelines and good practices proposed on PMBoK.

Research paper thumbnail of A Hybrid Approach using Progressive and Genetic Algorithms for Improvements in Multiple Sequence Alignments

The multiple sequence alignment is one of the main tasks in bioinformatics. It is used in differe... more The multiple sequence alignment is one of the main tasks in bioinformatics. It is used in different important biological analysis, such as function and structure prediction of unknown proteins. There are several approaches to perform multiple sequence alignment and the use of heuristics and meta-heuristics stands out because of the search ability of these methods, which generally leads to good results in a reasonable amount of time. The progressive alignment and genetic algorithm are among the most used heuristics and meta-heuristics to perform multiple sequence alignment. However, both methods have disadvantages, such as error propagation in the case of progressive alignment and local optima results in the case of genetics algorithm. Thus, this work proposes a new hybrid refinement phase using a progressive approach to locally realign the multiple sequence alignment produced by genetic algorithm based tools. Our results show that our method is able to improve the quality of the ali...

Research paper thumbnail of Guidelines for the development of educational games to motivate the learning of theoretical concepts in Engineering and Computing courses

Computer Applications in Engineering Education, 2021

Educational software, especially gaming, have been the target of research in different areas due ... more Educational software, especially gaming, have been the target of research in different areas due to their potential benefits in promoting more dynamic, interactive, and motivating learning. The use of educational games for teaching in Engineering and Computing courses, such as Electrical Engineering, Computer Engineering, Software Engineering, and Computer Science, given the familiarity of these students with computers, can promote greater engagement in the study of theoretical concepts. However, existing educational games still lack the good motivational quality considered essential to ensure real learning. In this context, this paper defines guidelines that address the development of educational games focusing on motivational quality. To support the definition of these guidelines, different motivational methods, together with the attributes that can be improved in a student such as autonomy, effort, and overcoming, were analyzed. These guidelines were applied in the development of an educational game prototype as proof of concept to confirm its effective applicability and its contributions to motivate students. The prototype was assessed by 118 students of the higher education in Computing for 15 days. The majority of participants in the assessment process attested that the prototype meets the motivational quality subcriteria, promoting fun (55%), challenge (68%), social interaction (59%), and feeling of satisfaction (74%). It was then possible to verify its attendance to the desired motivational quality and attest to the potential of the established guidelines.

Research paper thumbnail of Performance Improvement of SNP Search Using Multithread Programming

Journal of Computer Science, 2018

Pattern recognition is an important field in Bioinformatics and a well-known task is the search f... more Pattern recognition is an important field in Bioinformatics and a well-known task is the search for Single Nucleotide Polymorphism (SNP). It is possible to search for a known SNP position and analyze it using patterns of DNA bases, called masks. Nonetheless, this process becomes computationally expensive as the amount of available genomic data increases. Thus, in this study, we have developed a parallelization scheme, based on multithread programming, to SNP analysis using masks. In our tests, we noticed that the proposed scheme improved the execution time in 98.05 times when compared with the sequential approach.

Research paper thumbnail of An approach for COFFEE objective function to global DNA multiple sequence alignment

Computational biology and chemistry, 2018

Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can... more Multiple sequence alignment (MSA) is one of the most important tasks in bioinformatics and it can be used to prediction of structures or functions of unknown proteins and to phylogenetic tree reconstruction. There are many heuristics to perform multiple sequence alignment, as Progressive Alignment, Ant Colony, Genetic Algorithms, among others. Along the years, some tools were proposed to perform MSA and MSA-GA is one of them. The MSA-GA is a tool based on Genetic Algorithm to perform multiple sequence alignment and its results are generally better than other well-known tools in bioinformatics, as Clustal W. The COFFEE objective function was implemented in the MSA-GA in order to allow it to produce better alignments to less similar sequence sets of proteins. Nonetheless, the COFFEE objective function is not suited do perform multiple sequence alignment of nucleotides. Thus, we have modified the COFFEE objective function, previously implemented in the MSA-GA, to allow it to obtain bet...

Research paper thumbnail of Improving risk identification process in project management

Proceedings of the 28th International Conference on Software Engineering and Knowledge Engineering, 2016

Nowadays there are many information systems which aim the decision-making, automating the process... more Nowadays there are many information systems which aim the decision-making, automating the processes of project management. However, many times these systems limit the specific functions related to risk management processes and do not allow the control and effective treatment of uncertain events that may affect the project goals. Thus, this paper proposes the integrated use of the Delphi Technique and Risk Breakdown Structure-RBS in order to contribute to the identification of risks, considering the opportunities and threats in a project, to enhance the beneficial effects of the opportunities and avoid the harmful effects of threats. For the evaluation of the results, it was performed the improvement of a system called System to Aid Project Managing-SAPM, in order to support the automated execution of risk management with an emphasis on risk identification process, since this is a crucial stage for risk management in projects. As a result of this work, it is observed that the combined use of the Delphi Technique and RBS allows the risk identification process can be performed fast and safely through the anonymity of those involved and global visualization of the project.

Research paper thumbnail of A parallel approach of COFFEE objective function to multiple sequence alignment

Journal of Physics: Conference Series, 2015

The computational tools to assist genomic analyzes show even more necessary due to fast increasin... more The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

Research paper thumbnail of Improvements in the sensibility of MSA-GA tool using COFFEE objective function

Journal of Physics: Conference Series, 2015

The sequence alignment is one of the most important tasks in Bioinformatics, playing an important... more The sequence alignment is one of the most important tasks in Bioinformatics, playing an important role in the sequences analysis. There are many strategies to perform sequence alignment, since those use deterministic algorithms, as dynamic programming, until those ones, which use heuristic algorithms, as Progressive, Ant Colony (ACO), Genetic Algorithms (GA), Simulated Annealing (SA), among others. In this work, we have implemented the objective function COFFEE in the MSA-GA tool, in substitution of Weighted Sum-of-Pairs (WSP), to improve the final results. In the tests, we were able to verify the approach using COFFEE function achieved better results in 81% of the lower similarity alignments when compared with WSP approach. Moreover, even in the tests with more similar sets, the approach using COFFEE was better in 43% of the times.