Nurul Malim - Academia.edu (original) (raw)
Papers by Nurul Malim
Open Pharmaceutical Sciences Journal, 2016
Background: Turbo Similarity Searching (TSS) has been proved as one of the effective and simple s... more Background: Turbo Similarity Searching (TSS) has been proved as one of the effective and simple searching method in Cheminformatics. Emerging from the conventional similarity searching, TSS depended on the concept of fusion where relationship between the target being sought and the compound in the database are indirect. Previous works has looked at only one level of indirect relationship and indicates that there are further potential that more levels of such relationship be added to TSS to increase its ability to recover more actives. Hence, in this work, we aimed to investigate the impact of the indirect relationship on TSS. Method: This study has further investigated the enhancement of TSS using additional layers of indirect relationship and fusion process. We implemented TSS by adding another layer of fusion between the target and database compound. Results: The experiments with MDDR database showed that the proposed new strategy described in this paper provide a way of enhancing...
Lecture Notes in Electrical Engineering, 2015
Turbo Similarity Searching (TSS) is a two phases searching procedure that has been proven by prev... more Turbo Similarity Searching (TSS) is a two phases searching procedure that has been proven by previous works as one of the best searching method on chemical databases. TSS however consumes lots of computation time due to the number of searches and fusion carried out in the second phase of its procedure. Hence, TSS would not be able to cater the increase in the chemical database size due to this limitation. With the emergence of the parallel technology, this research looks into accelerating TSS on the widely-used many-cores i.e. the Graphics Processing Unit (GPU) and multi-cores platform. This would not only solve the computational time issue but also the cost as GPUs can be obtained at a lower cost. Hence, the implementation of TSS will help the medicinal chemist to execute the virtual screening in an accurate and fast manner. This study investigates the best possible method to parallelize TSS via experimentation of three parallel designs; two designs were implemented on GPU platform using the Compute Unified Device Architecture (CUDA) API namely CUDA 1 and CUDA 2 whilst one design was implemented on multi-core platform using OpenMP API. The CUDA 1 design had shown tremendous speedup and low GPU-memory utilization as compared to CUDA 2 design. In general observation, the parallel CUDA 1 was 131 times faster than sequential and 51 times faster than parallel OpenMP. This leads to the conclusion that CUDA 1 design as the best parallel design for TSS.
2015 International Symposium on Technology Management and Emerging Technologies (ISTMET), 2015
As information technology rapidly changes and assimilates into our life seamlessly through the ex... more As information technology rapidly changes and assimilates into our life seamlessly through the exponential growth of the Internet, identifying related technology acceptance behaviour among users becomes vital. Existing researches have shown that new systems require novice users to spend an amount of time to get to know the technology. Near Field Communication (NFC) is an emerging technology, which offers an enhanced interaction for users by simplifying data transfers, secured payment transaction access and many more. In this paper, we looked into a number of widely used acceptance models such as the Theory of Reasoned Action (TRA), Theory Planned Behavior (TPB) and, the Unified Theory of Acceptance and Use of Technology (UTAUT) to identify the theory that is best suited as an assessment tool of the user acceptance to the NFC technology. We have identified UTAUT as the best tool based on literature and utilized the theory to develop a questionnaire for the user acceptance survey. Our results indicates, factors such as social influence and facilitating condition affected the users' technology acceptance for NFC where most respondents are willing to use the technology if they had the chance to do so.
Procedia Computer Science, 2015
The interactions using text or writing has become an important medium to communicate among human.... more The interactions using text or writing has become an important medium to communicate among human. The inventions of online networks technologies and applications such as social networks rapidly growth the size of digital textual data and indirectly raises the curiosities to mine the juicy information encapsulated in the text data. Researchers have stated that linguistics of the people either in the online or offline having strong correlations with their self-disclosure. The mass creations of digital textual data raised the intentions of scholars to study the hidden abstractions of personality by applying automatic personality detection approaches. Most of the current automatic personality detection studies focused on Big 5 personality model as a framework to study the underlying characteristics of human. As such, this study incorporates the Three Factor Personality (PEN) Model as a personality framework to guide our understanding and revealing the role of words in depicting the characteristics of a user. This preliminary study revealed how the sentiment perceptions of public towards specific words could assist us in detecting the personality of Facebook users by exploiting their status messages. As the first phase of our study, this experiment focuses on gathering the general perceptions of Malaysians towards 52 English words and 17 interjections that was retrieve from the domain stated above. A Likert scale questionnaire executed to find the sentiment valences of 67 words through analyzing responses from participants and statistical significance will assist the categorization of words under PEN traits. The evaluation provides the necessary analysis that could assist our main research that focuses on automatic personality detections specifically on the psychoticism trait. Our initial findings has highlighted that the five words categorized under psychoticism has strong Cronbach's Alpha coefficients and significant effect from multivariate analysis that indirectly affirmed the reliability of the categorization of the words.
Jurnal Teknologi, 2015
The population of the elderly is growing rapidly and become a major concern in twentieth- century... more The population of the elderly is growing rapidly and become a major concern in twentieth- century. The impact of this global ageing phenomenon is significant to the human life in all aspect including social, political and economic of all social class. The implementation of ICT application can help to cope with this phenomenon and improve the quality of life of the elderly. This study aims to perform a bibliometric analysis on the field of ageing and ICT to reveal the trend of research and technologies related in the recent years. Bibliometric information such as keywords and number of publication is extracted from the search result of online publication databases and then further analyzed using computational technique such as growth rate analysis and Latent Semantic Analysis (LSA) to identify the relationship and the growth of the information extracted. The outcome is a set of terms that are grouped and ranked according to their relevance and growth in the recent year. This result c...
The increasing number of mobile devices consumptions, especially mobile phones and smartphones ha... more The increasing number of mobile devices consumptions, especially mobile phones and smartphones had caused a growing interest in the user experience research on the mobile platform. However, it is difficult to gain an encompassing understanding of the user experience especially from a localized context. This paper presents our survey finding on the understanding of user experience among USM undergraduates. The research finding identifies that a respondents' field of study has some influence on their understanding of user experience. Overall, the respondents tend to agree that user experience is subjective and based on the individual's interaction with an application. The ISO definition of user experience is discussed and compared with the survey results. The comparison highlights that the definition of user experience is similar with the ISO's definition of user experience.
Today, internet accessibility is no longer a privilege. It could be accessed anywhere and by anyo... more Today, internet accessibility is no longer a privilege. It could be accessed anywhere and by anyone regardless of age. Being exposed to the internet at an early age is harmful without proper parental guidance. Thus, there is a need to build awareness among children on digital etiquette when going online. Learning digital etiquette would allow children to know the correct use of the internet which will lead them to understand the concepts of accountability, respect, privacy and etc. These concepts can help guide them to build good attitude and avoid them from being victims of cybercrimes such as internet abuse - pornographic, information theft, cyber bullying and so forth. The purpose of this paper is to build awareness on digital etiquette among primary school children. An online survey was conducted to assess the children’s understanding and awareness about digital etiquette. The online survey was distributed via social network sites (such as Facebook, Twitter and Google+) to paren...
Near-Field Communication or NFC is a new technology that was introduced in recent years. However,... more Near-Field Communication or NFC is a new technology that was introduced in recent years. However, even with the simplicity and security that the technology provide, the adoption of this technology is not wide spread. In this paper, we describe the user-friendliness criteria essential for NFC technology through a proposed library system. To determine the criteria of userfriendliness for the technology, we conducted a survey on the understanding and usage of different users that would be exposed to a library system. The survey included questions about the existing library system (OPAC) and their perception of the NFC technology. Based on the results, we managed to identify that the OPAC system is not a user-friendly library system. Further, we have also identified that there are three main user-friendliness criteria deemed necessary by users for an NFC-enabled library system to be more effective than the OPAC system: usability, security and efficiency.
Lecture Notes in Computer Science, 2015
Most of the universities or colleges, the lecturer has to take the attendance of the students man... more Most of the universities or colleges, the lecturer has to take the attendance of the students manually by circulating a paper for them to register their names or calling the names. To date, there are various types of attendance systems that are applying different technologies such as biometrics, tokens and sensors such as RFID. The latest is by applying near-field communication (NFC), a sensor within the smartphone has been used as a mean for recording attendances. The aim of this paper is to list out the possible security attacks against NFC (Near Field Communication) enabled systems by focusing on a student-based attendance system. A brief overview over NFC technology and discussion on various security attacks against NFC in different media is presented. Overall, an attendance system is compromised mainly by tag swapping, tag cloning and manipulation of data occurring on the NFC device and operational server.
Carian persamaan merupakan asas aplikasi dalam bidang informatik kimia yang mengguna kaedah infor... more Carian persamaan merupakan asas aplikasi dalam bidang informatik kimia yang mengguna kaedah informatik untuk menyelesai masalah kimia. Kertas ini membincang komponen prinsip dalam carian persamaan yang menumpu kepada penyaringan maya 2D. Perbincangan juga menekankan latar belakang sejarah tentang prinsip dan kaedah yang diguna dalam bidang ini.
Journal of Cheminformatics, 2014
2013 1st International Conference on Artificial Intelligence, Modelling and Simulation, 2013
Similarity-based virtual screening is used in drug discovery by using computational model for rap... more Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.
2013 International Conference on Advanced Computer Science and Information Systems (ICACSIS), 2013
Virtual screening is one of the most vital methods applied in Chemoinformatics, the field that co... more Virtual screening is one of the most vital methods applied in Chemoinformatics, the field that contributes to drug discovery process. Turbo Similarity Searching (TSS) and data fusion are two of the latest chemical similarity searching strategies, which has evolved from the conventional similarity searching (SS) that apply the concept of multi-target searching instead of just an individual target search. The indirect relationship exists in TSS, with the inclusion of Nearest Neighbours (NN) has been proven to have better performance than the direct relationship (i.e. between query structure and database structures) that exists in similarity searching process. In this paper, we will focus on the implementation and improvement of the existing TSS. By adding in another layer of indirect relationship between the reference compound and the database compounds, along with an additional fusion layer, the performance of the new TSS strategy can be observed. The initial results indicated that there is an obvious increment in the recall value when applying the new strategy. The results are also evaluated with the significance test to show that the result produced by the new strategy is true and does not occurred by chance. Further work on different activity classes and different descriptors on the new strategy are expected to generate a better performance than the existing TSS. I. INTRODUCTION T present, the rapid evolution of technology has been the main endeavor that contributes to the Manuscript received June 30, 2013.
... Abdullah Embong School of Computer Science, Universiti Sains Malaysia, Penang, Malaysia <a... more ... Abdullah Embong School of Computer Science, Universiti Sains Malaysia, Penang, Malaysia <ae@cs.usm.my> ... Embong and Azwan (2003) have stated that "ITS differs from CAI system in terms of the ability of ITS to assist teaching learning process in an intelligent manner" (p. 1 ...
Research Journal of Applied Sciences, Engineering and Technology, 2015
Development of a new drug needs chemical databases as references to find lead compounds. This stu... more Development of a new drug needs chemical databases as references to find lead compounds. This study aims to determine the best similarity coefficient to be used for virtual screening task using chemical databases. We calculated the structural resemblance between each pair of chemical structures in their own activity class to get the Mean Pairwise Similarity (MPS) value to see the nature of heterogeneity for each natural product and synthetic chemical databases. The process involves the 2D descriptor of type ECFC4 fingerprint to represent each structure and Tanimoto coefficient to calculate the similarity score between each pair of chemical structures in the same activity class. MPS for an activity class was obtained by taking the average of all similarity scores within that class. Next, three types of similarity coefficients have been used to calculate the similarity score between a query structure and each of the database structure. The results indicate that Tanimoto coefficient shows better performance compared to Russell Rao and Forbes in retrieval task using chemical database. This implies that Tanimoto coefficient is recommended to carry out virtual screening in drug development. More work should be carried out to determine the best combination of similarity coefficient and fingerprint type to get optimal retrieval performance.
Open Pharmaceutical Sciences Journal, 2016
Background: Turbo Similarity Searching (TSS) has been proved as one of the effective and simple s... more Background: Turbo Similarity Searching (TSS) has been proved as one of the effective and simple searching method in Cheminformatics. Emerging from the conventional similarity searching, TSS depended on the concept of fusion where relationship between the target being sought and the compound in the database are indirect. Previous works has looked at only one level of indirect relationship and indicates that there are further potential that more levels of such relationship be added to TSS to increase its ability to recover more actives. Hence, in this work, we aimed to investigate the impact of the indirect relationship on TSS. Method: This study has further investigated the enhancement of TSS using additional layers of indirect relationship and fusion process. We implemented TSS by adding another layer of fusion between the target and database compound. Results: The experiments with MDDR database showed that the proposed new strategy described in this paper provide a way of enhancing...
Lecture Notes in Electrical Engineering, 2015
Turbo Similarity Searching (TSS) is a two phases searching procedure that has been proven by prev... more Turbo Similarity Searching (TSS) is a two phases searching procedure that has been proven by previous works as one of the best searching method on chemical databases. TSS however consumes lots of computation time due to the number of searches and fusion carried out in the second phase of its procedure. Hence, TSS would not be able to cater the increase in the chemical database size due to this limitation. With the emergence of the parallel technology, this research looks into accelerating TSS on the widely-used many-cores i.e. the Graphics Processing Unit (GPU) and multi-cores platform. This would not only solve the computational time issue but also the cost as GPUs can be obtained at a lower cost. Hence, the implementation of TSS will help the medicinal chemist to execute the virtual screening in an accurate and fast manner. This study investigates the best possible method to parallelize TSS via experimentation of three parallel designs; two designs were implemented on GPU platform using the Compute Unified Device Architecture (CUDA) API namely CUDA 1 and CUDA 2 whilst one design was implemented on multi-core platform using OpenMP API. The CUDA 1 design had shown tremendous speedup and low GPU-memory utilization as compared to CUDA 2 design. In general observation, the parallel CUDA 1 was 131 times faster than sequential and 51 times faster than parallel OpenMP. This leads to the conclusion that CUDA 1 design as the best parallel design for TSS.
2015 International Symposium on Technology Management and Emerging Technologies (ISTMET), 2015
As information technology rapidly changes and assimilates into our life seamlessly through the ex... more As information technology rapidly changes and assimilates into our life seamlessly through the exponential growth of the Internet, identifying related technology acceptance behaviour among users becomes vital. Existing researches have shown that new systems require novice users to spend an amount of time to get to know the technology. Near Field Communication (NFC) is an emerging technology, which offers an enhanced interaction for users by simplifying data transfers, secured payment transaction access and many more. In this paper, we looked into a number of widely used acceptance models such as the Theory of Reasoned Action (TRA), Theory Planned Behavior (TPB) and, the Unified Theory of Acceptance and Use of Technology (UTAUT) to identify the theory that is best suited as an assessment tool of the user acceptance to the NFC technology. We have identified UTAUT as the best tool based on literature and utilized the theory to develop a questionnaire for the user acceptance survey. Our results indicates, factors such as social influence and facilitating condition affected the users' technology acceptance for NFC where most respondents are willing to use the technology if they had the chance to do so.
Procedia Computer Science, 2015
The interactions using text or writing has become an important medium to communicate among human.... more The interactions using text or writing has become an important medium to communicate among human. The inventions of online networks technologies and applications such as social networks rapidly growth the size of digital textual data and indirectly raises the curiosities to mine the juicy information encapsulated in the text data. Researchers have stated that linguistics of the people either in the online or offline having strong correlations with their self-disclosure. The mass creations of digital textual data raised the intentions of scholars to study the hidden abstractions of personality by applying automatic personality detection approaches. Most of the current automatic personality detection studies focused on Big 5 personality model as a framework to study the underlying characteristics of human. As such, this study incorporates the Three Factor Personality (PEN) Model as a personality framework to guide our understanding and revealing the role of words in depicting the characteristics of a user. This preliminary study revealed how the sentiment perceptions of public towards specific words could assist us in detecting the personality of Facebook users by exploiting their status messages. As the first phase of our study, this experiment focuses on gathering the general perceptions of Malaysians towards 52 English words and 17 interjections that was retrieve from the domain stated above. A Likert scale questionnaire executed to find the sentiment valences of 67 words through analyzing responses from participants and statistical significance will assist the categorization of words under PEN traits. The evaluation provides the necessary analysis that could assist our main research that focuses on automatic personality detections specifically on the psychoticism trait. Our initial findings has highlighted that the five words categorized under psychoticism has strong Cronbach's Alpha coefficients and significant effect from multivariate analysis that indirectly affirmed the reliability of the categorization of the words.
Jurnal Teknologi, 2015
The population of the elderly is growing rapidly and become a major concern in twentieth- century... more The population of the elderly is growing rapidly and become a major concern in twentieth- century. The impact of this global ageing phenomenon is significant to the human life in all aspect including social, political and economic of all social class. The implementation of ICT application can help to cope with this phenomenon and improve the quality of life of the elderly. This study aims to perform a bibliometric analysis on the field of ageing and ICT to reveal the trend of research and technologies related in the recent years. Bibliometric information such as keywords and number of publication is extracted from the search result of online publication databases and then further analyzed using computational technique such as growth rate analysis and Latent Semantic Analysis (LSA) to identify the relationship and the growth of the information extracted. The outcome is a set of terms that are grouped and ranked according to their relevance and growth in the recent year. This result c...
The increasing number of mobile devices consumptions, especially mobile phones and smartphones ha... more The increasing number of mobile devices consumptions, especially mobile phones and smartphones had caused a growing interest in the user experience research on the mobile platform. However, it is difficult to gain an encompassing understanding of the user experience especially from a localized context. This paper presents our survey finding on the understanding of user experience among USM undergraduates. The research finding identifies that a respondents' field of study has some influence on their understanding of user experience. Overall, the respondents tend to agree that user experience is subjective and based on the individual's interaction with an application. The ISO definition of user experience is discussed and compared with the survey results. The comparison highlights that the definition of user experience is similar with the ISO's definition of user experience.
Today, internet accessibility is no longer a privilege. It could be accessed anywhere and by anyo... more Today, internet accessibility is no longer a privilege. It could be accessed anywhere and by anyone regardless of age. Being exposed to the internet at an early age is harmful without proper parental guidance. Thus, there is a need to build awareness among children on digital etiquette when going online. Learning digital etiquette would allow children to know the correct use of the internet which will lead them to understand the concepts of accountability, respect, privacy and etc. These concepts can help guide them to build good attitude and avoid them from being victims of cybercrimes such as internet abuse - pornographic, information theft, cyber bullying and so forth. The purpose of this paper is to build awareness on digital etiquette among primary school children. An online survey was conducted to assess the children’s understanding and awareness about digital etiquette. The online survey was distributed via social network sites (such as Facebook, Twitter and Google+) to paren...
Near-Field Communication or NFC is a new technology that was introduced in recent years. However,... more Near-Field Communication or NFC is a new technology that was introduced in recent years. However, even with the simplicity and security that the technology provide, the adoption of this technology is not wide spread. In this paper, we describe the user-friendliness criteria essential for NFC technology through a proposed library system. To determine the criteria of userfriendliness for the technology, we conducted a survey on the understanding and usage of different users that would be exposed to a library system. The survey included questions about the existing library system (OPAC) and their perception of the NFC technology. Based on the results, we managed to identify that the OPAC system is not a user-friendly library system. Further, we have also identified that there are three main user-friendliness criteria deemed necessary by users for an NFC-enabled library system to be more effective than the OPAC system: usability, security and efficiency.
Lecture Notes in Computer Science, 2015
Most of the universities or colleges, the lecturer has to take the attendance of the students man... more Most of the universities or colleges, the lecturer has to take the attendance of the students manually by circulating a paper for them to register their names or calling the names. To date, there are various types of attendance systems that are applying different technologies such as biometrics, tokens and sensors such as RFID. The latest is by applying near-field communication (NFC), a sensor within the smartphone has been used as a mean for recording attendances. The aim of this paper is to list out the possible security attacks against NFC (Near Field Communication) enabled systems by focusing on a student-based attendance system. A brief overview over NFC technology and discussion on various security attacks against NFC in different media is presented. Overall, an attendance system is compromised mainly by tag swapping, tag cloning and manipulation of data occurring on the NFC device and operational server.
Carian persamaan merupakan asas aplikasi dalam bidang informatik kimia yang mengguna kaedah infor... more Carian persamaan merupakan asas aplikasi dalam bidang informatik kimia yang mengguna kaedah informatik untuk menyelesai masalah kimia. Kertas ini membincang komponen prinsip dalam carian persamaan yang menumpu kepada penyaringan maya 2D. Perbincangan juga menekankan latar belakang sejarah tentang prinsip dan kaedah yang diguna dalam bidang ini.
Journal of Cheminformatics, 2014
2013 1st International Conference on Artificial Intelligence, Modelling and Simulation, 2013
Similarity-based virtual screening is used in drug discovery by using computational model for rap... more Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.
2013 International Conference on Advanced Computer Science and Information Systems (ICACSIS), 2013
Virtual screening is one of the most vital methods applied in Chemoinformatics, the field that co... more Virtual screening is one of the most vital methods applied in Chemoinformatics, the field that contributes to drug discovery process. Turbo Similarity Searching (TSS) and data fusion are two of the latest chemical similarity searching strategies, which has evolved from the conventional similarity searching (SS) that apply the concept of multi-target searching instead of just an individual target search. The indirect relationship exists in TSS, with the inclusion of Nearest Neighbours (NN) has been proven to have better performance than the direct relationship (i.e. between query structure and database structures) that exists in similarity searching process. In this paper, we will focus on the implementation and improvement of the existing TSS. By adding in another layer of indirect relationship between the reference compound and the database compounds, along with an additional fusion layer, the performance of the new TSS strategy can be observed. The initial results indicated that there is an obvious increment in the recall value when applying the new strategy. The results are also evaluated with the significance test to show that the result produced by the new strategy is true and does not occurred by chance. Further work on different activity classes and different descriptors on the new strategy are expected to generate a better performance than the existing TSS. I. INTRODUCTION T present, the rapid evolution of technology has been the main endeavor that contributes to the Manuscript received June 30, 2013.
... Abdullah Embong School of Computer Science, Universiti Sains Malaysia, Penang, Malaysia <a... more ... Abdullah Embong School of Computer Science, Universiti Sains Malaysia, Penang, Malaysia <ae@cs.usm.my> ... Embong and Azwan (2003) have stated that "ITS differs from CAI system in terms of the ability of ITS to assist teaching learning process in an intelligent manner" (p. 1 ...
Research Journal of Applied Sciences, Engineering and Technology, 2015
Development of a new drug needs chemical databases as references to find lead compounds. This stu... more Development of a new drug needs chemical databases as references to find lead compounds. This study aims to determine the best similarity coefficient to be used for virtual screening task using chemical databases. We calculated the structural resemblance between each pair of chemical structures in their own activity class to get the Mean Pairwise Similarity (MPS) value to see the nature of heterogeneity for each natural product and synthetic chemical databases. The process involves the 2D descriptor of type ECFC4 fingerprint to represent each structure and Tanimoto coefficient to calculate the similarity score between each pair of chemical structures in the same activity class. MPS for an activity class was obtained by taking the average of all similarity scores within that class. Next, three types of similarity coefficients have been used to calculate the similarity score between a query structure and each of the database structure. The results indicate that Tanimoto coefficient shows better performance compared to Russell Rao and Forbes in retrieval task using chemical database. This implies that Tanimoto coefficient is recommended to carry out virtual screening in drug development. More work should be carried out to determine the best combination of similarity coefficient and fingerprint type to get optimal retrieval performance.