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The impact of domain knowledge-driven variable derivation on classifier performance for corporate data mining
- Authors: Welcker, Laura Joana Maria
- Date: 2015
- Subjects: Data mining , Business -- Data processing , Database management
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/5009 , vital:20778
- Description: The technological progress in terms of increasing computational power and growing virtual space to collect data offers great potential for businesses to benefit from data mining applications. Data mining can create a competitive advantage for corporations by discovering business relevant information, such as patterns, relationships, and rules. The role of the human user within the data mining process is crucial, which is why the research area of domain knowledge becomes increasingly important. This thesis investigates the impact of domain knowledge-driven variable derivation on classifier performance for corporate data mining. Domain knowledge is defined as methodological, data and business know-how. The thesis investigates the topic from a new perspective by shifting the focus from a one-sided approach, namely a purely analytic or purely theoretical approach towards a target group-oriented (researcher and practitioner) approach which puts the methodological aspect by means of a scientific guideline in the centre of the research. In order to ensure feasibility and practical relevance of the guideline, it is adapted and applied to the requirements of a practical business case. Thus, the thesis examines the topic from both perspectives, a theoretical and practical perspective. Therewith, it overcomes the limitation of a one-sided approach which mostly lacks practical relevance or generalisability of the results. The primary objective of this thesis is to provide a scientific guideline which should enable both practitioners and researchers to move forward the domain knowledge-driven research for variable derivation on a corporate basis. In the theoretical part, a broad overview of the main aspects which are necessary to undertake the research are given, such as the concept of domain knowledge, the data mining task of classification, variable derivation as a subtask of data preparation, and evaluation techniques. This part of the thesis refers to the methodological aspect of domain knowledge. In the practical part, a research design is developed for testing six hypotheses related to domain knowledge-driven variable derivation. The major contribution of the empirical study is concerned with testing the impact of domain knowledge on a real business data set compared to the impact of a standard and randomly derived data set. The business application of the research is a binary classification problem in the domain of an insurance business, which deals with the prediction of damages in legal expenses insurances. Domain knowledge is expressed through deriving the corporate variables by means of the business and data-driven constructive induction strategy. Six variable derivation steps are investigated: normalisation, instance relation, discretisation, categorical encoding, ratio, and multivariate mathematical function. The impact of the domain knowledge is examined by pairwise (with and without derived variables) performance comparisons for five classification techniques (decision trees, naive Bayes, logistic regression, artificial neural networks, k-nearest neighbours). The impact is measured by two classifier performance criteria: sensitivity and area under the ROC-curve (AUC). The McNemar significance test is used to verify the results. Based on the results, two hypotheses are clearly verified and accepted, three hypotheses are partly verified, and one hypothesis had to be rejected on the basis of the case study results. The thesis reveals a significant positive impact of domain knowledge-driven variable derivation on classifier performance for options of all six tested steps. Furthermore, the findings indicate that the classification technique influences the impact of the variable derivation steps, and the bundling of steps has a significant higher performance impact if the variables are derived by using domain knowledge (compared to a non-knowledge application). Finally, the research turns out that an empirical examination of the domain knowledge impact is very complex due to a high level of interaction between the selected research parameters (variable derivation step, classification technique, and performance criteria).
- Full Text:
- Date Issued: 2015
- Authors: Welcker, Laura Joana Maria
- Date: 2015
- Subjects: Data mining , Business -- Data processing , Database management
- Language: English
- Type: Thesis , Doctoral , DPhil
- Identifier: http://hdl.handle.net/10948/5009 , vital:20778
- Description: The technological progress in terms of increasing computational power and growing virtual space to collect data offers great potential for businesses to benefit from data mining applications. Data mining can create a competitive advantage for corporations by discovering business relevant information, such as patterns, relationships, and rules. The role of the human user within the data mining process is crucial, which is why the research area of domain knowledge becomes increasingly important. This thesis investigates the impact of domain knowledge-driven variable derivation on classifier performance for corporate data mining. Domain knowledge is defined as methodological, data and business know-how. The thesis investigates the topic from a new perspective by shifting the focus from a one-sided approach, namely a purely analytic or purely theoretical approach towards a target group-oriented (researcher and practitioner) approach which puts the methodological aspect by means of a scientific guideline in the centre of the research. In order to ensure feasibility and practical relevance of the guideline, it is adapted and applied to the requirements of a practical business case. Thus, the thesis examines the topic from both perspectives, a theoretical and practical perspective. Therewith, it overcomes the limitation of a one-sided approach which mostly lacks practical relevance or generalisability of the results. The primary objective of this thesis is to provide a scientific guideline which should enable both practitioners and researchers to move forward the domain knowledge-driven research for variable derivation on a corporate basis. In the theoretical part, a broad overview of the main aspects which are necessary to undertake the research are given, such as the concept of domain knowledge, the data mining task of classification, variable derivation as a subtask of data preparation, and evaluation techniques. This part of the thesis refers to the methodological aspect of domain knowledge. In the practical part, a research design is developed for testing six hypotheses related to domain knowledge-driven variable derivation. The major contribution of the empirical study is concerned with testing the impact of domain knowledge on a real business data set compared to the impact of a standard and randomly derived data set. The business application of the research is a binary classification problem in the domain of an insurance business, which deals with the prediction of damages in legal expenses insurances. Domain knowledge is expressed through deriving the corporate variables by means of the business and data-driven constructive induction strategy. Six variable derivation steps are investigated: normalisation, instance relation, discretisation, categorical encoding, ratio, and multivariate mathematical function. The impact of the domain knowledge is examined by pairwise (with and without derived variables) performance comparisons for five classification techniques (decision trees, naive Bayes, logistic regression, artificial neural networks, k-nearest neighbours). The impact is measured by two classifier performance criteria: sensitivity and area under the ROC-curve (AUC). The McNemar significance test is used to verify the results. Based on the results, two hypotheses are clearly verified and accepted, three hypotheses are partly verified, and one hypothesis had to be rejected on the basis of the case study results. The thesis reveals a significant positive impact of domain knowledge-driven variable derivation on classifier performance for options of all six tested steps. Furthermore, the findings indicate that the classification technique influences the impact of the variable derivation steps, and the bundling of steps has a significant higher performance impact if the variables are derived by using domain knowledge (compared to a non-knowledge application). Finally, the research turns out that an empirical examination of the domain knowledge impact is very complex due to a high level of interaction between the selected research parameters (variable derivation step, classification technique, and performance criteria).
- Full Text:
- Date Issued: 2015
Application of machine learning, molecular modelling and structural data mining against antiretroviral drug resistance in HIV-1
- Sheik Amamuddy, Olivier Serge André
- Authors: Sheik Amamuddy, Olivier Serge André
- Date: 2020
- Subjects: Machine learning , Molecules -- Models , Data mining , Neural networks (Computer science) , Antiretroviral agents , Protease inhibitors , Drug resistance , Multidrug resistance , Molecular dynamics , Renin-angiotensin system , HIV (Viruses) -- South Africa , HIV (Viruses) -- Social aspects -- South Africa , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115964 , vital:34282
- Description: Millions are affected with the Human Immunodeficiency Virus (HIV) world wide, even though the death toll is on the decline. Antiretrovirals (ARVs), more specifically protease inhibitors have shown tremendous success since their introduction into therapy since the mid 1990’s by slowing down progression to the Acquired Immune Deficiency Syndrome (AIDS). However, Drug Resistance Mutations (DRMs) are constantly selected for due to viral adaptation, making drugs less effective over time. The current challenge is to manage the infection optimally with a limited set of drugs, with differing associated levels of toxicities in the face of a virus that (1) exists as a quasispecies, (2) may transmit acquired DRMs to drug-naive individuals and (3) that can manifest class-wide resistance due to similarities in design. The presence of latent reservoirs, unawareness of infection status, education and various socio-economic factors make the problem even more complex. Adequate timing and choice of drug prescription together with treatment adherence are very important as drug toxicities, drug failure and sub-optimal treatment regimens leave room for further development of drug resistance. While CD4 cell count and the determination of viral load from patients in resource-limited settings are very helpful to track how well a patient’s immune system is able to keep the virus in check, they can be lengthy in determining whether an ARV is effective. Phenosense assay kits answer this problem using viruses engineered to contain the patient sequences and evaluating their growth in the presence of different ARVs, but this can be expensive and too involved for routine checks. As a cheaper and faster alternative, genotypic assays provide similar information from HIV pol sequences obtained from blood samples, inferring ARV efficacy on the basis of drug resistance mutation patterns. However, these are inherently complex and the various methods of in silico prediction, such as Geno2pheno, REGA and Stanford HIVdb do not always agree in every case, even though this gap decreases as the list of resistance mutations is updated. A major gap in HIV treatment is that the information used for predicting drug resistance is mainly computed from data containing an overwhelming majority of B subtype HIV, when these only comprise about 12% of the worldwide HIV infections. In addition to growing evidence that drug resistance is subtype-related, it is intuitive to hypothesize that as subtyping is a phylogenetic classification, the more divergent a subtype is from the strains used in training prediction models, the less their resistance profiles would correlate. For the aforementioned reasons, we used a multi-faceted approach to attack the virus in multiple ways. This research aimed to (1) improve resistance prediction methods by focusing solely on the available subtype, (2) mine structural information pertaining to resistance in order to find any exploitable weak points and increase knowledge of the mechanistic processes of drug resistance in HIV protease. Finally, (3) we screen for protease inhibitors amongst a database of natural compounds [the South African natural compound database (SANCDB)] to find molecules or molecular properties usable to come up with improved inhibition against the drug target. In this work, structural information was mined using the Anisotropic Network Model, Dynamics Cross-Correlation, Perturbation Response Scanning, residue contact network analysis and the radius of gyration. These methods failed to give any resistance-associated patterns in terms of natural movement, internal correlated motions, residue perturbation response, relational behaviour and global compaction respectively. Applications of drug docking, homology-modelling and energy minimization for generating features suitable for machine-learning were not very promising, and rather suggest that the value of binding energies by themselves from Vina may not be very reliable quantitatively. All these failures lead to a refinement that resulted in a highly sensitive statistically-guided network construction and analysis, which leads to key findings in the early dynamics associated with resistance across all PI drugs. The latter experiment unravelled a conserved lateral expansion motion occurring at the flap elbows, and an associated contraction that drives the base of the dimerization domain towards the catalytic site’s floor in the case of drug resistance. Interestingly, we found that despite the conserved movement, bond angles were degenerate. Alongside, 16 Artificial Neural Network models were optimised for HIV proteases and reverse transcriptase inhibitors, with performances on par with Stanford HIVdb. Finally, we prioritised 9 compounds with potential protease inhibitory activity using virtual screening and molecular dynamics (MD) to additionally suggest a promising modification to one of the compounds. This yielded another molecule inhibiting equally well both opened and closed receptor target conformations, whereby each of the compounds had been selected against an array of multi-drug-resistant receptor variants. While a main hurdle was a lack of non-B subtype data, our findings, especially from the statistically-guided network analysis, may extrapolate to a certain extent to them as the level of conservation was very high within subtype B, despite all the present variations. This network construction method lays down a sensitive approach for analysing a pair of alternate phenotypes for which complex patterns prevail, given a sufficient number of experimental units. During the course of research a weighted contact mapping tool was developed to compare renin-angiotensinogen variants and packaged as part of the MD-TASK tool suite. Finally the functionality, compatibility and performance of the MODE-TASK tool were evaluated and confirmed for both Python2.7.x and Python3.x, for the analysis of normals modes from single protein structures and essential modes from MD trajectories. These techniques and tools collectively add onto the conventional means of MD analysis.
- Full Text:
- Date Issued: 2020
- Authors: Sheik Amamuddy, Olivier Serge André
- Date: 2020
- Subjects: Machine learning , Molecules -- Models , Data mining , Neural networks (Computer science) , Antiretroviral agents , Protease inhibitors , Drug resistance , Multidrug resistance , Molecular dynamics , Renin-angiotensin system , HIV (Viruses) -- South Africa , HIV (Viruses) -- Social aspects -- South Africa , South African Natural Compounds Database
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/115964 , vital:34282
- Description: Millions are affected with the Human Immunodeficiency Virus (HIV) world wide, even though the death toll is on the decline. Antiretrovirals (ARVs), more specifically protease inhibitors have shown tremendous success since their introduction into therapy since the mid 1990’s by slowing down progression to the Acquired Immune Deficiency Syndrome (AIDS). However, Drug Resistance Mutations (DRMs) are constantly selected for due to viral adaptation, making drugs less effective over time. The current challenge is to manage the infection optimally with a limited set of drugs, with differing associated levels of toxicities in the face of a virus that (1) exists as a quasispecies, (2) may transmit acquired DRMs to drug-naive individuals and (3) that can manifest class-wide resistance due to similarities in design. The presence of latent reservoirs, unawareness of infection status, education and various socio-economic factors make the problem even more complex. Adequate timing and choice of drug prescription together with treatment adherence are very important as drug toxicities, drug failure and sub-optimal treatment regimens leave room for further development of drug resistance. While CD4 cell count and the determination of viral load from patients in resource-limited settings are very helpful to track how well a patient’s immune system is able to keep the virus in check, they can be lengthy in determining whether an ARV is effective. Phenosense assay kits answer this problem using viruses engineered to contain the patient sequences and evaluating their growth in the presence of different ARVs, but this can be expensive and too involved for routine checks. As a cheaper and faster alternative, genotypic assays provide similar information from HIV pol sequences obtained from blood samples, inferring ARV efficacy on the basis of drug resistance mutation patterns. However, these are inherently complex and the various methods of in silico prediction, such as Geno2pheno, REGA and Stanford HIVdb do not always agree in every case, even though this gap decreases as the list of resistance mutations is updated. A major gap in HIV treatment is that the information used for predicting drug resistance is mainly computed from data containing an overwhelming majority of B subtype HIV, when these only comprise about 12% of the worldwide HIV infections. In addition to growing evidence that drug resistance is subtype-related, it is intuitive to hypothesize that as subtyping is a phylogenetic classification, the more divergent a subtype is from the strains used in training prediction models, the less their resistance profiles would correlate. For the aforementioned reasons, we used a multi-faceted approach to attack the virus in multiple ways. This research aimed to (1) improve resistance prediction methods by focusing solely on the available subtype, (2) mine structural information pertaining to resistance in order to find any exploitable weak points and increase knowledge of the mechanistic processes of drug resistance in HIV protease. Finally, (3) we screen for protease inhibitors amongst a database of natural compounds [the South African natural compound database (SANCDB)] to find molecules or molecular properties usable to come up with improved inhibition against the drug target. In this work, structural information was mined using the Anisotropic Network Model, Dynamics Cross-Correlation, Perturbation Response Scanning, residue contact network analysis and the radius of gyration. These methods failed to give any resistance-associated patterns in terms of natural movement, internal correlated motions, residue perturbation response, relational behaviour and global compaction respectively. Applications of drug docking, homology-modelling and energy minimization for generating features suitable for machine-learning were not very promising, and rather suggest that the value of binding energies by themselves from Vina may not be very reliable quantitatively. All these failures lead to a refinement that resulted in a highly sensitive statistically-guided network construction and analysis, which leads to key findings in the early dynamics associated with resistance across all PI drugs. The latter experiment unravelled a conserved lateral expansion motion occurring at the flap elbows, and an associated contraction that drives the base of the dimerization domain towards the catalytic site’s floor in the case of drug resistance. Interestingly, we found that despite the conserved movement, bond angles were degenerate. Alongside, 16 Artificial Neural Network models were optimised for HIV proteases and reverse transcriptase inhibitors, with performances on par with Stanford HIVdb. Finally, we prioritised 9 compounds with potential protease inhibitory activity using virtual screening and molecular dynamics (MD) to additionally suggest a promising modification to one of the compounds. This yielded another molecule inhibiting equally well both opened and closed receptor target conformations, whereby each of the compounds had been selected against an array of multi-drug-resistant receptor variants. While a main hurdle was a lack of non-B subtype data, our findings, especially from the statistically-guided network analysis, may extrapolate to a certain extent to them as the level of conservation was very high within subtype B, despite all the present variations. This network construction method lays down a sensitive approach for analysing a pair of alternate phenotypes for which complex patterns prevail, given a sufficient number of experimental units. During the course of research a weighted contact mapping tool was developed to compare renin-angiotensinogen variants and packaged as part of the MD-TASK tool suite. Finally the functionality, compatibility and performance of the MODE-TASK tool were evaluated and confirmed for both Python2.7.x and Python3.x, for the analysis of normals modes from single protein structures and essential modes from MD trajectories. These techniques and tools collectively add onto the conventional means of MD analysis.
- Full Text:
- Date Issued: 2020
Log analysis aided by latent semantic mapping
- Authors: Buys, Stephanus
- Date: 2013 , 2013-04-14
- Subjects: Latent semantic indexing , Data mining , Computer networks -- Security measures , Computer hackers , Computer security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4575 , http://hdl.handle.net/10962/d1002963 , Latent semantic indexing , Data mining , Computer networks -- Security measures , Computer hackers , Computer security
- Description: In an age of zero-day exploits and increased on-line attacks on computing infrastructure, operational security practitioners are becoming increasingly aware of the value of the information captured in log events. Analysis of these events is critical during incident response, forensic investigations related to network breaches, hacking attacks and data leaks. Such analysis has led to the discipline of Security Event Analysis, also known as Log Analysis. There are several challenges when dealing with events, foremost being the increased volumes at which events are often generated and stored. Furthermore, events are often captured as unstructured data, with very little consistency in the formats or contents of the events. In this environment, security analysts and implementers of Log Management (LM) or Security Information and Event Management (SIEM) systems face the daunting task of identifying, classifying and disambiguating massive volumes of events in order for security analysis and automation to proceed. Latent Semantic Mapping (LSM) is a proven paradigm shown to be an effective method of, among other things, enabling word clustering, document clustering, topic clustering and semantic inference. This research is an investigation into the practical application of LSM in the discipline of Security Event Analysis, showing the value of using LSM to assist practitioners in identifying types of events, classifying events as belonging to certain sources or technologies and disambiguating different events from each other. The culmination of this research presents adaptations to traditional natural language processing techniques that resulted in improved efficacy of LSM when dealing with Security Event Analysis. This research provides strong evidence supporting the wider adoption and use of LSM, as well as further investigation into Security Event Analysis assisted by LSM and other natural language or computer-learning processing techniques. , LaTeX with hyperref package , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2013
- Authors: Buys, Stephanus
- Date: 2013 , 2013-04-14
- Subjects: Latent semantic indexing , Data mining , Computer networks -- Security measures , Computer hackers , Computer security
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4575 , http://hdl.handle.net/10962/d1002963 , Latent semantic indexing , Data mining , Computer networks -- Security measures , Computer hackers , Computer security
- Description: In an age of zero-day exploits and increased on-line attacks on computing infrastructure, operational security practitioners are becoming increasingly aware of the value of the information captured in log events. Analysis of these events is critical during incident response, forensic investigations related to network breaches, hacking attacks and data leaks. Such analysis has led to the discipline of Security Event Analysis, also known as Log Analysis. There are several challenges when dealing with events, foremost being the increased volumes at which events are often generated and stored. Furthermore, events are often captured as unstructured data, with very little consistency in the formats or contents of the events. In this environment, security analysts and implementers of Log Management (LM) or Security Information and Event Management (SIEM) systems face the daunting task of identifying, classifying and disambiguating massive volumes of events in order for security analysis and automation to proceed. Latent Semantic Mapping (LSM) is a proven paradigm shown to be an effective method of, among other things, enabling word clustering, document clustering, topic clustering and semantic inference. This research is an investigation into the practical application of LSM in the discipline of Security Event Analysis, showing the value of using LSM to assist practitioners in identifying types of events, classifying events as belonging to certain sources or technologies and disambiguating different events from each other. The culmination of this research presents adaptations to traditional natural language processing techniques that resulted in improved efficacy of LSM when dealing with Security Event Analysis. This research provides strong evidence supporting the wider adoption and use of LSM, as well as further investigation into Security Event Analysis assisted by LSM and other natural language or computer-learning processing techniques. , LaTeX with hyperref package , Adobe Acrobat 9.54 Paper Capture Plug-in
- Full Text:
- Date Issued: 2013
A Functional Data Analysis approach to understand patterns imbedded within various data types
- Authors: Mangisa, Siphumlile
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Data mining
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52091 , vital:43426
- Description: The thesis investigates the use of the novel Functional Data Analysis (FDA) methods in tackling various data types. Strong motivation is provided for the use of interesting opportunities offered by FDA to analyse not only economic data, but generally, data from any domain. The use of these methods is illustrated using three unique self-contained case-studies from econometrics. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-04
- Authors: Mangisa, Siphumlile
- Date: 2021-04
- Subjects: Gqeberha (South Africa) , Eastern Cape (South Africa) , Data mining
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10948/52091 , vital:43426
- Description: The thesis investigates the use of the novel Functional Data Analysis (FDA) methods in tackling various data types. Strong motivation is provided for the use of interesting opportunities offered by FDA to analyse not only economic data, but generally, data from any domain. The use of these methods is illustrated using three unique self-contained case-studies from econometrics. , Thesis (PhD) -- Faculty of Science, School of Computer Science, Mathematics, Physics and Statistics, 2021
- Full Text: false
- Date Issued: 2021-04
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