Investigating unimodal isolated signer-independent sign language recognition
- Authors: Marais, Marc Jason
- Date: 2024-04-04
- Subjects: Convolutional neural network , Sign language recognition , Human activity recognition , Pattern recognition systems , Neural networks (Computer science)
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435343 , vital:73149
- Description: Sign language serves as the mode of communication for the Deaf and Hard of Hearing community, embodying a rich linguistic and cultural heritage. Recent Sign Language Recognition (SLR) system developments aim to facilitate seamless communication between the Deaf community and the broader society. However, most existing systems are limited by signer-dependent models, hindering their adaptability to diverse signing styles and signers, thus impeding their practical implementation in real-world scenarios. This research explores various unimodal approaches, both pose-based and vision-based, for isolated signer-independent SLR using RGB video input on the LSA64 and AUTSL datasets. The unimodal RGB-only input strategy provides a realistic SLR setting where alternative data sources are either unavailable or necessitate specialised equipment. Through systematic testing scenarios, isolated signer-independent SLR experiments are conducted on both datasets, primarily focusing on AUTSL – a signer-independent dataset. The vision-based R(2+1)D-18 model emerged as the top performer, achieving 90.64% accuracy on the unseen AUTSL dataset test split, closely followed by the pose-based Spatio- Temporal Graph Convolutional Network (ST-GCN) model with an accuracy of 89.95%. Furthermore, these models achieved comparable accuracies at a significantly lower computational demand. Notably, the pose-based approach demonstrates robust generalisation to substantial background and signer variation. Moreover, the pose-based approach demands significantly less computational power and training time than vision-based approaches. The proposed unimodal pose-based and vision-based systems were concluded to both be effective at classifying sign classes in the LSA64 and AUTSL datasets. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-04-04
- Authors: Marais, Marc Jason
- Date: 2024-04-04
- Subjects: Convolutional neural network , Sign language recognition , Human activity recognition , Pattern recognition systems , Neural networks (Computer science)
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/435343 , vital:73149
- Description: Sign language serves as the mode of communication for the Deaf and Hard of Hearing community, embodying a rich linguistic and cultural heritage. Recent Sign Language Recognition (SLR) system developments aim to facilitate seamless communication between the Deaf community and the broader society. However, most existing systems are limited by signer-dependent models, hindering their adaptability to diverse signing styles and signers, thus impeding their practical implementation in real-world scenarios. This research explores various unimodal approaches, both pose-based and vision-based, for isolated signer-independent SLR using RGB video input on the LSA64 and AUTSL datasets. The unimodal RGB-only input strategy provides a realistic SLR setting where alternative data sources are either unavailable or necessitate specialised equipment. Through systematic testing scenarios, isolated signer-independent SLR experiments are conducted on both datasets, primarily focusing on AUTSL – a signer-independent dataset. The vision-based R(2+1)D-18 model emerged as the top performer, achieving 90.64% accuracy on the unseen AUTSL dataset test split, closely followed by the pose-based Spatio- Temporal Graph Convolutional Network (ST-GCN) model with an accuracy of 89.95%. Furthermore, these models achieved comparable accuracies at a significantly lower computational demand. Notably, the pose-based approach demonstrates robust generalisation to substantial background and signer variation. Moreover, the pose-based approach demands significantly less computational power and training time than vision-based approaches. The proposed unimodal pose-based and vision-based systems were concluded to both be effective at classifying sign classes in the LSA64 and AUTSL datasets. , Thesis (MSc) -- Faculty of Science, Ichthyology and Fisheries Science, 2024
- Full Text:
- Date Issued: 2024-04-04
A multispectral and machine learning approach to early stress classification in plants
- Authors: Poole, Louise Carmen
- Date: 2022-04-06
- Subjects: Machine learning , Neural networks (Computer science) , Multispectral imaging , Image processing , Plant stress detection
- Language: English
- Type: Master's thesis , text
- Identifier: http://hdl.handle.net/10962/232410 , vital:49989
- Description: Crop loss and failure can impact both a country’s economy and food security, often to devastating effects. As such, the importance of successfully detecting plant stresses early in their development is essential to minimize spread and damage to crop production. Identification of the stress and the stress-causing agent is the most critical and challenging step in plant and crop protection. With the development of and increase in ease of access to new equipment and technology in recent years, the use of spectroscopy in the early detection of plant diseases has become notably popular. This thesis narrows down the most suitable multispectral imaging techniques and machine learning algorithms for early stress detection. Datasets were collected of visible images and multispectral images. Dehydration was selected as the plant stress type for the main experiments, and data was collected from six plant species typically used in agriculture. Key contributions of this thesis include multispectral and visible datasets showing plant dehydration as well as a separate preliminary dataset on plant disease. Promising results on dehydration showed statistically significant accuracy improvements in the multispectral imaging compared to visible imaging for early stress detection, with multispectral input obtaining a 92.50% accuracy over visible input’s 77.50% on general plant species. The system was effective at stress detection on known plant species, with multispectral imaging introducing greater improvement to early stress detection than advanced stress detection. Furthermore, strong species discrimination was achieved when exclusively testing either early or advanced dehydration against healthy species. , Thesis (MSc) -- Faculty of Science, Ichthyology & Fisheries Sciences, 2022
- Full Text:
- Date Issued: 2022-04-06
- Authors: Poole, Louise Carmen
- Date: 2022-04-06
- Subjects: Machine learning , Neural networks (Computer science) , Multispectral imaging , Image processing , Plant stress detection
- Language: English
- Type: Master's thesis , text
- Identifier: http://hdl.handle.net/10962/232410 , vital:49989
- Description: Crop loss and failure can impact both a country’s economy and food security, often to devastating effects. As such, the importance of successfully detecting plant stresses early in their development is essential to minimize spread and damage to crop production. Identification of the stress and the stress-causing agent is the most critical and challenging step in plant and crop protection. With the development of and increase in ease of access to new equipment and technology in recent years, the use of spectroscopy in the early detection of plant diseases has become notably popular. This thesis narrows down the most suitable multispectral imaging techniques and machine learning algorithms for early stress detection. Datasets were collected of visible images and multispectral images. Dehydration was selected as the plant stress type for the main experiments, and data was collected from six plant species typically used in agriculture. Key contributions of this thesis include multispectral and visible datasets showing plant dehydration as well as a separate preliminary dataset on plant disease. Promising results on dehydration showed statistically significant accuracy improvements in the multispectral imaging compared to visible imaging for early stress detection, with multispectral input obtaining a 92.50% accuracy over visible input’s 77.50% on general plant species. The system was effective at stress detection on known plant species, with multispectral imaging introducing greater improvement to early stress detection than advanced stress detection. Furthermore, strong species discrimination was achieved when exclusively testing either early or advanced dehydration against healthy species. , Thesis (MSc) -- Faculty of Science, Ichthyology & Fisheries Sciences, 2022
- Full Text:
- Date Issued: 2022-04-06
Statistical and Mathematical Learning: an application to fraud detection and prevention
- Authors: Hamlomo, Sisipho
- Date: 2022-04-06
- Subjects: Credit card fraud , Bootstrap (Statistics) , Support vector machines , Neural networks (Computer science) , Decision trees , Machine learning , Cross-validation , Imbalanced data
- Language: English
- Type: Master's thesis , text
- Identifier: http://hdl.handle.net/10962/233795 , vital:50128
- Description: Credit card fraud is an ever-growing problem. There has been a rapid increase in the rate of fraudulent activities in recent years resulting in a considerable loss to several organizations, companies, and government agencies. Many researchers have focused on detecting fraudulent behaviours early using advanced machine learning techniques. However, credit card fraud detection is not a straightforward task since fraudulent behaviours usually differ for each attempt and the dataset is highly imbalanced, that is, the frequency of non-fraudulent cases outnumbers the frequency of fraudulent cases. In the case of the European credit card dataset, we have a ratio of approximately one fraudulent case to five hundred and seventy-eight non-fraudulent cases. Different methods were implemented to overcome this problem, namely random undersampling, one-sided sampling, SMOTE combined with Tomek links and parameter tuning. Predictive classifiers, namely logistic regression, decision trees, k-nearest neighbour, support vector machine and multilayer perceptrons, are applied to predict if a transaction is fraudulent or non-fraudulent. The model's performance is evaluated based on recall, precision, F1-score, the area under receiver operating characteristics curve, geometric mean and Matthew correlation coefficient. The results showed that the logistic regression classifier performed better than other classifiers except when the dataset was oversampled. , Thesis (MSc) -- Faculty of Science, Statistics, 2022
- Full Text:
- Date Issued: 2022-04-06
- Authors: Hamlomo, Sisipho
- Date: 2022-04-06
- Subjects: Credit card fraud , Bootstrap (Statistics) , Support vector machines , Neural networks (Computer science) , Decision trees , Machine learning , Cross-validation , Imbalanced data
- Language: English
- Type: Master's thesis , text
- Identifier: http://hdl.handle.net/10962/233795 , vital:50128
- Description: Credit card fraud is an ever-growing problem. There has been a rapid increase in the rate of fraudulent activities in recent years resulting in a considerable loss to several organizations, companies, and government agencies. Many researchers have focused on detecting fraudulent behaviours early using advanced machine learning techniques. However, credit card fraud detection is not a straightforward task since fraudulent behaviours usually differ for each attempt and the dataset is highly imbalanced, that is, the frequency of non-fraudulent cases outnumbers the frequency of fraudulent cases. In the case of the European credit card dataset, we have a ratio of approximately one fraudulent case to five hundred and seventy-eight non-fraudulent cases. Different methods were implemented to overcome this problem, namely random undersampling, one-sided sampling, SMOTE combined with Tomek links and parameter tuning. Predictive classifiers, namely logistic regression, decision trees, k-nearest neighbour, support vector machine and multilayer perceptrons, are applied to predict if a transaction is fraudulent or non-fraudulent. The model's performance is evaluated based on recall, precision, F1-score, the area under receiver operating characteristics curve, geometric mean and Matthew correlation coefficient. The results showed that the logistic regression classifier performed better than other classifiers except when the dataset was oversampled. , Thesis (MSc) -- Faculty of Science, Statistics, 2022
- Full Text:
- Date Issued: 2022-04-06
The development of an ionospheric storm-time index for the South African region
- Authors: Tshisaphungo, Mpho
- Date: 2021-04
- Subjects: Ionospheric storms -- South Africa , Global Positioning System , Neural networks (Computer science) , Regression analysis , Ionosondes , Auroral electrojet , Geomagnetic indexes , Magnetic storms -- South Africa
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178409 , vital:42937 , 10.21504/10962/178409
- Description: This thesis presents the development of a regional ionospheric storm-time model which forms the foundation of an index to provide a quick view of the ionospheric storm effects over South African mid-latitude region. The model is based on the foF2 measurements from four South African ionosonde stations. The data coverage for the model development over Grahamstown (33.3◦S, 26.5◦E), Hermanus (34.42◦S, 19.22◦E), Louisvale (28.50◦S, 21.20◦E), and Madimbo (22.39◦S, 30.88◦E) is 1996-2016, 2009-2016, 2000-2016, and 2000-2016 respectively. Data from the Global Positioning System (GPS) and radio occultation (RO) technique were used during validation. As the measure of either positive or negative storm effect, the variation of the critical frequency of the F2 layer (foF2) from the monthly median values (denoted as _foF2) is modeled. The modeling of _foF2 is based on only storm time data with the criteria of Dst 6 -50 nT and Kp > 4. The modeling methods used in the study were artificial neural network (ANN), linear regression (LR) and polynomial functions. The approach taken was to first test the modeling techniques on a single station before expanding the study to cover the regional aspect. The single station modeling was developed based on ionosonde data over Grahamstown. The inputs for the model which related to seasonal variation, diurnal variation, geomagnetic activity and solar activity were considered. For the geomagnetic activity, three indices namely; the symmetric disturbance in the horizontal component of the Earth’s magnetic field (SYM − H), the Auroral Electrojet (AE) index and local geomagnetic index A, were included as inputs. The performance of a single station model revealed that, of the three geomagnetic indices, SYM − H index has the largest contribution of 41% and 54% based on ANN and LR techniques respectively. The average correlation coefficients (R) for both ANN and LR models was 0.8, when validated during the selected storms falling within the period of model development. When validated using storms that fall outside the period of model development, the model gave R values of 0.6 and 0.5 for ANN and LR respectively. In addition, the GPS total electron content (TEC) derived measurements were used to estimate foF2 data. This is because there are more GPS receivers than ionosonde locations and the utilisation of this data increases the spatial coverage of the regional model. The estimation of foF2 from GPS TEC was done at GPS-ionosonde co-locations using polynomial functions. The average R values of 0.69 and 0.65 were obtained between actual and derived _foF2 over the co-locations and other GPS stations respectively. Validation of GPS TEC derived foF2 with RO data over regions out of ionospheric pierce points coverage with respect to ionosonde locations gave R greater than 0.9 for the selected storm period of 4-8 August 2011. The regional storm-time model was then developed based on the ANN technique using the four South African ionosonde stations. The maximum and minimum R values of 0.6 and 0.5 were obtained over ionosonde and GPS locations respectively. This model forms the basis towards the regional ionospheric storm-time index. , Thesis (PhD) -- Faculty of Science, Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
- Authors: Tshisaphungo, Mpho
- Date: 2021-04
- Subjects: Ionospheric storms -- South Africa , Global Positioning System , Neural networks (Computer science) , Regression analysis , Ionosondes , Auroral electrojet , Geomagnetic indexes , Magnetic storms -- South Africa
- Language: English
- Type: thesis , text , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/178409 , vital:42937 , 10.21504/10962/178409
- Description: This thesis presents the development of a regional ionospheric storm-time model which forms the foundation of an index to provide a quick view of the ionospheric storm effects over South African mid-latitude region. The model is based on the foF2 measurements from four South African ionosonde stations. The data coverage for the model development over Grahamstown (33.3◦S, 26.5◦E), Hermanus (34.42◦S, 19.22◦E), Louisvale (28.50◦S, 21.20◦E), and Madimbo (22.39◦S, 30.88◦E) is 1996-2016, 2009-2016, 2000-2016, and 2000-2016 respectively. Data from the Global Positioning System (GPS) and radio occultation (RO) technique were used during validation. As the measure of either positive or negative storm effect, the variation of the critical frequency of the F2 layer (foF2) from the monthly median values (denoted as _foF2) is modeled. The modeling of _foF2 is based on only storm time data with the criteria of Dst 6 -50 nT and Kp > 4. The modeling methods used in the study were artificial neural network (ANN), linear regression (LR) and polynomial functions. The approach taken was to first test the modeling techniques on a single station before expanding the study to cover the regional aspect. The single station modeling was developed based on ionosonde data over Grahamstown. The inputs for the model which related to seasonal variation, diurnal variation, geomagnetic activity and solar activity were considered. For the geomagnetic activity, three indices namely; the symmetric disturbance in the horizontal component of the Earth’s magnetic field (SYM − H), the Auroral Electrojet (AE) index and local geomagnetic index A, were included as inputs. The performance of a single station model revealed that, of the three geomagnetic indices, SYM − H index has the largest contribution of 41% and 54% based on ANN and LR techniques respectively. The average correlation coefficients (R) for both ANN and LR models was 0.8, when validated during the selected storms falling within the period of model development. When validated using storms that fall outside the period of model development, the model gave R values of 0.6 and 0.5 for ANN and LR respectively. In addition, the GPS total electron content (TEC) derived measurements were used to estimate foF2 data. This is because there are more GPS receivers than ionosonde locations and the utilisation of this data increases the spatial coverage of the regional model. The estimation of foF2 from GPS TEC was done at GPS-ionosonde co-locations using polynomial functions. The average R values of 0.69 and 0.65 were obtained between actual and derived _foF2 over the co-locations and other GPS stations respectively. Validation of GPS TEC derived foF2 with RO data over regions out of ionospheric pierce points coverage with respect to ionosonde locations gave R greater than 0.9 for the selected storm period of 4-8 August 2011. The regional storm-time model was then developed based on the ANN technique using the four South African ionosonde stations. The maximum and minimum R values of 0.6 and 0.5 were obtained over ionosonde and GPS locations respectively. This model forms the basis towards the regional ionospheric storm-time index. , Thesis (PhD) -- Faculty of Science, Physics and Electronics, 2021
- Full Text:
- Date Issued: 2021-04
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
Technology in conservation: towards a system for in-field drone detection of invasive vegetation
- James, Katherine Margaret Frances
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
- Authors: James, Katherine Margaret Frances
- Date: 2020
- Subjects: Drone aircraft in remote sensing , Neural networks (Computer science) , Drone aircraft in remote sensing -- Case studies , Machine learning , Computer vision , Environmental monitoring -- Remote sensing , Invasive plants -- Monitoring
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/143408 , vital:38244
- Description: Remote sensing can assist in monitoring the spread of invasive vegetation. The adoption of camera-carrying unmanned aerial vehicles, commonly referred to as drones, as remote sensing tools has yielded images of higher spatial resolution than traditional techniques. Drones also have the potential to interact with the environment through the delivery of bio-control or herbicide, as seen with their adoption in precision agriculture. Unlike in agricultural applications, however, invasive plants do not have a predictable position relative to each other within the environment. To facilitate the adoption of drones as an environmental monitoring and management tool, drones need to be able to intelligently distinguish between invasive and non-invasive vegetation on the fly. In this thesis, we present the augmentation of a commercially available drone with a deep machine learning model to investigate the viability of differentiating between an invasive shrub and other vegetation. As a case study, this was applied to the shrub genus Hakea, originating in Australia and invasive in several countries including South Africa. However, for this research, the methodology is important, rather than the chosen target plant. A dataset was collected using the available drone and manually annotated to facilitate the supervised training of the model. Two approaches were explored, namely, classification and semantic segmentation. For each of these, several models were trained and evaluated to find the optimal one. The chosen model was then interfaced with the drone via an Android application on a mobile device and its performance was preliminarily evaluated in the field. Based on these findings, refinements were made and thereafter a thorough field evaluation was performed to determine the best conditions for model operation. Results from the classification task show that deep learning models are capable of distinguishing between target and other shrubs in ideal candidate windows. However, classification in this manner is restricted by the proposal of such candidate windows. End-to-end image segmentation using deep learning overcomes this problem, classifying the image in a pixel-wise manner. Furthermore, the use of appropriate loss functions was found to improve model performance. Field tests show that illumination and shadow pose challenges to the model, but that good recall can be achieved when the conditions are ideal. False positive detection remains an issue that could be improved. This approach shows the potential for drones as an environmental monitoring and management tool when coupled with deep machine learning techniques and outlines potential problems that may be encountered.
- Full Text:
- Date Issued: 2020
Modelling Ionospheric vertical drifts over the African low latitude region
- Dubazane, Makhosonke Berthwell
- Authors: Dubazane, Makhosonke Berthwell
- Date: 2018
- Subjects: Ionospheric drift , Magnetometers , Functions, Orthogonal , Neural networks (Computer science) , Ionospheric electron density -- Africa , Communication and Navigation Outage Forecasting Systems (C/NOFS)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63356 , vital:28396
- Description: Low/equatorial latitudes vertical plasma drifts and electric fields govern the formation and changes of ionospheric density structures which affect space-based systems such as communications, navigation and positioning. Dynamical and electrodynamical processes play important roles in plasma distribution at different altitudes. Because of the high variability of E × B drift in low latitude regions, coupled with various processes that sometimes originate from high latitudes especially during geomagnetic storm conditions, it is challenging to develop accurate vertical drift models. This is despite the fact that there are very few instruments dedicated to provide electric field and hence E × B drift data in low/equatorial latitude regions. To this effect, there exists no ground-based instrument for direct measurements of E×B drift data in the African sector. This study presents the first time investigation aimed at modelling the long-term variability of low latitude vertical E × B drift over the African sector using a combination of Communication and Navigation Outage Forecasting Systems (C/NOFS) and ground-based magnetometer observations/measurements during 2008-2013. Because the approach is based on the estimation of equatorial electrojet from ground-based magnetometer observations, the developed models are only valid for local daytime. Three modelling techniques have been considered. The application of Empirical Orthogonal Functions and partial least squares has been performed on vertical E × B drift modelling for the first time. The artificial neural networks that have the advantage of learning underlying changes between a set of inputs and known output were also used in vertical E × B drift modelling. Due to lack of E×B drift data over the African sector, the developed models were validated using satellite data and the climatological Scherliess-Fejer model incorporated within the International Reference Ionosphere model. Maximum correlation coefficient of ∼ 0.8 was achieved when validating the developed models with C/NOFS E × B drift observations that were not used in any model development. For most of the time, the climatological model overestimates the local daytime vertical E × B drift velocities. The methods and approach presented in this study provide a background for constructing vertical E ×B drift databases in longitude sectors that do not have radar instrumentation. This will in turn make it possible to study day-to-day variability of vertical E×B drift and hopefully lead to the development of regional and global models that will incorporate local time information in different longitude sectors.
- Full Text:
- Date Issued: 2018
- Authors: Dubazane, Makhosonke Berthwell
- Date: 2018
- Subjects: Ionospheric drift , Magnetometers , Functions, Orthogonal , Neural networks (Computer science) , Ionospheric electron density -- Africa , Communication and Navigation Outage Forecasting Systems (C/NOFS)
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63356 , vital:28396
- Description: Low/equatorial latitudes vertical plasma drifts and electric fields govern the formation and changes of ionospheric density structures which affect space-based systems such as communications, navigation and positioning. Dynamical and electrodynamical processes play important roles in plasma distribution at different altitudes. Because of the high variability of E × B drift in low latitude regions, coupled with various processes that sometimes originate from high latitudes especially during geomagnetic storm conditions, it is challenging to develop accurate vertical drift models. This is despite the fact that there are very few instruments dedicated to provide electric field and hence E × B drift data in low/equatorial latitude regions. To this effect, there exists no ground-based instrument for direct measurements of E×B drift data in the African sector. This study presents the first time investigation aimed at modelling the long-term variability of low latitude vertical E × B drift over the African sector using a combination of Communication and Navigation Outage Forecasting Systems (C/NOFS) and ground-based magnetometer observations/measurements during 2008-2013. Because the approach is based on the estimation of equatorial electrojet from ground-based magnetometer observations, the developed models are only valid for local daytime. Three modelling techniques have been considered. The application of Empirical Orthogonal Functions and partial least squares has been performed on vertical E × B drift modelling for the first time. The artificial neural networks that have the advantage of learning underlying changes between a set of inputs and known output were also used in vertical E × B drift modelling. Due to lack of E×B drift data over the African sector, the developed models were validated using satellite data and the climatological Scherliess-Fejer model incorporated within the International Reference Ionosphere model. Maximum correlation coefficient of ∼ 0.8 was achieved when validating the developed models with C/NOFS E × B drift observations that were not used in any model development. For most of the time, the climatological model overestimates the local daytime vertical E × B drift velocities. The methods and approach presented in this study provide a background for constructing vertical E ×B drift databases in longitude sectors that do not have radar instrumentation. This will in turn make it possible to study day-to-day variability of vertical E×B drift and hopefully lead to the development of regional and global models that will incorporate local time information in different longitude sectors.
- Full Text:
- Date Issued: 2018
Tomographic imaging of East African equatorial ionosphere and study of equatorial plasma bubbles
- Authors: Giday, Nigussie Mezgebe
- Date: 2018
- Subjects: Ionosphere -- Africa, Central , Tomography -- Africa, Central , Global Positioning System , Neural networks (Computer science) , Space environment , Multi-Instrument Data Analysis System (MIDAS) , Equatorial plasma bubbles
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63980 , vital:28516
- Description: In spite of the fact that the African ionospheric equatorial region has the largest ground footprint along the geomagnetic equator, it has not been well studied due to the absence of adequate ground-based instruments. This thesis presents research on both tomographic imaging of the African equatorial ionosphere and the study of the ionospheric irregularities/equatorial plasma bubbles (EPBs) under varying geomagnetic conditions. The Multi-Instrument Data Analysis System (MIDAS), an inversion algorithm, was investigated for its validity and ability as a tool to reconstruct multi-scaled ionospheric structures for different geomagnetic conditions. This was done for the narrow East African longitude sector with data from the available ground Global Positioning Sys-tem (GPS) receivers. The MIDAS results were compared to the results of two models, namely the IRI and GIM. MIDAS results compared more favourably with the observation vertical total electron content (VTEC), with a computed maximum correlation coefficient (r) of 0.99 and minimum root-mean-square error (RMSE) of 2.91 TECU, than did the results of the IRI-2012 and GIM models with maximum r of 0.93 and 0.99, and minimum RMSE of 13.03 TECU and 6.52 TECU, respectively, over all the test stations and validation days. The ability of MIDAS to reconstruct storm-time TEC was also compared with the results produced by the use of a Artificial Neural Net-work (ANN) for the African low- and mid-latitude regions. In terms of latitude, on average,MIDAS performed 13.44 % better than ANN in the African mid-latitudes, while MIDAS under performed in low-latitudes. This thesis also reports on the effects of moderate geomagnetic conditions on the evolution of EPBs and/or ionospheric irregularities during their season of occurrence using data from (or measurements by) space- and ground-based instruments for the east African equatorial sector. The study showed that the strength of daytime equatorial electrojet (EEJ), the steepness of the TEC peak-to-trough gradient and/or the meridional/transequatorial thermospheric winds sometimes have collective/interwoven effects, while at other times one mechanism dominates. In summary, this research offered tomographic results that outperform the results of the commonly used (“standard”) global models (i.e. IRI and GIM) for a longitude sector of importance to space weather, which has not been adequately studied due to a lack of sufficient instrumentation.
- Full Text:
- Date Issued: 2018
- Authors: Giday, Nigussie Mezgebe
- Date: 2018
- Subjects: Ionosphere -- Africa, Central , Tomography -- Africa, Central , Global Positioning System , Neural networks (Computer science) , Space environment , Multi-Instrument Data Analysis System (MIDAS) , Equatorial plasma bubbles
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/63980 , vital:28516
- Description: In spite of the fact that the African ionospheric equatorial region has the largest ground footprint along the geomagnetic equator, it has not been well studied due to the absence of adequate ground-based instruments. This thesis presents research on both tomographic imaging of the African equatorial ionosphere and the study of the ionospheric irregularities/equatorial plasma bubbles (EPBs) under varying geomagnetic conditions. The Multi-Instrument Data Analysis System (MIDAS), an inversion algorithm, was investigated for its validity and ability as a tool to reconstruct multi-scaled ionospheric structures for different geomagnetic conditions. This was done for the narrow East African longitude sector with data from the available ground Global Positioning Sys-tem (GPS) receivers. The MIDAS results were compared to the results of two models, namely the IRI and GIM. MIDAS results compared more favourably with the observation vertical total electron content (VTEC), with a computed maximum correlation coefficient (r) of 0.99 and minimum root-mean-square error (RMSE) of 2.91 TECU, than did the results of the IRI-2012 and GIM models with maximum r of 0.93 and 0.99, and minimum RMSE of 13.03 TECU and 6.52 TECU, respectively, over all the test stations and validation days. The ability of MIDAS to reconstruct storm-time TEC was also compared with the results produced by the use of a Artificial Neural Net-work (ANN) for the African low- and mid-latitude regions. In terms of latitude, on average,MIDAS performed 13.44 % better than ANN in the African mid-latitudes, while MIDAS under performed in low-latitudes. This thesis also reports on the effects of moderate geomagnetic conditions on the evolution of EPBs and/or ionospheric irregularities during their season of occurrence using data from (or measurements by) space- and ground-based instruments for the east African equatorial sector. The study showed that the strength of daytime equatorial electrojet (EEJ), the steepness of the TEC peak-to-trough gradient and/or the meridional/transequatorial thermospheric winds sometimes have collective/interwoven effects, while at other times one mechanism dominates. In summary, this research offered tomographic results that outperform the results of the commonly used (“standard”) global models (i.e. IRI and GIM) for a longitude sector of importance to space weather, which has not been adequately studied due to a lack of sufficient instrumentation.
- Full Text:
- Date Issued: 2018
Updating the ionospheric propagation factor, M(3000)F2, global model using the neural network technique and relevant geophysical input parameters
- Oronsaye, Samuel Iyen Jeffrey
- Authors: Oronsaye, Samuel Iyen Jeffrey
- Date: 2013
- Subjects: Neural networks (Computer science) , Ionospheric radio wave propagation , Ionosphere , Geophysics , Ionosondes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5434 , http://hdl.handle.net/10962/d1001609 , Neural networks (Computer science) , Ionospheric radio wave propagation , Ionosphere , Geophysics , Ionosondes
- Description: This thesis presents an update to the ionospheric propagation factor, M(3000)F2, global empirical model developed by Oyeyemi et al. (2007) (NNO). An additional aim of this research was to produce the updated model in a form that could be used within the International Reference Ionosphere (IRI) global model without adding to the complexity of the IRI. M(3000)F2 is the highest frequency at which a radio signal can be received over a distance of 3000 km after reflection in the ionosphere. The study employed the artificial neural network (ANN) technique using relevant geophysical input parameters which are known to influence the M(3000)F2 parameter. Ionosonde data from 135 ionospheric stations globally, including a number of equatorial stations, were available for this work. M(3000)F2 hourly values from 1976 to 2008, spanning all periods of low and high solar activity were used for model development and verification. A preliminary investigation was first carried out using a relatively small dataset to determine the appropriate input parameters for global M(3000)F2 parameter modelling. Inputs representing diurnal variation, seasonal variation, solar variation, modified dip latitude, longitude and latitude were found to be the optimum parameters for modelling the diurnal and seasonal variations of the M(3000)F2 parameter both on a temporal and spatial basis. The outcome of the preliminary study was applied to the overall dataset to develop a comprehensive ANN M(3000)F2 model which displays a remarkable improvement over the NNO model as well as the IRI version. The model shows 7.11% and 3.85% improvement over the NNO model as well as 13.04% and 10.05% over the IRI M(3000)F2 model, around high and low solar activity periods respectively. A comparison of the diurnal structure of the ANN and the IRI predicted values reveal that the ANN model is more effective in representing the diurnal structure of the M(3000)F2 values than the IRI M(3000)F2 model. The capability of the ANN model in reproducing the seasonal variation pattern of the M(3000)F2 values at 00h00UT, 06h00UT, 12h00UT, and l8h00UT more appropriately than the IRI version is illustrated in this work. A significant result obtained in this study is the ability of the ANN model in improving the post-sunset predicted values of the M(3000)F2 parameter which is known to be problematic to the IRI M(3000)F2 model in the low-latitude and the equatorial regions. The final M(3000)F2 model provides for an improved equatorial prediction and a simplified input space that allows for easy incorporation into the IRI model.
- Full Text:
- Date Issued: 2013
- Authors: Oronsaye, Samuel Iyen Jeffrey
- Date: 2013
- Subjects: Neural networks (Computer science) , Ionospheric radio wave propagation , Ionosphere , Geophysics , Ionosondes
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5434 , http://hdl.handle.net/10962/d1001609 , Neural networks (Computer science) , Ionospheric radio wave propagation , Ionosphere , Geophysics , Ionosondes
- Description: This thesis presents an update to the ionospheric propagation factor, M(3000)F2, global empirical model developed by Oyeyemi et al. (2007) (NNO). An additional aim of this research was to produce the updated model in a form that could be used within the International Reference Ionosphere (IRI) global model without adding to the complexity of the IRI. M(3000)F2 is the highest frequency at which a radio signal can be received over a distance of 3000 km after reflection in the ionosphere. The study employed the artificial neural network (ANN) technique using relevant geophysical input parameters which are known to influence the M(3000)F2 parameter. Ionosonde data from 135 ionospheric stations globally, including a number of equatorial stations, were available for this work. M(3000)F2 hourly values from 1976 to 2008, spanning all periods of low and high solar activity were used for model development and verification. A preliminary investigation was first carried out using a relatively small dataset to determine the appropriate input parameters for global M(3000)F2 parameter modelling. Inputs representing diurnal variation, seasonal variation, solar variation, modified dip latitude, longitude and latitude were found to be the optimum parameters for modelling the diurnal and seasonal variations of the M(3000)F2 parameter both on a temporal and spatial basis. The outcome of the preliminary study was applied to the overall dataset to develop a comprehensive ANN M(3000)F2 model which displays a remarkable improvement over the NNO model as well as the IRI version. The model shows 7.11% and 3.85% improvement over the NNO model as well as 13.04% and 10.05% over the IRI M(3000)F2 model, around high and low solar activity periods respectively. A comparison of the diurnal structure of the ANN and the IRI predicted values reveal that the ANN model is more effective in representing the diurnal structure of the M(3000)F2 values than the IRI M(3000)F2 model. The capability of the ANN model in reproducing the seasonal variation pattern of the M(3000)F2 values at 00h00UT, 06h00UT, 12h00UT, and l8h00UT more appropriately than the IRI version is illustrated in this work. A significant result obtained in this study is the ability of the ANN model in improving the post-sunset predicted values of the M(3000)F2 parameter which is known to be problematic to the IRI M(3000)F2 model in the low-latitude and the equatorial regions. The final M(3000)F2 model provides for an improved equatorial prediction and a simplified input space that allows for easy incorporation into the IRI model.
- Full Text:
- Date Issued: 2013
Universal approximation properties of feedforward artificial neural networks.
- Authors: Redpath, Stuart Frederick
- Date: 2011
- Subjects: Neural networks (Computer science) , Artificial intelligence -- Biological applications , Functional analysis , Weierstrass-Stone Theorem , Banach-Hahn theorem
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5430 , http://hdl.handle.net/10962/d1015869
- Description: In this thesis we summarise several results in the literature which show the approximation capabilities of multilayer feedforward artificial neural networks. We show that multilayer feedforward artificial neural networks are capable of approximating continuous and measurable functions from Rn to R to any degree of accuracy under certain conditions. In particular making use of the Stone-Weierstrass and Hahn-Banach theorems, we show that a multilayer feedforward artificial neural network can approximate any continuous function to any degree of accuracy, by using either an arbitrary squashing function or any continuous sigmoidal function for activation. Making use of the Stone-Weirstrass Theorem again, we extend these approximation capabilities of multilayer feedforward artificial neural networks to the space of measurable functions under any probability measure.
- Full Text:
- Date Issued: 2011
- Authors: Redpath, Stuart Frederick
- Date: 2011
- Subjects: Neural networks (Computer science) , Artificial intelligence -- Biological applications , Functional analysis , Weierstrass-Stone Theorem , Banach-Hahn theorem
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5430 , http://hdl.handle.net/10962/d1015869
- Description: In this thesis we summarise several results in the literature which show the approximation capabilities of multilayer feedforward artificial neural networks. We show that multilayer feedforward artificial neural networks are capable of approximating continuous and measurable functions from Rn to R to any degree of accuracy under certain conditions. In particular making use of the Stone-Weierstrass and Hahn-Banach theorems, we show that a multilayer feedforward artificial neural network can approximate any continuous function to any degree of accuracy, by using either an arbitrary squashing function or any continuous sigmoidal function for activation. Making use of the Stone-Weirstrass Theorem again, we extend these approximation capabilities of multilayer feedforward artificial neural networks to the space of measurable functions under any probability measure.
- Full Text:
- Date Issued: 2011
Development of a neural network based model for predicting the occurrence of spread F within the Brazilian sector
- Authors: Paradza, Masimba Wellington
- Date: 2009
- Subjects: Neural networks (Computer science) , Ionosphere , F region
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5460 , http://hdl.handle.net/10962/d1005245 , Neural networks (Computer science) , Ionosphere , F region
- Description: Spread F is a phenomenon of the ionosphere in which the pulses returned from the ionosphere are of a much greater duration than the transmitted ones. The occurrence of spread F can be predicted using the technique of Neural Networks (NNs). This thesis presents the development and evaluation of NN based models (two single station models and a regional model) for predicting the occurrence of spread F over selected stations within the Brazilian sector. The input space for the NNs included the day number (seasonal variation), hour (diurnal variation), sunspot number (measure of the solar activity), magnetic index (measure of the magnetic activity) and magnetic position (latitude, magnetic declination and inclination). Twelve years of spread F data measured during 1978 to 1989 inclusively at the equatorial site Fortaleza and low latitude site Cachoeira Paulista are used in the development of an input space and NN architecture for the NN models. Spread F data that is believed to be related to plasma bubble developments (range spread F) were used in the development of the models while those associated with narrow spectrum irregularities that occur near the F layer (frequency spread F) were excluded. The results of the models show the dependency of the probability of spread F as a function of local time, season and latitude. The models also illustrate some characteristics of spread F such as the onset and peak occurrence of spread F as a function of distance from the equator. Results from these models are presented in this thesis and compared to measured data and to modelled data obtained with an empirical model developed for the same purpose.
- Full Text:
- Date Issued: 2009
- Authors: Paradza, Masimba Wellington
- Date: 2009
- Subjects: Neural networks (Computer science) , Ionosphere , F region
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5460 , http://hdl.handle.net/10962/d1005245 , Neural networks (Computer science) , Ionosphere , F region
- Description: Spread F is a phenomenon of the ionosphere in which the pulses returned from the ionosphere are of a much greater duration than the transmitted ones. The occurrence of spread F can be predicted using the technique of Neural Networks (NNs). This thesis presents the development and evaluation of NN based models (two single station models and a regional model) for predicting the occurrence of spread F over selected stations within the Brazilian sector. The input space for the NNs included the day number (seasonal variation), hour (diurnal variation), sunspot number (measure of the solar activity), magnetic index (measure of the magnetic activity) and magnetic position (latitude, magnetic declination and inclination). Twelve years of spread F data measured during 1978 to 1989 inclusively at the equatorial site Fortaleza and low latitude site Cachoeira Paulista are used in the development of an input space and NN architecture for the NN models. Spread F data that is believed to be related to plasma bubble developments (range spread F) were used in the development of the models while those associated with narrow spectrum irregularities that occur near the F layer (frequency spread F) were excluded. The results of the models show the dependency of the probability of spread F as a function of local time, season and latitude. The models also illustrate some characteristics of spread F such as the onset and peak occurrence of spread F as a function of distance from the equator. Results from these models are presented in this thesis and compared to measured data and to modelled data obtained with an empirical model developed for the same purpose.
- Full Text:
- Date Issued: 2009
Forecasting solar cycle 24 using neural networks
- Authors: Uwamahoro, Jean
- Date: 2009
- Subjects: Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5468 , http://hdl.handle.net/10962/d1005253 , Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Description: The ability to predict the future behavior of solar activity has become of extreme importance due to its effect on the near-Earth environment. Predictions of both the amplitude and timing of the next solar cycle will assist in estimating the various consequences of Space Weather. Several prediction techniques have been applied and have achieved varying degrees of success in the domain of solar activity prediction. These techniques include, for example, neural networks and geomagnetic precursor methods. In this thesis, various neural network based models were developed and the model considered to be optimum was used to estimate the shape and timing of solar cycle 24. Given the recent success of the geomagnetic precusrsor methods, geomagnetic activity as measured by the aa index is considered among the main inputs to the neural network model. The neural network model developed is also provided with the time input parameters defining the year and the month of a particular solar cycle, in order to characterise the temporal behaviour of sunspot number as observed during the last 10 solar cycles. The structure of input-output patterns to the neural network is constructed in such a way that the network learns the relationship between the aa index values of a particular cycle, and the sunspot number values of the following cycle. Assuming January 2008 as the minimum preceding solar cycle 24, the shape and amplitude of solar cycle 24 is estimated in terms of monthly mean and smoothed monthly sunspot number. This new prediction model estimates an average solar cycle 24, with the maximum occurring around June 2012 [± 11 months], with a smoothed monthly maximum sunspot number of 121 ± 9.
- Full Text:
- Date Issued: 2009
- Authors: Uwamahoro, Jean
- Date: 2009
- Subjects: Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5468 , http://hdl.handle.net/10962/d1005253 , Solar cycle , Neural networks (Computer science) , Ionosphere , Ionospheric electron density , Ionospheric forecasting , Solar thermal energy
- Description: The ability to predict the future behavior of solar activity has become of extreme importance due to its effect on the near-Earth environment. Predictions of both the amplitude and timing of the next solar cycle will assist in estimating the various consequences of Space Weather. Several prediction techniques have been applied and have achieved varying degrees of success in the domain of solar activity prediction. These techniques include, for example, neural networks and geomagnetic precursor methods. In this thesis, various neural network based models were developed and the model considered to be optimum was used to estimate the shape and timing of solar cycle 24. Given the recent success of the geomagnetic precusrsor methods, geomagnetic activity as measured by the aa index is considered among the main inputs to the neural network model. The neural network model developed is also provided with the time input parameters defining the year and the month of a particular solar cycle, in order to characterise the temporal behaviour of sunspot number as observed during the last 10 solar cycles. The structure of input-output patterns to the neural network is constructed in such a way that the network learns the relationship between the aa index values of a particular cycle, and the sunspot number values of the following cycle. Assuming January 2008 as the minimum preceding solar cycle 24, the shape and amplitude of solar cycle 24 is estimated in terms of monthly mean and smoothed monthly sunspot number. This new prediction model estimates an average solar cycle 24, with the maximum occurring around June 2012 [± 11 months], with a smoothed monthly maximum sunspot number of 121 ± 9.
- Full Text:
- Date Issued: 2009
Predictability of Geomagnetically Induced Currents using neural networks
- Authors: Lotz, Stefanus Ignatius
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
- Date Issued: 2009
- Authors: Lotz, Stefanus Ignatius
- Date: 2009
- Subjects: Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5483 , http://hdl.handle.net/10962/d1005269 , Advanced Composition Explorer (Artificial satellite) , Geomagnetism , Electromagnetic induction , Neural networks (Computer science) , Artificial intelligence
- Description: It is a well documented fact that Geomagnetically Induced Currents (GIC’s) poses a significant threat to ground-based electric conductor networks like oil pipelines, railways and powerline networks. A study is undertaken to determine the feasibility of using artificial neural network models to predict GIC occurrence in the Southern African power grid. The magnitude of an induced current at a specific location on the Earth’s surface is directly related to the temporal derivative of the geomagnetic field (specifically its horizontal components) at that point. Hence, the focus of the problem is on the prediction of the temporal variations in the horizontal geomagnetic field (@Bx/@t and @By/@t). Artificial neural networks are used to predict @Bx/@t and @By/@t measured at Hermanus, South Africa (34.27◦ S, 19.12◦ E) with a 30 minute prediction lead time. As input parameters to the neural networks, insitu solar wind measurements made by the Advanced Composition Explorer (ACE) satellite are used. The results presented here compare well with similar models developed at high-latitude locations (e.g. Sweden, Finland, Canada) where extensive GIC research has been undertaken. It is concluded that it would indeed be feasible to use a neural network model to predict GIC occurrence in the Southern African power grid, provided that GIC measurements, powerline configuration and network parameters are made available.
- Full Text:
- Date Issued: 2009
Protein secondary structure prediction using neural networks and support vector machines
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
- Authors: Tsilo, Lipontseng Cecilia
- Date: 2009
- Subjects: Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5569 , http://hdl.handle.net/10962/d1002809 , Neural networks (Computer science) , Support vector machines , Proteins -- Structure -- Mathematical models
- Description: Predicting the secondary structure of proteins is important in biochemistry because the 3D structure can be determined from the local folds that are found in secondary structures. Moreover, knowing the tertiary structure of proteins can assist in determining their functions. The objective of this thesis is to compare the performance of Neural Networks (NN) and Support Vector Machines (SVM) in predicting the secondary structure of 62 globular proteins from their primary sequence. For each NN and SVM, we created six binary classifiers to distinguish between the classes’ helices (H) strand (E), and coil (C). For NN we use Resilient Backpropagation training with and without early stopping. We use NN with either no hidden layer or with one hidden layer with 1,2,...,40 hidden neurons. For SVM we use a Gaussian kernel with parameter fixed at = 0.1 and varying cost parameters C in the range [0.1,5]. 10- fold cross-validation is used to obtain overall estimates for the probability of making a correct prediction. Our experiments indicate for NN and SVM that the different binary classifiers have varying accuracies: from 69% correct predictions for coils vs. non-coil up to 80% correct predictions for stand vs. non-strand. It is further demonstrated that NN with no hidden layer or not more than 2 hidden neurons in the hidden layer are sufficient for better predictions. For SVM we show that the estimated accuracies do not depend on the value of the cost parameter. As a major result, we will demonstrate that the accuracy estimates of NN and SVM binary classifiers cannot distinguish. This contradicts a modern belief in bioinformatics that SVM outperforms other predictors.
- Full Text:
- Date Issued: 2009
A feasibility study into total electron content prediction using neural networks
- Authors: Habarulema, John Bosco
- Date: 2008
- Subjects: Electrons , Neural networks (Computer science) , Global Positioning System , Ionosphere , Ionospheric electron density
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5466 , http://hdl.handle.net/10962/d1005251 , Electrons , Neural networks (Computer science) , Global Positioning System , Ionosphere , Ionospheric electron density
- Description: Global Positioning System (GPS) networks provide an opportunity to study the dynamics and continuous changes in the ionosphere by supplementing ionospheric measurements which are usually obtained by various techniques such as ionosondes, incoherent scatter radars and satellites. Total electron content (TEC) is one of the physical quantities that can be derived from GPS data, and provides an indication of ionospheric variability. This thesis presents a feasibility study for the development of a Neural Network (NN) based model for the prediction of South African GPS derived TEC. The South African GPS receiver network is operated and maintained by the Chief Directorate Surveys and Mapping (CDSM) in Cape Town, South Africa. Three South African locations were identified and used in the development of an input space and NN architecture for the model. The input space includes the day number (seasonal variation), hour (diurnal variation), sunspot number (measure of the solar activity), and magnetic index(measure of the magnetic activity). An attempt to study the effects of solar wind on TEC variability was carried out using the Advanced Composition Explorer (ACE) data and it is recommended that more study be done using low altitude satellite data. An analysis was done by comparing predicted NN TEC with TEC values from the IRI2001 version of the International Reference Ionosphere (IRI), validating GPS TEC with ionosonde TEC (ITEC) and assessing the performance of the NN model during equinoxes and solstices. Results show that NNs predict GPS TEC more accurately than the IRI at South African GPS locations, but that more good quality GPS data is required before a truly representative empirical GPS TEC model can be released.
- Full Text:
- Date Issued: 2008
- Authors: Habarulema, John Bosco
- Date: 2008
- Subjects: Electrons , Neural networks (Computer science) , Global Positioning System , Ionosphere , Ionospheric electron density
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:5466 , http://hdl.handle.net/10962/d1005251 , Electrons , Neural networks (Computer science) , Global Positioning System , Ionosphere , Ionospheric electron density
- Description: Global Positioning System (GPS) networks provide an opportunity to study the dynamics and continuous changes in the ionosphere by supplementing ionospheric measurements which are usually obtained by various techniques such as ionosondes, incoherent scatter radars and satellites. Total electron content (TEC) is one of the physical quantities that can be derived from GPS data, and provides an indication of ionospheric variability. This thesis presents a feasibility study for the development of a Neural Network (NN) based model for the prediction of South African GPS derived TEC. The South African GPS receiver network is operated and maintained by the Chief Directorate Surveys and Mapping (CDSM) in Cape Town, South Africa. Three South African locations were identified and used in the development of an input space and NN architecture for the model. The input space includes the day number (seasonal variation), hour (diurnal variation), sunspot number (measure of the solar activity), and magnetic index(measure of the magnetic activity). An attempt to study the effects of solar wind on TEC variability was carried out using the Advanced Composition Explorer (ACE) data and it is recommended that more study be done using low altitude satellite data. An analysis was done by comparing predicted NN TEC with TEC values from the IRI2001 version of the International Reference Ionosphere (IRI), validating GPS TEC with ionosonde TEC (ITEC) and assessing the performance of the NN model during equinoxes and solstices. Results show that NNs predict GPS TEC more accurately than the IRI at South African GPS locations, but that more good quality GPS data is required before a truly representative empirical GPS TEC model can be released.
- Full Text:
- Date Issued: 2008
An analysis of neural networks and time series techniques for demand forecasting
- Authors: Winn, David
- Date: 2007
- Subjects: Time-series analysis , Neural networks (Computer science) , Artificial intelligence , Marketing -- Management , Marketing -- Data processing , Marketing -- Statistical methods , Consumer behaviour
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:5572 , http://hdl.handle.net/10962/d1004362 , Time-series analysis , Neural networks (Computer science) , Artificial intelligence , Marketing -- Management , Marketing -- Data processing , Marketing -- Statistical methods , Consumer behaviour
- Description: This research examines the plausibility of developing demand forecasting techniques which are consistently and accurately able to predict demand. Time Series Techniques and Artificial Neural Networks are both investigated. Deodorant sales in South Africa are specifically studied in this thesis. Marketing techniques which are used to influence consumer buyer behaviour are considered, and these factors are integrated into the forecasting models wherever possible. The results of this research suggest that Artificial Neural Networks can be developed which consistently outperform industry forecasting targets as well as Time Series forecasts, suggesting that producers could reduce costs by adopting this more effective method.
- Full Text:
- Date Issued: 2007
- Authors: Winn, David
- Date: 2007
- Subjects: Time-series analysis , Neural networks (Computer science) , Artificial intelligence , Marketing -- Management , Marketing -- Data processing , Marketing -- Statistical methods , Consumer behaviour
- Language: English
- Type: Thesis , Masters , MCom
- Identifier: vital:5572 , http://hdl.handle.net/10962/d1004362 , Time-series analysis , Neural networks (Computer science) , Artificial intelligence , Marketing -- Management , Marketing -- Data processing , Marketing -- Statistical methods , Consumer behaviour
- Description: This research examines the plausibility of developing demand forecasting techniques which are consistently and accurately able to predict demand. Time Series Techniques and Artificial Neural Networks are both investigated. Deodorant sales in South Africa are specifically studied in this thesis. Marketing techniques which are used to influence consumer buyer behaviour are considered, and these factors are integrated into the forecasting models wherever possible. The results of this research suggest that Artificial Neural Networks can be developed which consistently outperform industry forecasting targets as well as Time Series forecasts, suggesting that producers could reduce costs by adopting this more effective method.
- Full Text:
- Date Issued: 2007
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