title: Adaptive Neural Networks for Online Domain Incremental Continual Learning

authors: Gunasekara, Nuwan

subjects: computer science

abstract: Continual Learning (CL) poses a significant challenge to Neural Network (NN)s, where the data distribution changes from one task to another. In Online domain incremental continual learning (OD-ICL), this distribution change happens in the input space without affecting the label distribution. In order to adapt to such changes, the model being trained risks forgetting previously learned knowledge (stability). On the other hand, enforcing that the model preserves past knowledge will cause it to fail to learn new concepts (plasticity). We propose Online Domain Incremental Networks (ODIN), a novel method to alleviate catastrophic forgetting by automatically detecting the end of a task using concept drift detection. As a consequence, ODIN does not require the specification of task ids. ODIN maintains a pool of NNs, each trained on a single task and frozen for further updates. A Task Predictor (TP) is trained to select the most suitable NN from the frozen pool for prediction. We compare ODIN against popular regularization and replay methods. It outperforms regularization methods and achieves comparable predictive performance to replay methods.

text: Adaptive Neural Networks for Online Domain Incremental Continual Learning Continual Learning (CL) poses a significant challenge to Neural Network (NN)s, where the data distribution changes from one task to another. In Online domain incremental continual learning (OD-ICL), this distribution change happens in the input space without affecting the label distribution. In order to adapt to such changes, the model being trained risks forgetting previously learned knowledge (stability). On the other hand, enforcing that the model preserves past knowledge will cause it to fail to learn new concepts (plasticity). We propose Online Domain Incremental Networks (ODIN), a novel method to alleviate catastrophic forgetting by automatically detecting the end of a task using concept drift detection. As a consequence, ODIN does not require the specification of task ids. ODIN maintains a pool of NNs, each trained on a single task and frozen for further updates. A Task Predictor (TP) is trained to select the most suitable NN from the frozen pool for prediction. We compare ODIN against popular regularization and replay methods. It outperforms regularization methods and achieves comparable predictive performance to replay methods.

year: 2022

title: Black and White: investigations on the ecology, biology and biological control of sapstain fungi in New Zealand

authors: Thwaites, Joanne M.

abstract: This study examined ecology, colonisation, biological control and detection of sapstain fungi in New Zealand.
A nationwide survey of New Zealand sapstain fungi was undertaken between 1996 and1998. In total, 1035 sites were sampled in the North and South Islands. From these collections, 1755 potential sapstain fungi were isolated and seventeen individual species were identified. The predominant sapstain fungi identified were Sphaeropsis sapinea,
Ophiostoma ips, O. floccosum, O. piliferum, O. querci and Leptographium procerum. This data was subsequently evaluated according to ecological criteria, including geographical and temporal distribution of sapstain fungi. A greater diversity of sapstain fungi was found in areas of New Zealand that were primarily plantation forestry. S. sapinea was isolated during more generalised forest sampling, and from both native and plantation forests. Ophiostoma species were isolated more frequently from Pinus radiata plantations, processing plants including mills and ports and were mainly isolated from harvested forest material such as logs, wood chips, and other wood products. S. sapinea was isolated more frequently in spring and summer while Ophiostoma species predominated during autumn and winter periods, probably linked with insect vectoring. This was the first attempt to link the sapstain organisms identified in New Zealand with their overall distribution within sectors of the forest industry, in different wood species, and in different types of wood samples.
New Zealand is one of the world's largest exporters of softwood logs. Exports of forest products provide 4% of New Zealand’s gross domestic product (GDP) with Japan, Korea, United States and the Philippines as major export markets for P. radiata logs. Conditions found within the holds of ships were thought likely to be ideal for the rapid colonisation of the sapstain fungi that results in dark penetrating stains. Log export research was designed to determine the extent of sapstain colonisation at specific points in the processing of logs from harvesting to the export destination. Two trials were established, in New Zealand summer and in winter, where mature P. radiata logs were harvested in New Zealand and shipped to export ports in Japan. Microclimatic conditions (temperature and relative humidity) on board the ships were recorded using data loggers both above deck and below deck. Nine species of sapstain fungi were isolated from logs during the summer trial. The most common species isolated were O. floccosum, O. querci and O. setosum. In contrast, a different combination of nine species was detected during the winter trial. S. sapinea, O. querci, O. floccosum, O. setosum and Ophiostoma piceae were most commonly isolated. The results of this study showed that the New Zealand sapstain fungi were being exported on logs. However, many of these fungi were previously recorded in Japan. In addition, no serious pathogens were detected. 

It was recognised during the sapstain fungal survey and export trials that a more thorough fundamental understanding of sapstain colonisation was required to properly determine the impacts of sapstain fungi to the New Zealand forest industry. In vitro and field studies were established to measure the relative colonisation of different species of sapstain fungi using synthetic media and P. radiata wood. These studies were undertaken to determine which sapstain species colonised, and how species interacted with each other following inoculation. In addition, the impacts of environmental conditions on the establishment and development of fungi and the resulting associated stains were determined. Temperature was found to affect the growth of various species of sapstain fungi on synthetic media and on P. radiata wood and logs. In the field studies O. floccosum was found to be the most successful coloniser of P. radiata logs in both winter and summer. Environmental factors such as temperature and moisture content were found to affect stain development. All fungal treatments developed sapstain discolouration from 15 days following inoculation in the summer field trial. In contrast, no stain was evident on any treatment in the winter field trial 60 days following inoculation. The colonisation of P. radiata by sapstain fungi was determined using microscopic techniques. Sapstain fungal hyphae were abundantly present in the ray parenchyma cells, tracheid lumen and resin canals of P. radiata wood. No differences in hyphal penetration were observed between the different sapstain fungal species at the cellular level. From these results a better understanding of the biology of sapstain species emerged. This new knowledge of the mechanisms and environmental triggers of fungal colonisation and stain development will aid in the more advanced technologies and management strategies to successfully control sapstain.

The many negative environmental impacts associated with traditional anti-sapstain chemical treatments led to increased interest in the more benign treatments of logs and wood using biological control technologies. The potential biological treatment of sapstain fungi using albino strains of O. floccosum, O. piceae and O. pluriannulatum was evaluated. These albino fungi demonstrated varied growth characteristics at different temperatures on both synthetic media and on P. radiata wood specimens. Comparable growth was found when evaluating wild type and albino sapstain strains in synthetic media and P. radiata wood in laboratory and field studies. Four field trials showed considerable variation in the biological control potential of the albino strains against wild type sapstain fungi. The mode of action of the albino strains was found to be competitive, through the use of primary resource capture of wood nutrients. However, albino O. floccosum strains were shown to produce zonal barriers when challenged with S. sapinea.

Proteomic analysis of cell wall proteins was undertaken to differentiate sapstain fungi from other wood inhabiting fungi and in an attempt to develop a method of determining the presence of sapstain fungi in wood prior to the development of stain. Proteins were extracted from the cell walls of various sapstain fungi (L. procerum, O. ips, O. Querci and S. sapinea) and wood inhabiting fungi (Alternaria alternata, Epicoccum nigrum, Trichoderma koningi) grown in liquid culture. Two dimensional (2D) protein profiles were made and compared. A total of 93 proteins were analysed using mass spectroscopy and the profiles compared to protein databases. This is the first investigation using proteomics of the cell wall proteins of Ophiostoma species and S. sapinea.

This study addressed the importance of sapstain fungi in New Zealand on P. radiata and increased our understanding of ecological requirements of the different sapstain species. Differences between these species with respect to colonisation and the development of associated stains were identified and investigated, enabling a critical evaluation of those species that were found to be most significant to the New Zealand forest industry. The future of sapstain management depends on a thorough ecological understanding of key sapstain fungal species involved in the cosmetic degradation of wood and an ability to manage the impacts of these species on the New Zealand forest industry using a combination of forest management practises and biological and chemical control techniques.

text: Black and White: investigations on the ecology, biology and biological control of sapstain fungi in New Zealand This study examined ecology, colonisation, biological control and detection of sapstain fungi in New Zealand.
A nationwide survey of New Zealand sapstain fungi was undertaken between 1996 and1998. In total, 1035 sites were sampled in the North and South Islands. From these collections, 1755 potential sapstain fungi were isolated and seventeen individual species were identified. The predominant sapstain fungi identified were Sphaeropsis sapinea,
Ophiostoma ips, O. floccosum, O. piliferum, O. querci and Leptographium procerum. This data was subsequently evaluated according to ecological criteria, including geographical and temporal distribution of sapstain fungi. A greater diversity of sapstain fungi was found in areas of New Zealand that were primarily plantation forestry. S. sapinea was isolated during more generalised forest sampling, and from both native and plantation forests. Ophiostoma species were isolated more frequently from Pinus radiata plantations, processing plants including mills and ports and were mainly isolated from harvested forest material such as logs, wood chips, and other wood products. S. sapinea was isolated more frequently in spring and summer while Ophiostoma species predominated during autumn and winter periods, probably linked with insect vectoring. This was the first attempt to link the sapstain organisms identified in New Zealand with their overall distribution within sectors of the forest industry, in different wood species, and in different types of wood samples.
New Zealand is one of the world's largest exporters of softwood logs. Exports of forest products provide 4% of New Zealand’s gross domestic product (GDP) with Japan, Korea, United States and the Philippines as major export markets for P. radiata logs. Conditions found within the holds of ships were thought likely to be ideal for the rapid colonisation of the sapstain fungi that results in dark penetrating stains. Log export research was designed to determine the extent of sapstain colonisation at specific points in the processing of logs from harvesting to the export destination. Two trials were established, in New Zealand summer and in winter, where mature P. radiata logs were harvested in New Zealand and shipped to export ports in Japan. Microclimatic conditions (temperature and relative humidity) on board the ships were recorded using data loggers both above deck and below deck. Nine species of sapstain fungi were isolated from logs during the summer trial. The most common species isolated were O. floccosum, O. querci and O. setosum. In contrast, a different combination of nine species was detected during the winter trial. S. sapinea, O. querci, O. floccosum, O. setosum and Ophiostoma piceae were most commonly isolated. The results of this study showed that the New Zealand sapstain fungi were being exported on logs. However, many of these fungi were previously recorded in Japan. In addition, no serious pathogens were detected. 

It was recognised during the sapstain fungal survey and export trials that a more thorough fundamental understanding of sapstain colonisation was required to properly determine the impacts of sapstain fungi to the New Zealand forest industry. In vitro and field studies were established to measure the relative colonisation of different species of sapstain fungi using synthetic media and P. radiata wood. These studies were undertaken to determine which sapstain species colonised, and how species interacted with each other following inoculation. In addition, the impacts of environmental conditions on the establishment and development of fungi and the resulting associated stains were determined. Temperature was found to affect the growth of various species of sapstain fungi on synthetic media and on P. radiata wood and logs. In the field studies O. floccosum was found to be the most successful coloniser of P. radiata logs in both winter and summer. Environmental factors such as temperature and moisture content were found to affect stain development. All fungal treatments developed sapstain discolouration from 15 days following inoculation in the summer field trial. In contrast, no stain was evident on any treatment in the winter field trial 60 days following inoculation. The colonisation of P. radiata by sapstain fungi was determined using microscopic techniques. Sapstain fungal hyphae were abundantly present in the ray parenchyma cells, tracheid lumen and resin canals of P. radiata wood. No differences in hyphal penetration were observed between the different sapstain fungal species at the cellular level. From these results a better understanding of the biology of sapstain species emerged. This new knowledge of the mechanisms and environmental triggers of fungal colonisation and stain development will aid in the more advanced technologies and management strategies to successfully control sapstain.

The many negative environmental impacts associated with traditional anti-sapstain chemical treatments led to increased interest in the more benign treatments of logs and wood using biological control technologies. The potential biological treatment of sapstain fungi using albino strains of O. floccosum, O. piceae and O. pluriannulatum was evaluated. These albino fungi demonstrated varied growth characteristics at different temperatures on both synthetic media and on P. radiata wood specimens. Comparable growth was found when evaluating wild type and albino sapstain strains in synthetic media and P. radiata wood in laboratory and field studies. Four field trials showed considerable variation in the biological control potential of the albino strains against wild type sapstain fungi. The mode of action of the albino strains was found to be competitive, through the use of primary resource capture of wood nutrients. However, albino O. floccosum strains were shown to produce zonal barriers when challenged with S. sapinea.

Proteomic analysis of cell wall proteins was undertaken to differentiate sapstain fungi from other wood inhabiting fungi and in an attempt to develop a method of determining the presence of sapstain fungi in wood prior to the development of stain. Proteins were extracted from the cell walls of various sapstain fungi (L. procerum, O. ips, O. Querci and S. sapinea) and wood inhabiting fungi (Alternaria alternata, Epicoccum nigrum, Trichoderma koningi) grown in liquid culture. Two dimensional (2D) protein profiles were made and compared. A total of 93 proteins were analysed using mass spectroscopy and the profiles compared to protein databases. This is the first investigation using proteomics of the cell wall proteins of Ophiostoma species and S. sapinea.

This study addressed the importance of sapstain fungi in New Zealand on P. radiata and increased our understanding of ecological requirements of the different sapstain species. Differences between these species with respect to colonisation and the development of associated stains were identified and investigated, enabling a critical evaluation of those species that were found to be most significant to the New Zealand forest industry. The future of sapstain management depends on a thorough ecological understanding of key sapstain fungal species involved in the cosmetic degradation of wood and an ability to manage the impacts of these species on the New Zealand forest industry using a combination of forest management practises and biological and chemical control techniques.

year: 2003

title: The hydrodynamic evolution of the Maketū Estuary after the re-diversion of the Kaituna River

authors: Razzaghi, Mojgan

abstract: The Maketū Estuary and lower Kaituna River located in the Bay of Plenty, Aotearoa, New Zealand have undergone anthropic disturbances since late 1800s, including land reclamation, river diversion and re-diversion, and modifications to the river channels and estuary tidal inlet. This has resulted in estuarine degradation, as is a common issue worldwide. Globally different approaches to estuary restoration have aimed at mitigating the adverse impacts of estuarine degradation.  However, there are still gaps in restoration frameworks and how the success of the scheme is evaluated that mean there is no ready-made solution to the issues at Maketū.
This thesis examines the important role of the hydrodynamic processes (including water quality) that govern the overall physical response of Maketū Estuary to two stages of partial re-diversion of the Kaituna River into the estuary. The assessment of this physical response highlighted the necessity of a proper framework in which restoration attempts, such as at Maketū are evaluated.
Field time series data were collected before and after two stages of river re-diversion, Stage 1 in 2020 and Stage 2 in 2021, each over a span of a month, to record the immediate response of the estuary to the added freshwater flows. Freshwater flow into the estuary was constrained to approximately 4 hours during flood tides when the water level In the Kaituna River was at least 40 mm higher than the upper Maketū Estuary. The control gates also operate as a flood control scheme, so they remain shut if there is flood risk causing all the flood volume to discharge directly to the sea through Te Tumu Cut river mouth. 
The field data were obtained using Aquadopp ADPs, RBR Maestros, RBR Concertos, and Solinst water level loggers at seven different sites throughout the estuary and the Kaituna River. A hydrographic survey of the estuary using RTK-GNSS was undertaken and combined with LiDAR to produce a bathymetric map of the estuary and Lower Kaituna River. Comparison of this map to previous compilations showed that the tidal inlet and lower estuary have not undergone major changes since the original river diversion in 1958, apart from an expansion in the area occupied by the flood tidal delta. However, the upper estuary has undergone both artificial and natural changes, including construction of artificial channels, causeways and reclamation, which have influenced the flow regime, circulation patterns and the flushing ability of the upper estuary. 
Based on field observations, the freshwater inflow to the estuary during Stage 1 was higher than Stage 2 even though Stage 1 was a partial re-diversion restricted to 400,000 m3 per flood tide, compared to the maximum 600,000 m3 for Stage 2. There was great spatial variability in the response of the estuary to the added freshwater flow despite the estuary’s small size and lack of inter-tidal vegetation. To better isolate the impact of freshwater flow and eliminate variables such as spring/neap tidal events, rainfall and wind, all of the data were averaged over a semi-diurnal tidal cycle of 12.4 hours. There was an increase in mean water level after both stages. Flow in the mid and upper estuary shifted towards ebb-dominance after Stage 1, but no further shift to ebb-dominance was observed after Stage 2. Mean bottom salinity increased in the upper estuary while it decreased everywhere else after Stage 1. Mean bottom salinity reduced uniformly throughout the estuary after Stage 2, most likely due to higher rainfall rate during the monitoring period, and not the added freshwater flow.
To better understand the mixing patterns within the estuary, Estuarine Richardson number (R_iE) was calculated at 3 main sites before and after both stages of re-diversion. R_iE increased after Stage 1, but not sufficiently to cause a shift in classification; therefore, the estuary remained partially-mixed. Current dynamics within the estuary varied depending on proximity to the tidal inlet, with sites close to the inlet showing a strong tidal signal, and the ones near the control gates showing a decreased tidal influence and an increased response to freshwater inflows during flood tide when the control gates were open. Surface currents were influenced by strong winds during storm events and dictated the mixing (stratification) in the mid and upper shallow estuary. However, it was difficult to assess the significance of these changes in relation to the community aspirations for the re-diversion and estuarine restoration as there were insufficient quantitative or qualitative targets defined.
To complement the field observations and better evaluate the impact of alternative restoration options, a 2D numerical model of the estuary was developed using Delft3D. After successfully being calibrated and validated, Delft3D-FLOW and PART were used to simulate different scenarios to assess the flow regime and flushing ability of the estuary. The scenarios included Stage 1 re-diversion, river inflow flow without control gates; and a pulsed flood flow using control gates that imitated natural flood events. Particle tracking was used determine the residence time across the estuary, and assess within which zones decay rate changed with tidal fluctuations, and which zones were sheltered from the tidal fluctuations. Model results showed that the pulsed flood scenario created the optimal conditions for sediment transport, increased flushing ability, and reduced salinity throughout the estuary. The model results also highlighted differences in how various zones in the estuary responded to the added freshwater flow, further emphasising the need to monitor them separately with an improved monitoring framework.
The results of this study have led to a better understanding of the impact of added freshwater flow on estuarine hydrodynamics and water quality: specifically how the river input moves the boundaries of fluvially or tidally dominated, and mixing zones. The most vulnerable zones in terms of the flushing ability under different scenarios of freshwater restoration were also identified. This study also highlighted the importance of setting tangible targets in the restoration scheme in alignment with the environmental uncertainties such as the average river flow and limitations due to flooding issues in the upper catchment.

text: The hydrodynamic evolution of the Maketū Estuary after the re-diversion of the Kaituna River The Maketū Estuary and lower Kaituna River located in the Bay of Plenty, Aotearoa, New Zealand have undergone anthropic disturbances since late 1800s, including land reclamation, river diversion and re-diversion, and modifications to the river channels and estuary tidal inlet. This has resulted in estuarine degradation, as is a common issue worldwide. Globally different approaches to estuary restoration have aimed at mitigating the adverse impacts of estuarine degradation.  However, there are still gaps in restoration frameworks and how the success of the scheme is evaluated that mean there is no ready-made solution to the issues at Maketū.
This thesis examines the important role of the hydrodynamic processes (including water quality) that govern the overall physical response of Maketū Estuary to two stages of partial re-diversion of the Kaituna River into the estuary. The assessment of this physical response highlighted the necessity of a proper framework in which restoration attempts, such as at Maketū are evaluated.
Field time series data were collected before and after two stages of river re-diversion, Stage 1 in 2020 and Stage 2 in 2021, each over a span of a month, to record the immediate response of the estuary to the added freshwater flows. Freshwater flow into the estuary was constrained to approximately 4 hours during flood tides when the water level In the Kaituna River was at least 40 mm higher than the upper Maketū Estuary. The control gates also operate as a flood control scheme, so they remain shut if there is flood risk causing all the flood volume to discharge directly to the sea through Te Tumu Cut river mouth. 
The field data were obtained using Aquadopp ADPs, RBR Maestros, RBR Concertos, and Solinst water level loggers at seven different sites throughout the estuary and the Kaituna River. A hydrographic survey of the estuary using RTK-GNSS was undertaken and combined with LiDAR to produce a bathymetric map of the estuary and Lower Kaituna River. Comparison of this map to previous compilations showed that the tidal inlet and lower estuary have not undergone major changes since the original river diversion in 1958, apart from an expansion in the area occupied by the flood tidal delta. However, the upper estuary has undergone both artificial and natural changes, including construction of artificial channels, causeways and reclamation, which have influenced the flow regime, circulation patterns and the flushing ability of the upper estuary. 
Based on field observations, the freshwater inflow to the estuary during Stage 1 was higher than Stage 2 even though Stage 1 was a partial re-diversion restricted to 400,000 m3 per flood tide, compared to the maximum 600,000 m3 for Stage 2. There was great spatial variability in the response of the estuary to the added freshwater flow despite the estuary’s small size and lack of inter-tidal vegetation. To better isolate the impact of freshwater flow and eliminate variables such as spring/neap tidal events, rainfall and wind, all of the data were averaged over a semi-diurnal tidal cycle of 12.4 hours. There was an increase in mean water level after both stages. Flow in the mid and upper estuary shifted towards ebb-dominance after Stage 1, but no further shift to ebb-dominance was observed after Stage 2. Mean bottom salinity increased in the upper estuary while it decreased everywhere else after Stage 1. Mean bottom salinity reduced uniformly throughout the estuary after Stage 2, most likely due to higher rainfall rate during the monitoring period, and not the added freshwater flow.
To better understand the mixing patterns within the estuary, Estuarine Richardson number (R_iE) was calculated at 3 main sites before and after both stages of re-diversion. R_iE increased after Stage 1, but not sufficiently to cause a shift in classification; therefore, the estuary remained partially-mixed. Current dynamics within the estuary varied depending on proximity to the tidal inlet, with sites close to the inlet showing a strong tidal signal, and the ones near the control gates showing a decreased tidal influence and an increased response to freshwater inflows during flood tide when the control gates were open. Surface currents were influenced by strong winds during storm events and dictated the mixing (stratification) in the mid and upper shallow estuary. However, it was difficult to assess the significance of these changes in relation to the community aspirations for the re-diversion and estuarine restoration as there were insufficient quantitative or qualitative targets defined.
To complement the field observations and better evaluate the impact of alternative restoration options, a 2D numerical model of the estuary was developed using Delft3D. After successfully being calibrated and validated, Delft3D-FLOW and PART were used to simulate different scenarios to assess the flow regime and flushing ability of the estuary. The scenarios included Stage 1 re-diversion, river inflow flow without control gates; and a pulsed flood flow using control gates that imitated natural flood events. Particle tracking was used determine the residence time across the estuary, and assess within which zones decay rate changed with tidal fluctuations, and which zones were sheltered from the tidal fluctuations. Model results showed that the pulsed flood scenario created the optimal conditions for sediment transport, increased flushing ability, and reduced salinity throughout the estuary. The model results also highlighted differences in how various zones in the estuary responded to the added freshwater flow, further emphasising the need to monitor them separately with an improved monitoring framework.
The results of this study have led to a better understanding of the impact of added freshwater flow on estuarine hydrodynamics and water quality: specifically how the river input moves the boundaries of fluvially or tidally dominated, and mixing zones. The most vulnerable zones in terms of the flushing ability under different scenarios of freshwater restoration were also identified. This study also highlighted the importance of setting tangible targets in the restoration scheme in alignment with the environmental uncertainties such as the average river flow and limitations due to flooding issues in the upper catchment.

year: 2023