title: Improving on bagging with input smearing

authors: Frank, Eibe

subjects: computer science

abstract: Bagging is an ensemble learning method that has proved to be a useful tool in the arsenal of machine learning practitioners. Commonly applied in conjunction with decision tree learners to build an ensemble of decision trees, it often leads to reduced errors in the predictions when compared to using a single tree. A single tree is built from a training set of size N. Bagging is based on the idea that, ideally, we would like to eliminate the variance due to a particular training set by combining trees built from all training sets of size N. However, in practice, only one training set is available, and bagging simulates this platonic method by sampling with replacement from the original training data to form new training sets. In this paper we pursue the idea of sampling from a kernel density estimator of the underlying distribution to form new training sets, in addition to sampling from the data itself. This can be viewed as “smearing out” the resampled training data to generate new datasets, and the amount of “smear” is controlled by a parameter. We show that the resulting method, called “input smearing”, can lead to improved results when compared to bagging. We present results for both classification and regression problems.

text: Improving on bagging with input smearing Bagging is an ensemble learning method that has proved to be a useful tool in the arsenal of machine learning practitioners. Commonly applied in conjunction with decision tree learners to build an ensemble of decision trees, it often leads to reduced errors in the predictions when compared to using a single tree. A single tree is built from a training set of size N. Bagging is based on the idea that, ideally, we would like to eliminate the variance due to a particular training set by combining trees built from all training sets of size N. However, in practice, only one training set is available, and bagging simulates this platonic method by sampling with replacement from the original training data to form new training sets. In this paper we pursue the idea of sampling from a kernel density estimator of the underlying distribution to form new training sets, in addition to sampling from the data itself. This can be viewed as “smearing out” the resampled training data to generate new datasets, and the amount of “smear” is controlled by a parameter. We show that the resulting method, called “input smearing”, can lead to improved results when compared to bagging. We present results for both classification and regression problems.

year: 2006

title: New Zealand seagrass (Zostera muelleri) response to acute sedimentation: Linking non-structural carbohydrate reserves to resilience

authors: Soerensen, Stine Tang

subjects: seagrass

abstract: Seagrass meadows form healthy near-coastal marine environments that provide a wide range of ecosystem services in New Zealand and Australia. However, seagrass habitats are declining regionally and globally. It is therefore essential that research fills the current knowledge gaps associated with seagrass disturbance-response regimes and develops standardised methods to measure seagrass health and resilience. Sedimentation associated with increased human activity is a major environmental stressor to seagrass; yet little is known about how sedimentation affects New Zealand’s only seagrass species, Zostera muelleri. This thesis, therefore explores how Z. muelleri responds to catastrophic burial (acute) events in Tauranga Harbour, New Zealand. 

Non-structural carbohydrates (NSC) are synthesised and stored in seagrass tissues when photosynthetic outputs exceed metabolic demands and, in turn, are mobilised when photosynthesis is unable to meet metabolic demands. Hence, NSC reserves can be used to measure the impact of a disturbance and/or the resilience of seagrass. A literature review in Chapter 2 illustrates that multiple methods are used to estimate NSC reserves. Experimental comparisons of a selection of these methods demonstrate that NSC estimates by different analytical methods cannot be compared. The outcome of Chapter 2 is the development of a 5-step standard analytical protocol for the quantitation of NSC reserves in seagrass (specifically Z. muelleri). The implementation of a standardised protocol will enable researchers to compare and synthesise results and, thus, increase the application of NSC as a seagrass health measure. 

Chapter 3 investigates the effects of acute sedimentation (i.e. burial) on Z. muelleri. In situ manipulative experiments across three sites in Tauranga Harbour, New Zealand were used to assess the spatial variation in resilience (i.e. resistance and recovery) to burial. Resistance and recovery following burial varied significantly between the three distinct morphotypes that existed in the three sites; a large, a small and an intermediate morphotype that overlapped with the small and the large morphotypes. These morphometric differences were believed to be phenotypic responses to site-specific environmental conditions. Having a large morphotype maximises the potential to capture light and store reserves and presumably an acclimation of Z. muelleri existing in a chronically impacted environment (high sediment mud/organic matter (SOM) and low sediment grain size). The largest seagrass displayed high resistance to both single and repeated burial events of 2 cm (no significant effects). In contrast, the smaller seagrass had low resistance and the slowest ability to recover following burial (up to 251 days), whereas, the intermediate morphotype displayed a faster ability to recover (up to 168 days). Results, therefore, suggest that the resilience to burial events increases in populations that have acclimated to a chronically impacted environment. It is, however, noted that a degraded environment will eventually reach a limiting threshold from which recovery is not plausible and results should therefore be interpreted with some caution. 

While rhizome NSC reserves were not affected by burial treatments, these varied significantly throughout a full growing year across the three locations. NSC reserves were at the lowest levels in winter and spring, consistent with seasonal trends. Sucrose levels at the peak of the growing season (February) were significantly related to relative shoot cover the following winter (r² = 0.54, P < .001) and spring (r² = 0.66, P < .001). As such, chapter 3 also documented a link between seagrass cover and sucrose reserves.

Estimates of NSC reserves from the literature vary greatly, presumably due to the wide variety of analytical methods used. Chapter 4 explores the variability of Z. muelleri NSC reserves and the specific partitioning of carbohydrate groups (sucrose and starch) across different spatial scales (within meadow, between sites, between regions), including temperate (Port Phillip Bay) and tropical populations (Townville and Magnetic Island) in Australia. When measured in spring, the total NSC reserves were similar across all spatial scales (193.59 ± 10.88 mg g⁻¹ DW); however, the proportional contents of sucrose and starch varied significantly at different spatial scales. Sucrose contents varied at site level and were best explained by a combination of sediment pH and aboveground to belowground biomass ratio (r² = 0.49, P <0.001). Starch contents varied between regions, with seagrass in the tropical Townsville containing significantly higher starch levels and as such lower sucrose to starch ratios. The best model for starch included only one variable; sediment surface temperature (r² = 0.33, P < 0.001) and results therefore suggest that starch is influenced by large-scale processes linked to climatic processes. The adaptive strategies of seagrass to moderate NSC allocation appear to be of particular importance to seagrass’ ability to acclimate to a diverse range of environments. 

Chapter 5 synthesises the results of the three research chapters and provides recommendations for best practices. Of particular importance, is the method that was developed to ensure accurate measurements of NSC reserves in seagrasses, allowing this measure to be used as a monitoring tool of potential resilience and health of seagrass meadows. This thesis clearly illustrates that the partitioning of NSC groups (sucrose/starch) vary spatially and temporally and that these are influenced by distinct processes. Furthermore, it demonstrates that the phenotypic plasticity of Z. muelleri in New Zealand enhances their resilience to acute sedimentation events (i.e. burial). It is therefore suggested that the timing and location of human-induced disturbances (i.e. catchment developments, dredging of harbours and ports) should match optimum seagrass resilience (e.g., high sucrose reserves and consideration of phenotypic expression), as this is likely to increase the survival rates of the impacted seagrass meadows. The new insights gained from this research provides crucial information to ensure sustainable management of Z. muelleri into the future.

text: New Zealand seagrass (Zostera muelleri) response to acute sedimentation: Linking non-structural carbohydrate reserves to resilience Seagrass meadows form healthy near-coastal marine environments that provide a wide range of ecosystem services in New Zealand and Australia. However, seagrass habitats are declining regionally and globally. It is therefore essential that research fills the current knowledge gaps associated with seagrass disturbance-response regimes and develops standardised methods to measure seagrass health and resilience. Sedimentation associated with increased human activity is a major environmental stressor to seagrass; yet little is known about how sedimentation affects New Zealand’s only seagrass species, Zostera muelleri. This thesis, therefore explores how Z. muelleri responds to catastrophic burial (acute) events in Tauranga Harbour, New Zealand. 

Non-structural carbohydrates (NSC) are synthesised and stored in seagrass tissues when photosynthetic outputs exceed metabolic demands and, in turn, are mobilised when photosynthesis is unable to meet metabolic demands. Hence, NSC reserves can be used to measure the impact of a disturbance and/or the resilience of seagrass. A literature review in Chapter 2 illustrates that multiple methods are used to estimate NSC reserves. Experimental comparisons of a selection of these methods demonstrate that NSC estimates by different analytical methods cannot be compared. The outcome of Chapter 2 is the development of a 5-step standard analytical protocol for the quantitation of NSC reserves in seagrass (specifically Z. muelleri). The implementation of a standardised protocol will enable researchers to compare and synthesise results and, thus, increase the application of NSC as a seagrass health measure. 

Chapter 3 investigates the effects of acute sedimentation (i.e. burial) on Z. muelleri. In situ manipulative experiments across three sites in Tauranga Harbour, New Zealand were used to assess the spatial variation in resilience (i.e. resistance and recovery) to burial. Resistance and recovery following burial varied significantly between the three distinct morphotypes that existed in the three sites; a large, a small and an intermediate morphotype that overlapped with the small and the large morphotypes. These morphometric differences were believed to be phenotypic responses to site-specific environmental conditions. Having a large morphotype maximises the potential to capture light and store reserves and presumably an acclimation of Z. muelleri existing in a chronically impacted environment (high sediment mud/organic matter (SOM) and low sediment grain size). The largest seagrass displayed high resistance to both single and repeated burial events of 2 cm (no significant effects). In contrast, the smaller seagrass had low resistance and the slowest ability to recover following burial (up to 251 days), whereas, the intermediate morphotype displayed a faster ability to recover (up to 168 days). Results, therefore, suggest that the resilience to burial events increases in populations that have acclimated to a chronically impacted environment. It is, however, noted that a degraded environment will eventually reach a limiting threshold from which recovery is not plausible and results should therefore be interpreted with some caution. 

While rhizome NSC reserves were not affected by burial treatments, these varied significantly throughout a full growing year across the three locations. NSC reserves were at the lowest levels in winter and spring, consistent with seasonal trends. Sucrose levels at the peak of the growing season (February) were significantly related to relative shoot cover the following winter (r² = 0.54, P < .001) and spring (r² = 0.66, P < .001). As such, chapter 3 also documented a link between seagrass cover and sucrose reserves.

Estimates of NSC reserves from the literature vary greatly, presumably due to the wide variety of analytical methods used. Chapter 4 explores the variability of Z. muelleri NSC reserves and the specific partitioning of carbohydrate groups (sucrose and starch) across different spatial scales (within meadow, between sites, between regions), including temperate (Port Phillip Bay) and tropical populations (Townville and Magnetic Island) in Australia. When measured in spring, the total NSC reserves were similar across all spatial scales (193.59 ± 10.88 mg g⁻¹ DW); however, the proportional contents of sucrose and starch varied significantly at different spatial scales. Sucrose contents varied at site level and were best explained by a combination of sediment pH and aboveground to belowground biomass ratio (r² = 0.49, P <0.001). Starch contents varied between regions, with seagrass in the tropical Townsville containing significantly higher starch levels and as such lower sucrose to starch ratios. The best model for starch included only one variable; sediment surface temperature (r² = 0.33, P < 0.001) and results therefore suggest that starch is influenced by large-scale processes linked to climatic processes. The adaptive strategies of seagrass to moderate NSC allocation appear to be of particular importance to seagrass’ ability to acclimate to a diverse range of environments. 

Chapter 5 synthesises the results of the three research chapters and provides recommendations for best practices. Of particular importance, is the method that was developed to ensure accurate measurements of NSC reserves in seagrasses, allowing this measure to be used as a monitoring tool of potential resilience and health of seagrass meadows. This thesis clearly illustrates that the partitioning of NSC groups (sucrose/starch) vary spatially and temporally and that these are influenced by distinct processes. Furthermore, it demonstrates that the phenotypic plasticity of Z. muelleri in New Zealand enhances their resilience to acute sedimentation events (i.e. burial). It is therefore suggested that the timing and location of human-induced disturbances (i.e. catchment developments, dredging of harbours and ports) should match optimum seagrass resilience (e.g., high sucrose reserves and consideration of phenotypic expression), as this is likely to increase the survival rates of the impacted seagrass meadows. The new insights gained from this research provides crucial information to ensure sustainable management of Z. muelleri into the future.

year: 2020

title: Aihe Pepene

authors: Hart, Philip

abstract: Sharing the same illustrious whakapapa as his brother Reha Aperahama, Aihe Pepene was prominent when living in the Thames district before settling at Te Aroha in 1878. When speculators tried to acquire the Thames foreshore from Pepene and others in 1870, he became involved in the subsequent legal actions over unpaid promissory notes. Later he would acquire interests in many blocks of land, and received a steady income by leasing or selling these plus his share in the goldfields revenue. When the Aroha Block was considered by the land court for the last time, in 1878, he conducted the case for Ngati Rahiri.
He invested in four Hauraki goldfields, and was briefly an owner and skipper of two small river steamers, an unsuccessful endeavour that resulted in his being forced to sell more land to meet his debts. Once his 1880 and 1881 financial difficulties were resolved, no more such problems recurred. 
A leading rangatira in Hauraki generally as well as at Te Aroha, he would be elected to a Maori Committee that was soon revealed to have no significance. Closely involved with Pakeha, he assisted settlement, and his loyalty to the Crown was illustrated by his becoming an officer in the Thames Native Volunteer Corps. A member of the Church of England for many years, like many Maori he became a Mormon, a faith perhaps more appropriate to his private life, for he had more than one wife, notoriously eloping with the wife of a more senior rangatira despite already being married.

text: Aihe Pepene Sharing the same illustrious whakapapa as his brother Reha Aperahama, Aihe Pepene was prominent when living in the Thames district before settling at Te Aroha in 1878. When speculators tried to acquire the Thames foreshore from Pepene and others in 1870, he became involved in the subsequent legal actions over unpaid promissory notes. Later he would acquire interests in many blocks of land, and received a steady income by leasing or selling these plus his share in the goldfields revenue. When the Aroha Block was considered by the land court for the last time, in 1878, he conducted the case for Ngati Rahiri.
He invested in four Hauraki goldfields, and was briefly an owner and skipper of two small river steamers, an unsuccessful endeavour that resulted in his being forced to sell more land to meet his debts. Once his 1880 and 1881 financial difficulties were resolved, no more such problems recurred. 
A leading rangatira in Hauraki generally as well as at Te Aroha, he would be elected to a Maori Committee that was soon revealed to have no significance. Closely involved with Pakeha, he assisted settlement, and his loyalty to the Crown was illustrated by his becoming an officer in the Thames Native Volunteer Corps. A member of the Church of England for many years, like many Maori he became a Mormon, a faith perhaps more appropriate to his private life, for he had more than one wife, notoriously eloping with the wife of a more senior rangatira despite already being married.

year: 2016