title: Large scale K-means clustering using GPUs

authors: Li, Mi

subjects: k-means

abstract: The k-means algorithm is widely used for clustering, compressing, and summarizing vector data. We present a fast and memory-efficient GPU-based algorithm for exact k-means, Asynchronous Selective Batched K-means (ASB K-means). Unlike most GPU-based k-means algorithms that require loading the whole dataset onto the GPU for clustering, the amount of GPU memory required to run our algorithm can be chosen to be much smaller than the size of the whole dataset. Thus, our algorithm can cluster datasets whose size exceeds the available GPU memory. The algorithm works in a batched fashion and applies the triangle inequality in each k-means iteration to omit a data point if its membership assignment, i.e., the cluster it belongs to, remains unchanged, thus significantly reducing the number of data points that need to be transferred between the CPU’s RAM and the GPU’s global memory and enabling the algorithm to very efficiently process large datasets. Our algorithm can be substantially faster than a GPU-based implementation of standard k-means even in situations when application of the standard algorithm is feasible because the whole dataset fits into GPU memory. Experiments show that ASB K-means can run up to 15x times faster than a standard GPU-based implementation of k-means, and it also outperforms the GPU-based k-means implementation in NVIDIA’s open-source RAPIDS machine learning library on all the datasets used in our experiments.

text: Large scale K-means clustering using GPUs The k-means algorithm is widely used for clustering, compressing, and summarizing vector data. We present a fast and memory-efficient GPU-based algorithm for exact k-means, Asynchronous Selective Batched K-means (ASB K-means). Unlike most GPU-based k-means algorithms that require loading the whole dataset onto the GPU for clustering, the amount of GPU memory required to run our algorithm can be chosen to be much smaller than the size of the whole dataset. Thus, our algorithm can cluster datasets whose size exceeds the available GPU memory. The algorithm works in a batched fashion and applies the triangle inequality in each k-means iteration to omit a data point if its membership assignment, i.e., the cluster it belongs to, remains unchanged, thus significantly reducing the number of data points that need to be transferred between the CPU’s RAM and the GPU’s global memory and enabling the algorithm to very efficiently process large datasets. Our algorithm can be substantially faster than a GPU-based implementation of standard k-means even in situations when application of the standard algorithm is feasible because the whole dataset fits into GPU memory. Experiments show that ASB K-means can run up to 15x times faster than a standard GPU-based implementation of k-means, and it also outperforms the GPU-based k-means implementation in NVIDIA’s open-source RAPIDS machine learning library on all the datasets used in our experiments.

year: 2022

title: Nitrogen-15 isotope enrichment in benthic boundary layer gases of a stratified eutrophic iron and manganese rich lake

authors: Pearson, Lisa Kyle

subjects: nitrogen isotope

abstract: The applicability of the natural abundance of nitrogen gas isotope ratios was used to indicate the spatial distribution of nitrogen transformations in the water column and sediment pore waters of Lake Ngapouri, a small (area 0.19 km²), monomictic, eutrophic lake in the Taupo Volcanic Zone, North Island, New Zealand. Samples were collected from the epilimnion, hypolimnion, benthic boundary layer and at 5-cm intervals from the sediment pore waters at monthly intervals for 1 year. Values of δ¹⁵N [N2] ranged from -1 to 0.28%₀in the epilimnion, -1.5 to 1.25%₀ in the hypolimnion, -1.8 to 12.2%₀ in the benthic boundary layer and -0.7 to 3.5% in sediment pore waters. Values of δ¹⁵ [N₂] showed a strong seasonal pattern that was related to the loss of dissolved oxygen in the hypolimnion during seasonal stratification. Increases in 15N-enriched dinitrogen take place in the benthic boundary layer during the periods of anoxia (taken to be dissolved oxygen concentrations <6.3 µM) and may be related to abundant ammonium substrate (up to 275 µM) to support denitrification. Nitrate concentrations increased up to 36 µM with increasing duration of anoxia. We hypothesise that an alternative electron acceptor besides oxygen is required to support the nitrification needed for the production of nitrate. Iron and manganese hydroxides and oxides from material sedimenting out of the water column may have induced chemo-nitrification sufficient to oxidise ammonium in the anoxic benthic boundary layer. The nitrate formed would mostly be rapidly denitrified so that the δ¹⁵N[N₂] would continue to become enriched during the presence of anoxia, as observed in hypolimnion and benthic boundary layer of Lake Ngapouri. The changes in δ¹⁵N [N₂] values indicate the potential use of isotope ratios to identify and quantify potential chemonitrification/denitrification in the water column and sediment pore waters of lakes.

text: Nitrogen-15 isotope enrichment in benthic boundary layer gases of a stratified eutrophic iron and manganese rich lake The applicability of the natural abundance of nitrogen gas isotope ratios was used to indicate the spatial distribution of nitrogen transformations in the water column and sediment pore waters of Lake Ngapouri, a small (area 0.19 km²), monomictic, eutrophic lake in the Taupo Volcanic Zone, North Island, New Zealand. Samples were collected from the epilimnion, hypolimnion, benthic boundary layer and at 5-cm intervals from the sediment pore waters at monthly intervals for 1 year. Values of δ¹⁵N [N2] ranged from -1 to 0.28%₀in the epilimnion, -1.5 to 1.25%₀ in the hypolimnion, -1.8 to 12.2%₀ in the benthic boundary layer and -0.7 to 3.5% in sediment pore waters. Values of δ¹⁵ [N₂] showed a strong seasonal pattern that was related to the loss of dissolved oxygen in the hypolimnion during seasonal stratification. Increases in 15N-enriched dinitrogen take place in the benthic boundary layer during the periods of anoxia (taken to be dissolved oxygen concentrations <6.3 µM) and may be related to abundant ammonium substrate (up to 275 µM) to support denitrification. Nitrate concentrations increased up to 36 µM with increasing duration of anoxia. We hypothesise that an alternative electron acceptor besides oxygen is required to support the nitrification needed for the production of nitrate. Iron and manganese hydroxides and oxides from material sedimenting out of the water column may have induced chemo-nitrification sufficient to oxidise ammonium in the anoxic benthic boundary layer. The nitrate formed would mostly be rapidly denitrified so that the δ¹⁵N[N₂] would continue to become enriched during the presence of anoxia, as observed in hypolimnion and benthic boundary layer of Lake Ngapouri. The changes in δ¹⁵N [N₂] values indicate the potential use of isotope ratios to identify and quantify potential chemonitrification/denitrification in the water column and sediment pore waters of lakes.

year: 2012

title: Medications and meanings in Maori households with chronic illnesses

authors: Carlson, Teah

subjects: medications

abstract: Domestic spaces have always featured as sites for health care. The home is increasingly referred to as a new therapeutic space within which chronic illnesses are managed within everyday life. This research explores the meanings and use of medications within four Māori households containing at least one chronically ill householder. A broad ethnographic approach was used to capture popular understandings and medication use in daily life. Multiple methods were used, including group discussions with household members, individual interviews, household mapping, and photographic and diary elicitation tasks. Findings shed light on the sources and uses of medications, householder knowledge of medications, communal practices of sharing, caring, rationalising use, grappling with side-effects and the management of illness. I consider what it means for householders to take medications themselves or give these to others, and the care-giving practices that feature in the everyday consumption of medicines. The research is based on the premise that medications are material objects with therapeutic uses that enter into and take on meaning within people’s lives. Medications become culturally embedded phenomena that carry meanings and shape social relationships and practices with Māori households. As such, medications were used in a way that reflected the cultural values and bonds within the households. Within household relationships, medications were invested within meaning to show aroha, support and care. Within a Māori whānau context, the values of maanakitanga, rangatiratanga, and whanaungatanga were recognised as having an integral role in understanding the social practices with medications in each household.

text: Medications and meanings in Maori households with chronic illnesses Domestic spaces have always featured as sites for health care. The home is increasingly referred to as a new therapeutic space within which chronic illnesses are managed within everyday life. This research explores the meanings and use of medications within four Māori households containing at least one chronically ill householder. A broad ethnographic approach was used to capture popular understandings and medication use in daily life. Multiple methods were used, including group discussions with household members, individual interviews, household mapping, and photographic and diary elicitation tasks. Findings shed light on the sources and uses of medications, householder knowledge of medications, communal practices of sharing, caring, rationalising use, grappling with side-effects and the management of illness. I consider what it means for householders to take medications themselves or give these to others, and the care-giving practices that feature in the everyday consumption of medicines. The research is based on the premise that medications are material objects with therapeutic uses that enter into and take on meaning within people’s lives. Medications become culturally embedded phenomena that carry meanings and shape social relationships and practices with Māori households. As such, medications were used in a way that reflected the cultural values and bonds within the households. Within household relationships, medications were invested within meaning to show aroha, support and care. Within a Māori whānau context, the values of maanakitanga, rangatiratanga, and whanaungatanga were recognised as having an integral role in understanding the social practices with medications in each household.

year: 2010