Predicting water quality and ecological responses

Abstract Changes to climate are predicted to have effects on freshwater streams. Stream flows are likely to change, with implications for freshwater ecosystems and water quality. Other stressors such as population growth, community preferences and management policies can be expected to interact in various ways with climate change and stream flows, and outcomes for freshwater ecosystems and water quality are uncertain. Managers of freshwater ecosystems and water supplies could benefit from being able to predict the scales of likely changes. This project has developed and applied a linked modelling framework to assess climate change impacts on water quality regimes and ecological responses. The framework is designed to inform water planning and climate adaptation activities. It integrates quantitative tools, and predicts relationships between future climate, human activities, water quality and ecology, thereby filling a gap left by the considerable research effort so far invested in predicting stream flows. The modelling framework allows managers to explore potential changes in the water quality and ecology of freshwater systems in response to plausible scenarios for climate change and management adaptations. Although set up for the Upper Murrumbidgee River catchment in southern NSW and ACT, the framework was planned to be transferable to other regions where suitable data are available. The approach and learning from the project appear to have the potential to be broadly applicable. We selected six climate scenarios representing minor, moderate and major changes in flow characteristics for 1oC and 2oC temperature increases. These were combined with four plausible alternative management adaptations that might be used to modify water supply, urban water demand and stream flow regimes in the Upper Murrumbidgee catchment. The Bayesian Network (BN) model structure we used was developed using both a ‘top down’ and ‘bottom up’ approach. From analyses combined with expert advice, we identified the causal structure linking climate variables to stream flow, water quality attributes, land management and ecological responses (top down). The ‘bottom up’ approach focused on key ecological outcomes and key drivers, and helped produce efficient models. The result was six models for macroinvertebrates, and one for fish. In the macroinvertebrate BN models, nodes were discretised using statistical/empirical derived thresholds using new techniques. The framework made it possible to explore how ecological communities respond to changes in climate and management activities. Particularly, we focused on the effects of water quality and quantity on ecological responses. The models showed a strong regional response reflecting differences across 18 regions in the catchment. In two regions the management alternatives were predicted to have stronger effects than climate change. In three other regions the predicted response to climate change was stronger. Analyses of water quality suggested minor changes in the probability of water quality exceeding thresholds designed to protect aquatic ecosystems. The ‘bottom up’ approach limited the framework’s transferability by being specific to the Upper Murrumbidgee catchment data. Indeed, to meet stakeholder questions models need to be specifically tailored. Therefore the report proposes a general model-building framework for transferring the approach, rather than the models, to other regions.  Please cite this report as: Dyer, F, El Sawah, S, Lucena-Moya, P, Harrison, E, Croke, B, Tschierschke, A, Griffiths, R, Brawata, R, Kath, J, Reynoldson, T, Jakeman, T 2013 Predicting water quality and ecological responses, National Climate Change Adaptation Research Facility, Gold Coast, pp. 110 Changes to climate are predicted to have effects on freshwater streams. Stream flows are likely to change, with implications for freshwater ecosystems and water quality. Other stressors such as population growth, community preferences and management policies can be expected to interact in various ways with climate change and stream flows, and outcomes for freshwater ecosystems and water quality are uncertain. Managers of freshwater ecosystems and water supplies could benefit from being able to predict the scales of likely changes. This project has developed and applied a linked modelling framework to assess climate change impacts on water quality regimes and ecological responses. The framework is designed to inform water planning and climate adaptation activities. It integrates quantitative tools, and predicts relationships between future climate, human activities, water quality and ecology, thereby filling a gap left by the considerable research effort so far invested in predicting stream flows. The modelling framework allows managers to explore potential changes in the water quality and ecology of freshwater systems in response to plausible scenarios for climate change and management adaptations. Although set up for the Upper Murrumbidgee River catchment in southern NSW and ACT, the framework was planned to be transferable to other regions where suitable data are available. The approach and learning from the project appear to have the potential to be broadly applicable. We selected six climate scenarios representing minor, moderate and major changes in flow characteristics for 1oC and 2oC temperature increases. These were combined with four plausible alternative management adaptations that might be used to modify water supply, urban water demand and stream flow regimes in the Upper Murrumbidgee catchment. The Bayesian Network (BN) model structure we used was developed using both a ‘top down’ and ‘bottom up’ approach. From analyses combined with expert advice, we identified the causal structure linking climate variables to stream flow, water quality attributes, land management and ecological responses (top down). The ‘bottom up’ approach focused on key ecological outcomes and key drivers, and helped produce efficient models. The result was six models for macroinvertebrates, and one for fish. In the macroinvertebrate BN models, nodes were discretised using statistical/empirical derived thresholds using new techniques. The framework made it possible to explore how ecological communities respond to changes in climate and management activities. Particularly, we focused on the effects of water quality and quantity on ecological responses. The models showed a strong regional response reflecting differences across 18 regions in the catchment. In two regions the management alternatives were predicted to have stronger effects than climate change. In three other regions the predicted response to climate change was stronger. Analyses of water quality suggested minor changes in the probability of water quality exceeding thresholds designed to protect aquatic ecosystems. The ‘bottom up’ approach limited the framework’s transferability by being specific to the Upper Murrumbidgee catchment data. Indeed, to meet stakeholder questions models need to be specifically tailored. Therefore the report proposes a general model-building framework for transferring the approach, rather than the models, to other regions.&nbsp

An improved randomization of a multi-blocking jpeg based steganographic system.

Thesis (M.Sc.)-University of KwaZulu-Natal, Durban, 2010.Steganography is classified as the art of hiding information. In a digital context, this refers to our ability to hide secret messages within innocent digital cover data. The digital domain offers many opportunities for possible cover mediums, such as cloud based hiding (saving secret information within the internet and its structure), image based hiding, video and audio based hiding, text based documents as well as the potential of hiding within any set of compressed data. This dissertation focuses on the image based domain and investigates currently available image based steganographic techniques. After a review of the history of the field, and a detailed survey of currently available JPEG based steganographic systems, the thesis focuses on the systems currently considered to be secure and introduces mechanisms that have been developed to detect them. The dissertation presents a newly developed system that is designed to counter act the current weakness in the YASS JPEG based steganographic system. By introducing two new levels of randomization to the embedding process, the proposed system offers security benefits over YASS. The introduction of randomization to the B‐block sizes as well as the E‐block sizes used in the embedding process aids in increasing security and the potential for new, larger E‐block sizes also aids in providing an increased set of candidate coefficients to be used for embedding. The dissertation also introduces a new embedding scheme which focuses on hiding in medium frequency coefficients. By hiding in these medium frequency coefficients, we allow for more aggressive embedding without risking more visual distortion but trade this off with a risk of higher error rates due to compression losses. Finally, the dissertation presents simulation aimed at testing the proposed system performance compared to other JPEG based steganographic systems with similar embedding properties. We show that the new system achieves an embedding capacity of 1.6, which represents round a 7 times improvement over YASS. We also show that the new system, although introducing more bits in error per B‐block, successfully allows for the embedding of up to 2 bits per B‐block more than YASS at a similar error rate per B‐block. We conclude the results by demonstrating the new systems ability to resist detection both through human observation, via a survey, as well as resist computer aided analysis

Statistical Machine Learning & Deep Neural Networks Applied to Neural Data Analysis

Computational neuroscience seeks to discover the underlying mechanisms by which neural activity is generated. With the recent advancement in neural data acquisition methods, the bottleneck of this pursuit is the analysis of ever-growing volume of neural data acquired in numerous labs from various experiments. These analyses can be broadly divided into two categories. First, extraction of high quality neuronal signals from noisy large scale recordings. Second, inference for statistical models aimed at explaining the neuronal signals and underlying processes that give rise to them. Conventionally, majority of the methodologies employed for this effort are based on statistics and signal processing. However, in recent years recruiting Artificial Neural Networks (ANN) for neural data analysis is gaining traction. This is due to their immense success in computer vision and natural language processing, and the stellar track record of ANN architectures generalizing to a wide variety of problems. In this work we investigate and improve upon statistical and ANN machine learning methods applied to multi-electrode array recordings and inference for dynamical systems that play critical roles in computational neuroscience. In the first and second part of this thesis, we focus on spike sorting problem. The analysis of large-scale multi-neuronal spike train data is crucial for current and future of neuroscience research. However, this type of data is not available directly from recordings and require further processing to be converted into spike trains. Dense multi-electrode arrays (MEA) are standard methods for collecting such recordings. The processing needed to extract spike trains from these raw electrical signals is carried out by ``spike sorting'' algorithms. We introduce a robust and scalable MEA spike sorting pipeline YASS (Yet Another Spike Sorter) to address many challenges that are inherent to this task. We primarily pay attention to MEA data collected from the primate retina for important reasons such as the unique challenges and available side information that ultimately assist us in scoring different spike sorting pipelines. We also introduce a Neural Network architecture and an accompanying training scheme specifically devised to address the challenging task of deconvolution in MEA recordings. In the last part, we shift our attention to inference for non-linear dynamics. Dynamical systems are the governing force behind many real world phenomena and temporally correlated data. Recently, a number of neural network architectures have been proposed to address inference for nonlinear dynamical systems. We introduce two different methods based on normalizing flows for posterior inference in latent non-linear dynamical systems. We also present gradient-based amortized posterior inference approaches using the auto-encoding variational Bayes framework that can be applied to a wide range of generative models with nonlinear dynamics. We call our method (FNF). FNF performs favorably against state-of-the-art inference methods in terms of accuracy of predictions and quality of uncovered codes and dynamics on synthetic data