The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

SEI+II Information Integration Through Events

Many environmental observations are collected at different space and time scales that preclude easy integration of the data and hinder broader understanding of ecosystem dynamics. Ocean Observing Systems provide a specific example of multi-sensor systems observing several variables in different space - time regimes. This project integrates diverse space-time environmental sensor streams based on the conversion of their information content to a common higher-level abstraction: a space-time event data type. The space-time event data type normalizes across the diversity of observation level data to produce a common data type for exploration and analysis. Gulf of Maine Ocean Observing System (GOMOOS) data provide the multivariate time and space-time series from which space-time events are detected and assembled. Event detection employs a combined top down-bottom up approach. The top down component specifies an event ontology while the bottom up component is based on extraction of primitive events (e.g. decreasing, increasing, local maxima and minima sequences) from time and space-time series. Exploration and analysis of the extracted events employs a graphic exploratory environment based on a graphic primitive called an event band and its composition into event band stacks and panels that support investigation of various space-time patterns.The project contributes a new information integration approach based on the concept of an event that can be extended to many domains including socio-economic, financial, legislative, surveillance and health related information. The project will contribute new data mining strategies for event detection in time and space-time series and a set of flexible exploratory tools for examination and development of hypotheses on space-time event patterns and interactions

The impact of agricultural activities on water quality: a case for collaborative catchment-scale management using integrated wireless sensor networks

The challenge of improving water quality is a growing global concern, typified by the European Commission Water Framework Directive and the United States Clean Water Act. The main drivers of poor water quality are economics, poor water management, agricultural practices and urban development. This paper reviews the extensive role of non-point sources, in particular the outdated agricultural practices, with respect to nutrient and contaminant contributions. Water quality monitoring (WQM) is currently undertaken through a number of data acquisition methods from grab sampling to satellite based remote sensing of water bodies. Based on the surveyed sampling methods and their numerous limitations, it is proposed that wireless sensor networks (WSNs), despite their own limitations, are still very attractive and effective for real-time spatio-temporal data collection for WQM applications. WSNs have been employed for WQM of surface and ground water and catchments, and have been fundamental in advancing the knowledge of contaminants trends through their high resolution observations. However, these applications have yet to explore the implementation and impact of this technology for management and control decisions, to minimize and prevent individual stakeholder’s contributions, in an autonomous and dynamic manner. Here, the potential of WSN-controlled agricultural activities and different environmental compartments for integrated water quality management is presented and limitations of WSN in agriculture and WQM are identified. Finally, a case for collaborative networks at catchment scale is proposed for enabling cooperation among individually networked activities/stakeholders (farming activities, water bodies) for integrated water quality monitoring, control and management

Development and Applications of Similarity Measures for Spatial-Temporal Event and Setting Sequences

Similarity or distance measures between data objects are applied frequently in many fields or domains such as geography, environmental science, biology, economics, computer science, linguistics, logic, business analytics, and statistics, among others. One area where similarity measures are particularly important is in the analysis of spatiotemporal event sequences and associated environs or settings. This dissertation focuses on developing a framework of modeling, representation, and new similarity measure construction for sequences of spatiotemporal events and corresponding settings, which can be applied to different event data types and used in different areas of data science. The first core part of this dissertation presents a matrix-based spatiotemporal event sequence representation that unifies punctual and interval-based representation of events. This framework supports different event data types and provides support for data mining and sequence classification and clustering. The similarity measure is based on the modified Jaccard index with temporal order constraints and accommodates different event data types. This approach is demonstrated through simulated data examples and the performance of the similarity measures is evaluated with a k-nearest neighbor algorithm (k-NN) classification test on synthetic datasets. These similarity measures are incorporated into a clustering method and successfully demonstrate the usefulness in a case study analysis of event sequences extracted from space time series of a water quality monitoring system. This dissertation further proposes a new similarity measure for event setting sequences, which involve the space and time in which events occur. While similarity measures for spatiotemporal event sequences have been studied, the settings and setting sequences have not yet been considered. While modeling event setting sequences, spatial and temporal scales are considered to define the bounds of the setting and incorporate dynamic variables along with static variables. Using a matrix-based representation and an extended Jaccard index, new similarity measures are developed to allow for the use of all variable data types. With these similarity measures coupled with other multivariate statistical analysis approaches, results from a case study involving setting sequences and pollution event sequences associated with the same monitoring stations, support the hypothesis that more similar spatial-temporal settings or setting sequences may generate more similar events or event sequences. To test the scalability of STES similarity measure in a larger dataset and an extended application in different fields, this dissertation compares and contrasts the prospective space-time scan statistic with the STES similarity approach for identifying COVID-19 hotspots. The COVID-19 pandemic has highlighted the importance of detecting hotspots or clusters of COVID-19 to provide decision makers at various levels with better information for managing distribution of human and technical resources as the outbreak in the USA continues to grow. The prospective space-time scan statistic has been used to help identify emerging disease clusters yet results from this approach can encounter strategic limitations imposed by the spatial constraints of the scanning window. The STES-based approach adapted for this pandemic context computes the similarity of evolving normalized COVID-19 daily cases by county and clusters these to identify counties with similarly evolving COVID-19 case histories. This dissertation analyzes the spread of COVID-19 within the continental US through four periods beginning from late January 2020 using the COVID-19 datasets maintained by John Hopkins University, Center for Systems Science and Engineering (CSSE). Results of the two approaches can complement with each other and taken together can aid in tracking the progression of the pandemic. Overall, the dissertation highlights the importance of developing similarity measures for analyzing spatiotemporal event sequences and associated settings, which can be applied to different event data types and used for data mining, sequence classification, and clustering

Robust sound event detection in bioacoustic sensor networks

Bioacoustic sensors, sometimes known as autonomous recording units (ARUs), can record sounds of wildlife over long periods of time in scalable and minimally invasive ways. Deriving per-species abundance estimates from these sensors requires detection, classification, and quantification of animal vocalizations as individual acoustic events. Yet, variability in ambient noise, both over time and across sensors, hinders the reliability of current automated systems for sound event detection (SED), such as convolutional neural networks (CNN) in the time-frequency domain. In this article, we develop, benchmark, and combine several machine listening techniques to improve the generalizability of SED models across heterogeneous acoustic environments. As a case study, we consider the problem of detecting avian flight calls from a ten-hour recording of nocturnal bird migration, recorded by a network of six ARUs in the presence of heterogeneous background noise. Starting from a CNN yielding state-of-the-art accuracy on this task, we introduce two noise adaptation techniques, respectively integrating short-term (60 milliseconds) and long-term (30 minutes) context. First, we apply per-channel energy normalization (PCEN) in the time-frequency domain, which applies short-term automatic gain control to every subband in the mel-frequency spectrogram. Secondly, we replace the last dense layer in the network by a context-adaptive neural network (CA-NN) layer. Combining them yields state-of-the-art results that are unmatched by artificial data augmentation alone. We release a pre-trained version of our best performing system under the name of BirdVoxDetect, a ready-to-use detector of avian flight calls in field recordings.Comment: 32 pages, in English. Submitted to PLOS ONE journal in February 2019; revised August 2019; published October 201

Multi-spatiotemporal analysis of changes in mangrove forests in Palawan, Philippines: predicting future trends using a support vector machine algorithm and the Markov chain model

Multi-temporal remote sensing imagery can be used to explore how mangrove assemblages are changing over time and facilitate critical interventions for ecological sustainability and effective management. This study aims to explore the spatial dynamics of mangrove extents in Palawan, Philippines, specifically in Puerto Princesa City, Taytay and Aborlan, and facilitate future predictions for Palawan using the Markov Chain model. The multi-date Landsat imageries during the period 1988–2020 were used for this research. The support vector machine algorithm was sufficiently effective for mangrove feature extraction to generate satisfactory accuracy results (>70% kappa coefficient values; 91% average overall accuracies). In Palawan, a 5.2% (2693 ha) decrease was recorded during 1988–1998 and an 8.6% increase in 2013–2020 to 4371 ha. In Puerto Princesa City, a 95.9% (2758 ha) increase was observed during 1988–1998 and 2.0% (136 ha) decrease during 2013–2020. The mangroves in Taytay and Aborlan both gained an additional 2138 ha (55.3%) and 228 ha (16.8%) during 1988–1998 but also decreased from 2013 to 2020 by 3.4% (247 ha) and 0.2% (3 ha), respectively. However, projected results suggest that the mangrove areas in Palawan will likely increase in 2030 (to 64,946 ha) and 2050 (to 66,972 ha). This study demonstrated the capability of the Markov chain model in the context of ecological sustainability involving policy intervention. However, as this research did not capture the environmental factors that may have influenced the changes in mangrove patterns, it is suggested adding cellular automata in future Markovian mangrove modelling

Integrating Data Science and Earth Science

This open access book presents the results of three years collaboration between earth scientists and data scientist, in developing and applying data science methods for scientific discovery. The book will be highly beneficial for other researchers at senior and graduate level, interested in applying visual data exploration, computational approaches and scientifc workflows

Spatial-Temporal Data Mining for Ocean Science: Data, Methodologies, and Opportunities

With the increasing amount of spatial-temporal~(ST) ocean data, numerous spatial-temporal data mining (STDM) studies have been conducted to address various oceanic issues, e.g., climate forecasting and disaster warning. Compared with typical ST data (e.g., traffic data), ST ocean data is more complicated with some unique characteristics, e.g., diverse regionality and high sparsity. These characteristics make it difficult to design and train STDM models. Unfortunately, an overview of these studies is still missing, hindering computer scientists to identify the research issues in ocean while discouraging researchers in ocean science from applying advanced STDM techniques. To remedy this situation, we provide a comprehensive survey to summarize existing STDM studies in ocean. Concretely, we first summarize the widely-used ST ocean datasets and identify their unique characteristics. Then, typical ST ocean data quality enhancement techniques are discussed. Next, we classify existing STDM studies for ocean into four types of tasks, i.e., prediction, event detection, pattern mining, and anomaly detection, and elaborate the techniques for these tasks. Finally, promising research opportunities are highlighted. This survey will help scientists from the fields of both computer science and ocean science have a better understanding of the fundamental concepts, key techniques, and open challenges of STDM in ocean