Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the potential advantages of cheaper and increased sampling. An acoustic event detection algorithm is introduced that outputs a compact rectangular marquee description of each event. It can disentangle superimposed events, which are a common occurrence during morning and evening choruses. Next, three uses to which acoustic event detection can be put are illustrated. These tasks have been selected because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are a frequent contaminant of recordings of the terrestrial environment; (2) the detection of bird calls using the spatial distribution of their component events; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle

The calculation of acoustic indices derived from long-duration recordings of the natural environment

The work described in this technical report is part of ongoing research within the QUT Ecoacoustics Research Group to build practical tools for the manipulation, analysis and visualisation of recordings of the natural environment. This report describes methods we use to calculate spectral and summary acoustic indices derived from recordings of the environment. A spectral index is a vector of N values, one for each frequency bin of the spectrogram. A summary index is a scalar value, in some cases derived directly from the waveform envelope and in other cases from the corresponding spectral index

The calculation of acoustic indices to characterise acoustic recordings of the environment

This technical report describes the methods used to obtain a list of acoustic indices that are used to characterise the structure and distribution of acoustic energy in recordings of the natural environment. In particular it describes methods for noise reduction from recordings of the environment and a fast clustering algorithm used to estimate the spectral richness of long recordings

The calculation of acoustic indices to characterise acoustic recordings of the environment

This technical report describes the methods used to obtain a list of acoustic indices that are used to characterise the structure and distribution of acoustic energy in recordings of the natural environment. In particular it describes methods for noise reduction from recordings of the environment and a fast clustering algorithm used to estimate the spectral richness of long recordings

Noise removal from wave-forms and spectrograms derived from natural recordings of the environment

The work described in this technical report is part of an ongoing project to build practical tools for the manipulation, analysis and visualisation of recordings of the natural environment. This report describes the methods we use to remove background noise from spectrograms. It updates techniques previously described in Towsey and Planitz (2011), Technical report: acoustic analysis of the natural environment, downloadable from: http://eprints.qut.edu.au/41131/. It also describes noise removal from wave-forms, a technique not described in the above 2011 technical report

Determining hearing threshold from Brain Stem Evoked Potentials - Optimising a neural network to improve classification performance

Brain Stem Evoked Potentials (BAEPs) are considered the most objective measure currently available with which to determine the functional integrity of the peripheral auditory nervous system. Estimating hearing threshold from BAEP signals is a time consuming and laborious task, and therefore one which recommends itself to automation. In this paper we demonstrate that neural networks trained by back-propagation are an effective method to classify BAEPs. In order to achieve maxumum generalsiation, it was necesary to fine tune the learning parameters. Although this step can be time consuming, it has important clinical consequences

BioPatML : pattern sharing for the genomic sciences

Computational biology increasingly demands the sharing of sophisticated data and annotations between research groups. Web 2.0 style sharing and publication requires that biological systems be described in well-defined, yet flexible and extensible formats which enhance exchange and re-use. In contrast to many of the standards for exchange in the genomic sciences, descriptions of biological sequences show a great diversity in format and function, impeding the definition and exchange of sequence patterns. In this presentation, we introduce BioPatML, an XML-based pattern description language that supports a wide range of patterns and allows the construction of complex, hierarchically structured patterns and pattern libraries. BioPatML unifies the diversity of current pattern description languages and fills a gap in the set of XML-based description languages for biological systems. We discuss the structure and elements of the language, and demonstrate its advantages on a series of applications, showing lightweight integration between the BioPatML parser and search engine, and the SilverGene genome browser. We conclude by describing our site to enable large scale pattern sharing, and our efforts to seed this repository

BioPatML.NET – a bioinformatic pattern search engine

In the present paper, we introduce BioPatML.NET, an application library for the Microsoft Windows .NET framework [2] that implements the BioPatML pattern definition language and sequence search engine. BioPatML.NET is integrated with the Microsoft Biology Foundation (MBF) application library [3], unifying the parsers and annotation services supported or emerging through MBF with the language, search framework and pattern repository of BioPatML. End users who wish to exploit the BioPatML.NET engine and repository without engaging the services of a programmer may do so via the freely accessible web-based BioPatML Editor, which we describe below

Technical report : acoustic analysis of the natural environment

This technical report is concerned with one aspect of environmental monitoring—the detection and analysis of acoustic events in sound recordings of the environment. Sound recordings offer ecologists the advantage of cheaper and increased sampling but make available so much data that automated analysis becomes essential. The report describes a number of tools for automated analysis of recordings, including noise removal from spectrograms, acoustic event detection, event pattern recognition, spectral peak tracking, syntactic pattern recognition applied to call syllables, and oscillation detection. These algorithms are applied to a number of animal call recognition tasks, chosen because they illustrate quite different modes of analysis: (1) the detection of diffuse events caused by wind and rain, which are frequent contaminants of recordings of the terrestrial environment; (2) the detection of bird and calls; and (3) the preparation of acoustic maps for whole ecosystem analysis. This last task utilises the temporal distribution of events over a daily, monthly or yearly cycle

Report on a workshop to investigate the current status of environmental bio-acoustic monitoring

This workshop was supported by the Australian Centre for Ecological Analysis and Synthesis (ACEAS, http://www.aceas.org.au/), a facility of the Australian Government-funded Terrestrial Ecosystem Research Network (http://www.tern.org.au/), a research infrastructure facility established under the National Collaborative Research Infrastructure Strategy and Education Infrastructure Fund - Super Science Initiative, through the Department of Industry, Innovation, Science, Research and Tertiary Education.\ud \ud Hosted by: Queensland University of Technology, Brisbane, Queensland. (QUT, http://www.qut.edu.au/)\ud \ud Dates: 8-11 May 2012\ud Report Editors: Prof Stuart Parsons (Uni. Auckland, NZ) and Dr Michael Towsey (QUT).\ud \ud This report is a compilation of notes and discussion summaries contributed by those attending the Workshop. They have been assembled into a logical order by the editors. Another report (with photographs) can be obtained at: http://www.aceas.org.au/index.php?option=com_content&view=article&id=94&Itemid=9