A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models

Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks

A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models

Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks

Parallels in the sequential organization of birdsong and human speech.

Human speech possesses a rich hierarchical structure that allows for meaning to be altered by words spaced far apart in time. Conversely, the sequential structure of nonhuman communication is thought to follow non-hierarchical Markovian dynamics operating over only short distances. Here, we show that human speech and birdsong share a similar sequential structure indicative of both hierarchical and Markovian organization. We analyze the sequential dynamics of song from multiple songbird species and speech from multiple languages by modeling the information content of signals as a function of the sequential distance between vocal elements. Across short sequence-distances, an exponential decay dominates the information in speech and birdsong, consistent with underlying Markovian processes. At longer sequence-distances, the decay in information follows a power law, consistent with underlying hierarchical processes. Thus, the sequential organization of acoustic elements in two learned vocal communication signals (speech and birdsong) shows functionally equivalent dynamics, governed by similar processes

Automatic Detection and Compression for Passive Acoustic Monitoring of the African Forest Elephant

In this work, we consider applying machine learning to the analysis and compression of audio signals in the context of monitoring elephants in sub-Saharan Africa. Earth's biodiversity is increasingly under threat by sources of anthropogenic change (e.g. resource extraction, land use change, and climate change) and surveying animal populations is critical for developing conservation strategies. However, manually monitoring tropical forests or deep oceans is intractable. For species that communicate acoustically, researchers have argued for placing audio recorders in the habitats as a cost-effective and non-invasive method, a strategy known as passive acoustic monitoring (PAM). In collaboration with conservation efforts, we construct a large labeled dataset of passive acoustic recordings of the African Forest Elephant via crowdsourcing, compromising thousands of hours of recordings in the wild. Using state-of-the-art techniques in artificial intelligence we improve upon previously proposed methods for passive acoustic monitoring for classification and segmentation. In real-time detection of elephant calls, network bandwidth quickly becomes a bottleneck and efficient ways to compress the data are needed. Most audio compression schemes are aimed at human listeners and are unsuitable for low-frequency elephant calls. To remedy this, we provide a novel end-to-end differentiable method for compression of audio signals that can be adapted to acoustic monitoring of any species and dramatically improves over naive coding strategies

A toolbox for animal call recognition

Monitoring the natural environment is increasingly important as habit degradation and climate change reduce theworld’s biodiversity.We have developed software tools and applications to assist ecologists with the collection and analysis of acoustic data at large spatial and temporal scales.One of our key objectives is automated animal call recognition, and our approach has three novel attributes. First, we work with raw environmental audio, contaminated by noise and artefacts and containing calls that vary greatly in volume depending on the animal’s proximity to the microphone. Second, initial experimentation suggested that no single recognizer could dealwith the enormous variety of calls. Therefore, we developed a toolbox of generic recognizers to extract invariant features for each call type. Third, many species are cryptic and offer little data with which to train a recognizer. Many popular machine learning methods require large volumes of training and validation data and considerable time and expertise to prepare. Consequently we adopt bootstrap techniques that can be initiated with little data and refined subsequently. In this paper, we describe our recognition tools and present results for real ecological problems

Automatic Recognition of Non-Verbal Acoustic Communication Events With Neural Networks

Non-verbal acoustic communication is of high importance to humans and animals: Infants use the voice as a primary communication tool. Animals of all kinds employ acoustic communication, such as chimpanzees, which use pant-hoot vocalizations for long-distance communication. Many applications require the assessment of such communication for a variety of analysis goals. Computational systems can support these areas through automatization of the assessment process. This is of particular importance in monitoring scenarios over large spatial and time scales, which are infeasible to perform manually. Algorithms for sound recognition have traditionally been based on conventional machine learning approaches. In recent years, so-called representation learning approaches have gained increasing popularity. This particularly includes deep learning approaches that feed raw data to deep neural networks. However, there remain open challenges in applying these approaches to automatic recognition of non-verbal acoustic communication events, such as compensating for small data set sizes. The leading question of this thesis is: How can we apply deep learning more effectively to automatic recognition of non-verbal acoustic communication events? The target communication types were specifically (1) infant vocalizations and (2) chimpanzee long-distance calls. This thesis comprises four studies that investigated aspects of this question: Study (A) investigated the assessment of infant vocalizations by laypersons. The central goal was to derive an infant vocalization classification scheme based on the laypersons' perception. The study method was based on the Nijmegen Protocol, where participants rated vocalization recordings through various items, such as affective ratings and class labels. Results showed a strong association between valence ratings and class labels, which was used to derive a classification scheme. Study (B) was a comparative study on various neural network types for the automatic classification of infant vocalizations. The goal was to determine the best performing network type among the currently most prevailing ones, while considering the influence of their architectural configuration. Results showed that convolutional neural networks outperformed recurrent neural networks and that the choice of the frequency and time aggregation layer inside the network is the most important architectural choice. Study (C) was a detailed investigation on computer vision-like convolutional neural networks for infant vocalization classification. The goal was to determine the most important architectural properties for increasing classification performance. Results confirmed the importance of the aggregation layer and additionally identified the input size of the fully-connected layers and the accumulated receptive field to be of major importance. Study (D) was an investigation on compensating class imbalance for chimpanzee call detection in naturalistic long-term recordings. The goal was to determine which compensation method among a selected group improved performance the most for a deep learning system. Results showed that spectrogram denoising was most effective, while methods for compensating relative imbalance either retained or decreased performance.:1. Introduction 2. Foundations in Automatic Recognition of Acoustic Communication 3. State of Research 4. Study (A): Investigation of the Assessment of Infant Vocalizations by Laypersons 5. Study (B): Comparison of Neural Network Types for Automatic Classification of Infant Vocalizations 6. Study (C): Detailed Investigation of CNNs for Automatic Classification of Infant Vocalizations 7. Study (D): Compensating Class Imbalance for Acoustic Chimpanzee Detection With Convolutional Recurrent Neural Networks 8. Conclusion and Collected Discussion 9. AppendixNonverbale akustische Kommunikation ist für Menschen und Tiere von großer Bedeutung: Säuglinge nutzen die Stimme als primäres Kommunikationsmittel. Schimpanse verwenden sogenannte 'Pant-hoots' und Trommeln zur Kommunikation über weite Entfernungen. Viele Anwendungen erfordern die Beurteilung solcher Kommunikation für verschiedenste Analyseziele. Algorithmen können solche Bereiche durch die Automatisierung der Beurteilung unterstützen. Dies ist besonders wichtig beim Monitoring langer Zeitspannen oder großer Gebiete, welche manuell nicht durchführbar sind. Algorithmen zur Geräuscherkennung verwendeten bisher größtenteils konventionelle Ansätzen des maschinellen Lernens. In den letzten Jahren hat eine alternative Herangehensweise Popularität gewonnen, das sogenannte Representation Learning. Dazu gehört insbesondere Deep Learning, bei dem Rohdaten in tiefe neuronale Netze eingespeist werden. Jedoch gibt es bei der Anwendung dieser Ansätze auf die automatische Erkennung von nonverbaler akustischer Kommunikation ungelöste Herausforderungen, wie z.B. die Kompensation der relativ kleinen Datenmengen. Die Leitfrage dieser Arbeit ist: Wie können wir Deep Learning effektiver zur automatischen Erkennung nonverbaler akustischer Kommunikation verwenden? Diese Arbeit konzentriert sich speziell auf zwei Kommunikationsarten: (1) vokale Laute von Säuglingen (2) Langstreckenrufe von Schimpansen. Diese Arbeit umfasst vier Studien, welche Aspekte dieser Frage untersuchen: Studie (A) untersuchte die Beurteilung von Säuglingslauten durch Laien. Zentrales Ziel war die Ableitung eines Klassifikationsschemas für Säuglingslaute auf der Grundlage der Wahrnehmung von Laien. Die Untersuchungsmethode basierte auf dem sogenannten Nijmegen-Protokoll. Hier beurteilten die Teilnehmenden Lautaufnahmen von Säuglingen anhand verschiedener Variablen, wie z.B. affektive Bewertungen und Klassenbezeichnungen. Die Ergebnisse zeigten eine starke Assoziation zwischen Valenzbewertungen und Klassenbezeichnungen, die zur Ableitung eines Klassifikationsschemas verwendet wurde. Studie (B) war eine vergleichende Studie verschiedener Typen neuronaler Netzwerke für die automatische Klassifizierung von Säuglingslauten. Ziel war es, den leistungsfähigsten Netzwerktyp unter den momentan verbreitetsten Typen zu ermitteln. Hierbei wurde der Einfluss verschiedener architektonischer Konfigurationen innerhalb der Typen berücksichtigt. Die Ergebnisse zeigten, dass Convolutional Neural Networks eine höhere Performance als Recurrent Neural Networks erreichten. Außerdem wurde gezeigt, dass die Wahl der Frequenz- und Zeitaggregationsschicht die wichtigste architektonische Entscheidung ist. Studie (C) war eine detaillierte Untersuchung von Computer Vision-ähnlichen Convolutional Neural Networks für die Klassifizierung von Säuglingslauten. Ziel war es, die wichtigsten architektonischen Eigenschaften zur Steigerung der Erkennungsperformance zu bestimmen. Die Ergebnisse bestätigten die Bedeutung der Aggregationsschicht. Zusätzlich Eigenschaften, die als wichtig identifiziert wurden, waren die Eingangsgröße der vollständig verbundenen Schichten und das akkumulierte rezeptive Feld. Studie (D) war eine Untersuchung zur Kompensation der Klassenimbalance zur Erkennung von Schimpansenrufen in Langzeitaufnahmen. Ziel war es, herauszufinden, welche Kompensationsmethode aus einer Menge ausgewählter Methoden die Performance eines Deep Learning Systems am meisten verbessert. Die Ergebnisse zeigten, dass Spektrogrammentrauschen am effektivsten war, während Methoden zur Kompensation des relativen Ungleichgewichts die Performance entweder gleichhielten oder verringerten.:1. Introduction 2. Foundations in Automatic Recognition of Acoustic Communication 3. State of Research 4. Study (A): Investigation of the Assessment of Infant Vocalizations by Laypersons 5. Study (B): Comparison of Neural Network Types for Automatic Classification of Infant Vocalizations 6. Study (C): Detailed Investigation of CNNs for Automatic Classification of Infant Vocalizations 7. Study (D): Compensating Class Imbalance for Acoustic Chimpanzee Detection With Convolutional Recurrent Neural Networks 8. Conclusion and Collected Discussion 9. Appendi