Supporting accessibility and reproducibility in language research in the Alveo virtual laboratory

Our paper discussing Alveo in the context of reproducibility in language sciences is now available in Computer Speech & Language: DOI:10.1016/j.csl.2017.01.003


  • Reviews a number of publications in CSL regarding their practice in using and citing data collections.
  • Finds that authors are keen to identify and share data but that practices vary in how precise they are or how easy it is to get the data.
  • Reviews research workflows in speech and language, including the use of software tools.
  • Suggests a ‘hierarchy of needs’ for reproducibility in speech and language research.
  • Describes how the Alveo Virtual Laboratory supports a model of research that facilitates data sharing and citation of software tools.


Reproducibility is an important part of scientific research and studies published in speech and language research usually make some attempt at ensuring that the work reported could be reproduced by other researchers. This paper looks at the current practice in the field relating to the citation and availability of both data and software methods. It is common to use widely available shared datasets in this field which helps to ensure that studies can be reproduced; however a brief survey of recent papers shows a wide range of styles of citation of data only some of which clearly identify the exact data used in the study. Similarly, practices in describing and sharing software artefacts vary considerably from detailed descriptions of algorithms to linked repositories. The Alveo Virtual Laboratory is a web based platform to support research based on collections of text, speech and video. Alveo provides a central repository for language data and provides a set of services for discovery and analysis of data. We argue that some of the features of the Alveo platform may make it easier for researchers to share their data more precisely and cite the exact software tools used to develop published results. Alveo makes use of ideas developed in other areas of science and we discuss these and how they can be applied to speech and language research.


Docker and MAUS

Today’s problem was to write a wrapper for the MAUS automatic segmentation system in preparation for including it as a Galaxy tool.   MAUS comes from Florian Schiel in Munich and is a collection of shell scripts and Linux executables that take a sound file and an orthographic transcription and generate an aligned phonetic segmentation.  The core of this process is the HTK speech recognition system and getting it to work on anything other than Linux is a pain that is best not lived with.  Continue reading

A Galaxy Workflow for Acoustic Phonetic Analysis

I’ve been working for a while now on adapting the Galaxy Workflow engine for use in speech analysis, specifically for acoustic phonetic analysis of vowel sounds.  Galaxy is a system used in bioinformatics for constructing workflows to do genetic analysis and other things.  As part of the Alveo project we’ve been building tools for doing text and speech analysis for Galaxy.  My recent work has been specifically looking at acoustic phonetic analysis with the Emu library with a goal of reproducing some work on children’s vowels that I did with Catherine Watson many years ago. Continue reading

Mobile Apps for Aboriginal Languages

My introduction to Darwin was on a borrowed bike used to discover the streets around CDU and eventually making my way to the city and Midil Beach markets for a Sunday evening feast of Gado-Gado watching the sunset on the sand.  I’m in Darwin for a workshop organised by Steven Bird aiming to build mobile apps aimed at “Keeping our Languages Strong”.   While a lot of the work with Australian languages is aimed at preservation and documentation, Steven’s work is aimed more at maintaining the living languages within their communities.
The invitees to the workshop were a mixture of technologists like me, linguists, people working with the language communities and members of the communities themselves.  The premise was to bring us together to imagine what mobile apps we might build in the context of Aboriginal languages and them maybe even try to build some demonstrations as a proof of concept in the week.  The first two days explored possibilities; the next two left the hackers alone to try to build something; the final morning was a show and tell and reflection on what we’d managed to achieve.
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Galaxy Tool Generating Dataset Collections

As part of the Alveo project we’ve been using the Galaxy Workflow Engine to provide a web-based user-friendly interface to some language processing tools. Galaxy was originally developed for Bioinformatics researchers but we’ve been able to adapt it for language tools quite easily. Galaxy tools are scripts or executable command line applications that read input data from files and write results out to new files. These files are presented as data objects in the Galaxy interface. Chains of tools can be run one after another to process data from input to final results.

One of the recent updates to Galaxy is the ability to group data objects together into datasets. These datasets can then form the input to a workflow which can be run for each object in the dataset.  This is something we’ve wanted for Alveo for a long time since applying the same process to all files in a collection is a common requirement for language processing.   After a bit of exploration I’ve worked out how to write a tool that generates a dataset and since the documentation for this is somewhat sparse and confusing, I thought I’d write up my findings.

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Updating the ICE Annotation System: Tagging, Parsing and Validation

Authors: Deanna Wong, Steve Cassidy and Pam Peters

To appear in Corpora, expected publication in 2012. Manuscript available on request.

The textual markup scheme of the International Corpus of English (ICE) corpus project evolved continuously from 1989 on, more or less independent of the Text Encoding Initiative (TEI). It was intended to standardise the annotation of all the regional ICE corpora, in order to facilitate inter-comparisons of their linguistic content. However this goal has proved elusive because of gradual changes in the ICE annotation system, and additions to it made by those working on individual ICE corpora. Further, since the project pre-dates the development of XML-based markup standards, the format of the ICE markup does not match that in many modern corpora and can be difficult to manipulate. As a goal of the original project was interoperability of the various ICE corpora, it is important that the markup of existing and new ICE corpora can be converted into a common format that can serve their ongoing needs, while allowing older markup to be fully included. This paper describes the most significant variations in annotation, and focuses on several points of difficulty inherent in the system: especially the non-hierarchical treatment of the visual and structural elements of written texts, and of overlapping speech in spontaneous conversation. We report on our development of a parser to validate the existing ICE markup scheme and convert it to other formats. The development of this tool not only brings the Australian version into line with the current ICE standard, it also allows for proper validation of all annotation in any of the regional corpora. Once the corpora have been validated, they can be converted easily to a standardised XML format for alternate systems of corpus annotation, such as that developed by the TEI.

Notes on Conversion of GrAF to RDF

The Graph Annotation Format (GrAF) is the XML data exchange format developed for the model of linguistic annotation described in the ISO Linguistic Annotation Framework (LAF). LAF is the abstract model of annotations represented as a graph structure, GrAF is an XML serialisation of the model intended for moving data between different tools. Both were developed by Nancy Ide and Keith Suderman in Vasser with input from the community involved in the ISO standardisation process around linguistic data. Continue reading

DADA Project Update

The DADA project is developing software for managing language resources and exposing them on the web. Language resources are digital collections of language as audio, video and text used to study language and build technology systems. The project has been going for a while with some initial funding from the ARC to build the basic infrastructure and later from Macquarie University for some work on the Auslan corpus of Australian Sign Language collected by Trevor Johnston. Recently we have two projects which DADA will be part of, and so the pace of development has picked up a little. Continue reading

An RDF Realisation of LAF in the DADA Annotation Server

The Linguistic Annotation Framework defines a generalised graph based
model for annotation data intended as an interchange format for transfer
of annotations between tools.   The DADA system uses an RDF based representation
of annotation data and provides a web based annotation store.  The annotation
model in DADA can be seen as an RDF realisation of the LAF model. This paper
describes the relationship between the two models and makes some comments on
how the standard might be stated in a more format-neutral way.

Download PDF: An RDF Realisation of LAF in the DADA Annotation Server

Ingesting the Auslan Corpus into the DADA Annotation Store

Steve Cassidy and Trevor Johnston.

The DADA system is being developed to support collaborative access to and annotation of language resources over the web.  DADA provides a web accessible annotation store that delivers both a human browsable version of a corpus and a machine accessible API for reading and writing annotations.  DADA implements an abstract model of annotation suitable for storing many kinds of data from a wide range of language resources.  This paper describes the process of ingesting data from a corpus of Australian Sign Language (Auslan) into the DADA system.  We describe the format of the RDF data used by DADA and the issues raised in converting the ELAN annotations from the corpus.  Once ingested, the data is presented in a simple web interface and also via a Javascript client that makes use of an alternate interface to the DADA server.

Download PDF: Ingesting the Auslan Corpus into the DADA Annotation Store