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John W. Holloway

Publications and source records attributed to John W. Holloway.

2 recordsLinked to original sources

BreathGRU: A Novel Semi-Supervised Bidirectional Gated Recurrent Unit Framework for Speech and Breath Segmentation for Respiratory Audio

Speech-breath segmentation is a fundamental preprocessing step in respiratory audio analysis, enabling applications such as respiratory acoustic biomarker extraction, lung function prediction and disease monitoring. Existing approaches, including threshold methods, Fourier Transform-based techniques, and unsupervised and pretrained voice activity detection (VAD) models, primarily focus on speech detection and often classify breathing events as non-speech or silence, limiting their applicability for precise breath detection. To address this limitation, we propose BreathGRU, a semi-supervised Bidirectional Gated Recurrent Unit (BiGRU) framework specifically designed for speech-breath segmentation. The proposed framework combines frame-level acoustic feature extraction with bidirectional recurrent modelling, pseudo-label refinement and duration-constrained Segmental Viterbi decoding to produce speech and breath segmentation. BreathGRU was evaluated against the existing approaches, using manually annotated recordings. Performance was assessed using event-based, time-based, overlap-based, duration-based and boundary-based segmentation metrics. Experiment results demonstrated that BreathGRU achieved the highest breath event recall (0.83), the lowest onset-localisation error (0.14s) and the highest Mean Match Intersection over Union (0.81), with competitive overall segmentation performance compared to large pretrained VAD models like Silero. Qualitative evaluation on manually annotated recordings further showed close agreement between BreathGRU and manual annotation, with better breath detection compared to Silero. These findings demonstrate that explicit breath event modelling provides advantages over general-purpose VAD models and establish BreathGRU as an effective speech-breath segmentation framework which can be applied for respiratory audio analysis and pulmonary healthcare applications.

cs.SD↗

Identifying heterogeneous transgenerational DNA methylation sites via clustering in beta regression

This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their offsprings at the population level. To facilitate this goal, an expectation maximization algorithm for parameter estimation along with a BIC criterion to determine the number of clusters is proposed. Applying our method to the DNA methylation data composed of 4063 CpG sites of 41 mother-father-infant triads, we identified a set of CpG sites in which DNA methylation transmission is dominated by fathers, while at a large number of CpG sites, DNA methylation is mainly maternally transmitted to the offspring.

stat.AP↗