Objective intelligibility measurement of reverberant vocoded speech for normal-hearing listeners: Towards facilitating the development of speech enhancement algorithms for cochlear implants.

Cochlear implant (CI) recipients often struggle to understand speech in reverberant environments. Speech enhancement algorithms could restore speech perception for CI listeners by removing reverberant artifacts from the CI stimulation pattern. Listening studies, either with cochlear-implant recipients or normal-hearing (NH) listeners using a CI acoustic model, provide a benchmark for speech intelligibility improvements conferred by the enhancement algorithm but are costly and time consuming. To reduce the associated costs during algorithm development, speech intelligibility could be estimated offline using objective intelligibility measures. Previous evaluations of objective measures that considered CIs primarily assessed the combined impact of noise and reverberation and employed highly accurate enhancement algorithms. To facilitate the development of enhancement algorithms, we evaluate twelve objective measures in reverberant-only conditions characterized by a gradual reduction of reverberant artifacts, simulating the performance of an enhancement algorithm during development. Measures are validated against the performance of NH listeners using a CI acoustic model. To enhance compatibility with reverberant CI-processed signals, measure performance was assessed after modifying the reference signal and spectral filterbank. Measures leveraging the speech-to-reverberant ratio, cepstral distance and, after modifying the reference or filterbank, envelope correlation are strong predictors of intelligibility for reverberant CI-processed speech.

A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors.

MOTIVATION: Conservation is broadly used to identify biologically important (epi)genomic regions. In the case of tumor growth, preferential conservation of DNA methylation can be used to identify areas of particular functional importance to the tumor. However, reliable assessment of methylation conservation based on multiple tissue samples per patient requires the decomposition of methylation variation at multiple levels. RESULTS: We developed a Bayesian hierarchical model that allows for variance decomposition of methylation on three levels: between-patient normal tissue variation, between-patient tumor-effect variation and within-patient tumor variation. We then defined a model-based conservation score to identify loci of reduced within-tumor methylation variation relative to between-patient variation. We fit the model to multi-sample methylation array data from 21 colorectal cancer (CRC) patients using a Monte Carlo Markov Chain algorithm (Stan). Sets of genes implicated in CRC tumorigenesis exhibited preferential conservation, demonstrating the model's ability to identify functionally relevant genes based on methylation conservation. A pathway analysis of preferentially conserved genes implicated several CRC relevant pathways and pathways related to neoantigen presentation and immune evasion. Our findings suggest that preferential methylation conservation may be used to identify novel gene targets that are not consistently mutated in CRC. The flexible structure makes the model amenable to the analysis of more complex multi-sample data structures. AVAILABILITY AND IMPLEMENTATION: The data underlying this article are available in the NCBI GEO Database, under accession code GSE166212. The R analysis code is available at https://github.com/kevin-murgas/DNAmethylation-hierarchicalmodel. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Parameter tuning of time-frequency masking algorithms for reverberant artifact removal within the cochlear implant stimulus.

Cochlear implant recipients struggle to understand speech in reverberant environments. To restore speech perception, artifacts due to reverberant reflections can be removed from the cochlear implant stimulus by applying a matrix of gain values, a technique referred to as time-frequency masking. In this study, two common time-frequency masking strategies are implemented within cochlear implant processing, either introducing complete retention or deletion of stimulus components using a binary mask or continuous attenuation of stimulus components using a ratio mask. Parameters of each masking strategy control the level of attenuation imposed by the gain values. In this study, we perceptually tune the parameters of the masking strategy to determine a balance between speech retention and artifact removal. We measure the intelligibility of reverberant signals mitigated by each strategy with speech recognition testing in normal-hearing listeners using vocoding as a simulation of cochlear implant perception. For both masking strategies, we find parameterizations that maximize the intelligibility of the mitigated signals. At the best-performing parameterizations, binary-masked reverberant signals yield larger intelligibility improvements than ratio-masked signals. The results provide a perceptually optimized objective for the removal of reverberant artifacts from cochlear implant stimuli, facilitating improved speech recognition performance for cochlear implant recipients in reverberant environments.

Application of a Graphical Model to Investigate the Utility of Cross-channel Information for Mitigating Reverberation in Cochlear Implants.

Individuals with cochlear implants (CIs) experience more difficulty understanding speech in reverberant environ-ments than normal hearing listeners. As a result, recent research has targeted mitigating the effects of late reverberant signal reflections in CIs by using a machine learning approach to detect and delete affected segments in the CI stimulus pattern. Previous work has trained electrode-specific classification models to mitigate late reverberant signal reflections based on features extracted from only the acoustic activity within the electrode of interest. Since adjacent CI electrodes tend to be activated concurrently during speech, we hypothesized that incorporating additional information from the other electrode channels, termed cross-channel information, as features could improve classification performance. Cross-channel information extracted in real-world conditions will likely contain errors that will impact classification performance. To simulate extracting cross-channel information in realistic conditions, we developed a graphical model based on the Ising model to systematically introduce errors to specific types of cross-channel information. The Ising-like model allows us to add errors while maintaining the important geometric information contained in cross-channel information, which is due to the spectro-temporal structure of speech. Results suggest the potential utility of leveraging cross-channel information to improve the performance of the reverberation mitigation algorithm from the baseline channel-based features, even when the cross-channel information contains errors.