Semi-supervised source localization with deep generative modeling

We propose a semi-supervised localization approach based on deep generative modeling with variational autoencoders (VAEs). Localization in reverberant environments remains a challenge, which machine learning (ML) has shown promise in addressing. Even with large data volumes, the number of labels available for supervised learning in reverberant environments is usually small. We address this issue by performing semi-supervised learning (SSL) with convolutional VAEs. The VAE is trained to generate the phase of relative transfer functions (RTFs), in parallel with a DOA classifier, on both labeled and unlabeled RTF samples. The VAE-SSL approach is compared with SRP-PHAT and fully-supervised CNNs. We find that VAE-SSL can outperform both SRP-PHAT and CNN in label-limited scenarios.Comment: Published in proceedings of IEEE International Workshop on Machine Learning for Signal Processing. arXiv admin note: substantial text overlap with arXiv:2101.1063

Semi-supervised source localization in reverberant environments with deep generative modeling

We propose a semi-supervised approach to acoustic source localization in reverberant environments based on deep generative modeling. Localization in reverberant environments remains an open challenge. Even with large data volumes, the number of labels available for supervised learning in reverberant environments is usually small. We address this issue by performing semi-supervised learning (SSL) with convolutional variational autoencoders (VAEs) on reverberant speech signals recorded with microphone arrays. The VAE is trained to generate the phase of relative transfer functions (RTFs) between microphones, in parallel with a direction of arrival (DOA) classifier based on RTF-phase. These models are trained using both labeled and unlabeled RTF-phase sequences. In learning to perform these tasks, the VAE-SSL explicitly learns to separate the physical causes of the RTF-phase (i.e., source location) from distracting signal characteristics such as noise and speech activity. Relative to existing semi-supervised localization methods in acoustics, VAE-SSL is effectively an end-to-end processing approach which relies on minimal preprocessing of RTF-phase features. As far as we are aware, our paper presents the first approach to modeling the physics of acoustic propagation using deep generative modeling. The VAE-SSL approach is compared with two signal processing-based approaches, steered response power with phase transform (SRP-PHAT) and MUltiple SIgnal Classification (MUSIC), as well as fully supervised CNNs. We find that VAE-SSL can outperform the conventional approaches and the CNN in label-limited scenarios. Further, the trained VAE-SSL system can generate new RTF-phase samples, which shows the VAE-SSL approach learns the physics of the acoustic environment. The generative modeling in VAE-SSL thus provides a means of interpreting the learned representations.Comment: Revision, submitted to IEEE Acces

Thirty Years with HIV Infection—Nonprogression Is Still Puzzling: Lessons to Be Learned from Controllers and Long-Term Nonprogressors

In the early days of the HIV epidemic, it was observed that a minority of the infected patients did not progress to AIDS or death and maintained stable CD4+ cell counts. As the technique for measuring viral load became available it was evident that some of these nonprogressors in addition to preserved CD4+ cell counts had very low or even undetectable viral replication. They were therefore termed controllers, while those with viral replication were termed long-term nonprogressors (LTNPs). Genetics and virology play a role in nonprogression, but does not provide a full explanation. Therefore, host differences in the immunological response have been proposed. Moreover, the immunological response can be divided into an immune homeostasis resistant to HIV and an immune response leading to viral control. Thus, non-progression in LTNP and controllers may be due to different immunological mechanisms. Understanding the lack of disease progression and the different interactions between HIV and the immune system could ideally teach us how to develop a functional cure for HIV infection. Here we review immunological features of controllers and LTNP, highlighting differences and clinical implications

Selected Topics of the Past Thirty Years in Ocean Acoustics

This paper reviews some of the highlights of selected topics in ocean acoustics during the thirty years that have passed since the founding of the Journal of Theoretical and Computational Acoustics. Advances in computational methods and computers helped to make computational ocean acoustics a vibrant area of research during that period. The parabolic equation method provides an unrivaled combination of accuracy and efficiency for propagation problems in which the bathymetry, sound speed, and other environmental parameters vary in the horizontal directions. The extension of this approach to cases involving layers that support shear waves has been an active area of research throughout the thirty year period. Interest in basin-scale and global-scale propagation was stimulated by the Heard Island Feasibility Test for monitoring climate change in terms of changes in travel time that occur as the temperature of the ocean rises. Diminishing ice cover in the Arctic, which is one of the consequences of climate change, has stimulated renewed interest in Arctic acoustics during the past decade. Reverberation is a challenging problem that was the topic of a major research program during the beginning of the thirty year period. An innovative approach for making it feasible to solve such problems was applied to data for reverberation from the seafloor and from schools of fish, and some of the findings were featured in Science and Nature. Source localization is one of the core problems in ocean acoustics. When applied on a 2-D array of receivers, an approach based on the eigenvectors of the covariance matrix is capable of separating the signals from different sources from each other, determining when this partitioning step is successful, and tracking sources that cross each other in bearing; one of the advantages of this approach is that it does not require environmental information or solutions of the wave equation. Geoacoustic inversion for estimating the layer structure, wave speeds, density, and other parameters of ocean bottoms has also been a topic of interest throughout the thirty year period

Incomplete Immune Recovery in HIV Infection: Mechanisms, Relevance for Clinical Care, and Possible Solutions

Treatment of HIV-infected patients with highly active antiretroviral therapy (HAART) usually results in diminished viral replication, increasing CD4+ cell counts, a reversal of most immunological disturbances, and a reduction in risk of morbidity and mortality. However, approximately 20% of all HIV-infected patients do not achieve optimal immune reconstitution despite suppression of viral replication. These patients are referred to as immunological nonresponders (INRs). INRs present with severely altered immunological functions, including malfunction and diminished production of cells within lymphopoetic tissue, perturbed frequencies of immune regulators such as regulatory T cells and Th17 cells, and increased immune activation, immunosenescence, and apoptosis. Importantly, INRs have an increased risk of morbidity and mortality compared to HIV-infected patients with an optimal immune reconstitution. Additional treatment to HAART that may improve immune reconstitution has been investigated, but results thus far have proved disappointing. The reason for immunological nonresponse is incompletely understood. This paper summarizes the known and unknown factors regarding the incomplete immune reconstitution in HIV infection, including mechanisms, relevance for clinical care, and possible solutions

Impact of Age and HIV Status on Immune Activation, Senescence and Apoptosis

Introduction: Residual immune dysfunctions, resembling those that occur during normal aging, may persist even in well-treated people with HIV (PWH), and accelerated aging has been proposed. We aimed to determine if HIV infection is an independent risk factor for T-cell immune dysfunctions including increased immune activation, senescence and apoptosis. Moreover, in PWH we aimed to identify the associations between age and immune activation, senescence and apoptosis. Materials and Methods: We included 780 PWH with suppressed viral replication (<50 copies/mL) and absence of hepatitis B and hepatitis C co-infection and 65 uninfected controls from the Copenhagen Co-morbidity in HIV Infection (COCOMO) Study. Flow cytometry was used to determine T-cell activation (CD38+HLA-DR+), senescence (CD28-CD57+), and apoptosis (CD28-CD95+). T-cell subsets are reported as proportions of CD4+ and CD8+ T-cells. We defined an elevated proportion of a given T-cell subset as above the 75th percentile. Regression models were used to determine the association between HIV status and T-cell subset and in PWH to determine the association between age or HIV-specific risk factors and T-cell subsets. Furthermore, an interaction between HIV status and age on T-cell subsets was investigated with an interaction term in models including both PWH and controls. Models were adjusted for age, sex, BMI, and smoking status. Results: In adjusted models a positive HIV status was associated with elevated proportions of CD8+ activated (p = 0.009), CD4+ senescent (p = 0.004), CD4+ apoptotic (p = 0.002), and CD8+ apoptotic (p = 0.003) T-cells. In PWH a 10-year increase in age was associated with higher proportions of CD4+ and CD8+ senescent (p = 0.001 and p < 0.001) and CD4+ and CD8+ apoptotic T-cells (p < 0.001 and p < 0.001). However, no interaction between HIV status and age was found. Furthermore, in PWH a CD4+/CD8+ ratio < 1 was associated with elevated proportions of T-cell activation, senescence, and apoptosis. Discussion: We found evidence of residual T-cell immune dysfunction in well-treated PWH without HBV or HCV co-infection, and age was associated with T-cell senescence and apoptosis. Our data supports that HIV infection has similar effects as aging on T-cell subsets. However, since no interaction between HIV status and age was found on these parameters, we found no evidence to support accelerated immunological aging in PWH

Impaired platelet aggregation and rebalanced hemostasis in patients with chronic hepatitis C virus infection

Increased risk of both cardiovascular disease (CVD) and bleeding has been found in patients with chronic hepatitis C (CHC) infection, and a re-balanced hemostasis has been proposed. The aim of this study was to investigate functional whole blood coagulation and platelet function in CHC infection. The prospective study included 82 patients with CHC infection (39 with advanced liver fibrosis and 43 with no or mild liver fibrosis) and 39 healthy controls. A total of 33 patients were treated for CHC infection and achieved sustained virological response (SVR). Baseline and post-treatment blood samples were collected. Hemostasis was assessed by both standard coagulation tests and functional whole blood hemostatic assays (thromboelastograhy (TEG), and platelet aggregation (Multiplate). Patients with CHC and advanced fibrosis had impaired platelet aggregation both compared to patients with no or mild fibrosis and to healthy controls. Patients with CHC and advanced fibrosis also had lower antithrombin, platelet count, and coagulation factors II-VII-X compared to healthy controls. In contrast, TEG did not differ between groups. In treated patients achieving SVR, post-treatment platelet count was higher than pre-treatment counts (p = 0.033) and ADPtest, ASPItest, and RISTOhightest all increased post treatment (all p &lt; 0.05). All Multiplate tests values, however, remained below those in the healthy controls. CHC-infected patients displayed evidence of rebalanced hemostasis with only partly hemostatic normalization in patients achieving SVR. The implications of rebalanced hemostasis and especially the impact on risk of CVD and bleeding warrants further studies