Search

Magnetic particle imaging is a tracer-based tomographic imaging technique that allows the concentration of magnetic nanoparticles to be determined with high spatio-temporal resolution. To reconstruct an image of the tracer concentration, the magnetization dynamics of the particles must be accurately modeled. A popular ensemble model is based on solving the Fokker-Plank equation, taking into account either Brownian or N\'eel dynamics. The disadvantage of this model is that it is computationally expensive due to an underlying stiff differential equation. A simplified model is the equilibrium model, which can be evaluated directly but in most relevant cases it suffers from a non-negligible modeling error. In the present work, we investigate an extended version of the equilibrium model that can account for particle anisotropy. We show that this model can be expressed as a series of Bessel functions, which can be truncated based on a predefined accuracy, leading to very short computation times, which are about three orders of magnitude lower than equivalent Fokker-Planck computation times. We investigate the accuracy of the model for 2D Lissajous magnetic particle imaging sequences and show that the difference between the Fokker-Planck and the equilibrium model with anisotropy is sufficiently small so that the latter model can be used for image reconstruction on experimental data with only marginal loss of image quality, even compared to a system matrix-based reconstruction., Comment: This work has been submitted to the IEEE for possible publication

Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.

Human sleep is cyclical with a period of approximately 90 minutes, implying long temporal dependency in the sleep data. Yet, exploring this long-term dependency when developing sleep staging models has remained untouched. In this work, we show that while encoding the logic of a whole sleep cycle is crucial to improve sleep staging performance, the sequential modelling approach in existing state-of-the-art deep learning models are inefficient for that purpose. We thus introduce a method for efficient long sequence modelling and propose a new deep learning model, L-SeqSleepNet, which takes into account whole-cycle sleep information for sleep staging. Evaluating L-SeqSleepNet on four distinct databases of various sizes, we demonstrate state-of-the-art performance obtained by the model over three different EEG setups, including scalp EEG in conventional Polysomnography (PSG), in-ear EEG, and around-the-ear EEG (cEEGrid), even with a single EEG channel input. Our analyses also show that L-SeqSleepNet is able to alleviate the predominance of N2 sleep (the major class in terms of classification) to bring down errors in other sleep stages. Moreover the network becomes much more robust, meaning that for all subjects where the baseline method had exceptionally poor performance, their performance are improved significantly. Finally, the computation time only grows at a sub-linear rate when the sequence length increases., Comment: This article has been published in IEEE Journal of Biomedical and Health Informatics (JBHI). Source code is available at http://github.com/pquochuy/l-seqsleepnet

Research question: How can we establish an AI support for reading of chest X-rays in clinical routine and which benefits emerge for the clinicians and radiologists. Can it perform 24/7 support for practicing clinicians? 2. Findings: We installed an AI solution for Chest X-ray in a given structure (MVZ Uhlenbrock & Partner, Germany). We could demonstrate the practicability, performance, and benefits in 10 connected clinical sites. 3. Meaning: A commercially available AI solution for the evaluation of Chest X-ray images is able to help radiologists and clinical colleagues 24/7 in a complex environment. The system performs in a robust manner, supporting radiologists and clinical colleagues in their important decisions, in practises and hospitals regardless of the user and X-ray system type producing the image-data.

Polyphonic events are the main error source of audio event detection (AED) systems. In deep-learning context, the most common approach to deal with event overlaps is to treat the AED task as a multi-label classification problem. By doing this, we inherently consider multiple one-vs.-rest classification problems, which are jointly solved by a single (i.e. shared) network. In this work, to better handle polyphonic mixtures, we propose to frame the task as a multi-class classification problem by considering each possible label combination as one class. To circumvent the large number of arising classes due to combinatorial explosion, we divide the event categories into multiple groups and construct a multi-task problem in a divide-and-conquer fashion, where each of the tasks is a multi-class classification problem. A network architecture is then devised for multi-class multi-task modelling. The network is composed of a backbone subnet and multiple task-specific subnets. The task-specific subnets are designed to learn time-frequency and channel attention masks to extract features for the task at hand from the common feature maps learned by the backbone. Experiments on the TUT-SED-Synthetic-2016 with high degree of event overlap show that the proposed approach results in more favorable performance than the common multi-label approach., Comment: This paper has been accepted to IEEE ICASSP 2022

Background: Despite the tremendous progress recently made towards automatic sleep staging in adults, it is currently unknown if the most advanced algorithms generalize to the pediatric population, which displays distinctive characteristics in overnight polysomnography (PSG). Methods: To answer the question, in this work, we conduct a large-scale comparative study on the state-of-the-art deep learning methods for pediatric automatic sleep staging. Six different deep neural networks with diverging features are adopted to evaluate a sample of more than 1,200 children across a wide spectrum of obstructive sleep apnea (OSA) severity. Results: Our experimental results show that the individual performance of automated pediatric sleep stagers when evaluated on new subjects is equivalent to the expert-level one reported on adults. Combining the six stagers into ensemble models further boosts the staging accuracy, reaching an overall accuracy of 88.8%, a Cohen's kappa of 0.852, and a macro F1-score of 85.8%. At the same time, the ensemble models lead to reduced predictive uncertainty. The results also show that the studied algorithms and their ensembles are robust to concept drift when the training and test data were recorded seven months apart and after clinical intervention. Conclusion: However, we show that the improvements in the staging performance are not necessarily clinically significant although the ensemble models lead to more favorable clinical measures than the six standalone models. Significance: Detailed analyses further demonstrate "almost perfect" agreement between the automatic stagers to one another and their similar patterns on the staging errors, suggesting little room for improvement., Comment: This article has been published in IEEE Transactions on Biomedical Engineering

Background: Black-box skepticism is one of the main hindrances impeding deep-learning-based automatic sleep scoring from being used in clinical environments. Methods: Towards interpretability, this work proposes a sequence-to-sequence sleep-staging model, namely SleepTransformer. It is based on the transformer backbone and offers interpretability of the model's decisions at both the epoch and sequence level. We further propose a simple yet efficient method to quantify uncertainty in the model's decisions. The method, which is based on entropy, can serve as a metric for deferring low-confidence epochs to a human expert for further inspection. Results: Making sense of the transformer's self-attention scores for interpretability, at the epoch level, the attention scores are encoded as a heat map to highlight sleep-relevant features captured from the input EEG signal. At the sequence level, the attention scores are visualized as the influence of different neighboring epochs in an input sequence (i.e. the context) to recognition of a target epoch, mimicking the way manual scoring is done by human experts. Conclusion: Additionally, we demonstrate that SleepTransformer performs on par with existing methods on two databases of different sizes. Significance: Equipped with interpretability and the ability of uncertainty quantification, SleepTransformer holds promise for being integrated into clinical settings., Comment: This article has been published in IEEE Transactions on Biomedical Engineering

We propose in this work a multi-view learning approach for audio and music classification. Considering four typical low-level representations (i.e. different views) commonly used for audio and music recognition tasks, the proposed multi-view network consists of four subnetworks, each handling one input types. The learned embedding in the subnetworks are then concatenated to form the multi-view embedding for classification similar to a simple concatenation network. However, apart from the joint classification branch, the network also maintains four classification branches on the single-view embedding of the subnetworks. A novel method is then proposed to keep track of the learning behavior on the classification branches and adapt their weights to proportionally blend their gradients for network training. The weights are adapted in such a way that learning on a branch that is generalizing well will be encouraged whereas learning on a branch that is overfitting will be slowed down. Experiments on three different audio and music classification tasks show that the proposed multi-view network not only outperforms the single-view baselines but also is superior to the multi-view baselines based on concatenation and late fusion., Comment: Accepted to ICASSP 2021

This paper presents an inception-based deep neural network for detecting lung diseases using respiratory sound input. Recordings of respiratory sound collected from patients are firstly transformed into spectrograms where both spectral and temporal information are well presented, referred to as front-end feature extraction. These spectrograms are then fed into the proposed network, referred to as back-end classification, for detecting whether patients suffer from lung-relevant diseases. Our experiments, conducted over the ICBHI benchmark meta-dataset of respiratory sound, achieve competitive ICBHI scores of 0.53/0.45 and 0.87/0.85 regarding respiratory anomaly and disease detection, respectively.

Existing generative adversarial networks (GANs) for speech enhancement solely rely on the convolution operation, which may obscure temporal dependencies across the sequence input. To remedy this issue, we propose a self-attention layer adapted from non-local attention, coupled with the convolutional and deconvolutional layers of a speech enhancement GAN (SEGAN) using raw signal input. Further, we empirically study the effect of placing the self-attention layer at the (de)convolutional layers with varying layer indices as well as at all of them when memory allows. Our experiments show that introducing self-attention to SEGAN leads to consistent improvement across the objective evaluation metrics of enhancement performance. Furthermore, applying at different (de)convolutional layers does not significantly alter performance, suggesting that it can be conveniently applied at the highest-level (de)convolutional layer with the smallest memory overhead., Comment: 46th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2021). Source code is available at http://github.com/pquochuy/sasegan

Audio event localization and detection (SELD) have been commonly tackled using multitask models. Such a model usually consists of a multi-label event classification branch with sigmoid cross-entropy loss for event activity detection and a regression branch with mean squared error loss for direction-of-arrival estimation. In this work, we propose a multitask regression model, in which both (multi-label) event detection and localization are formulated as regression problems and use the mean squared error loss homogeneously for model training. We show that the common combination of heterogeneous loss functions causes the network to underfit the data whereas the homogeneous mean squared error loss leads to better convergence and performance. Experiments on the development and validation sets of the DCASE 2020 SELD task demonstrate that the proposed system also outperforms the DCASE 2020 SELD baseline across all the detection and localization metrics, reducing the overall SELD error (the combined metric) by approximately 10% absolute., Comment: Accepted for publication in DCASE 2020 Workshop

Automating sleep staging is vital to scale up sleep assessment and diagnosis to serve millions experiencing sleep deprivation and disorders and enable longitudinal sleep monitoring in home environments. Learning from raw polysomnography signals and their derived time-frequency image representations has been prevalent. However, learning from multi-view inputs (e.g., both the raw signals and the time-frequency images) for sleep staging is difficult and not well understood. This work proposes a sequence-to-sequence sleep staging model, XSleepNet, that is capable of learning a joint representation from both raw signals and time-frequency images. Since different views may generalize or overfit at different rates, the proposed network is trained such that the learning pace on each view is adapted based on their generalization/overfitting behavior. In simple terms, the learning on a particular view is speeded up when it is generalizing well and slowed down when it is overfitting. View-specific generalization/overfitting measures are computed on-the-fly during the training course and used to derive weights to blend the gradients from different views. As a result, the network is able to retain the representation power of different views in the joint features which represent the underlying distribution better than those learned by each individual view alone. Furthermore, the XSleepNet architecture is principally designed to gain robustness to the amount of training data and to increase the complementarity between the input views. Experimental results on five databases of different sizes show that XSleepNet consistently outperforms the single-view baselines and the multi-view baseline with a simple fusion strategy. Finally, XSleepNet also outperforms prior sleep staging methods and improves previous state-of-the-art results on the experimental databases., Comment: This article has been published in IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI)

Brain waves vary between people. An obvious way to improve automatic sleep staging for longitudinal sleep monitoring is personalization of algorithms based on individual characteristics extracted from the first night of data. As a single night is a very small amount of data to train a sleep staging model, we propose a Kullback-Leibler (KL) divergence regularized transfer learning approach to address this problem. We employ the pretrained SeqSleepNet (i.e. the subject independent model) as a starting point and finetune it with the single-night personalization data to derive the personalized model. This is done by adding the KL divergence between the output of the subject independent model and the output of the personalized model to the loss function during finetuning. In effect, KL-divergence regularization prevents the personalized model from overfitting to the single-night data and straying too far away from the subject independent model. Experimental results on the Sleep-EDF Expanded database with 75 subjects show that sleep staging personalization with a single-night data is possible with help of the proposed KL-divergence regularization. On average, we achieve a personalized sleep staging accuracy of 79.6%, a Cohen's kappa of 0.706, a macro F1-score of 73.0%, a sensitivity of 71.8%, and a specificity of 94.2%. We find both that the approach is robust against overfitting and that it improves the accuracy by 4.5 percentage points compared to non-personalization and 2.2 percentage points compared to personalization without regularization., Comment: This article has been published in Physiological Measurement

This paper presents and explores a robust deep learning framework for auscultation analysis. This aims to classify anomalies in respiratory cycles and detect disease, from respiratory sound recordings. The framework begins with front-end feature extraction that transforms input sound into a spectrogram representation. Then, a back-end deep learning network is used to classify the spectrogram features into categories of respiratory anomaly cycles or diseases. Experiments, conducted over the ICBHI benchmark dataset of respiratory sounds, confirm three main contributions towards respiratory-sound analysis. Firstly, we carry out an extensive exploration of the effect of spectrogram type, spectral-time resolution, overlapped/non-overlapped windows, and data augmentation on final prediction accuracy. This leads us to propose a novel deep learning system, built on the proposed framework, which outperforms current state-of-the-art methods. Finally, we apply a Teacher-Student scheme to achieve a trade-off between model performance and model complexity which additionally helps to increase the potential of the proposed framework for building real-time applications.

In this work, we propose an approach that features deep feature embedding learning and hierarchical classification with triplet loss function for Acoustic Scene Classification (ASC). In the one hand, a deep convolutional neural network is firstly trained to learn a feature embedding from scene audio signals. Via the trained convolutional neural network, the learned embedding embeds an input into the embedding feature space and transforms it into a high-level feature vector for representation. In the other hand, in order to exploit the structure of the scene categories, the original scene classification problem is structured into a hierarchy where similar categories are grouped into meta-categories. Then, hierarchical classification is accomplished using deep neural network classifiers associated with triplet loss function. Our experiments show that the proposed system achieves good performance on both the DCASE 2018 Task 1A and 1B datasets, resulting in accuracy gains of 15.6% and 16.6% absolute over the DCASE 2018 baseline on Task 1A and 1B, respectively.

This article proposes an encoder-decoder network model for Acoustic Scene Classification (ASC), the task of identifying the scene of an audio recording from its acoustic signature. We make use of multiple low-level spectrogram features at the front-end, transformed into higher level features through a well-trained CNN-DNN front-end encoder. The high level features and their combination (via a trained feature combiner) are then fed into different decoder models comprising random forest regression, DNNs and a mixture of experts, for back-end classification. We report extensive experiments to evaluate the accuracy of this framework for various ASC datasets, including LITIS Rouen and IEEE AASP Challenge on Detection and Classification of Acoustic Scenes and Events (DCASE) 2016 Task 1, 2017 Task 1, 2018 Tasks 1A & 1B and 2019 Tasks 1A & 1B. The experimental results highlight two main contributions; the first is an effective method for high-level feature extraction from multi-spectrogram input via the novel C-DNN architecture encoder network, and the second is the proposed decoder which enables the framework to achieve competitive results on various datasets. The fact that a single framework is highly competitive for several different challenges is an indicator of its robustness for performing general ASC tasks.

Generative adversarial networks (GAN) have recently been shown to be efficient for speech enhancement. However, most, if not all, existing speech enhancement GANs (SEGAN) make use of a single generator to perform one-stage enhancement mapping. In this work, we propose to use multiple generators that are chained to perform multi-stage enhancement mapping, which gradually refines the noisy input signals in a stage-wise fashion. Furthermore, we study two scenarios: (1) the generators share their parameters and (2) the generators' parameters are independent. The former constrains the generators to learn a common mapping that is iteratively applied at all enhancement stages and results in a small model footprint. On the contrary, the latter allows the generators to flexibly learn different enhancement mappings at different stages of the network at the cost of an increased model size. We demonstrate that the proposed multi-stage enhancement approach outperforms the one-stage SEGAN baseline, where the independent generators lead to more favorable results than the tied generators. The source code is available at http://github.com/pquochuy/idsegan., Comment: This letter has been accepted for publication in IEEE Signal Processing Letters

Background: Despite recent significant progress in the development of automatic sleep staging methods, building a good model still remains a big challenge for sleep studies with a small cohort due to the data-variability and data-inefficiency issues. This work presents a deep transfer learning approach to overcome these issues and enable transferring knowledge from a large dataset to a small cohort for automatic sleep staging. Methods: We start from a generic end-to-end deep learning framework for sequence-to-sequence sleep staging and derive two networks as the means for transfer learning. The networks are first trained in the source domain (i.e. the large database). The pretrained networks are then finetuned in the target domain (i.e. the small cohort) to complete knowledge transfer. We employ the Montreal Archive of Sleep Studies (MASS) database consisting of 200 subjects as the source domain and study deep transfer learning on three different target domains: the Sleep Cassette subset and the Sleep Telemetry subset of the Sleep-EDF Expanded database, and the Surrey-cEEGrid database. The target domains are purposely adopted to cover different degrees of data mismatch to the source domains. Results: Our experimental results show significant performance improvement on automatic sleep staging on the target domains achieved with the proposed deep transfer learning approach. Conclusions: These results suggest the efficacy of the proposed approach in addressing the above-mentioned data-variability and data-inefficiency issues. Significance: As a consequence, it would enable one to improve the quality of automatic sleep staging models when the amount of data is relatively small. The source code and the pretrained models are available at http://github.com/pquochuy/sleep_transfer_learning., Comment: This article has been published in IEEE Transactions on Biomedical Engineering

Many sleep studies suffer from the problem of insufficient data to fully utilize deep neural networks as different labs use different recordings set ups, leading to the need of training automated algorithms on rather small databases, whereas large annotated databases are around but cannot be directly included into these studies for data compensation due to channel mismatch. This work presents a deep transfer learning approach to overcome the channel mismatch problem and transfer knowledge from a large dataset to a small cohort to study automatic sleep staging with single-channel input. We employ the state-of-the-art SeqSleepNet and train the network in the source domain, i.e. the large dataset. Afterwards, the pretrained network is finetuned in the target domain, i.e. the small cohort, to complete knowledge transfer. We study two transfer learning scenarios with slight and heavy channel mismatch between the source and target domains. We also investigate whether, and if so, how finetuning entirely or partially the pretrained network would affect the performance of sleep staging on the target domain. Using the Montreal Archive of Sleep Studies (MASS) database consisting of 200 subjects as the source domain and the Sleep-EDF Expanded database consisting of 20 subjects as the target domain in this study, our experimental results show significant performance improvement on sleep staging achieved with the proposed deep transfer learning approach. Furthermore, these results also reveal the essential of finetuning the feature-learning parts of the pretrained network to be able to bypass the channel mismatch problem., Comment: Accepted for 27th European Signal Processing Conference (EUSIPCO 2019)

Acoustic scenes are rich and redundant in their content. In this work, we present a spatio-temporal attention pooling layer coupled with a convolutional recurrent neural network to learn from patterns that are discriminative while suppressing those that are irrelevant for acoustic scene classification. The convolutional layers in this network learn invariant features from time-frequency input. The bidirectional recurrent layers are then able to encode the temporal dynamics of the resulting convolutional features. Afterwards, a two-dimensional attention mask is formed via the outer product of the spatial and temporal attention vectors learned from two designated attention layers to weigh and pool the recurrent output into a final feature vector for classification. The network is trained with between-class examples generated from between-class data augmentation. Experiments demonstrate that the proposed method not only outperforms a strong convolutional neural network baseline but also sets new state-of-the-art performance on the LITIS Rouen dataset., Comment: To appear at the 20th Annual Conference of the International Speech Communication Association (INTERSPEECH 2019)