arXiv subjects

Andreas Maier

Publications and source records attributed to Andreas Maier.

At least 307 records · Page 17Linked to original sources

arXiv2022

Self-Supervised Speech Representations Preserve Speech Characteristics while Anonymizing Voices

Collecting speech data is an important step in training speech recognition systems and other speech-based machine learning models. However, the issue of privacy protection is an increasing concern that must be addressed. The current study investigates the use of voice conversion as a method for anonymizing voices. In particular, we train several voice conversion models using self-supervised speech representations including Wav2Vec2.0, Hubert and UniSpeech. Converted voices retain a low word error rate within 1% of the original voice. Equal error rate increases from 1.52% to 46.24% on the LibriSpeech test set and from 3.75% to 45.84% on speakers from the VCTK corpus which signifies degraded performance on speaker verification. Lastly, we conduct experiments on dysarthric speech data to show that speech features relevant to articulation, prosody, phonation and phonology can be extracted from anonymized voices for discriminating between healthy and pathological speech.

cs.CL↗

arXiv2022

Limited Parameter Denoising for Low-dose X-ray Computed Tomography Using Deep Reinforcement Learning

The use of deep learning has successfully solved several problems in the field of medical imaging. Deep learning has been applied to the CT denoising problem successfully. However, the use of deep learning requires large amounts of data to train deep convolutional networks (CNNs). Moreover, due to large parameter count, such deep CNNs may cause unexpected results. In this study, we introduce a novel CT denoising framework, which has interpretable behaviour, and provides useful results with limited data. We employ bilateral filtering in both the projection and volume domains to remove noise. To account for non-stationary noise, we tune the $σ$ parameters of the volume for every projection view, and for every volume pixel. The tuning is carried out by two deep CNNs. Due to impracticality of labelling, the two deep CNNs are trained via a Deep-Q reinforcement learning task. The reward for the task is generated by using a custom reward function represented by a neural network. Our experiments were carried out on abdominal scans for the Mayo Clinic TCIA dataset, and the AAPM Low Dose CT Grand Challenge. Our denoising framework has excellent denoising performance increasing the PSNR from 28.53 to 28.93, and increasing the SSIM from 0.8952 to 0.9204. We outperform several state-of-the-art deep CNNs, which have several orders of magnitude higher number of parameters (p-value (PSNR) = 0.000, p-value (SSIM) = 0.000). Our method does not introduce any blurring, which is introduced by MSE loss based methods, or any deep learning artifacts, which are introduced by WGAN based models. Our ablation studies show that parameter tuning and using our reward network results in the best possible results.

eess.IV↗

arXiv2022

Simulation-Driven Training of Vision Transformers Enabling Metal Segmentation in X-Ray Images

In several image acquisition and processing steps of X-ray radiography, knowledge of the existence of metal implants and their exact position is highly beneficial (e.g. dose regulation, image contrast adjustment). Another application which would benefit from an accurate metal segmentation is cone beam computed tomography (CBCT) which is based on 2D X-ray projections. Due to the high attenuation of metals, severe artifacts occur in the 3D X-ray acquisitions. The metal segmentation in CBCT projections usually serves as a prerequisite for metal artifact avoidance and reduction algorithms. Since the generation of high quality clinical training is a constant challenge, this study proposes to generate simulated X-ray images based on CT data sets combined with self-designed computer aided design (CAD) implants and make use of convolutional neural network (CNN) and vision transformer (ViT) for metal segmentation. Model test is performed on accurately labeled X-ray test datasets obtained from specimen scans. The CNN encoder-based network like U-Net has limited performance on cadaver test data with an average dice score below 0.30, while the metal segmentation transformer with dual decoder (MST-DD) shows high robustness and generalization on the segmentation task, with an average dice score of 0.90. Our study indicates that the CAD model-based data generation has high flexibility and could be a way to overcome the problem of shortage in clinical data sampling and labelling. Furthermore, the MST-DD approach generates a more reliable neural network in case of training on simulated data.

eess.IV↗

arXiv2022

Neural Network based Successor Representations of Space and Language

How does the mind organize thoughts? The hippocampal-entorhinal complex is thought to support domain-general representation and processing of structural knowledge of arbitrary state, feature and concept spaces. In particular, it enables the formation of cognitive maps, and navigation on these maps, thereby broadly contributing to cognition. It has been proposed that the concept of multi-scale successor representations provides an explanation of the underlying computations performed by place and grid cells. Here, we present a neural network based approach to learn such representations, and its application to different scenarios: a spatial exploration task based on supervised learning, a spatial navigation task based on reinforcement learning, and a non-spatial task where linguistic constructions have to be inferred by observing sample sentences. In all scenarios, the neural network correctly learns and approximates the underlying structure by building successor representations. Furthermore, the resulting neural firing patterns are strikingly similar to experimentally observed place and grid cell firing patterns. We conclude that cognitive maps and neural network-based successor representations of structured knowledge provide a promising way to overcome some of the short comings of deep learning towards artificial general intelligence.

cs.AI↗

arXiv2022

Deep learning-guided weighted averaging for signal dropout compensation in diffusion-weighted imaging of the liver

Purpose: To develop an algorithm for the retrospective correction of signal dropout artifacts in abdominal diffusion-weighted imaging (DWI) resulting from cardiac motion. Methods: Given a set of image repetitions for a slice, a locally adaptive weighted averaging is proposed which aims to suppress the contribution of image regions affected by signal dropouts. Corresponding weight maps were estimated by a sliding-window algorithm which analyzed signal deviations from a patch-wise reference. In order to ensure the computation of a robust reference, repetitions were filtered by a classifier that was trained to detect images corrupted by signal dropouts. The proposed method, termed Deep Learning-guided Adaptive Weighted Averaging (DLAWA), was evaluated in terms of dropout suppression capability, bias reduction in the Apparent Diffusion Coefficient (ADC) and noise characteristics. Results: In the case of uniform averaging, motion-related dropouts caused signal attenuation and ADC overestimation in parts of the liver with the left lobe being affected particularly. Both effects could be substantially mitigated by DLAWA while preventing global penalties with respect to signal-to-noise ratio (SNR) due to local signal suppression. Performing evaluations on patient data, the capability to recover lesions concealed by signal dropouts was demonstrated as well. Further, DLAWA allowed for transparent control of the trade-off between SNR and signal dropout suppression by means of a few hyperparameters. Conclusion: This work presents an effective and flexible method for the local compensation of signal dropouts resulting from motion and pulsation. Since DLAWA follows a retrospective approach, no changes to the acquisition are required.

eess.IV↗

arXiv2022

CAD-RADS Scoring using Deep Learning and Task-Specific Centerline Labeling

With coronary artery disease (CAD) persisting to be one of the leading causes of death worldwide, interest in supporting physicians with algorithms to speed up and improve diagnosis is high. In clinical practice, the severeness of CAD is often assessed with a coronary CT angiography (CCTA) scan and manually graded with the CAD-Reporting and Data System (CAD-RADS) score. The clinical questions this score assesses are whether patients have CAD or not (rule-out) and whether they have severe CAD or not (hold-out). In this work, we reach new state-of-the-art performance for automatic CAD-RADS scoring. We propose using severity-based label encoding, test time augmentation (TTA) and model ensembling for a task-specific deep learning architecture. Furthermore, we introduce a novel task- and model-specific, heuristic coronary segment labeling, which subdivides coronary trees into consistent parts across patients. It is fast, robust, and easy to implement. We were able to raise the previously reported area under the receiver operating characteristic curve (AUC) from 0.914 to 0.942 in the rule-out and from 0.921 to 0.950 in the hold-out task respectively.

eess.IV↗

arXiv2022

SliTraNet: Automatic Detection of Slide Transitions in Lecture Videos using Convolutional Neural Networks

With the increasing number of online learning material in the web, search for specific content in lecture videos can be time consuming. Therefore, automatic slide extraction from the lecture videos can be helpful to give a brief overview of the main content and to support the students in their studies. For this task, we propose a deep learning method to detect slide transitions in lectures videos. We first process each frame of the video by a heuristic-based approach using a 2-D convolutional neural network to predict transition candidates. Then, we increase the complexity by employing two 3-D convolutional neural networks to refine the transition candidates. Evaluation results demonstrate the effectiveness of our method in finding slide transitions.

cs.CV↗

arXiv2022

DeepFilterNet: A Low Complexity Speech Enhancement Framework for Full-Band Audio based on Deep Filtering

Complex-valued processing has brought deep learning-based speech enhancement and signal extraction to a new level. Typically, the process is based on a time-frequency (TF) mask which is applied to a noisy spectrogram, while complex masks (CM) are usually preferred over real-valued masks due to their ability to modify the phase. Recent work proposed to use a complex filter instead of a point-wise multiplication with a mask. This allows to incorporate information from previous and future time steps exploiting local correlations within each frequency band. In this work, we propose DeepFilterNet, a two stage speech enhancement framework utilizing deep filtering. First, we enhance the spectral envelope using ERB-scaled gains modeling the human frequency perception. The second stage employs deep filtering to enhance the periodic components of speech. Additionally to taking advantage of perceptual properties of speech, we enforce network sparsity via separable convolutions and extensive grouping in linear and recurrent layers to design a low complexity architecture. We further show that our two stage deep filtering approach outperforms complex masks over a variety of frequency resolutions and latencies and demonstrate convincing performance compared to other state-of-the-art models.

eess.AS↗

arXiv2022

FlexParser -- the adaptive log file parser for continuous results in a changing world

Any modern system writes events into files, called log files. Those contain crucial information which are subject to various analyses. Examples range from cybersecurity, intrusion detection over usage analyses to trouble shooting. Before data analysis is possible, desired information needs to be extracted first out of the semi-structured log messages. State-of-the-art event parsing often assumes static log events. However, any modern system is updated consistently and with updates also log file structures can change. We call those changes "mutation" and study parsing performance for different mutation cases. Latest research discovers mutations using anomaly detection post mortem, however, does not cover actual continuous parsing. Thus, we propose a novel and flexible parser, called FlexParser, which can extract desired values despite gradual changes in the log messages. It implies basic text preprocessing followed by a supervised Deep Learning method. We train a stateful LSTM on parsing one event per data set. Statefulness enforces the model to learn log message structures across several examples. Our model was tested on seven different, publicly available log file data sets and various kinds of mutations. Exhibiting an average F1-Score of 0.98, it outperforms other Deep Learning methods as well as state-of-the-art unsupervised parsers.

cs.LG↗

arXiv2022

Few-shot Unsupervised Domain Adaptation for Multi-modal Cardiac Image Segmentation

Unsupervised domain adaptation (UDA) methods intend to reduce the gap between source and target domains by using unlabeled target domain and labeled source domain data, however, in the medical domain, target domain data may not always be easily available, and acquiring new samples is generally time-consuming. This restricts the development of UDA methods for new domains. In this paper, we explore the potential of UDA in a more challenging while realistic scenario where only one unlabeled target patient sample is available. We call it Few-shot Unsupervised Domain adaptation (FUDA). We first generate target-style images from source images and explore diverse target styles from a single target patient with Random Adaptive Instance Normalization (RAIN). Then, a segmentation network is trained in a supervised manner with the generated target images. Our experiments demonstrate that FUDA improves the segmentation performance by 0.33 of Dice score on the target domain compared with the baseline, and it also gives 0.28 of Dice score improvement in a more rigorous one-shot setting. Our code is available at \url{https://github.com/MingxuanGu/Few-shot-UDA}.

eess.IV↗

arXiv2022

Automatic Classification of Neuromuscular Diseases in Children Using Photoacoustic Imaging

Neuromuscular diseases (NMDs) cause a significant burden for both healthcare systems and society. They can lead to severe progressive muscle weakness, muscle degeneration, contracture, deformity and progressive disability. The NMDs evaluated in this study often manifest in early childhood. As subtypes of disease, e.g. Duchenne Muscular Dystropy (DMD) and Spinal Muscular Atrophy (SMA), are difficult to differentiate at the beginning and worsen quickly, fast and reliable differential diagnosis is crucial. Photoacoustic and ultrasound imaging has shown great potential to visualize and quantify the extent of different diseases. The addition of automatic classification of such image data could further improve standard diagnostic procedures. We compare deep learning-based 2-class and 3-class classifiers based on VGG16 for differentiating healthy from diseased muscular tissue. This work shows promising results with high accuracies above 0.86 for the 3-class problem and can be used as a proof of concept for future approaches for earlier diagnosis and therapeutic monitoring of NMDs.

eess.IV↗

arXiv2022

Initial Investigations Towards Non-invasive Monitoring of Chronic Wound Healing Using Deep Learning and Ultrasound Imaging

Chronic wounds including diabetic and arterial/venous insufficiency injuries have become a major burden for healthcare systems worldwide. Demographic changes suggest that wound care will play an even bigger role in the coming decades. Predicting and monitoring response to therapy in wound care is currently largely based on visual inspection with little information on the underlying tissue. Thus, there is an urgent unmet need for innovative approaches that facilitate personalized diagnostics and treatments at the point-of-care. It has been recently shown that ultrasound imaging can monitor response to therapy in wound care, but this work required onerous manual image annotations. In this study, we present initial results of a deep learning-based automatic segmentation of cross-sectional wound size in ultrasound images and identify requirements and challenges for future research on this application. Evaluation of the segmentation results underscores the potential of the proposed deep learning approach to complement non-invasive imaging with Dice scores of 0.34 (U-Net, FCN) and 0.27 (ResNet-U-Net) but also highlights the need for improving robustness further. We conclude that deep learning-supported analysis of non-invasive ultrasound images is a promising area of research to automatically extract cross-sectional wound size and depth information with potential value in monitoring response to therapy.

eess.IV↗

arXiv2022

Ultra Low-Parameter Denoising: Trainable Bilateral Filter Layers in Computed Tomography

Computed tomography is widely used as an imaging tool to visualize three-dimensional structures with expressive bone-soft tissue contrast. However, CT resolution and radiation dose are tightly entangled, highlighting the importance of low-dose CT combined with sophisticated denoising algorithms. Most data-driven denoising techniques are based on deep neural networks and, therefore, contain hundreds of thousands of trainable parameters, making them incomprehensible and prone to prediction failures. Developing understandable and robust denoising algorithms achieving state-of-the-art performance helps to minimize radiation dose while maintaining data integrity. This work presents an open-source CT denoising framework based on the idea of bilateral filtering. We propose a bilateral filter that can be incorporated into a deep learning pipeline and optimized in a purely data-driven way by calculating the gradient flow toward its hyperparameters and its input. Denoising in pure image-to-image pipelines and across different domains such as raw detector data and reconstructed volume, using a differentiable backprojection layer, is demonstrated. Although only using three spatial parameters and one range parameter per filter layer, the proposed denoising pipelines can compete with deep state-of-the-art denoising architectures with several hundred thousand parameters. Competitive denoising performance is achieved on x-ray microscope bone data (0.7053 and 33.10) and the 2016 Low Dose CT Grand Challenge dataset (0.9674 and 43.07) in terms of SSIM and PSNR. Due to the extremely low number of trainable parameters with well-defined effect, prediction reliance and data integrity is guaranteed at any time in the proposed pipelines, in contrast to most other deep learning-based denoising architectures.

eess.IV↗

arXiv2022

Superpixel Pre-Segmentation of HER2 Slides for Efficient Annotation

Supervised deep learning has shown state-of-the-art performance for medical image segmentation across different applications, including histopathology and cancer research; however, the manual annotation of such data is extremely laborious. In this work, we explore the use of superpixel approaches to compute a pre-segmentation of HER2 stained images for breast cancer diagnosis that facilitates faster manual annotation and correction in a second step. Four methods are compared: Standard Simple Linear Iterative Clustering (SLIC) as a baseline, a domain adapted SLIC, and superpixels based on feature embeddings of a pretrained ResNet-50 and a denoising autoencoder. To tackle oversegmentation, we propose to hierarchically merge superpixels, based on their content in the respective feature space. When evaluating the approaches on fully manually annotated images, we observe that the autoencoder-based superpixels achieve a 23% increase in boundary F1 score compared to the baseline SLIC superpixels. Furthermore, the boundary F1 score increases by 73% when hierarchical clustering is applied on the adapted SLIC and the autoencoder-based superpixels. These evaluations show encouraging first results for a pre-segmentation for efficient manual refinement without the need for an initial set of annotated training data.

cs.CV↗

arXiv2022

Learned Cone-Beam CT Reconstruction Using Neural Ordinary Differential Equations

Learned iterative reconstruction algorithms for inverse problems offer the flexibility to combine analytical knowledge about the problem with modules learned from data. This way, they achieve high reconstruction performance while ensuring consistency with the measured data. In computed tomography, extending such approaches from 2D fan-beam to 3D cone-beam data is challenging due to the prohibitively high GPU memory that would be needed to train such models. This paper proposes to use neural ordinary differential equations to solve the reconstruction problem in a residual formulation via numerical integration. For training, there is no need to backpropagate through several unrolled network blocks nor through the internals of the solver. Instead, the gradients are obtained very memory-efficiently in the neural ODE setting allowing for training on a single consumer graphics card. The method is able to reduce the root mean squared error by over 30% compared to the best performing classical iterative reconstruction algorithm and produces high quality cone-beam reconstructions even in a sparse view scenario.

eess.IV↗

arXiv2022

First steps on Gamification of Lung Fluid Cells Annotations in the Flower Domain

Annotating data, especially in the medical domain, requires expert knowledge and a lot of effort. This limits the amount and/or usefulness of available medical data sets for experimentation. Therefore, developing strategies to increase the number of annotations while lowering the needed domain knowledge is of interest. A possible strategy is the use of gamification, i.e. transforming the annotation task into a game. We propose an approach to gamify the task of annotating lung fluid cells from pathological whole slide images (WSIs). As the domain is unknown to non-expert annotators, we transform images of cells to the domain of flower images using a CycleGAN architecture. In this more assessable domain, non-expert annotators can be (t)asked to annotate different kinds of flowers in a playful setting. In order to provide a proof of concept, this work shows that the domain transfer is possible by evaluating an image classification network trained on real cell images and tested on the cell images generated by the CycleGAN network (reconstructed cell images) as well as real cell images. The classification network reaches an average accuracy of 94.73 % on the original lung fluid cells and 95.25 % on the transformed lung fluid cells, respectively. Our study lays the foundation for future research on gamification using CycleGANs.

eess.IV↗

arXiv2022

Robust partial Fourier reconstruction for diffusion-weighted imaging using a recurrent convolutional neural network

Purpose: To develop an algorithm for robust partial Fourier (PF) reconstruction applicable to diffusion-weighted (DW) images with non-smooth phase variations. Methods: Based on an unrolled proximal splitting algorithm, a neural network architecture is derived which alternates between data consistency operations and regularization implemented by recurrent convolutions. In order to exploit correlations, multiple repetitions of the same slice are jointly reconstructed under consideration of permutation-equivariance. The algorithm is trained on DW liver data of 60 volunteers and evaluated on retrospectively and prospectively sub-sampled data of different anatomies and resolutions. Results: The proposed method is able to significantly outperform conventional PF techniques on retrospectively sub-sampled data in terms of quantitative measures as well as perceptual image quality. In this context, joint reconstruction of repetitions as well as the particular type of recurrent network unrolling are found to be beneficial with respect to reconstruction quality. On prospectively PF-sampled data, the proposed method enables DW imaging with higher signal without sacrificing image resolution or introducing additional artifacts. Alternatively, it can be used to counter the TE increase in acquisitions with higher resolution. Further, generalizability can be shown to prospective brain data exhibiting anatomies and contrasts not present in the training set. Conclusion: This work demonstrates that robust PF reconstruction of DW data is feasible even at strong PF factors in anatomies prone to phase variations. Since the proposed method does not rely on smoothness priors of the phase but uses learned recurrent convolutions instead, artifacts of conventional PF methods can be avoided.

eess.IV↗

arXiv2022

A Keypoint Detection and Description Network Based on the Vessel Structure for Multi-Modal Retinal Image Registration

Ophthalmological imaging utilizes different imaging systems, such as color fundus, infrared, fluorescein angiography, optical coherence tomography (OCT) or OCT angiography. Multiple images with different modalities or acquisition times are often analyzed for the diagnosis of retinal diseases. Automatically aligning the vessel structures in the images by means of multi-modal registration can support the ophthalmologists in their work. Our method uses a convolutional neural network to extract features of the vessel structure in multi-modal retinal images. We jointly train a keypoint detection and description network on small patches using a classification and a cross-modal descriptor loss function and apply the network to the full image size in the test phase. Our method demonstrates the best registration performance on our and a public multi-modal dataset in comparison to competing methods.

eess.IV↗