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Oct 30

Deep Spatiotemporal Clutter Filtering of Transthoracic Echocardiographic Images: Leveraging Contextual Attention and Residual Learning

This study presents a deep convolutional autoencoder network for filtering reverberation clutter from transthoracic echocardiographic (TTE) image sequences. Given the spatiotemporal nature of this type of clutter, the filtering network employs 3D convolutional layers to suppress it throughout the cardiac cycle. The design of the network incorporates two key features that contribute to the effectiveness of the filter: 1) an attention mechanism for focusing on cluttered regions and leveraging contextual information, and 2) residual learning for preserving fine image structures. To train the network, a diverse set of artifact patterns was simulated and superimposed onto ultra-realistic synthetic TTE sequences from six ultrasound vendors, generating input for the filtering network. The artifact-free sequences served as ground-truth. Performance of the filtering network was evaluated using unseen synthetic and in vivo artifactual sequences. Results from the in vivo dataset confirmed the network's strong generalization capabilities, despite being trained solely on synthetic data and simulated artifacts. The suitability of the filtered sequences for downstream processing was assessed by computing segmental strain curves. A significant reduction in the discrepancy between strain profiles computed from cluttered and clutter-free segments was observed after filtering the cluttered sequences with the proposed network. The trained network processes a TTE sequence in a fraction of a second, enabling real-time clutter filtering and potentially improving the precision of clinically relevant indices derived from TTE sequences. The source code of the proposed method and example video files of the filtering results are available at: https://github.com/MahdiTabassian/Deep-Clutter-Filtering/tree/main{https://github.com/MahdiTabassian/Deep-Clutter-Filtering/tree/main}.

  • 4 authors
·
Jan 23, 2024

Deep Clustering via Joint Convolutional Autoencoder Embedding and Relative Entropy Minimization

Image clustering is one of the most important computer vision applications, which has been extensively studied in literature. However, current clustering methods mostly suffer from lack of efficiency and scalability when dealing with large-scale and high-dimensional data. In this paper, we propose a new clustering model, called DEeP Embedded RegularIzed ClusTering (DEPICT), which efficiently maps data into a discriminative embedding subspace and precisely predicts cluster assignments. DEPICT generally consists of a multinomial logistic regression function stacked on top of a multi-layer convolutional autoencoder. We define a clustering objective function using relative entropy (KL divergence) minimization, regularized by a prior for the frequency of cluster assignments. An alternating strategy is then derived to optimize the objective by updating parameters and estimating cluster assignments. Furthermore, we employ the reconstruction loss functions in our autoencoder, as a data-dependent regularization term, to prevent the deep embedding function from overfitting. In order to benefit from end-to-end optimization and eliminate the necessity for layer-wise pretraining, we introduce a joint learning framework to minimize the unified clustering and reconstruction loss functions together and train all network layers simultaneously. Experimental results indicate the superiority and faster running time of DEPICT in real-world clustering tasks, where no labeled data is available for hyper-parameter tuning.

  • 5 authors
·
Apr 20, 2017

Singing Voice Separation Using a Deep Convolutional Neural Network Trained by Ideal Binary Mask and Cross Entropy

Separating a singing voice from its music accompaniment remains an important challenge in the field of music information retrieval. We present a unique neural network approach inspired by a technique that has revolutionized the field of vision: pixel-wise image classification, which we combine with cross entropy loss and pretraining of the CNN as an autoencoder on singing voice spectrograms. The pixel-wise classification technique directly estimates the sound source label for each time-frequency (T-F) bin in our spectrogram image, thus eliminating common pre- and postprocessing tasks. The proposed network is trained by using the Ideal Binary Mask (IBM) as the target output label. The IBM identifies the dominant sound source in each T-F bin of the magnitude spectrogram of a mixture signal, by considering each T-F bin as a pixel with a multi-label (for each sound source). Cross entropy is used as the training objective, so as to minimize the average probability error between the target and predicted label for each pixel. By treating the singing voice separation problem as a pixel-wise classification task, we additionally eliminate one of the commonly used, yet not easy to comprehend, postprocessing steps: the Wiener filter postprocessing. The proposed CNN outperforms the first runner up in the Music Information Retrieval Evaluation eXchange (MIREX) 2016 and the winner of MIREX 2014 with a gain of 2.2702 ~ 5.9563 dB global normalized source to distortion ratio (GNSDR) when applied to the iKala dataset. An experiment with the DSD100 dataset on the full-tracks song evaluation task also shows that our model is able to compete with cutting-edge singing voice separation systems which use multi-channel modeling, data augmentation, and model blending.

  • 5 authors
·
Dec 4, 2018

Deep reproductive feature generation framework for the diagnosis of COVID-19 and viral pneumonia using chest X-ray images

The rapid and accurate detection of COVID-19 cases is critical for timely treatment and preventing the spread of the disease. In this study, a two-stage feature extraction framework using eight state-of-the-art pre-trained deep Convolutional Neural Networks (CNNs) and an autoencoder is proposed to determine the health conditions of patients (COVID-19, Normal, Viral Pneumonia) based on chest X-rays. The X-ray scans are divided into four equally sized sections and analyzed by deep pre-trained CNNs. Subsequently, an autoencoder with three hidden layers is trained to extract reproductive features from the concatenated ouput of CNNs. To evaluate the performance of the proposed framework, three different classifiers, which are single-layer perceptron (SLP), multi-layer perceptron (MLP), and support vector machine (SVM) are used. Furthermore, the deep CNN architectures are used to create benchmark models and trained on the same dataset for comparision. The proposed framework outperforms other frameworks wih pre-trained feature extractors in binary classification and shows competitive results in three-class classification. The proposed methodology is task-independent and suitable for addressing various problems. The results show that the discriminative features are a subset of the reproductive features, suggesting that extracting task-independent features is superior to the extraction only task-based features. The flexibility and task-independence of the reproductive features make the conceptive information approach more favorable. The proposed methodology is novel and shows promising results for analyzing medical image data.

  • 4 authors
·
Apr 20, 2023

Self-Supervised Pre-Training with Contrastive and Masked Autoencoder Methods for Dealing with Small Datasets in Deep Learning for Medical Imaging

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

  • 7 authors
·
Aug 12, 2023

The History Began from AlexNet: A Comprehensive Survey on Deep Learning Approaches

Deep learning has demonstrated tremendous success in variety of application domains in the past few years. This new field of machine learning has been growing rapidly and applied in most of the application domains with some new modalities of applications, which helps to open new opportunity. There are different methods have been proposed on different category of learning approaches, which includes supervised, semi-supervised and un-supervised learning. The experimental results show state-of-the-art performance of deep learning over traditional machine learning approaches in the field of Image Processing, Computer Vision, Speech Recognition, Machine Translation, Art, Medical imaging, Medical information processing, Robotics and control, Bio-informatics, Natural Language Processing (NLP), Cyber security, and many more. This report presents a brief survey on development of DL approaches, including Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) including Long Short Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). In addition, we have included recent development of proposed advanced variant DL techniques based on the mentioned DL approaches. Furthermore, DL approaches have explored and evaluated in different application domains are also included in this survey. We have also comprised recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys have published on Deep Learning in Neural Networks [1, 38] and a survey on RL [234]. However, those papers have not discussed the individual advanced techniques for training large scale deep learning models and the recently developed method of generative models [1].

  • 9 authors
·
Mar 3, 2018