Convolutional Sparse Support Estimator-Based COVID-19 Recognition From X-Ray Images

Coronavirus disease (COVID-19) has been the main agenda of the whole world ever since it came into sight. X-ray imaging is a common and easily accessible tool that has great potential for COVID-19 diagnosis and prognosis. Deep learning techniques can generally provide state-of-the-art performance in many classification tasks when trained properly over large data sets. However, data scarcity can be a crucial obstacle when using them for COVID-19 detection. Alternative approaches such as representation-based classification [collaborative or sparse representation (SR)] might provide satisfactory performance with limited size data sets, but they generally fall short in performance or speed compared to the neural network (NN)-based methods. To address this deficiency, convolution support estimation network (CSEN) has recently been proposed as a bridge between representation-based and NN approaches by providing a noniterative real-time mapping from query sample to ideally SR coefficient support, which is critical information for class decision in representation-based techniques. The main premises of this study can be summarized as follows: 1) A benchmark X-ray data set, namely QaTa-Cov19, containing over 6200 X-ray images is created. The data set covering 462 X-ray images from COVID-19 patients along with three other classes; bacterial pneumonia, viral pneumonia, and normal. 2) The proposed CSEN-based classification scheme equipped with feature extraction from state-of-the-art deep NN solution for X-ray images, CheXNet, achieves over 98% sensitivity and over 95% specificity for COVID-19 recognition directly from raw X-ray images when the average performance of 5-fold cross validation over QaTa-Cov19 data set is calculated. 3) Having such an elegant COVID-19 assistive diagnosis performance, this study further provides evidence that COVID-19 induces a unique pattern in X-rays that can be discriminated with high accuracy.

Echo Memory-Augmented Network for time series classification

Echo State Networks (ESNs) are efficient recurrent neural networks (RNNs) which have been successfully applied to time series modeling tasks. However, ESNs are unable to capture the history information far from the current time step, since the echo state at the present step of ESNs mostly impacted by the previous one. Thus, ESN may have difficulty in capturing the long-term dependencies of temporal data. In this paper, we propose an end-to-end model named Echo Memory-Augmented Network (EMAN) for time series classification. An EMAN consists of an echo memory-augmented encoder and a multi-scale convolutional learner. First, the time series is fed into the reservoir of an ESN to produce the echo states, which are all collected into an echo memory matrix along with the time steps. After that, we design an echo memory-augmented mechanism employing the sparse learnable attention to the echo memory matrix to obtain the Echo Memory-Augmented Representations (EMARs). In this way, the input time series is encoded into the EMARs with enhancing the temporal memory of the ESN. We then use multi-scale convolutions with the max-over-time pooling to extract the most discriminative features from the EMARs. Finally, a fully-connected layer and a softmax layer calculate the probability distribution on categories. Experiments conducted on extensive time series datasets show that EMAN is state-of-the-art compared to existing time series classification methods. The visualization analysis also demonstrates the effectiveness of enhancing the temporal memory of the ESN.

Deep Neural Architectures for Highly Imbalanced Data in Bioinformatics

In the postgenome era, many problems in bioinformatics have arisen due to the generation of large amounts of imbalanced data. In particular, the computational classification of precursor microRNA (pre-miRNA) involves a high imbalance in the classes. For this task, a classifier is trained to identify RNA sequences having the highest chance of being miRNA precursors. The big issue is that well-known pre-miRNAs are usually just a few in comparison to the hundreds of thousands of candidate sequences in a genome, which results in highly imbalanced data. This imbalance has a strong influence on most standard classifiers and, if not properly addressed, the classifier is not able to work properly in a real-life scenario. This work provides a comparative assessment of recent deep neural architectures for dealing with the large imbalanced data issue in the classification of pre-miRNAs. We present and analyze recent architectures in a benchmark framework with genomes of animals and plants, with increasing imbalance ratios up to 1:2000. We also propose a new graphical way for comparing classifiers performance in the context of high-class imbalance. The comparative results obtained show that, at a very high imbalance, deep belief neural networks can provide the best performance.

Confidence resets reveal hierarchical adaptive learning in humans

Hierarchical processing is pervasive in the brain, but its computational significance for learning under uncertainty is disputed. On the one hand, hierarchical models provide an optimal framework and are becoming increasingly popular to study cognition. On the other hand, non-hierarchical (flat) models remain influential and can learn efficiently, even in uncertain and changing environments. Here, we show that previously proposed hallmarks of hierarchical learning, which relied on reports of learned quantities or choices in simple experiments, are insufficient to categorically distinguish hierarchical from flat models. Instead, we present a novel test which leverages a more complex task, whose hierarchical structure allows generalization between different statistics tracked in parallel. We use reports of confidence to quantitatively and qualitatively arbitrate between the two accounts of learning. Our results support the hierarchical learning framework, and demonstrate how confidence can be a useful metric in learning theory.

Automated classification of Alzheimer's disease and mild cognitive impairment using a single MRI and deep neural networks

We built and validated a deep learning algorithm predicting the individual diagnosis of Alzheimer's disease (AD) and mild cognitive impairment who will convert to AD (c-MCI) based on a single cross-sectional brain structural MRI scan. Convolutional neural networks (CNNs) were applied on 3D T1-weighted images from ADNI and subjects recruited at our Institute (407 healthy controls [HC], 418 AD, 280 c-MCI, 533 stable MCI [s-MCI]). CNN performance was tested in distinguishing AD, c-MCI and s-MCI. High levels of accuracy were achieved in all the classifications, with the highest rates achieved in the AD vs HC classification tests using both the ADNI dataset only (99%) and the combined ADNI + non-ADNI dataset (98%). CNNs discriminated c-MCI from s-MCI patients with an accuracy up to 75% and no difference between ADNI and non-ADNI images. CNNs provide a powerful tool for the automatic individual patient diagnosis along the AD continuum. Our method performed well without any prior feature engineering and regardless the variability of imaging protocols and scanners, demonstrating that it is exploitable by not-trained operators and likely to be generalizable to unseen patient data. CNNs may accelerate the adoption of structural MRI in routine practice to help assessment and management of patients.

Automatic classification of grouper species by their sounds using deep neural networks

In this paper, the effectiveness of deep learning for automatic classification of grouper species by their vocalizations has been investigated. In the proposed approach, wavelet denoising is used to reduce ambient ocean noise, and a deep neural network is then used to classify sounds generated by different species of groupers. Experimental results for four species of groupers show that the proposed approach achieves a classification accuracy of around 90% or above in all of the tested cases, a result that is significantly better than the one obtained by a previously reported method for automatic classification of grouper calls.

Visualizing histopathologic deep learning classification and anomaly detection using nonlinear feature space dimensionality reduction

BACKGROUND

There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies highlight expert-level performance of convolutional neural networks (CNNs) on focused classification tasks, most studies rely on probability distribution scores with empirically defined cutoff values based on post-hoc analysis. More generalizable tools that allow humans to visualize histology-based deep learning inferences and decision making are scarce.

RESULTS

Here, we leverage t-distributed Stochastic Neighbor Embedding (t-SNE) to reduce dimensionality and depict how CNNs organize histomorphologic information. Unique to our workflow, we develop a quantitative and transparent approach to visualizing classification decisions prior to softmax compression. By discretizing the relationships between classes on the t-SNE plot, we show we can super-impose randomly sampled regions of test images and use their distribution to render statistically-driven classifications. Therefore, in addition to providing intuitive outputs for human review, this visual approach can carry out automated and objective multi-class classifications similar to more traditional and less-transparent categorical probability distribution scores. Importantly, this novel classification approach is driven by a priori statistically defined cutoffs. It therefore serves as a generalizable classification and anomaly detection tool less reliant on post-hoc tuning.

CONCLUSION

Routine incorporation of this convenient approach for quantitative visualization and error reduction in histopathology aims to accelerate early adoption of CNNs into generalized real-world applications where unanticipated and previously untrained classes are often encountered.