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• An interpretable CNN model that can reveal important parts of input single-channel EEG signals for classification with the Class Activation Map (CAM) method. • The model can discover biologically explainable features from a diversity of EEG data of different subjects. • An average accuracy of 73.22% is achieved by the model on 11 subjects for 2-class cross-subject EEG signal classification. • We use the model to discover interesting features from EEG signals that can be indicators of alert or drowsy states. Driver drowsiness is one of the main factors leading to road fatalities and hazards in the transportation industry. Electroencephalography (EEG) has been considered as one of the best physiological signals to detect drivers' drowsy states, since it directly measures neurophysiological activities in the brain. However, designing a calibration-free system for driver drowsiness detection with EEG is still a challenging task, as EEG suffers from serious mental and physical drifts across different subjects. In this paper, we propose a compact and interpretable Convolutional Neural Network (CNN) to discover shared EEG features across different subjects for driver drowsiness detection. We incorporate the Global Average Pooling (GAP) layer in the model structure, allowing the Class Activation Map (CAM) method to be used for localizing regions of the input signal that contribute most for classification. Results show that the proposed model can achieve an average accuracy of 73.22% on 11 subjects for 2-class cross-subject EEG signal classification, which is higher than conventional machine learning methods and other state-of-art deep learning methods. It is revealed by the visualization technique that the model has learned biologically explainable features, e.g., Alpha spindles and Theta burst, as evidence for the drowsy state. It is also interesting to see that the model uses artifacts that usually dominate the wakeful EEG, e.g., muscle artifacts and sensor drifts, to recognize the alert state. The proposed model illustrates a potential direction to use CNN models as a powerful tool to discover shared features related to different mental states across different subjects from EEG signals. [ABSTRACT FROM AUTHOR]

Background: Mutual information is a measure of similarity between two variables. It has been widely used in various application domains including computational biology, machine learning, statistics, image processing, and financial computing. Previously used simple histogram based mutual information estimators lack the precision in quality compared to kernel based methods. The recently introduced B-spline function based mutual information estimation method is competitive to the kernel based methods in terms of quality but at a lower computational complexity. Results: We present a new approach to accelerate the B-spline function based mutual information estimation algorithm with commodity graphics hardware. To derive an efficient mapping onto this type of architecture, we have used the Compute Unified Device Architecture (CUDA) programming model to design and implement a new parallel algorithm. Our implementation, called CUDA-MI, can achieve speedups of up to 82 using double precision on a single GPU compared to a multi-threaded implementation on a quad-core CPU for large microarray datasets. We have used the results obtained by CUDA-MI to infer gene regulatory networks (GRNs) from microarray data. The comparisons to existing methods including ARACNE and TINGe show that CUDA-MI produces GRNs of higher quality in less time. Conclusions: CUDA-MI is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant speedup over sequential multi-threaded implementation by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. [ABSTRACT FROM AUTHOR]

Sequence alignment is a common and often repeated task in molecular biology. Typical alignment operations consist of finding similarities between a pair of sequences (pairwise sequence alignment) or a family of sequences (multiple sequence alignment). The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases: Every year their size increases by a factor of 1.5 to 2. In this paper we present a new approach to high-performance biological sequence alignment based on commodity PC graphics hardware. Using modern graphics processing units (GPUs) for high-performance computing is facilitated by their enhanced programmability and motivated by their attractive price/performance ratio and incredible growth in speed. To derive an efficient mapping onto this type of architecture, we have reformulated dynamic-programming-based alignment algorithms as streaming algorithms in terms of computer graphics primitives. Our experimental results show that the GPU-based approach allows speedups of more than one order of magnitude with respect to optimized CPU implementations. [ABSTRACT FROM AUTHOR]

Mental fatigue is one of the major factors leading to human errors. To avoid failures caused by mental fatigue, researchers are working on ways to detect/monitor fatigue using different types of signals. Electroencephalography (EEG) signal is one of the most popular methods to recognize mental fatigue since it directly measures the neurophysiological activities in the brain. Current EEG-based fatigue recognition algorithms are usually subject-specific, which means a classifier needs to be trained per subject. However, as fatigue may need a relatively long period to induce, collecting training data from each new user could be time-consuming and troublesome. Calibration-free methods are desired but also challenging since significant variability of physiological signals exists among different subjects. In this paper, we proposed algorithms using inter-subject transfer learning for EEG-based mental fatigue recognition, which did not need a calibration. To explore the influence of the number of EEG channels on the algorithms' accuracy, we also compared the cases of using one channel only and multiple channels. Random forest was applied to choose the channel that has the most distinguishable features. A public EEG fatigue dataset recorded during driving was used to validate the algorithms. EEG data from 11 subjects were selected from the dataset and leave-one-subject-out cross-validation was employed. The channel from the occipital lobe is selected when only one channel is desired. The proposed transfer learning-based algorithms using Maximum Independence Domain Adaptation (MIDA) achieved an accuracy of 73.01% with all thirty channels, and using Transfer Component Analysis (TCA) achieved 68.00% with the one selected channel. [ABSTRACT FROM AUTHOR]