While there has been significant progress in evaluating and comparing different representations for learning on protein data, the role of surface-based learning approaches remains not well-understood. In particular, there is a lack of direct and fair benchmark comparison between the best available surface-based learning methods against alternative representations such as graphs. Moreover, the few existing surface-based approaches either use surface information in isolation or, at best, perform global pooling between surface and graph-based architectures. In this work, we fill this gap by first adapting a state-of-the-art surface encoder for protein learning tasks. We then perform a direct and fair comparison of the resulting method against alternative approaches within the Atom3D benchmark, highlighting the limitations of pure surface-based learning. Finally, we propose an integrated approach, which allows learned feature sharing between graphs and surface representations on the level of nodes and vertices \textit{across all layers}. We demonstrate that the resulting architecture achieves state-of-the-art results on all tasks in the Atom3D benchmark, while adhering to the strict benchmark protocol, as well as more broadly on binding site identification and binding pocket classification. Furthermore, we use coarsened surfaces and optimize our approach for efficiency, making our tool competitive in training and inference time with existing techniques. Code can be found online: https://github.com/Vincentx15/atomsurf

The common spatial patterns (CSP) algorithm is one of the most frequently used and effective spatial filtering methods for extracting relevant features for use in motor imagery brain-computer interfaces (MI-BCIs). However, the inherent defect of the traditional CSP algorithm is that it is highly sensitive to potential outliers, which adversely affects its performance in practical applications. In this work, we propose a novel feature optimization and outlier detection method for the CSP algorithm. Specifically, we use the minimum covariance determinant (MCD) to detect and remove outliers in the dataset, then we use the Fisher score to evaluate and select features. In addition, in order to prevent the emergence of new outliers, we propose an iterative minimum covariance determinant (IMCD) algorithm. We evaluate our proposed algorithm in terms of iteration times, classification accuracy and feature distribution using two BCI competition datasets. The experimental results show that the average classification performance of our proposed method is 12% and 22.9% higher than that of the traditional CSP method in two datasets ([Formula: see text]), and our proposed method obtains better performance in comparison with other competing methods. The results show that our method improves the performance of MI-BCI systems.

Tactile P300 brain-computer interface (BCI) generally has a worse accuracy and information transfer rate (ITR) than the visual-based BCI. It may be due to the fact that human beings have a relatively poor tactile perception. This study investigated the influence of visual attention on the performance of a tactile P300 BCI. We designed our paradigms based on a novel cheeks-stim paradigm which attached the stimulators on the subject's cheeks. Two paradigms were designed as follows: a paradigm with no visual attention and another paradigm with visual attention to the target position. Eleven subjects were invited to perform the two paradigms. We also recorded and analyzed the eyeball movement data during the paradigm with visual attention to explore whether the eyeball movement would have an effect on the BCI classification. The average online accuracy was 89.09% for the paradigm with visual attention, which was significantly higher than that of the paradigm with no visual attention (70.45%). Significant difference in ITR was also found between the two paradigms ([Formula: see text]). The results demonstrated that visual attention was an effective method to improve the performance of tactile P300 BCI. Our findings suggested that it may be feasible to complete an efficient tactile BCI system by adding visual attention.

The common spatial pattern (CSP) algorithm is a well-recognized spatial filtering method for feature extraction in motor imagery (MI)-based brain-computer interfaces (BCIs). However, due to the influence of nonstationary in electroencephalography (EEG) and inherent defects of the CSP objective function, the spatial filters, and their corresponding features are not necessarily optimal in the feature space used within CSP. In this work, we design a new feature selection method to address this issue by selecting features based on an improved objective function. Especially, improvements are made in suppressing outliers and discovering features with larger interclass distances. Moreover, a fusion algorithm based on the Dempster-Shafer theory is proposed, which takes into consideration the distribution of features. With two competition data sets, we first evaluate the performance of the improved objective functions in terms of classification accuracy, feature distribution, and embeddability. Then, a comparison with other feature selection methods is carried out in both accuracy and computational time. Experimental results show that the proposed methods consume less additional computational cost and result in a significant increase in the performance of MI-based BCI systems.