Interictal Epileptiform Discharge is essential for identifying epilepsy. However, the unpredictable and non-stationary nature of electroencephalogram (EEG) patterns poses considerable challenges for reliable identification. Manual interpretation of EEG is subjective and time-consuming. With advancements in machine learning and deep learning, computer-aided approaches for automated IED detection have been rapidly developed. The state-of-the-art convolutional neural network (CNN)-based methods have shown promising results but struggle to capture long-term dependencies in time-series data. In contrast, Transformer excels at modeling sequential information through self-attention mechanisms, overcoming the CNN limitations. This study proposes an IED Detector (IEDD) that integrates convolutional layers and a Transformer to detect IEDs. The IEDD initially employs convolutional layers to extract local features of IEDs, followed by a Transformer to model long-term dependencies. To further extract spatial features, EEG data are represented as a three-dimensional tensor with embedded channel topology, where a CNN captures spatial features at each sampling point and a Long Short-Term Memory (LSTM) network models their temporal evolution. Additionally, due to the scarcity of IED data, a novel Transformer-based Generative Adversarial Network (GAN) is developed to augment the IED dataset. Experimental results show the proposed approach achieves an average accuracy of 96.11% on the augmented Dataset 1 and 95.25% on Dataset 2 for binary classification, with an average sensitivity of 87.26% and precision of 89.96% for multi-label classification. These findings provide valuable insights into advancing deep learning and Transformer-based approaches for automated IED detection.

The 3D conformation of the chromatin is crucial for transcriptional regulation. However, current experimental techniques for detecting the 3D structure of the genome are costly and limited to the biological conditions. Here, we described "ChrombusXMBD," a graph convolution model capable of predicting chromatin interactions ab initio based on available chromatin features. Using dynamic edge convolution with multihead attention mechanism, Chrombus encodes the 2D-chromatin features into a learnable embedding space, thereby generating a genome-wide 3D-contactmap. In validation, Chrombus effectively recapitulated the topological associated domains, expression quantitative trait loci, and promoter/enhancer interactions. Especially, Chrombus outperforms existing algorithms in predicting chromatin interactions over 1-2 Mb, increasing prediction correlation by 11.8%-48.7%, and predicts long-range interactions over 2 Mb (Pearson's coefficient 0.243-0.582). Chrombus also exhibits strong generalizability across human and mouse-derived cell lines. Additionally, the parameters of Chrombus inform the biological mechanisms underlying cistrome. Our model provides a new, generalizable analytical tool for understanding the complex dynamics of chromatin interactions and the landscape of cis-regulation of gene expression.

In clinical acupuncture practice, needle twirling (NT) and needle retention (NR) are strategically combined to achieve different therapeutic effects, highlighting the importance of distinguishing between different acupuncture states. Scalp EEG has been proven significantly relevant to brain activity and acupuncture stimulation. In this work, we designed an acupuncture paradigm to collect scalp EEG to study the differences in EEG changes during different acupuncture states. Since deep learning (DL) has been increasingly used in EEG analysis, we propose the Acupuncture Transformer Detector (ATD), a model based on Convolutional Neural Networks (CNN) and Transformer technology. ATD encapsulates the local and global features of EEG under the acupuncture states of Zusanli acupoint (ST-36) in an end-to-end classification framework. The experiment results from 28 healthy participants show that the proposed model can efficiently classify the EEG in different states, with an accuracy of $85.47\pm 0.73\%$. In this study, time-frequency analysis revealed that power changes were mainly confined to the delta frequency band under different acupuncture states. Brain topography revealed that ST-36 was activated primarily on the left frontal and parieto-occipital areas. This method provides new ideas for automatic recognition of acupuncture status from the perspective of DL, offering new solutions for standardizing acupuncture procedures.

High-quality scalp EEG datasets are extremely valuable for motor imagery (MI) analysis. However, due to electrode size and montage, different datasets inevitably experience channel information loss, posing a significant challenge for MI decoding. A 2D representation that focuses on the time domain may loss the spatial information in EEG. In contrast, a 3D representation based on topography may suffer from channel loss and introduce noise through different padding methods. In this paper, we propose a framework called Reference Electrode Standardization Interpolation Network (REI-Net). Through an interpolation of 3D representation, REI-Net retains the temporal information in 2D scalp EEG while improving the spatial resolution within a certain montage. Additionally, to overcome the data variability caused by individual differences, transfer learning is employed to enhance the decoding robustness. Our approach achieves promising performance on two widely-recognized MI datasets, with an accuracy of 77.99% on BCI-C IV-2a and an accuracy of 63.94% on Kaya2018. The proposed algorithm outperforms the SOTAs leading to more accurate and robust results.

High-frequency oscillations (HFOs) are spontaneous magnetoencephalography (MEG) patterns that have been acknowledged as a putative biomarker to identify epileptic foci. Correct detection of HFOs in the MEG signals is crucial for the accurate and timely clinical evaluation. Since the visual examination of HFOs is time-consuming, error-prone, and with poor inter-reviewer reliability, an automatic HFOs detector is highly desirable in clinical practice. However, the existing approaches for HFOs detection may not be applicable for MEG signals with noisy background activity. Therefore, we employ the stacked sparse autoencoder (SSAE) and propose an SSAE-based MEG HFOs (SMO) detector to facilitate the clinical detection of HFOs. To the best of our knowledge, this is the first attempt to conduct HFOs detection in MEG using deep learning methods. After configuration optimization, our proposed SMO detector is outperformed other classic peer models by achieving 89.9% in accuracy, 88.2% in sensitivity, and 91.6% in specificity. Furthermore, we have tested the performance consistency of our model using various validation schemes. The distribution of performance metrics demonstrates that our model can achieve steady performance.

In this paper, we propose PGIS, a parallelism and garbage collection aware I/O Scheduler, which identifies the hot data based on trace characteristics to exploit the channel level internal parallelism of flash-based storage systems. PGIS not only fully exploits abundant channel resource in the SSD, but also it introduces a hot data identification mechanism to reduce the garbage collection overhead. By dispatching hot read data to different channel, the channel level internal parallelism is fully exploited. By dispatching hot write data to the same physical block, the garbage collection overhead has been alleviated. The experiment results show that compared with existing I/O schedulers, PGIS improves the response time and garbage collection performance significantly. Consequently, PGIS reduces the garbage collection overhead up to 30.9%, while exploiting channel level internal parallelism.

This paper presents an SSD-based Block I/O Scheduler, short for SBIOS. SBIOS fully exploits the internal parallelism to improve the system performance. It dispatches the read requests to different blocks to make full use of SSD internal parallelism. For write requests, it tries to dispatch write requests to the same block to alleviate the block cross penalty and garbage collection overhead. The evaluation results show that compared with other I/O schedulers in the Linux kernel, SBIOS reduces the average response time significantly. Consequently, the performance of the SSD-based storage systems is improved.