He, Fei
MSA-CNN: A Lightweight Multi-Scale CNN with Attention for Sleep Stage Classification
Goerttler, Stephan, Wang, Yucheng, Eldele, Emadeldeen, Wu, Min, He, Fei
Recent advancements in machine learning-based signal analysis, coupled with open data initiatives, have fuelled efforts in automatic sleep stage classification. Despite the proliferation of classification models, few have prioritised reducing model complexity, which is a crucial factor for practical applications. In this work, we introduce Multi-Scale and Attention Convolutional Neural Network (MSA-CNN), a lightweight architecture featuring as few as ~10,000 parameters. MSA-CNN leverages a novel multi-scale module employing complementary pooling to eliminate redundant filter parameters and dense convolutions. Model complexity is further reduced by separating temporal and spatial feature extraction and using cost-effective global spatial convolutions. This separation of tasks not only reduces model complexity but also mirrors the approach used by human experts in sleep stage scoring. We evaluated both small and large configurations of MSA-CNN against nine state-of-the-art baseline models across three public datasets, treating univariate and multivariate models separately. Our evaluation, based on repeated cross-validation and re-evaluation of all baseline models, demonstrated that the large MSA-CNN outperformed all baseline models on all three datasets in terms of accuracy and Cohen's kappa, despite its significantly reduced parameter count. Lastly, we explored various model variants and conducted an in-depth analysis of the key modules and techniques, providing deeper insights into the underlying mechanisms. The code for our models, baselines, and evaluation procedures is available at https://github.com/sgoerttler/MSA-CNN.
EEG-GMACN: Interpretable EEG Graph Mutual Attention Convolutional Network
Ye, Haili, Goerttler, Stephan, He, Fei
Electroencephalogram (EEG) is a valuable technique to record brain electrical activity through electrodes placed on the scalp. Analyzing EEG signals contributes to the understanding of neurological conditions and developing brain-computer interface. Graph Signal Processing (GSP) has emerged as a promising method for EEG spatial-temporal analysis, by further considering the topological relationships between electrodes. However, existing GSP studies lack interpretability of electrode importance and the credibility of prediction confidence. This work proposes an EEG Graph Mutual Attention Convolutional Network (EEG-GMACN), by introducing an 'Inverse Graph Weight Module' to output interpretable electrode graph weights, enhancing the clinical credibility and interpretability of EEG classification results. Additionally, we incorporate a mutual attention mechanism module into the model to improve its capability to distinguish critical electrodes and introduce credibility calibration to assess the uncertainty of prediction results. This study enhances the transparency and effectiveness of EEG analysis, paving the way for its widespread use in clinical and neuroscience research.
NonSysId: A nonlinear system identification package with improved model term selection for NARMAX models
Gunawardena, Rajintha, Lang, Zi-Qiang, He, Fei
System identification involves constructing mathematical models of dynamic systems using input-output data, enabling analysis and prediction of system behaviour in both time and frequency domains. This approach can model the entire system or capture specific dynamics within it. For meaningful analysis, it is essential for the model to accurately reflect the underlying system's behaviour. This paper introduces NonSysId, an open-sourced MATLAB software package designed for nonlinear system identification, specifically focusing on NARMAX models. The software incorporates an advanced term selection methodology that prioritises on simulation (free-run) accuracy while preserving model parsimony. A key feature is the integration of iterative Orthogonal Forward Regression (iOFR) with Predicted Residual Sum of Squares (PRESS) statistic-based term selection, facilitating robust model generalisation without the need for a separate validation dataset. Furthermore, techniques for reducing computational overheads are implemented. These features make NonSysId particularly suitable for real-time applications such as structural health monitoring, fault diagnosis, and biomedical signal processing, where it is a challenge to capture the signals under consistent conditions, resulting in limited or no validation data.
Balancing Spectral, Temporal and Spatial Information for EEG-based Alzheimer's Disease Classification
Goerttler, Stephan, He, Fei, Wu, Min
The prospect of future treatment warrants the development of cost-effective screening for Alzheimer's disease (AD). A promising candidate in this regard is electroencephalography (EEG), as it is one of the most economic imaging modalities. Recent efforts in EEG analysis have shifted towards leveraging spatial information, employing novel frameworks such as graph signal processing or graph neural networks. Here, we investigate the importance of spatial information relative to spectral or temporal information by varying the proportion of each dimension for AD classification. To do so, we systematically test various dimension resolution configurations on two routine EEG datasets. Our findings show that spatial information is more important than temporal information and equally valuable as spectral information. On the larger second dataset, substituting spectral with spatial information even led to an increase of 1.1% in accuracy, which emphasises the importance of spatial information for EEG-based AD classification. We argue that our resolution-based feature extraction has the potential to improve AD classification specifically, and multivariate signal classification generally.
Deep Automated Mechanism Design for Integrating Ad Auction and Allocation in Feed
Li, Xuejian, Wang, Ze, Zhu, Bingqi, He, Fei, Wang, Yongkang, Wang, Xingxing
E-commerce platforms usually present an ordered list, mixed with several organic items and an advertisement, in response to each user's page view request. This list, the outcome of ad auction and allocation processes, directly impacts the platform's ad revenue and gross merchandise volume (GMV). Specifically, the ad auction determines which ad is displayed and the corresponding payment, while the ad allocation decides the display positions of the advertisement and organic items. The prevalent methods of segregating the ad auction and allocation into two distinct stages face two problems: 1) Ad auction does not consider externalities, such as the influence of actual display position and context on ad Click-Through Rate (CTR); 2) The ad allocation, which utilizes the auction-winning ad's payment to determine the display position dynamically, fails to maintain incentive compatibility (IC) for the advertisement. For instance, in the auction stage employing the traditional Generalized Second Price (GSP) , even if the winning ad increases its bid, its payment remains unchanged. This implies that the advertisement cannot secure a better position and thus loses the opportunity to achieve higher utility in the subsequent ad allocation stage. Previous research often focused on one of the two stages, neglecting the two-stage problem, which may result in suboptimal outcomes...
Graph Neural Network-based EEG Classification: A Survey
Klepl, Dominik, Wu, Min, He, Fei
Graph neural networks (GNN) are increasingly used to classify EEG for tasks such as emotion recognition, motor imagery and neurological diseases and disorders. A wide range of methods have been proposed to design GNN-based classifiers. Therefore, there is a need for a systematic review and categorisation of these approaches. We exhaustively search the published literature on this topic and derive several categories for comparison. These categories highlight the similarities and differences among the methods. The results suggest a prevalence of spectral graph convolutional layers over spatial. Additionally, we identify standard forms of node features, with the most popular being the raw EEG signal and differential entropy. Our results summarise the emerging trends in GNN-based approaches for EEG classification. Finally, we discuss several promising research directions, such as exploring the potential of transfer learning methods and appropriate modelling of cross-frequency interactions.
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs
He, Fei, Yang, Zhiyuan, Gao, Mingyue, Poudel, Biplab, Dhas, Newgin Sam Ebin Sam, Gyawali, Rajan, Dhakal, Ashwin, Cheng, Jianlin, Xu, Dong
Cryo-electron microscopy (cryo-EM) remains pivotal in structural biology, yet the task of protein particle picking, integral for 3D protein structure construction, is laden with manual inefficiencies. While recent AI tools such as Topaz and crYOLO are advancing the field, they do not fully address the challenges of cryo-EM images, including low contrast, complex shapes, and heterogeneous conformations. This study explored prompt-based learning to adapt the state-of-the-art image segmentation foundation model Segment Anything Model (SAM) for cryo-EM. This focus was driven by the desire to optimize model performance with a small number of labeled data without altering pre-trained parameters, aiming for a balance between adaptability and foundational knowledge retention. Through trials with three prompt-based learning strategies, namely head prompt, prefix prompt, and encoder prompt, we observed enhanced performance and reduced computational requirements compared to the fine-tuning approach. This work not only highlights the potential of prompting SAM in protein identification from cryo-EM micrographs but also suggests its broader promise in biomedical image segmentation and object detection.
Adaptive Gated Graph Convolutional Network for Explainable Diagnosis of Alzheimer's Disease using EEG Data
Klepl, Dominik, He, Fei, Wu, Min, Blackburn, Daniel J., Sarrigiannis, Ptolemaios G.
Graph neural network (GNN) models are increasingly being used for the classification of electroencephalography (EEG) data. However, GNN-based diagnosis of neurological disorders, such as Alzheimer's disease (AD), remains a relatively unexplored area of research. Previous studies have relied on functional connectivity methods to infer brain graph structures and used simple GNN architectures for the diagnosis of AD. In this work, we propose a novel adaptive gated graph convolutional network (AGGCN) that can provide explainable predictions. AGGCN adaptively learns graph structures by combining convolution-based node feature enhancement with a correlation-based measure of power spectral density similarity. Furthermore, the gated graph convolution can dynamically weigh the contribution of various spatial scales. The proposed model achieves high accuracy in both eyes-closed and eyes-open conditions, indicating the stability of learned representations. Finally, we demonstrate that the proposed AGGCN model generates consistent explanations of its predictions that might be relevant for further study of AD-related alterations of brain networks.
Model-Free Market Risk Hedging Using Crowding Networks
Zlotnikov, Vadim, Liu, Jiayu, Halperin, Igor, He, Fei, Huang, Lisa
Crowding is widely regarded as one of the most important risk factors in designing portfolio strategies. In this paper, we analyze stock crowding using network analysis of fund holdings, which is used to compute crowding scores for stocks. These scores are used to construct costless long-short portfolios, computed in a distribution-free (model-free) way and without using any numerical optimization, with desirable properties of hedge portfolios. More speciTically, these long-short portfolios provide protection for both small and large market price Tluctuations, due to their negative correlation with the market and positive convexity as a function of market returns. By adding our long-short portfolio to a baseline portfolio such as a traditional 60/40 portfolio, our method provides an alternative way to hedge portfolio risk including tail risk, which does not require costly option-based strategies or complex numerical optimization.
Fast OBDD Reordering using Neural Message Passing on Hypergraph
Xu, Feifan, He, Fei, Xie, Enze, Li, Liang
Ordered binary decision diagrams (OBDDs) are an efficient data structure for representing and manipulating Boolean formulas. With respect to different variable orders, the OBDDs' sizes may vary from linear to exponential in the number of the Boolean variables. Finding the optimal variable order has been proved a NP-complete problem. Many heuristics have been proposed to find a near-optimal solution of this problem. In this paper, we propose a neural network-based method to predict near-optimal variable orders for unknown formulas. Viewing these formulas as hypergraphs, and lifting the message passing neural network into 3-hypergraph (MPNN3), we are able to learn the patterns of Boolean formula. Compared to the traditional methods, our method can find a near-the-best solution with an extremely shorter time, even for some hard examples.To the best of our knowledge, this is the first work on applying neural network to OBDD reordering.