Inferencing Gene Regulatory Networks (GRNs) from gene expression data is a pivotal challenge in systems biology, and several innovative computational methods have been introduced. However, most of these studies have not considered the skewed degree distribution of genes. Specifically, some genes may regulate multiple target genes while some genes may be regulated by multiple regulator genes. Such a skewed degree distribution issue significantly complicates the application of directed graph embedding methods. To tackle this issue, we propose the Cross-Attention Complex Dual Graph Embedding Model (XATGRN). Our XATGRN employs a cross-attention mechanism to effectively capture intricate gene interactions from gene expression profiles. Additionally, it uses a Dual Complex Graph Embedding approach to manage the skewed degree distribution, thereby ensuring precise prediction of regulatory relationships and their directionality. Our model consistently outperforms existing state-of-the-art methods across various datasets, underscoring its efficacy in elucidating complex gene regulatory mechanisms.

Classifying antimicrobial peptides(AMPs) from the vast array of peptides mined from metagenomic sequencing data is a significant approach to addressing the issue of antibiotic resistance. However, current AMP classification methods, primarily relying on sequence-based data, neglect the spatial structure of peptides, thereby limiting the accurate classification of AMPs. Additionally, the number of known AMPs is significantly lower than that of non-AMPs, leading to imbalanced datasets that reduce predictive accuracy for AMPs. To alleviate these two limitations, we first employ Omegafold to predict the three-dimensional spatial structures of AMPs and non-AMPs, constructing peptide graphs based on the amino acids' C$_\alpha$ positions. Building upon this, we propose a novel classification model named Spatial GNN-based AMP Classifier (SGAC). Our SGAC model employs a graph encoder based on Graph Neural Networks (GNNs) to process peptide graphs, generating high-dimensional representations that capture essential features from the three-dimensional spatial structure of amino acids. Then, to address the inherent imbalanced datasets, SGAC first incorporates Weight-enhanced Contrastive Learning, which clusters similar peptides while ensuring separation between dissimilar ones, using weighted contributions to emphasize AMP-specific features. Furthermore, SGAC employs Weight-enhanced Pseudo-label Distillation to dynamically generate high-confidence pseudo labels for ambiguous peptides, further refining predictions and promoting balanced learning between AMPs and non-AMPs. Experiments on publicly available AMP and non-AMP datasets demonstrate that SGAC significantly outperforms traditional sequence-based methods and achieves state-of-the-art performance among graph-based models, validating its effectiveness in AMP classification.

At the core of this transformation is the development of multi-layered neural network architectures that facilitate automatic feature extraction from raw data, significantly improving the efficiency on machine learning tasks. Given the rapid pace of these advancements, an accessible manual is necessary to distill the key advances of the past decade. With this in mind, we introduce a study which highlights the evolution of deep learning, largely attributed to powerful algorithms. Among the multitude of breakthroughs, certain algorithms, including Residual Networks (ResNets), Transformers, Generative Adversarial Networks (GANs), Variational Autoencoders (VAEs), Graph Neural Networks (GNNs), Contrastive Language-Image Pretraining (CLIP) and Diffusion models, have emerged as the cornerstones and driving forces behind the discipline. We select these algorithms via a survey targeting a broad spectrum of academics and professionals with the aim of encapsulating the essence of the most influential algorithms over the past decade. In this work, we provide details on the selection methodology, exploring the mentioned architectures in a broader context of the history of deep learning. We present an overview of selected core architectures, their mathematical underpinnings, and the algorithmic procedures that define the subsequent extensions and variants of these models, their applications, and their challenges and potential future research directions. In addition, we explore the practical aspects related to these algorithms, such as training and optimization methods, normalization techniques, and rate scheduling strategies that are essential for their effective implementation. Therefore, our manuscript serves as a practical survey for understanding and applying these crucial algorithms and aims to provide a manual for experienced researchers transitioning into deep learning from other domains, as well as for beginners seeking to grasp the trending algorithms.

Graph Neural Networks (GNNs) with equivariant properties have achieved significant success in modeling complex dynamic systems and molecular properties. However, their expressiveness ability is limited by: (1) Existing methods often overlook the over-smoothing issue caused by traditional GNN models, as well as the gradient explosion or vanishing problems in deep GNNs. (2) Most models operate on first-order information, neglecting that the real world often consists of second-order systems, which further limits the model's representation capabilities. To address these issues, we propose the \textbf{Du}al \textbf{S}econd-order \textbf{E}quivariant \textbf{G}raph \textbf{O}rdinary Differential Equation (\method{}) for equivariant representation. Specifically, \method{} apply the dual second-order equivariant graph ordinary differential equations (Graph ODEs) on graph embeddings and node coordinates, simultaneously. Theoretically, we first prove that \method{} maintains the equivariant property. Furthermore, we provide theoretical insights showing that \method{} effectively alleviates the over-smoothing problem in both feature representation and coordinate update. Additionally, we demonstrate that the proposed \method{} mitigates the exploding and vanishing gradients problem, facilitating the training of deep multi-layer GNNs. Extensive experiments on benchmark datasets validate the superiority of the proposed \method{} compared to baselines.

Spiking Graph Networks (SGNs) have garnered significant attraction from both researchers and industry due to their ability to address energy consumption challenges in graph classification. However, SGNs are only effective for in-distribution data and cannot tackle out-of-distribution data. In this paper, we first propose the domain adaptation problem in SGNs, and introduce a novel framework named Degree-aware Spiking Graph Domain Adaptation for Classification. The proposed DeSGDA addresses the spiking graph domain adaptation problem by three aspects: node degree-aware personalized spiking representation, adversarial feature distribution alignment, and pseudo-label distillation. First, we introduce the personalized spiking representation method for generating degree-dependent spiking signals. Specifically, the threshold of triggering a spike is determined by the node degree, allowing this personalized approach to capture more expressive information for classification. Then, we propose the graph feature distribution alignment module that is adversarially trained using membrane potential against a domain discriminator. Such an alignment module can efficiently maintain high performance and low energy consumption in the case of inconsistent distribution. Additionally, we extract consistent predictions across two spaces to create reliable pseudo-labels, effectively leveraging unlabeled data to enhance graph classification performance. Extensive experiments on benchmark datasets validate the superiority of the proposed DeSGDA compared with competitive baselines.

Many Click-Through Rate (CTR) prediction works focused on designing advanced architectures to model complex feature interactions but neglected the importance of feature representation learning, e.g., adopting a plain embedding layer for each feature, which results in sub-optimal feature representations and thus inferior CTR prediction performance. For instance, low frequency features, which account for the majority of features in many CTR tasks, are less considered in standard supervised learning settings, leading to sub-optimal feature representations. In this paper, we introduce self-supervised learning to produce high-quality feature representations directly and propose a model-agnostic Contrastive Learning for CTR (CL4CTR) framework consisting of three self-supervised learning signals to regularize the feature representation learning: contrastive loss, feature alignment, and field uniformity. The contrastive module first constructs positive feature pairs by data augmentation and then minimizes the distance between the representations of each positive feature pair by the contrastive loss. The feature alignment constraint forces the representations of features from the same field to be close, and the field uniformity constraint forces the representations of features from different fields to be distant. Extensive experiments verify that CL4CTR achieves the best performance on four datasets and has excellent effectiveness and compatibility with various representative baselines.

Symbiotic Autonomous Systems (SAS) are advanced intelligent and cognitive systems exhibiting autonomous collective intelligence enabled by coherent symbiosis of human-machine interactions in hybrid societies. Basic research in the emerging field of SAS has triggered advanced general AI technologies functioning without human intervention or hybrid symbiotic systems synergizing humans and intelligent machines into coherent cognitive systems. This work presents a theoretical framework of SAS underpinned by the latest advances in intelligence, cognition, computer, and system sciences. SAS are characterized by the composition of autonomous and symbiotic systems that adopt bio-brain-social-inspired and heterogeneously synergized structures and autonomous behaviors. This paper explores their cognitive and mathematical foundations. The challenge to seamless human-machine interactions in a hybrid environment is addressed. SAS-based collective intelligence is explored in order to augment human capability by autonomous machine intelligence towards the next generation of general AI, autonomous computers, and trustworthy mission-critical intelligent systems. Emerging paradigms and engineering applications of SAS are elaborated via an autonomous knowledge learning system that symbiotically works between humans and cognitive robots.