Siwei Liu

Siwei Liu, Xi Wang, Craig Macdonald et al.

The use of pre-training is an emerging technique to enhance a neural model's performance, which has been shown to be effective for many neural language models such as BERT. This technique has also been used to enhance the performance of recommender systems. In such recommender systems, pre-training models are used to learn a better initialisation for both users and items. However, recent existing pre-trained recommender systems tend to only incorporate the user interaction data at the pre-training stage, making it difficult to deliver good recommendations, especially when the interaction data is sparse. To alleviate this common data sparsity issue, we propose to pre-train the recommendation model not only with the interaction data but also with other available information such as the social relations among users, thereby providing the recommender system with a better initialisation compared with solely relying on the user interaction data. We propose a novel recommendation model, the Social-aware Gaussian Pre-trained model (SGP), which encodes the user social relations and interaction data at the pre-training stage in a Graph Neural Network (GNN). Afterwards, in the subsequent fine-tuning stage, our SGP model adopts a Gaussian Mixture Model (GMM) to factorise these pre-trained embeddings for further training, thereby benefiting the cold-start users from these pre-built social relations. Our extensive experiments on three public datasets show that, in comparison to 16 competitive baselines, our SGP model significantly outperforms the best baseline by upto 7.7% in terms of NDCG@10. In addition, we show that SGP permits to effectively alleviate the cold-start problem, especially when users newly register to the system through their friends' suggestions.

Xiang Li, Yong Tao, Siyuan Zhang et al.

Earth observation foundation models have shown strong generalization across multiple Earth observation tasks, but their robustness under real-world perturbations remains underexplored. To bridge this gap, we introduce REOBench, the first comprehensive benchmark for evaluating the robustness of Earth observation foundation models across six tasks and twelve types of image corruptions, including both appearance-based and geometric perturbations. To ensure realistic and fine-grained evaluation, our benchmark focuses on high-resolution optical remote sensing images, which are widely used in critical applications such as urban planning and disaster response. We conduct a systematic evaluation of a broad range of models trained using masked image modeling, contrastive learning, and vision-language pre-training paradigms. Our results reveal that (1) existing Earth observation foundation models experience significant performance degradation when exposed to input corruptions. (2) The severity of degradation varies across tasks, model architectures, backbone sizes, and types of corruption, with performance drop varying from less than 1% to over 20%. (3) Vision-language models show enhanced robustness, particularly in multimodal tasks. REOBench underscores the vulnerability of current Earth observation foundation models to real-world corruptions and provides actionable insights for developing more robust and reliable models. Code and data are publicly available at https://github.com/lx709/REOBench.

Yingxu Wang, Siwei Liu, Jinyuan Fang et al.

Multi-agent systems (MAS) have emerged as a powerful paradigm for orchestrating large language models (LLMs) and specialized tools to collaboratively address complex tasks. However, existing MAS frameworks often require manual workflow configuration and lack native support for dynamic evolution and performance optimization. In addition, many MAS optimization algorithms are not integrated into a unified framework. In this paper, we present EvoAgentX, an open-source platform that automates the generation, execution, and evolutionary optimization of multi-agent workflows. EvoAgentX employs a modular architecture consisting of five core layers: the basic components, agent, workflow, evolving, and evaluation layers. Specifically, within the evolving layer, EvoAgentX integrates three MAS optimization algorithms, TextGrad, AFlow, and MIPRO, to iteratively refine agent prompts, tool configurations, and workflow topologies. We evaluate EvoAgentX on HotPotQA, MBPP, and MATH for multi-hop reasoning, code generation, and mathematical problem solving, respectively, and further assess it on real-world tasks using GAIA. Experimental results show that EvoAgentX consistently achieves significant performance improvements, including a 7.44% increase in HotPotQA F1, a 10.00% improvement in MBPP pass@1, a 10.00% gain in MATH solve accuracy, and an overall accuracy improvement of up to 20.00% on GAIA. The source code is available at: https://github.com/EvoAgentX/EvoAgentX

Yingxu Wang, Victor Liang, Nan Yin et al.

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$_α$ 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.

Yingxu Wang, Nan Yin, Mingyan Xiao et al.

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.

Yingxu Wang, Kunyu Zhang, Jiaxin Huang et al.

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity, bioactivity, and physicochemical properties through the integration of structural and semantic information. However, existing multimodal methods suffer from two key limitations: (1) they typically perform cross-modal interaction only at the final encoder layer, thus overlooking hierarchical semantic dependencies; (2) they lack a unified prototype space for robust alignment between modalities. To address these limitations, we propose ProtoMol, a prototype-guided multimodal framework that enables fine-grained integration and consistent semantic alignment between molecular graphs and textual descriptions. ProtoMol incorporates dual-branch hierarchical encoders, utilizing Graph Neural Networks to process structured molecular graphs and Transformers to encode unstructured texts, resulting in comprehensive layer-wise representations. Then, ProtoMol introduces a layer-wise bidirectional cross-modal attention mechanism that progressively aligns semantic features across layers. Furthermore, a shared prototype space with learnable, class-specific anchors is constructed to guide both modalities toward coherent and discriminative representations. Extensive experiments on multiple benchmark datasets demonstrate that ProtoMol consistently outperforms state-of-the-art baselines across a variety of molecular property prediction tasks.

Zhaohan Meng, Zaiqiao Meng, Siwei Liu et al.

Large Language Models (LLMs) have shown strong performance on static medical Question Answering (QA) tasks, yet their reasoning often deteriorates in multi-turn clinical dialogues where patient information is scattered across turns. This paper introduces TriMediQ, a triplet-structured approach that enhances the reasoning reliability of LLMs through explicit knowledge integration. TriMediQ first employs a frozen triplet extraction LLM to convert patient responses into clinically grounded triplets, ensuring factual precision via constrained prompting. These triplets are incorporated into a patient-specific Knowledge Graph (KG), from which a trainable projection module consisting of a graph encoder and a projector captures relational dependencies while keeping all LLM parameters frozen. During inference, the projection module guides multi-hop reasoning over the KG, enabling coherent clinical dialogue understanding. Experiments on two interactive medical QA benchmarks show that TriMediQ achieves up to 10.4\% improvement in accuracy over five existing baselines on the iMedQA dataset. These results demonstrate that structuring patient information as triplets can effectively improve the reasoning capability of LLMs in multi-turn medical QA.

Dilshod Azizov, Muhammad Arslan Manzoor, Velibor Bojkovic et al.

Deep learning has fundamentally reshaped the landscape of artificial intelligence over the past decade, enabling remarkable achievements across diverse domains. At the heart of these developments lie multi-layered neural network architectures that excel at automatic feature extraction, leading to significant improvements in machine learning tasks. To demystify these advances and offer accessible guidance, we present a comprehensive overview of the most influential deep learning algorithms selected through a broad-based survey of the field. Our discussion centers on pivotal architectures, including Residual Networks, Transformers, Generative Adversarial Networks, Variational Autoencoders, Graph Neural Networks, Contrastive Language-Image Pre-training, and Diffusion models. We detail their historical context, highlight their mathematical foundations and algorithmic principles, and examine subsequent variants, extensions, and practical considerations such as training methodologies, normalization techniques, and learning rate schedules. Beyond historical and technical insights, we also address their applications, challenges, and potential research directions. This survey aims to serve as a practical manual for both newcomers seeking an entry point into cutting-edge deep learning methods and experienced researchers transitioning into this rapidly evolving domain.

Zaiqiao Meng, Siwei Liu, Craig Macdonald et al.

Leveraging the side information associated with entities (i.e. users and items) to enhance the performance of recommendation systems has been widely recognized as an important modelling dimension. While many existing approaches focus on the integration scheme to incorporate entity side information -- by combining the recommendation loss function with an extra side information-aware loss -- in this paper, we propose instead a novel pre-training scheme for leveraging the side information. In particular, we first pre-train a representation model using the side information of the entities, and then fine-tune it using an existing general representation-based recommendation model. Specifically, we propose two pre-training models, named GCN-P and COM-P, by considering the entities and their relations constructed from side information as two different types of graphs respectively, to pre-train entity embeddings. For the GCN-P model, two single-relational graphs are constructed from all the users' and items' side information respectively, to pre-train entity representations by using the Graph Convolutional Networks. For the COM-P model, two multi-relational graphs are constructed to pre-train the entity representations by using the Composition-based Graph Convolutional Networks. An extensive evaluation of our pre-training models fine-tuned under four general representation-based recommender models, i.e. MF, NCF, NGCF and LightGCN, shows that effectively pre-training embeddings with both the user's and item's side information can significantly improve these original models in terms of both effectiveness and stability.

Gao Xu, Yuanpeng Long, Siwei Liu et al.

The flow-based generative model is a deep learning generative model, which obtains the ability to generate data by explicitly learning the data distribution. Theoretically its ability to restore data is stronger than other generative models. However, its implementation has many limitations, including limited model design, too many model parameters and tedious calculation. In this paper, a bi-parallel linear flow model for facial emotion generation from emotion set images is constructed, and a series of improvements have been made in terms of the expression ability of the model and the convergence speed in training. The model is mainly composed of several coupling layers superimposed to form a multi-scale structure, in which each coupling layer contains 1*1 reversible convolution and linear operation modules. Furthermore, this paper sorted out the current public data set of facial emotion images, made a new emotion data, and verified the model through this data set. The experimental results show that, under the traditional convolutional neural network, the 3-layer 3*3 convolution kernel is more conducive to extracte the features of the face images. The introduction of principal component decomposition can improve the convergence speed of the model.