Jia Wu

Chuang Liu, Yibing Zhan, Jia Wu et al.

Graph neural networks have emerged as a leading architecture for many graph-level tasks, such as graph classification and graph generation. As an essential component of the architecture, graph pooling is indispensable for obtaining a holistic graph-level representation of the whole graph. Although a great variety of methods have been proposed in this promising and fast-developing research field, to the best of our knowledge, little effort has been made to systematically summarize these works. To set the stage for the development of future works, in this paper, we attempt to fill this gap by providing a broad review of recent methods for graph pooling. Specifically, 1) we first propose a taxonomy of existing graph pooling methods with a mathematical summary for each category; 2) then, we provide an overview of the libraries related to graph pooling, including the commonly used datasets, model architectures for downstream tasks, and open-source implementations; 3) next, we further outline the applications that incorporate the idea of graph pooling in a variety of domains; 4) finally, we discuss certain critical challenges facing current studies and share our insights on future potential directions for research on the improvement of graph pooling.

Sheng Zhou, Hongjia Xu, Zhuonan Zheng et al.

Clustering is a fundamental machine learning task which has been widely studied in the literature. Classic clustering methods follow the assumption that data are represented as features in a vectorized form through various representation learning techniques. As the data become increasingly complicated and complex, the shallow (traditional) clustering methods can no longer handle the high-dimensional data type. With the huge success of deep learning, especially the deep unsupervised learning, many representation learning techniques with deep architectures have been proposed in the past decade. Recently, the concept of Deep Clustering, i.e., jointly optimizing the representation learning and clustering, has been proposed and hence attracted growing attention in the community. Motivated by the tremendous success of deep learning in clustering, one of the most fundamental machine learning tasks, and the large number of recent advances in this direction, in this paper we conduct a comprehensive survey on deep clustering by proposing a new taxonomy of different state-of-the-art approaches. We summarize the essential components of deep clustering and categorize existing methods by the ways they design interactions between deep representation learning and clustering. Moreover, this survey also provides the popular benchmark datasets, evaluation metrics and open-source implementations to clearly illustrate various experimental settings. Last but not least, we discuss the practical applications of deep clustering and suggest challenging topics deserving further investigations as future directions.

Ce Zhou, Qian Li, Chen Li et al. · allen-ai

Pretrained Foundation Models (PFMs) are regarded as the foundation for various downstream tasks with different data modalities. A PFM (e.g., BERT, ChatGPT, and GPT-4) is trained on large-scale data which provides a reasonable parameter initialization for a wide range of downstream applications. BERT learns bidirectional encoder representations from Transformers, which are trained on large datasets as contextual language models. Similarly, the generative pretrained transformer (GPT) method employs Transformers as the feature extractor and is trained using an autoregressive paradigm on large datasets. Recently, ChatGPT shows promising success on large language models, which applies an autoregressive language model with zero shot or few shot prompting. The remarkable achievements of PFM have brought significant breakthroughs to various fields of AI. Numerous studies have proposed different methods, raising the demand for an updated survey. This study provides a comprehensive review of recent research advancements, challenges, and opportunities for PFMs in text, image, graph, as well as other data modalities. The review covers the basic components and existing pretraining methods used in natural language processing, computer vision, and graph learning. Additionally, it explores advanced PFMs used for different data modalities and unified PFMs that consider data quality and quantity. The review also discusses research related to the fundamentals of PFMs, such as model efficiency and compression, security, and privacy. Finally, the study provides key implications, future research directions, challenges, and open problems in the field of PFMs. Overall, this survey aims to shed light on the research of the PFMs on scalability, security, logical reasoning ability, cross-domain learning ability, and the user-friendly interactive ability for artificial general intelligence.

Ge Zhang, Jia Wu, Jian Yang et al. · allen-ai

Graph-structured data consisting of objects (i.e., nodes) and relationships among objects (i.e., edges) are ubiquitous. Graph-level learning is a matter of studying a collection of graphs instead of a single graph. Traditional graph-level learning methods used to be the mainstream. However, with the increasing scale and complexity of graphs, Graph-level Neural Networks (GLNNs, deep learning-based graph-level learning methods) have been attractive due to their superiority in modeling high-dimensional data. Thus, a survey on GLNNs is necessary. To frame this survey, we propose a systematic taxonomy covering GLNNs upon deep neural networks, graph neural networks, and graph pooling. The representative and state-of-the-art models in each category are focused on this survey. We also investigate the reproducibility, benchmarks, and new graph datasets of GLNNs. Finally, we conclude future directions to further push forward GLNNs. The repository of this survey is available at https://github.com/GeZhangMQ/Awesome-Graph-level-Neural-Networks.

Ruitong Zhang, Hao Peng, Yingtong Dou et al.

DBSCAN is widely used in many scientific and engineering fields because of its simplicity and practicality. However, due to its high sensitivity parameters, the accuracy of the clustering result depends heavily on practical experience. In this paper, we first propose a novel Deep Reinforcement Learning guided automatic DBSCAN parameters search framework, namely DRL-DBSCAN. The framework models the process of adjusting the parameter search direction by perceiving the clustering environment as a Markov decision process, which aims to find the best clustering parameters without manual assistance. DRL-DBSCAN learns the optimal clustering parameter search policy for different feature distributions via interacting with the clusters, using a weakly-supervised reward training policy network. In addition, we also present a recursive search mechanism driven by the scale of the data to efficiently and controllably process large parameter spaces. Extensive experiments are conducted on five artificial and real-world datasets based on the proposed four working modes. The results of offline and online tasks show that the DRL-DBSCAN not only consistently improves DBSCAN clustering accuracy by up to 26% and 25% respectively, but also can stably find the dominant parameters with high computational efficiency. The code is available at https://github.com/RingBDStack/DRL-DBSCAN.

Zhizhi Yu, Di Jin, Cuiying Huo et al. · mit

Social Internet of Things (SIoT), a promising and emerging paradigm that injects the notion of social networking into smart objects (i.e., things), paving the way for the next generation of Internet of Things. However, due to the risks and uncertainty, a crucial and urgent problem to be settled is establishing reliable relationships within SIoT, that is, trust evaluation. Graph neural networks for trust evaluation typically adopt a straightforward way such as one-hot or node2vec to comprehend node characteristics, which ignores the valuable semantic knowledge attached to nodes. Moreover, the underlying structure of SIoT is usually complex, including both the heterogeneous graph structure and pairwise trust relationships, which renders hard to preserve the properties of SIoT trust during information propagation. To address these aforementioned problems, we propose a novel knowledge-enhanced graph neural network (KGTrust) for better trust evaluation in SIoT. Specifically, we first extract useful knowledge from users' comment behaviors and external structured triples related to object descriptions, in order to gain a deeper insight into the semantics of users and objects. Furthermore, we introduce a discriminative convolutional layer that utilizes heterogeneous graph structure, node semantics, and augmented trust relationships to learn node embeddings from the perspective of a user as a trustor or a trustee, effectively capturing multi-aspect properties of SIoT trust during information propagation. Finally, a trust prediction layer is developed to estimate the trust relationships between pairwise nodes. Extensive experiments on three public datasets illustrate the superior performance of KGTrust over state-of-the-art methods.

Nasrin Shabani, Jia Wu, Amin Beheshti et al.

As large-scale graphs become more widespread, more and more computational challenges with extracting, processing, and interpreting large graph data are being exposed. It is therefore natural to search for ways to summarize these expansive graphs while preserving their key characteristics. In the past, most graph summarization techniques sought to capture the most important part of a graph statistically. However, today, the high dimensionality and complexity of modern graph data are making deep learning techniques more popular. Hence, this paper presents a comprehensive survey of progress in deep learning summarization techniques that rely on graph neural networks (GNNs). Our investigation includes a review of the current state-of-the-art approaches, including recurrent GNNs, convolutional GNNs, graph autoencoders, and graph attention networks. A new burgeoning line of research is also discussed where graph reinforcement learning is being used to evaluate and improve the quality of graph summaries. Additionally, the survey provides details of benchmark datasets, evaluation metrics, and open-source tools that are often employed in experimentation settings, along with a detailed comparison, discussion, and takeaways for the research community focused on graph summarization. Finally, the survey concludes with a number of open research challenges to motivate further study in this area.

Fanzhen Liu, Xiaoxiao Ma, Jia Wu et al.

Graph anomaly detection in this paper aims to distinguish abnormal nodes that behave differently from the benign ones accounting for the majority of graph-structured instances. Receiving increasing attention from both academia and industry, yet existing research on this task still suffers from two critical issues when learning informative anomalous behavior from graph data. For one thing, anomalies are usually hard to capture because of their subtle abnormal behavior and the shortage of background knowledge about them, which causes severe anomalous sample scarcity. Meanwhile, the overwhelming majority of objects in real-world graphs are normal, bringing the class imbalance problem as well. To bridge the gaps, this paper devises a novel Data Augmentation-based Graph Anomaly Detection (DAGAD) framework for attributed graphs, equipped with three specially designed modules: 1) an information fusion module employing graph neural network encoders to learn representations, 2) a graph data augmentation module that fertilizes the training set with generated samples, and 3) an imbalance-tailored learning module to discriminate the distributions of the minority (anomalous) and majority (normal) classes. A series of experiments on three datasets prove that DAGAD outperforms ten state-of-the-art baseline detectors concerning various mostly-used metrics, together with an extensive ablation study validating the strength of our proposed modules.

Zhenyu Yang, Ge Zhang, Jia Wu et al.

Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison, regression, classification, and more. Traditional approaches to learning a set of graphs heavily rely on hand-crafted features, such as substructures. But while these methods benefit from good interpretability, they often suffer from computational bottlenecks as they cannot skirt the graph isomorphism problem. Conversely, deep learning has helped graph-level learning adapt to the growing scale of graphs by extracting features automatically and encoding graphs into low-dimensional representations. As a result, these deep graph learning methods have been responsible for many successes. Yet, there is no comprehensive survey that reviews graph-level learning starting with traditional learning and moving through to the deep learning approaches. This article fills this gap and frames the representative algorithms into a systematic taxonomy covering traditional learning, graph-level deep neural networks, graph-level graph neural networks, and graph pooling. To ensure a thoroughly comprehensive survey, the evolutions, interactions, and communications between methods from four different branches of development are also examined. This is followed by a brief review of the benchmark data sets, evaluation metrics, and common downstream applications. The survey concludes with a broad overview of 12 current and future directions in this booming field.

Jiaqian Ren, Lei Jiang, Hao Peng et al. · salesforce

The rising popularity of online social network services has attracted lots of research on mining social media data, especially on mining social events. Social event detection, due to its wide applications, has now become a trivial task. State-of-the-art approaches exploiting Graph Neural Networks (GNNs) usually follow a two-step strategy: 1) constructing text graphs based on various views (\textit{co-user}, \textit{co-entities} and \textit{co-hashtags}); and 2) learning a unified text representation by a specific GNN model. Generally, the results heavily rely on the quality of the constructed graphs and the specific message passing scheme. However, existing methods have deficiencies in both aspects: 1) They fail to recognize the noisy information induced by unreliable views. 2) Temporal information which works as a vital indicator of events is neglected in most works. To this end, we propose ETGNN, a novel Evidential Temporal-aware Graph Neural Network. Specifically, we construct view-specific graphs whose nodes are the texts and edges are determined by several types of shared elements respectively. To incorporate temporal information into the message passing scheme, we introduce a novel temporal-aware aggregator which assigns weights to neighbours according to an adaptive time exponential decay formula. Considering the view-specific uncertainty, the representations of all views are converted into mass functions through evidential deep learning (EDL) neural networks, and further combined via Dempster-Shafer theory (DST) to make the final detection. Experimental results on three real-world datasets demonstrate the effectiveness of ETGNN in accuracy, reliability and robustness in social event detection.

Jiaqian Ren, Lei Jiang, Hao Peng et al. · salesforce

Integrating multiple online social networks (OSNs) has important implications for many downstream social mining tasks, such as user preference modelling, recommendation, and link prediction. However, it is unfortunately accompanied by growing privacy concerns about leaking sensitive user information. How to fully utilize the data from different online social networks while preserving user privacy remains largely unsolved. To this end, we propose a Cross-network Social User Embedding framework, namely DP-CroSUE, to learn the comprehensive representations of users in a privacy-preserving way. We jointly consider information from partially aligned social networks with differential privacy guarantees. In particular, for each heterogeneous social network, we first introduce a hybrid differential privacy notion to capture the variation of privacy expectations for heterogeneous data types. Next, to find user linkages across social networks, we make unsupervised user embedding-based alignment in which the user embeddings are achieved by the heterogeneous network embedding technology. To further enhance user embeddings, a novel cross-network GCN embedding model is designed to transfer knowledge across networks through those aligned users. Extensive experiments on three real-world datasets demonstrate that our approach makes a significant improvement on user interest prediction tasks as well as defending user attribute inference attacks from embedding.

Usama Tariq, Rizwan Qureshi, Anas Zafar et al.

Generative models have been very successful over the years and have received significant attention for synthetic data generation. As deep learning models are getting more and more complex, they require large amounts of data to perform accurately. In medical image analysis, such generative models play a crucial role as the available data is limited due to challenges related to data privacy, lack of data diversity, or uneven data distributions. In this paper, we present a method to generate brain tumor MRI images using generative adversarial networks. We have utilized StyleGAN2 with ADA methodology to generate high-quality brain MRI with tumors while using a significantly smaller amount of training data when compared to the existing approaches. We use three pre-trained models for transfer learning. Results demonstrate that the proposed method can learn the distributions of brain tumors. Furthermore, the model can generate high-quality synthetic brain MRI with a tumor that can limit the small sample size issues. The approach can addresses the limited data availability by generating realistic-looking brain MRI with tumors. The code is available at: ~\url{https://github.com/rizwanqureshi123/Brain-Tumor-Synthetic-Data}.

Dongcheng Zou, Hao Peng, Xiang Huang et al.

Graph Neural Networks (GNNs) are de facto solutions to structural data learning. However, it is susceptible to low-quality and unreliable structure, which has been a norm rather than an exception in real-world graphs. Existing graph structure learning (GSL) frameworks still lack robustness and interpretability. This paper proposes a general GSL framework, SE-GSL, through structural entropy and the graph hierarchy abstracted in the encoding tree. Particularly, we exploit the one-dimensional structural entropy to maximize embedded information content when auxiliary neighbourhood attributes are fused to enhance the original graph. A new scheme of constructing optimal encoding trees is proposed to minimize the uncertainty and noises in the graph whilst assuring proper community partition in hierarchical abstraction. We present a novel sample-based mechanism for restoring the graph structure via node structural entropy distribution. It increases the connectivity among nodes with larger uncertainty in lower-level communities. SE-GSL is compatible with various GNN models and enhances the robustness towards noisy and heterophily structures. Extensive experiments show significant improvements in the effectiveness and robustness of structure learning and node representation learning.

Zitai Qiu, Jia Wu, Jian Yang et al.

Social events reflect the dynamics of society and, here, natural disasters and emergencies receive significant attention. The timely detection of these events can provide organisations and individuals with valuable information to reduce or avoid losses. However, due to the complex heterogeneities of the content and structure of social media, existing models can only learn limited information; large amounts of semantic and structural information are ignored. In addition, due to high labour costs, it is rare for social media datasets to include high-quality labels, which also makes it challenging for models to learn information from social media. In this study, we propose two hyperbolic graph representation-based methods for detecting social events from heterogeneous social media environments. For cases where a dataset has labels, we designed a Hyperbolic Social Event Detection (HSED) model that converts complex social information into a unified social message graph. This model addresses the heterogeneity of social media, and, with this graph, the information in social media can be used to capture structural information based on the properties of hyperbolic space. For cases where the dataset is unlabelled, we designed an Unsupervised Hyperbolic Social Event Detection (UHSED). This model is based on the HSED model but includes graph contrastive learning to make it work in unlabelled scenarios. Extensive experiments demonstrate the superiority of the proposed approaches.

Xusheng Zhao, Jia Wu, Hao Peng et al.

Modern neuroimaging techniques, such as diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI), enable us to model the human brain as a brain network or connectome. Capturing brain networks' structural information and hierarchical patterns is essential for understanding brain functions and disease states. Recently, the promising network representation learning capability of graph neural networks (GNNs) has prompted many GNN-based methods for brain network analysis to be proposed. Specifically, these methods apply feature aggregation and global pooling to convert brain network instances into meaningful low-dimensional representations used for downstream brain network analysis tasks. However, existing GNN-based methods often neglect that brain networks of different subjects may require various aggregation iterations and use GNN with a fixed number of layers to learn all brain networks. Therefore, how to fully release the potential of GNNs to promote brain network analysis is still non-trivial. To solve this problem, we propose a novel brain network representation framework, namely BN-GNN, which searches for the optimal GNN architecture for each brain network. Concretely, BN-GNN employs deep reinforcement learning (DRL) to train a meta-policy to automatically determine the optimal number of feature aggregations (reflected in the number of GNN layers) required for a given brain network. Extensive experiments on eight real-world brain network datasets demonstrate that our proposed BN-GNN improves the performance of traditional GNNs on different brain network analysis tasks.

Jiaqian Ren, Hao Peng, Lei Jiang et al. · salesforce

Real-world social events typically exhibit a severe class-imbalance distribution, which makes the trained detection model encounter a serious generalization challenge. Most studies solve this problem from the frequency perspective and emphasize the representation or classifier learning for tail classes. While in our observation, compared to the rarity of classes, the calibrated uncertainty estimated from well-trained evidential deep learning networks better reflects model performance. To this end, we propose a novel uncertainty-guided class imbalance learning framework - UCL$_{SED}$, and its variant - UCL-EC$_{SED}$, for imbalanced social event detection tasks. We aim to improve the overall model performance by enhancing model generalization to those uncertain classes. Considering performance degradation usually comes from misclassifying samples as their confusing neighboring classes, we focus on boundary learning in latent space and classifier learning with high-quality uncertainty estimation. First, we design a novel uncertainty-guided contrastive learning loss, namely UCL and its variant - UCL-EC, to manipulate distinguishable representation distribution for imbalanced data. During training, they force all classes, especially uncertain ones, to adaptively adjust a clear separable boundary in the feature space. Second, to obtain more robust and accurate class uncertainty, we combine the results of multi-view evidential classifiers via the Dempster-Shafer theory under the supervision of an additional calibration method. We conduct experiments on three severely imbalanced social event datasets including Events2012\_100, Events2018\_100, and CrisisLexT\_7. Our model significantly improves social event representation and classification tasks in almost all classes, especially those uncertain ones.

Xingcheng Fu, Yuecen Wei, Qingyun Sun et al.

Learning unbiased node representations for imbalanced samples in the graph has become a more remarkable and important topic. For the graph, a significant challenge is that the topological properties of the nodes (e.g., locations, roles) are unbalanced (topology-imbalance), other than the number of training labeled nodes (quantity-imbalance). Existing studies on topology-imbalance focus on the location or the local neighborhood structure of nodes, ignoring the global underlying hierarchical properties of the graph, i.e., hierarchy. In the real-world scenario, the hierarchical structure of graph data reveals important topological properties of graphs and is relevant to a wide range of applications. We find that training labeled nodes with different hierarchical properties have a significant impact on the node classification tasks and confirm it in our experiments. It is well known that hyperbolic geometry has a unique advantage in representing the hierarchical structure of graphs. Therefore, we attempt to explore the hierarchy-imbalance issue for node classification of graph neural networks with a novelty perspective of hyperbolic geometry, including its characteristics and causes. Then, we propose a novel hyperbolic geometric hierarchy-imbalance learning framework, named HyperIMBA, to alleviate the hierarchy-imbalance issue caused by uneven hierarchy-levels and cross-hierarchy connectivity patterns of labeled nodes.Extensive experimental results demonstrate the superior effectiveness of HyperIMBA for hierarchy-imbalance node classification tasks.

Jianxin Li, Xingcheng Fu, Qingyun Sun et al.

Generative adversarial network (GAN) is widely used for generalized and robust learning on graph data. However, for non-Euclidean graph data, the existing GAN-based graph representation methods generate negative samples by random walk or traverse in discrete space, leading to the information loss of topological properties (e.g. hierarchy and circularity). Moreover, due to the topological heterogeneity (i.e., different densities across the graph structure) of graph data, they suffer from serious topological distortion problems. In this paper, we proposed a novel Curvature Graph Generative Adversarial Networks method, named \textbf{\modelname}, which is the first GAN-based graph representation method in the Riemannian geometric manifold. To better preserve the topological properties, we approximate the discrete structure as a continuous Riemannian geometric manifold and generate negative samples efficiently from the wrapped normal distribution. To deal with the topological heterogeneity, we leverage the Ricci curvature for local structures with different topological properties, obtaining to low-distortion representations. Extensive experiments show that CurvGAN consistently and significantly outperforms the state-of-the-art methods across multiple tasks and shows superior robustness and generalization.

Yutong Qu, Wei Emma Zhang, Jian Yang et al.

Knowledge-aware methods have boosted a range of natural language processing applications over the last decades. With the gathered momentum, knowledge recently has been pumped into enormous attention in document summarization, one of natural language processing applications. Previous works reported that knowledge-embedded document summarizers excel at generating superior digests, especially in terms of informativeness, coherence, and fact consistency. This paper pursues to present the first systematic survey for the state-of-the-art methodologies that embed knowledge into document summarizers. Particularly, we propose novel taxonomies to recapitulate knowledge and knowledge embeddings under the document summarization view. We further explore how embeddings are generated in embedding learning architectures of document summarization models, especially of deep learning models. At last, we discuss the challenges of this topic and future directions.

Xing Su, Jian Yang, Jia Wu et al.

Users' involvement in creating and propagating news is a vital aspect of fake news detection in online social networks. Intuitively, credible users are more likely to share trustworthy news, while untrusted users have a higher probability of spreading untrustworthy news. In this paper, we construct a dual-layer graph (i.e., the news layer and the user layer) to extract multiple relations of news and users in social networks to derive rich information for detecting fake news. Based on the dual-layer graph, we propose a fake news detection model named Us-DeFake. It learns the propagation features of news in the news layer and the interaction features of users in the user layer. Through the inter-layer in the graph, Us-DeFake fuses the user signals that contain credibility information into the news features, to provide distinctive user-aware embeddings of news for fake news detection. The training process conducts on multiple dual-layer subgraphs obtained by a graph sampler to scale Us-DeFake in large scale social networks. Extensive experiments on real-world datasets illustrate the superiority of Us-DeFake which outperforms all baselines, and the users' credibility signals learned by interaction relation can notably improve the performance of our model.

Yuecen Wei, Xingcheng Fu, Qingyun Sun et al.

Social networks are considered to be heterogeneous graph neural networks (HGNNs) with deep learning technological advances. HGNNs, compared to homogeneous data, absorb various aspects of information about individuals in the training stage. That means more information has been covered in the learning result, especially sensitive information. However, the privacy-preserving methods on homogeneous graphs only preserve the same type of node attributes or relationships, which cannot effectively work on heterogeneous graphs due to the complexity. To address this issue, we propose a novel heterogeneous graph neural network privacy-preserving method based on a differential privacy mechanism named HeteDP, which provides a double guarantee on graph features and topology. In particular, we first define a new attack scheme to reveal privacy leakage in the heterogeneous graphs. Specifically, we design a two-stage pipeline framework, which includes the privacy-preserving feature encoder and the heterogeneous link reconstructor with gradients perturbation based on differential privacy to tolerate data diversity and against the attack. To better control the noise and promote model performance, we utilize a bi-level optimization pattern to allocate a suitable privacy budget for the above two modules. Our experiments on four public benchmarks show that the HeteDP method is equipped to resist heterogeneous graph privacy leakage with admirable model generalization.

Cheng Ji, Jianxin Li, Hao Peng et al.

Contrastive Learning (CL) has been proved to be a powerful self-supervised approach for a wide range of domains, including computer vision and graph representation learning. However, the incremental learning issue of CL has rarely been studied, which brings the limitation in applying it to real-world applications. Contrastive learning identifies the samples with the negative ones from the noise distribution that changes in the incremental scenarios. Therefore, only fitting the change of data without noise distribution causes bias, and directly retraining results in low efficiency. To bridge this research gap, we propose a self-supervised Incremental Contrastive Learning (ICL) framework consisting of (i) a novel Incremental InfoNCE (NCE-II) loss function by estimating the change of noise distribution for old data to guarantee no bias with respect to the retraining, (ii) a meta-optimization with deep reinforced Learning Rate Learning (LRL) mechanism which can adaptively learn the learning rate according to the status of the training processes and achieve fast convergence which is critical for incremental learning. Theoretically, the proposed ICL is equivalent to retraining, which is based on solid mathematical derivation. In practice, extensive experiments in different domains demonstrate that, without retraining a new model, ICL achieves up to 16.7x training speedup and 16.8x faster convergence with competitive results.

Fu Lin, Xuexiong Luo, Jia Wu et al.

Different from the current node-level anomaly detection task, the goal of graph-level anomaly detection is to find abnormal graphs that significantly differ from others in a graph set. Due to the scarcity of research on the work of graph-level anomaly detection, the detailed description of graph-level anomaly is insufficient. Furthermore, existing works focus on capturing anomalous graph information to learn better graph representations, but they ignore the importance of an effective anomaly score function for evaluating abnormal graphs. Thus, in this work, we first define anomalous graph information including node and graph property anomalies in a graph set and adopt node-level and graph-level information differences to identify them, respectively. Then, we introduce a discriminative graph-level anomaly detection framework with dual-students-teacher model, where the teacher model with a heuristic loss are trained to make graph representations more divergent. Then, two competing student models trained by normal and abnormal graphs respectively fit graph representations of the teacher model in terms of node-level and graph-level representation perspectives. Finally, we combine representation errors between two student models to discriminatively distinguish anomalous graphs. Extensive experiment analysis demonstrates that our method is effective for the graph-level anomaly detection task on graph datasets in the real world.

Kun Li, Xiantao Cai, Jia Wu et al.

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 985 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 95.4\%, with an average efficacy increase of 7.5\%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at: https://anonymous.4open.science/r/FMOP-98C2.

Shravan Venkatraman, Muthu Subash Kavitha, Joe Dhanith P R et al.

Histopathology image segmentation is essential for delineating tissue structures in skin cancer diagnostics, but modeling spatial context and inter-tissue relationships remains a challenge, especially in regions with overlapping or morphologically similar tissues. Current convolutional neural network (CNN)-based approaches operate primarily on visual texture, often treating tissues as independent regions and failing to encode biological context. To this end, we introduce Neural Tissue Relation Modeling (NTRM), a novel segmentation framework that augments CNNs with a tissue-level graph neural network to model spatial and functional relationships across tissue types. NTRM constructs a graph over predicted regions, propagates contextual information via message passing, and refines segmentation through spatial projection. Unlike prior methods, NTRM explicitly encodes inter-tissue dependencies, enabling structurally coherent predictions in boundary-dense zones. On the benchmark Histopathology Non-Melanoma Skin Cancer Segmentation Dataset, NTRM outperforms state-of-the-art methods, achieving a robust Dice similarity coefficient that is 4.9\% to 31.25\% higher than the best-performing models among the evaluated approaches. Our experiments indicate that relational modeling offers a principled path toward more context-aware and interpretable histological segmentation, compared to local receptive-field architectures that lack tissue-level structural awareness. Our code is available at https://github.com/shravan-18/NTRM.

Ziyang Chen, Wei Long, He Yao et al.

Learning-based stereo matching techniques have made significant progress. However, existing methods inevitably lose geometrical structure information during the feature channel generation process, resulting in edge detail mismatches. In this paper, the Motif Cha}nnel Attention Stereo Matching Network (MoCha-Stereo) is designed to address this problem. We provide the Motif Channel Correlation Volume (MCCV) to determine more accurate edge matching costs. MCCV is achieved by projecting motif channels, which capture common geometric structures in feature channels, onto feature maps and cost volumes. In addition, edge variations in %potential feature channels of the reconstruction error map also affect details matching, we propose the Reconstruction Error Motif Penalty (REMP) module to further refine the full-resolution disparity estimation. REMP integrates the frequency information of typical channel features from the reconstruction error. MoCha-Stereo ranks 1st on the KITTI-2015 and KITTI-2012 Reflective leaderboards. Our structure also shows excellent performance in Multi-View Stereo. Code is avaliable at https://github.com/ZYangChen/MoCha-Stereo.

Yuzhe Chen, Jie Cao, Youquan Wang et al.

Existing multi-behavior recommendations tend to prioritize performance at the expense of explainability, while current explainable methods suffer from limited generalizability due to their reliance on external information. Neuro-Symbolic integration offers a promising avenue for explainability by combining neural networks with symbolic logic rule reasoning. Concurrently, we posit that user behavior chains inherently embody an endogenous logic suitable for explicit reasoning. However, these observational multiple behaviors are plagued by confounders, causing models to learn spurious correlations. By incorporating causal inference into this Neuro-Symbolic framework, we propose a novel Causal Neuro-Symbolic Reasoning model for Explainable Multi-Behavior Recommendation (CNRE). CNRE operationalizes the endogenous logic by simulating a human-like decision-making process. Specifically, CNRE first employs hierarchical preference propagation to capture heterogeneous cross-behavior dependencies. Subsequently, it models the endogenous logic rule implicit in the user's behavior chain based on preference strength, and adaptively dispatches to the corresponding neural-logic reasoning path (e.g., conjunction, disjunction). This process generates an explainable causal mediator that approximates an ideal state isolated from confounding effects. Extensive experiments on three large-scale datasets demonstrate CNRE's significant superiority over state-of-the-art baselines, offering multi-level explainability from model design and decision process to recommendation results.

Yifan Chen, Fei Yin, Hao Chen et al.

Contrast medium plays a pivotal role in radiological imaging, as it amplifies lesion conspicuity and improves detection for the diagnosis of tumor-related diseases. However, depending on the patient's health condition or the medical resources available, the use of contrast medium is not always feasible. Recent work has explored AI-based image translation to synthesize contrast-enhanced images directly from non-contrast scans, aims to reduce side effects and streamlines clinical workflows. Progress in this direction has been constrained by data limitations: (1) existing public datasets focus almost exclusively on brain-related paired MR modalities; (2) other collections include partially paired data but suffer from missing modalities/timestamps and imperfect spatial alignment; (3) explicit labeling of CT vs. CTC or DCE phases is often absent; (4) substantial resources remain private. To bridge this gap, we introduce the first public, fully paired, pan-cancer medical imaging dataset spanning 11 human organs. The MR data include complete dynamic contrast-enhanced (DCE) sequences covering all three phases (DCE1-DCE3), while the CT data provide paired non-contrast and contrast-enhanced acquisitions (CTC). The dataset is curated for anatomical correspondence, enabling rigorous evaluation of 1-to-1, N-to-1, and N-to-N translation settings (e.g., predicting DCE phases from non-contrast inputs). Built upon this resource, we establish a comprehensive benchmark. We report results from representative baselines of contemporary image-to-image translation. We release the dataset and benchmark to catalyze research on safe, effective contrast synthesis, with direct relevance to multi-organ oncology imaging workflows. Our code and dataset are publicly available at https://github.com/YifanChen02/PMPBench.

Chuang Liu, Yuyao Wang, Yibing Zhan et al.

Graph masked autoencoders (GMAE) have emerged as a significant advancement in self-supervised pre-training for graph-structured data. Previous GMAE models primarily utilize a straightforward random masking strategy for nodes or edges during training. However, this strategy fails to consider the varying significance of different nodes within the graph structure. In this paper, we investigate the potential of leveraging the graph's structural composition as a fundamental and unique prior in the masked pre-training process. To this end, we introduce a novel structure-guided masking strategy (i.e., StructMAE), designed to refine the existing GMAE models. StructMAE involves two steps: 1) Structure-based Scoring: Each node is evaluated and assigned a score reflecting its structural significance. Two distinct types of scoring manners are proposed: predefined and learnable scoring. 2) Structure-guided Masking: With the obtained assessment scores, we develop an easy-to-hard masking strategy that gradually increases the structural awareness of the self-supervised reconstruction task. Specifically, the strategy begins with random masking and progresses to masking structure-informative nodes based on the assessment scores. This design gradually and effectively guides the model in learning graph structural information. Furthermore, extensive experiments consistently demonstrate that our StructMAE method outperforms existing state-of-the-art GMAE models in both unsupervised and transfer learning tasks. Codes are available at https://github.com/LiuChuang0059/StructMAE.

Kun Li, Jia Wu, Bo Du et al.

GNN-based methods have achieved excellent results as a mainstream task in drug response prediction tasks in recent years. Traditional GNN methods use only the atoms in a drug molecule as nodes to obtain the representation of the molecular graph through node information passing, whereas the method using the transformer can only extract information about the nodes. However, the covalent bonding and chirality of a drug molecule have a great influence on the pharmacological properties of the molecule, and these information are implied in the chemical bonds formed by the edges between the atoms. In addition, CNN methods for modelling cell lines genomics sequences can only perceive local rather than global information about the sequence. In order to solve the above problems, we propose the decoupled dual transformer structure with edge embedded for drug respond prediction (TransEDRP), which is used for the representation of cell line genomics and drug respectively. For the drug branch, we encoded the chemical bond information within the molecule as the embedding of the edge in the molecular graph, extracted the global structural and biochemical information of the drug molecule using graph transformer. For the branch of cell lines genomics, we use the multi-headed attention mechanism to globally represent the genomics sequence. Finally, the drug and genomics branches are fused to predict IC50 values through the transformer layer and the fully connected layer, which two branches are different modalities. Extensive experiments have shown that our method is better than the current mainstream approach in all evaluation indicators.

Dexuan Ding, Ciyuan Peng, Endrowednes Kuantama et al.

High-dimensional structural MRI (sMRI) images are widely used for Alzheimer's Disease (AD) diagnosis. Most existing methods for sMRI representation learning rely on 3D architectures (e.g., 3D CNNs), slice-wise feature extraction with late aggregation, or apply training-free feature extractions using 2D foundation models (e.g., DINO). However, these three paradigms suffer from high computational cost, loss of cross-slice relations, and limited ability to extract discriminative features, respectively. To address these challenges, we propose Multimodal Visual Surrogate Compression (MVSC). It learns to compress and adapt large 3D sMRI volumes into compact 2D features, termed as visual surrogates, which are better aligned with frozen 2D foundation models to extract powerful representations for final AD classification. MVSC has two key components: a Volume Context Encoder that captures global cross-slice context under textual guidance, and an Adaptive Slice Fusion module that aggregates slice-level information in a text-enhanced, patch-wise manner. Extensive experiments on three large-scale Alzheimer's disease benchmarks demonstrate our MVSC performs favourably on both binary and multi-class classification tasks compared against state-of-the-art methods.

Hongzhi Zhang, Xiuwen Gong, Shirui Pan et al.

Drug-target interaction (DTI) prediction is a critical component of the drug discovery process. In the drug development engineering field, predicting novel drug-target interactions is extremely crucial.However, although existing methods have achieved high accuracy levels in predicting known drugs and drug targets, they fail to utilize global protein information during DTI prediction. This leads to an inability to effectively predict interaction the interactions between novel drugs and their targets. As a result, the cross-field information fusion strategy is employed to acquire local and global protein information. Thus, we propose the siamese drug-target interaction SiamDTI prediction method, which utilizes a double channel network structure for cross-field supervised learning.Experimental results on three benchmark datasets demonstrate that SiamDTI achieves higher accuracy levels than other state-of-the-art (SOTA) methods on novel drugs and targets.Additionally, SiamDTI's performance with known drugs and targets is comparable to that of SOTA approachs. The code is available at https://anonymous.4open.science/r/DDDTI-434D.

Amgad Muneer, Muhammad Waqas, Maliazurina B Saad et al.

Cancer research is increasingly driven by the integration of diverse data modalities, spanning from genomics and proteomics to imaging and clinical factors. However, extracting actionable insights from these vast and heterogeneous datasets remains a key challenge. The rise of foundation models (FMs) -- large deep-learning models pretrained on extensive amounts of data serving as a backbone for a wide range of downstream tasks -- offers new avenues for discovering biomarkers, improving diagnosis, and personalizing treatment. This paper presents a comprehensive review of widely adopted integration strategies of multimodal data to assist advance the computational approaches for data-driven discoveries in oncology. We examine emerging trends in machine learning (ML) and deep learning (DL), including methodological frameworks, validation protocols, and open-source resources targeting cancer subtype classification, biomarker discovery, treatment guidance, and outcome prediction. This study also comprehensively covers the shift from traditional ML to FMs for multimodal integration. We present a holistic view of recent FMs advancements and challenges faced during the integration of multi-omics with advanced imaging data. We identify the state-of-the-art FMs, publicly available multi-modal repositories, and advanced tools and methods for data integration. We argue that current state-of-the-art integrative methods provide the essential groundwork for developing the next generation of large-scale, pre-trained models poised to further revolutionize oncology. To the best of our knowledge, this is the first review to systematically map the transition from conventional ML to advanced FM for multimodal data integration in oncology, while also framing these developments as foundational for the forthcoming era of large-scale AI models in cancer research.

Kun Li, Longtao Hu, Xiantao Cai et al.

Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through transformations such as adding, deleting, and modifying atoms and chemical bonds, reflecting specific evolutionary paths. Existing molecular representation methods mainly focus on mining data, such as atomic-level structures and chemical bonds directly from the molecules, often overlooking their evolutionary history. Consequently, we aim to explore the possibility of enhancing molecular representations by simulating the evolutionary process. We extract and analyze the changes in the evolutionary pathway and explore combining it with existing molecular representations. Therefore, this paper proposes the molecular evolutionary network (MEvoN) for molecular representations. First, we construct the MEvoN using molecules with a small number of atoms and generate evolutionary paths utilizing similarity calculations. Then, by modeling the atomic-level changes, MEvoN reveals their impact on molecular properties. Experimental results show that the MEvoN-based molecular property prediction method significantly improves the performance of traditional end-to-end algorithms on several molecular datasets. The code is available at https://anonymous.4open.science/r/MEvoN-7416/.

Minhui Xie, Hao Peng, Pu Li et al.

Superpixel segmentation is a foundation for many higher-level computer vision tasks, such as image segmentation, object recognition, and scene understanding. Existing graph-based superpixel segmentation methods typically concentrate on the relationships between a given pixel and its directly adjacent pixels while overlooking the influence of non-adjacent pixels. These approaches do not fully leverage the global information in the graph, leading to suboptimal segmentation quality. To address this limitation, we present SIT-HSS, a hierarchical superpixel segmentation method based on structural information theory. Specifically, we first design a novel graph construction strategy that incrementally explores the pixel neighborhood to add edges based on 1-dimensional structural entropy (1D SE). This strategy maximizes the retention of graph information while avoiding an overly complex graph structure. Then, we design a new 2D SE-guided hierarchical graph partitioning method, which iteratively merges pixel clusters layer by layer to reduce the graph's 2D SE until a predefined segmentation scale is achieved. Experimental results on three benchmark datasets demonstrate that the SIT-HSS performs better than state-of-the-art unsupervised superpixel segmentation algorithms. The source code is available at \url{https://github.com/SELGroup/SIT-HSS}.

Zelin Yao, Chuang Liu, Xianke Meng et al.

Graph neural networks (GNNs) are gaining popularity for processing graph-structured data. In real-world scenarios, graph data within the same dataset can vary significantly in scale. This variability leads to depth-sensitivity, where the optimal depth of GNN layers depends on the scale of the graph data. Empirically, fewer layers are sufficient for message passing in smaller graphs, while larger graphs typically require deeper networks to capture long-range dependencies and global features. However, existing methods generally use a fixed number of GNN layers to generate representations for all graphs, overlooking the depth-sensitivity issue in graph structure data. To address this challenge, we propose the depth adaptive mixture of expert (DA-MoE) method, which incorporates two main improvements to GNN backbone: \textbf{1)} DA-MoE employs different GNN layers, each considered an expert with its own parameters. Such a design allows the model to flexibly aggregate information at different scales, effectively addressing the depth-sensitivity issue in graph data. \textbf{2)} DA-MoE utilizes GNN to capture the structural information instead of the linear projections in the gating network. Thus, the gating network enables the model to capture complex patterns and dependencies within the data. By leveraging these improvements, each expert in DA-MoE specifically learns distinct graph patterns at different scales. Furthermore, comprehensive experiments on the TU dataset and open graph benchmark (OGB) have shown that DA-MoE consistently surpasses existing baselines on various tasks, including graph, node, and link-level analyses. The code are available at \url{https://github.com/Celin-Yao/DA-MoE}.

Chuang Liu, Wenhang Yu, Kuang Gao et al.

Graph pooling has been increasingly recognized as crucial for Graph Neural Networks (GNNs) to facilitate hierarchical graph representation learning. Existing graph pooling methods commonly consist of two stages: selecting top-ranked nodes and discarding the remaining to construct coarsened graph representations. However, this paper highlights two key issues with these methods: 1) The process of selecting nodes to discard frequently employs additional Graph Convolutional Networks or Multilayer Perceptrons, lacking a thorough evaluation of each node's impact on the final graph representation and subsequent prediction tasks. 2) Current graph pooling methods tend to directly discard the noise segment (dropped) of the graph without accounting for the latent information contained within these elements. To address the first issue, we introduce a novel Graph Explicit Pooling (GrePool) method, which selects nodes by explicitly leveraging the relationships between the nodes and final representation vectors crucial for classification. The second issue is addressed using an extended version of GrePool (i.e., GrePool+), which applies a uniform loss on the discarded nodes. This addition is designed to augment the training process and improve classification accuracy. Furthermore, we conduct comprehensive experiments across 12 widely used datasets to validate our proposed method's effectiveness, including the Open Graph Benchmark datasets. Our experimental results uniformly demonstrate that GrePool outperforms 14 baseline methods for most datasets. Likewise, implementing GrePool+ enhances GrePool's performance without incurring additional computational costs.

Amgad Muneer, Kai Zhang, Ibraheem Hamdi et al.

Foundation models (FMs) are driving a prominent shift in artificial intelligence across different domains, including biomedical imaging. These models are designed to move beyond narrow pattern recognition towards emulating sophisticated clinical reasoning, understanding complex spatial relationships, and integrating multimodal data with unprecedented flexibility. However, a critical gap exists between this potential and the current reality, where the clinical evaluation and deployment of FMs are hampered by significant challenges. Herein, we critically assess the current state-of-the-art, analyzing hype by examining the core capabilities and limitations of FMs in the biomedical domain. We also provide a taxonomy of reasoning, ranging from emulated sequential logic and spatial understanding to the integration of explicit symbolic knowledge, to evaluate whether these models exhibit genuine cognition or merely mimic surface-level patterns. We argue that a critical frontier lies beyond statistical correlation, in the pursuit of causal inference, which is essential for building robust models that understand cause and effect. Furthermore, we discuss the paramount issues in deployment stemming from trustworthiness, bias, and safety, dissecting the challenges of algorithmic bias, data bias and privacy, and model hallucinations. We also draw attention to the need for more inclusive, rigorous, and clinically relevant validation frameworks to ensure their safe and ethical application. We conclude that while the vision of autonomous AI-doctors remains distant, the immediate reality is the emergence of powerful technology and assistive tools that would benefit clinical practice. The future of FMs in biomedical imaging hinges not on scale alone, but on developing hybrid, causally aware, and verifiably safe systems that augment, rather than replace, human expertise.

Yida Xiong, Jiameng Chen, Xiuwen Gong et al.

Graph generation aims to sample discrete node and edge attributes while satisfying coupled structural constraints. Diffusion models for graphs often adopt largely factorized forward-noising, and many flow-matching methods start from factorized reference noise and coordinate-wise interpolation, so node-edge coupling is not encoded by the generative geometry and must be recovered implicitly by the core network, which can be brittle after discrete decoding. Bayesian Flow Networks (BFNs) evolve distribution parameters and naturally support discrete generation. But classical BFNs typically rely on factorized beliefs and independent channels, which limit geometric evidence fusion. We propose Variational Bayesian Flow Network (VBFN), which performs a variational lifting to a tractable joint Gaussian variational belief family governed by structured precisions. Each Bayesian update reduces to solving a symmetric positive definite linear system, enabling coupled node and edge updates within a single fusion step. We construct sample-agnostic sparse precisions from a representation-induced dependency graph, thereby avoiding label leakage while enforcing node-edge consistency. On synthetic and molecular graph datasets, VBFN improves fidelity and diversity, and surpasses baseline methods.

Hongzhi Zhang, Zhonglie Liu, Kun Meng et al.

Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug development. Although existing methods perform adequately during certain CPI tasks, they still face the following challenges: (1) Representation learning from local or complete protein sequences often overlooks the complex interdependencies between subsequences, which are essential for predicting spatial structures and binding properties. (2) Dependence on large-scale or scarce multimodal protein datasets demands significant training data and computational resources, limiting scalability and efficiency. To address these challenges, we propose a novel approach that pretrains protein representations for CPI prediction tasks using subsequence reordering, explicitly capturing the dependencies between protein subsequences. Furthermore, we apply length-variable protein augmentation to ensure excellent pretraining performance on small training datasets. To evaluate the model's effectiveness and zero-shot learning ability, we combine it with various baseline methods. The results demonstrate that our approach can improve the baseline model's performance on the CPI task, especially in the challenging zero-shot scenario. Compared to existing pre-training models, our model demonstrates superior performance, particularly in data-scarce scenarios where training samples are limited. Our implementation is available at https://github.com/Hoch-Zhang/PSRP-CPI.

Jiameng Chen, Xiantao Cai, Jia Wu et al.

Antibody design remains a critical challenge in therapeutic and diagnostic development, particularly for complex antigens with diverse binding interfaces. Current computational methods face two main limitations: (1) capturing geometric features while preserving symmetries, and (2) generalizing novel antigen interfaces. Despite recent advancements, these methods often fail to accurately capture molecular interactions and maintain structural integrity. To address these challenges, we propose \textbf{AbMEGD}, an end-to-end framework integrating \textbf{M}ulti-scale \textbf{E}quivariant \textbf{G}raph \textbf{D}iffusion for antibody sequence and structure co-design. Leveraging advanced geometric deep learning, AbMEGD combines atomic-level geometric features with residue-level embeddings, capturing local atomic details and global sequence-structure interactions. Its E(3)-equivariant diffusion method ensures geometric precision, computational efficiency, and robust generalizability for complex antigens. Furthermore, experiments using the SAbDab database demonstrate a 10.13\% increase in amino acid recovery, 3.32\% rise in improvement percentage, and a 0.062~Å reduction in root mean square deviation within the critical CDR-H3 region compared to DiffAb, a leading antibody design model. These results highlight AbMEGD's ability to balance structural integrity with improved functionality, establishing a new benchmark for sequence-structure co-design and affinity optimization. The code is available at: https://github.com/Patrick221215/AbMEGD.

Yiming Wang, Hao Peng, Senzhang Wang et al.

Traffic data imputation is fundamentally important to support various applications in intelligent transportation systems such as traffic flow prediction. However, existing time-to-space sequential methods often fail to effectively extract features in block-wise missing data scenarios. Meanwhile, the static graph structure for spatial feature propagation significantly constrains the models flexibility in handling the distribution shift issue for the nonstationary traffic data. To address these issues, this paper proposes a SpatioTemporal Attention Mixture of experts network named STAMImputer for traffic data imputation. Specifically, we introduce a Mixture of Experts (MoE) framework to capture latent spatio-temporal features and their influence weights, effectively imputing block missing. A novel Low-rank guided Sampling Graph ATtention (LrSGAT) mechanism is designed to dynamically balance the local and global correlations across road networks. The sampled attention vectors are utilized to generate dynamic graphs that capture real-time spatial correlations. Extensive experiments are conducted on four traffic datasets for evaluation. The result shows STAMImputer achieves significantly performance improvement compared with existing SOTA approaches. Our codes are available at https://github.com/RingBDStack/STAMImupter.

Kun Li, Xiuwen Gong, Shirui Pan et al.

Drug response prediction (DRP) is a crucial phase in drug discovery, and the most important metric for its evaluation is the IC50 score. DRP results are heavily dependent on the quality of the generated molecules. Existing molecule generation methods typically employ classifier-based guidance, enabling sampling within the IC50 classification range. However, these methods fail to ensure the sampling space range's effectiveness, generating numerous ineffective molecules. Through experimental and theoretical study, we hypothesize that conditional generation based on the target IC50 score can obtain a more effective sampling space. As a result, we introduce regressor-free guidance molecule generation to ensure sampling within a more effective space and support DRP. Regressor-free guidance combines a diffusion model's score estimation with a regression controller model's gradient based on number labels. To effectively map regression labels between drugs and cell lines, we design a common-sense numerical knowledge graph that constrains the order of text representations. Experimental results on the real-world dataset for the DRP task demonstrate our method's effectiveness in drug discovery. The code is available at:https://anonymous.4open.science/r/RMCD-DBD1.

Jiameng Chen, Yida Xiong, Kun Li et al.

Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 Å when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.

Anas Zafar, Muhammad Waqas, Amgad Muneer et al.

Low-dose CT (LDCT) reduces radiation exposure but introduces protocol-dependent noise and artifacts that vary across institutions. While federated learning enables collaborative training without centralizing patient data, existing methods personalize in image space, making it difficult to separate scanner noise from patient anatomy. We propose ProFed (Projection Guided Personalized Federated Learning), a framework that complements the image space approach by performing dual-level personalization in the projection space, where noise originates during CT measurements before reconstruction combines protocol and anatomy effects. ProFed introduces: (i) anatomy-aware and protocol-aware networks that personalize CT reconstruction to patient and scanner-specific features, (ii) multi-constraint projection losses that enforce consistency with CT measurements, and (iii) uncertainty-guided selective aggregation that weights clients by prediction confidence. Extensive experiments on the Mayo Clinic 2016 dataset demonstrate that ProFed achieves 42.56 dB PSNR with CNN backbones and 44.83 dB with Transformers, outperforming 11 federated learning baselines, including the physics-informed SCAN-PhysFed by +1.42 dB.

Muthu Subash Kavitha, Anas Zafar, Amgad Muneer et al.

Clinical deployment of chest radiograph classifiers requires models that can be updated as new datasets become available without retraining on previously ob- served data or degrading validated performance. We study, for the first time, a task-incremental continual learning setting for chest radiograph classification, in which heterogeneous chest X-ray datasets arrive sequentially and task identifiers are unavailable at inference. We propose a continual adapter-based routing learning strategy for Chest X-rays (CARL-XRay) that maintains a fixed high-capacity backbone and incrementally allocates lightweight task-specific adapters and classifier heads. A latent task selector operates on task-adapted features and leverages both current and historical context preserved through compact prototypes and feature-level experience replay. This design supports stable task identification and adaptation across sequential updates while avoiding raw-image storage. Experiments on large-scale public chest radiograph datasets demonstrate robust performance retention and reliable task-aware inference under continual dataset ingestion. CARL-XRay outperforms joint training under task-unknown deployment, achieving higher routing accuracy (75.0\% vs.\ 62.5\%), while maintaining competitive diagnostic performance with AUROC of 0.74 in the oracle setting with ground-truth task identity and 0.75 under task-unknown inference, using significantly fewer trainable parameters. Finally, the proposed framework provides a practical alternative to joint training and repeated full retraining in continual clinical deployment.

Kun Li, Longtao Hu, Yida Xiong et al.

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.

Haoyu Zheng, Fangcheng Fu, Jia Wu et al.

LLM-based workflows compose specialized agents to execute complex tasks, and these agents usually share substantial context, allowing KV-Cache reuse to save computation. Existing approaches either manage KV-Cache at agent level and fail to exploit the reuse opportunities within workflows, or manage cache at the workflow level but assume that each workflow calls a static sequence of agents. However, practical workflows are typically dynamic, where the sequence of invoked agents and thus induced cache reuse opportunities depend on the context of each task. To serve such dynamic workflows efficiently, we build a system dubbed PBKV (\textbf{P}rediction-\textbf{B}ased \textbf{KV}-Cache Management). For each workflow, PBKV predicts the agent invocations in several future steps by fusing the guidance from historical workflows and context of the target workflow. Based on the predictions, PBKV estimates the reuse potential of cache entries and keeps the high-potential entries in GPU memory. To be robust to prediction errors, PBKV utilizes the predictions conservatively during both cache eviction and prefetching. Experiments on three workflow benchmarks show that PBKV achieves up to $1.85\times$ speedup over LRU on dynamic workflows, and up to $1.26\times$ speedup over the SOTA baseline KVFlow on the static workflow.

Congbo Ma, Yuxia Wang, Jia Wu et al.

Social event detection involves identifying and categorizing important events from social media, which relies on labeled data, but annotation is costly and labor-intensive. To address this problem, we propose Augmentation framework for Social Event Detection (SED-Aug), a plug-and-play dual augmentation framework, which combines explicit text-based and implicit feature-space augmentation to enhance data diversity and model robustness. The explicit augmentation utilizes large language models to enhance textual information through five diverse generation strategies. For implicit augmentation, we design five novel perturbation techniques that operate in the feature space on structural fused embeddings. These perturbations are crafted to keep the semantic and relational properties of the embeddings and make them more diverse. Specifically, SED-Aug outperforms the best baseline model by approximately 17.67% on the Twitter2012 dataset and by about 15.57% on the Twitter2018 dataset in terms of the average F1 score. The code is available at GitHub: https://github.com/congboma/SED-Aug.

Hikmat Khan, Syed Farhan Alam Zaidi, Pir Masoom Shah et al.

Domain generalization in computational histopathology is hindered by heterogeneity in whole slide images (WSIs), caused by variations in tissue preparation, staining, and imaging conditions across institutions. Unlike machine learning systems, pathologists rely on domain-invariant morphological cues such as nuclear atypia (enlargement, irregular contours, hyperchromasia, chromatin texture, spatial disorganization), structural atypia (abnormal architecture and gland formation), and overall morphological atypia that remain diagnostic across diverse settings. Motivated by this, we hypothesize that explicitly modeling biologically robust nuclear morphology and spatial organization will enable the learning of cancer representations that are resilient to domain shifts. We propose MorphGen (Morphology-Guided Generalization), a method that integrates histopathology images, augmentations, and nuclear segmentation masks within a supervised contrastive learning framework. By aligning latent representations of images and nuclear masks, MorphGen prioritizes diagnostic features such as nuclear and morphological atypia and spatial organization over staining artifacts and domain-specific features. To further enhance out-of-distribution robustness, we incorporate stochastic weight averaging (SWA), steering optimization toward flatter minima. Attention map analyses revealed that MorphGen primarily relies on nuclear morphology, cellular composition, and spatial cell organization within tumors or normal regions for final classification. Finally, we demonstrate resilience of the learned representations to image corruptions (such as staining artifacts) and adversarial attacks, showcasing not only OOD generalization but also addressing critical vulnerabilities in current deep learning systems for digital pathology. Code, datasets, and trained models are available at: https://github.com/hikmatkhan/MorphGen