Lifang He

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.

Hejie Cui, Wei Dai, Yanqiao Zhu et al.

Human brains lie at the core of complex neurobiological systems, where the neurons, circuits, and subsystems interact in enigmatic ways. Understanding the structural and functional mechanisms of the brain has long been an intriguing pursuit for neuroscience research and clinical disorder therapy. Mapping the connections of the human brain as a network is one of the most pervasive paradigms in neuroscience. Graph Neural Networks (GNNs) have recently emerged as a potential method for modeling complex network data. Deep models, on the other hand, have low interpretability, which prevents their usage in decision-critical contexts like healthcare. To bridge this gap, we propose an interpretable framework to analyze disorder-specific Regions of Interest (ROIs) and prominent connections. The proposed framework consists of two modules: a brain-network-oriented backbone model for disease prediction and a globally shared explanation generator that highlights disorder-specific biomarkers including salient ROIs and important connections. We conduct experiments on three real-world datasets of brain disorders. The results verify that our framework can obtain outstanding performance and also identify meaningful biomarkers. All code for this work is available at https://github.com/HennyJie/IBGNN.git.

Zhiling Yan, Kai Zhang, Rong Zhou et al.

In this paper, we critically evaluate the capabilities of the state-of-the-art multimodal large language model, i.e., GPT-4 with Vision (GPT-4V), on Visual Question Answering (VQA) task. Our experiments thoroughly assess GPT-4V's proficiency in answering questions paired with images using both pathology and radiology datasets from 11 modalities (e.g. Microscopy, Dermoscopy, X-ray, CT, etc.) and fifteen objects of interests (brain, liver, lung, etc.). Our datasets encompass a comprehensive range of medical inquiries, including sixteen distinct question types. Throughout our evaluations, we devised textual prompts for GPT-4V, directing it to synergize visual and textual information. The experiments with accuracy score conclude that the current version of GPT-4V is not recommended for real-world diagnostics due to its unreliable and suboptimal accuracy in responding to diagnostic medical questions. In addition, we delineate seven unique facets of GPT-4V's behavior in medical VQA, highlighting its constraints within this complex arena. The complete details of our evaluation cases are accessible at https://github.com/ZhilingYan/GPT4V-Medical-Report.

Jianpeng Chen, Yawen Ling, Jie Xu et al.

Multi-view graph clustering (MGC) methods are increasingly being studied due to the explosion of multi-view data with graph structural information. The critical point of MGC is to better utilize view-specific and view-common information in features and graphs of multiple views. However, existing works have an inherent limitation that they are unable to concurrently utilize the consensus graph information across multiple graphs and the view-specific feature information. To address this issue, we propose Variational Graph Generator for Multi-View Graph Clustering (VGMGC). Specifically, a novel variational graph generator is proposed to extract common information among multiple graphs. This generator infers a reliable variational consensus graph based on a priori assumption over multiple graphs. Then a simple yet effective graph encoder in conjunction with the multi-view clustering objective is presented to learn the desired graph embeddings for clustering, which embeds the inferred view-common graph and view-specific graphs together with features. Finally, theoretical results illustrate the rationality of the VGMGC by analyzing the uncertainty of the inferred consensus graph with the information bottleneck principle.Extensive experiments demonstrate the superior performance of our VGMGC over SOTAs. The source code is publicly available at https://github.com/cjpcool/VGMGC.

Jun Yu, Zhaoming Kong, Liang Zhan et al.

The assessment of Alzheimer's Disease (AD) and Mild Cognitive Impairment (MCI) associated with brain changes remains a challenging task. Recent studies have demonstrated that combination of multi-modality imaging techniques can better reflect pathological characteristics and contribute to more accurate diagnosis of AD and MCI. In this paper, we propose a novel tensor-based multi-modality feature selection and regression method for diagnosis and biomarker identification of AD and MCI from normal controls. Specifically, we leverage the tensor structure to exploit high-level correlation information inherent in the multi-modality data, and investigate tensor-level sparsity in the multilinear regression model. We present the practical advantages of our method for the analysis of ADNI data using three imaging modalities (VBM- MRI, FDG-PET and AV45-PET) with clinical parameters of disease severity and cognitive scores. The experimental results demonstrate the superior performance of our proposed method against the state-of-the-art for the disease diagnosis and the identification of disease-specific regions and modality-related differences. The code for this work is publicly available at https://github.com/junfish/BIOS22.

Zhaoming Kong, Fangxi Deng, Haomin Zhuang et al.

The advancement of imaging devices and countless images generated everyday pose an increasingly high demand on image denoising, which still remains a challenging task in terms of both effectiveness and efficiency. To improve denoising quality, numerous denoising techniques and approaches have been proposed in the past decades, including different transforms, regularization terms, algebraic representations and especially advanced deep neural network (DNN) architectures. Despite their sophistication, many methods may fail to achieve desirable results for simultaneous noise removal and fine detail preservation. In this paper, to investigate the applicability of existing denoising techniques, we compare a variety of denoising methods on both synthetic and real-world datasets for different applications. We also introduce a new dataset for benchmarking, and the evaluations are performed from four different perspectives including quantitative metrics, visual effects, human ratings and computational cost. Our experiments demonstrate: (i) the effectiveness and efficiency of representative traditional denoisers for various denoising tasks, (ii) a simple matrix-based algorithm may be able to produce similar results compared with its tensor counterparts, and (iii) the notable achievements of DNN models, which exhibit impressive generalization ability and show state-of-the-art performance on various datasets. In spite of the progress in recent years, we discuss shortcomings and possible extensions of existing techniques. Datasets, code and results are made publicly available and will be continuously updated at https://github.com/ZhaomingKong/Denoising-Comparison.

Yao Su, Xin Dai, Lifang He et al.

Deformable image registration, i.e., the task of aligning multiple images into one coordinate system by non-linear transformation, serves as an essential preprocessing step for neuroimaging data. Recent research on deformable image registration is mainly focused on improving the registration accuracy using multi-stage alignment methods, where the source image is repeatedly deformed in stages by a same neural network until it is well-aligned with the target image. Conventional methods for multi-stage registration can often blur the source image as the pixel/voxel values are repeatedly interpolated from the image generated by the previous stage. However, maintaining image quality such as sharpness during image registration is crucial to medical data analysis. In this paper, we study the problem of anti-blur deformable image registration and propose a novel solution, called Anti-Blur Network (ABN), for multi-stage image registration. Specifically, we use a pair of short-term registration and long-term memory networks to learn the nonlinear deformations at each stage, where the short-term registration network learns how to improve the registration accuracy incrementally and the long-term memory network combines all the previous deformations to allow an interpolation to perform on the raw image directly and preserve image sharpness. Extensive experiments on both natural and medical image datasets demonstrated that ABN can accurately register images while preserving their sharpness. Our code and data can be found at https://github.com/anonymous3214/ABN

Yao Su, Zhentian Qian, Lifang He et al.

Brain extraction and registration are important preprocessing steps in neuroimaging data analysis, where the goal is to extract the brain regions from MRI scans (i.e., extraction step) and align them with a target brain image (i.e., registration step). Conventional research mainly focuses on developing methods for the extraction and registration tasks separately under supervised settings. The performance of these methods highly depends on the amount of training samples and visual inspections performed by experts for error correction. However, in many medical studies, collecting voxel-level labels and conducting manual quality control in high-dimensional neuroimages (e.g., 3D MRI) are very expensive and time-consuming. Moreover, brain extraction and registration are highly related tasks in neuroimaging data and should be solved collectively. In this paper, we study the problem of unsupervised collective extraction and registration in neuroimaging data. We propose a unified end-to-end framework, called ERNet (Extraction-Registration Network), to jointly optimize the extraction and registration tasks, allowing feedback between them. Specifically, we use a pair of multi-stage extraction and registration modules to learn the extraction mask and transformation, where the extraction network improves the extraction accuracy incrementally and the registration network successively warps the extracted image until it is well-aligned with the target image. Experiment results on real-world datasets show that our proposed method can effectively improve the performance on extraction and registration tasks in neuroimaging data. Our code and data can be found at https://github.com/ERNetERNet/ERNet

Yao Su, Zhentian Qian, Lei Ma et al.

Brain extraction, registration and segmentation are indispensable preprocessing steps in neuroimaging studies. The aim is to extract the brain from raw imaging scans (i.e., extraction step), align it with a target brain image (i.e., registration step) and label the anatomical brain regions (i.e., segmentation step). Conventional studies typically focus on developing separate methods for the extraction, registration and segmentation tasks in a supervised setting. The performance of these methods is largely contingent on the quantity of training samples and the extent of visual inspections carried out by experts for error correction. Nevertheless, collecting voxel-level labels and performing manual quality control on high-dimensional neuroimages (e.g., 3D MRI) are expensive and time-consuming in many medical studies. In this paper, we study the problem of one-shot joint extraction, registration and segmentation in neuroimaging data, which exploits only one labeled template image (a.k.a. atlas) and a few unlabeled raw images for training. We propose a unified end-to-end framework, called JERS, to jointly optimize the extraction, registration and segmentation tasks, allowing feedback among them. Specifically, we use a group of extraction, registration and segmentation modules to learn the extraction mask, transformation and segmentation mask, where modules are interconnected and mutually reinforced by self-supervision. Empirical results on real-world datasets demonstrate that our proposed method performs exceptionally in the extraction, registration and segmentation tasks. Our code and data can be found at https://github.com/Anonymous4545/JERS

Yazhou Ren, Jingyu Pu, Zhimeng Yang et al.

Cluster analysis plays an indispensable role in machine learning and data mining. Learning a good data representation is crucial for clustering algorithms. Recently, deep clustering, which can learn clustering-friendly representations using deep neural networks, has been broadly applied in a wide range of clustering tasks. Existing surveys for deep clustering mainly focus on the single-view fields and the network architectures, ignoring the complex application scenarios of clustering. To address this issue, in this paper we provide a comprehensive survey for deep clustering in views of data sources. With different data sources and initial conditions, we systematically distinguish the clustering methods in terms of methodology, prior knowledge, and architecture. Concretely, deep clustering methods are introduced according to four categories, i.e., traditional single-view deep clustering, semi-supervised deep clustering, deep multi-view clustering, and deep transfer clustering. Finally, we discuss the open challenges and potential future opportunities in different fields of deep clustering.

Hejie Cui, Wei Dai, Yanqiao Zhu et al.

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

Houliang Zhou, Lifang He, Yu Zhang et al.

Identification of brain regions related to the specific neurological disorders are of great importance for biomarker and diagnostic studies. In this paper, we propose an interpretable Graph Convolutional Network (GCN) framework for the identification and classification of Alzheimer's disease (AD) using multi-modality brain imaging data. Specifically, we extended the Gradient Class Activation Mapping (Grad-CAM) technique to quantify the most discriminative features identified by GCN from brain connectivity patterns. We then utilized them to find signature regions of interest (ROIs) by detecting the difference of features between regions in healthy control (HC), mild cognitive impairment (MCI), and AD groups. We conducted the experiments on the ADNI database with imaging data from three modalities, including VBM-MRI, FDG-PET, and AV45-PET, and showed that the ROI features learned by our method were effective for enhancing the performances of both clinical score prediction and disease status identification. It also successfully identified biomarkers associated with AD and MCI.

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.

Chenhang Cui, Yazhou Ren, Jingyu Pu et al.

Multi-view clustering (MVC) is a popular technique for improving clustering performance using various data sources. However, existing methods primarily focus on acquiring consistent information while often neglecting the issue of redundancy across multiple views. This study presents a new approach called Sufficient Multi-View Clustering (SUMVC) that examines the multi-view clustering framework from an information-theoretic standpoint. Our proposed method consists of two parts. Firstly, we develop a simple and reliable multi-view clustering method SCMVC (simple consistent multi-view clustering) that employs variational analysis to generate consistent information. Secondly, we propose a sufficient representation lower bound to enhance consistent information and minimise unnecessary information among views. The proposed SUMVC method offers a promising solution to the problem of multi-view clustering and provides a new perspective for analyzing multi-view data. To verify the effectiveness of our model, we conducted a theoretical analysis based on the Bayes Error Rate, and experiments on multiple multi-view datasets demonstrate the superior performance of SUMVC.

Yi Yang, Yanqiao Zhu, Hejie Cui et al.

Brain networks characterize complex connectivities among brain regions as graph structures, which provide a powerful means to study brain connectomes. In recent years, graph neural networks have emerged as a prevalent paradigm of learning with structured data. However, most brain network datasets are limited in sample sizes due to the relatively high cost of data acquisition, which hinders the deep learning models from sufficient training. Inspired by meta-learning that learns new concepts fast with limited training examples, this paper studies data-efficient training strategies for analyzing brain connectomes in a cross-dataset setting. Specifically, we propose to meta-train the model on datasets of large sample sizes and transfer the knowledge to small datasets. In addition, we also explore two brain-network-oriented designs, including atlas transformation and adaptive task reweighing. Compared to other pre-training strategies, our meta-learning-based approach achieves higher and stabler performance, which demonstrates the effectiveness of our proposed solutions. The framework is also able to derive new insights regarding the similarities among datasets and diseases in a data-driven fashion.

Xianghua Zeng, Hao Peng, Angsheng Li et al.

State abstraction optimizes decision-making by ignoring irrelevant environmental information in reinforcement learning with rich observations. Nevertheless, recent approaches focus on adequate representational capacities resulting in essential information loss, affecting their performances on challenging tasks. In this article, we propose a novel mathematical Structural Information principles-based State Abstraction framework, namely SISA, from the information-theoretic perspective. Specifically, an unsupervised, adaptive hierarchical state clustering method without requiring manual assistance is presented, and meanwhile, an optimal encoding tree is generated. On each non-root tree node, a new aggregation function and condition structural entropy are designed to achieve hierarchical state abstraction and compensate for sampling-induced essential information loss in state abstraction. Empirical evaluations on a visual gridworld domain and six continuous control benchmarks demonstrate that, compared with five SOTA state abstraction approaches, SISA significantly improves mean episode reward and sample efficiency up to 18.98 and 44.44%, respectively. Besides, we experimentally show that SISA is a general framework that can be flexibly integrated with different representation-learning objectives to improve their performances further.

Xinyue Chen, Jie Xu, Yazhou Ren et al.

Federated multi-view clustering has the potential to learn a global clustering model from data distributed across multiple devices. In this setting, label information is unknown and data privacy must be preserved, leading to two major challenges. First, views on different clients often have feature heterogeneity, and mining their complementary cluster information is not trivial. Second, the storage and usage of data from multiple clients in a distributed environment can lead to incompleteness of multi-view data. To address these challenges, we propose a novel federated deep multi-view clustering method that can mine complementary cluster structures from multiple clients, while dealing with data incompleteness and privacy concerns. Specifically, in the server environment, we propose sample alignment and data extension techniques to explore the complementary cluster structures of multiple views. The server then distributes global prototypes and global pseudo-labels to each client as global self-supervised information. In the client environment, multiple clients use the global self-supervised information and deep autoencoders to learn view-specific cluster assignments and embedded features, which are then uploaded to the server for refining the global self-supervised information. Finally, the results of our extensive experiments demonstrate that our proposed method exhibits superior performance in addressing the challenges of incomplete multi-view data in distributed environments.

Xuetong Wang, Kanhao Zhao, Rong Zhou et al.

Normative modeling is an emerging and promising approach to effectively study disorder heterogeneity in individual participants. In this study, we propose a novel normative modeling method by combining conditional variational autoencoder with adversarial learning (ACVAE) to identify brain dysfunction in Alzheimer's Disease (AD). Specifically, we first train a conditional VAE on the healthy control (HC) group to create a normative model conditioned on covariates like age, gender and intracranial volume. Then we incorporate an adversarial training process to construct a discriminative feature space that can better generalize to unseen data. Finally, we compute deviations from the normal criterion at the patient level to determine which brain regions were associated with AD. Our experiments on OASIS-3 database show that the deviation maps generated by our model exhibit higher sensitivity to AD compared to other deep normative models, and are able to better identify differences between the AD and HC groups.

Weixiang Sun, Xiaocao You, Ruizhe Zheng et al.

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for medical AI development. Diffusion models can now generate realistic images from text prompts, while recent advancements have demonstrated their ability to create diverse, high-quality videos. However, these models often struggle with generating accurate representations of medical procedures and detailed anatomical structures. This paper introduces Bora, the first spatio-temporal diffusion probabilistic model designed for text-guided biomedical video generation. Bora leverages Transformer architecture and is pre-trained on general-purpose video generation tasks. It is fine-tuned through model alignment and instruction tuning using a newly established medical video corpus, which includes paired text-video data from various biomedical fields. To the best of our knowledge, this is the first attempt to establish such a comprehensive annotated biomedical video dataset. Bora is capable of generating high-quality video data across four distinct biomedical domains, adhering to medical expert standards and demonstrating consistency and diversity. This generalist video generative model holds significant potential for enhancing medical consultation and decision-making, particularly in resource-limited settings. Additionally, Bora could pave the way for immersive medical training and procedure planning. Extensive experiments on distinct medical modalities such as endoscopy, ultrasound, MRI, and cell tracking validate the effectiveness of our model in understanding biomedical instructions and its superior performance across subjects compared to state-of-the-art generation models.

Zongmo Huang, Yazhou Ren, Xiaorong Pu et al.

With the representation learning capability of the deep learning models, deep embedded multi-view clustering (MVC) achieves impressive performance in many scenarios and has become increasingly popular in recent years. Although great progress has been made in this field, most existing methods merely focus on learning the latent representations and ignore that learning the latent graph of nodes also provides available information for the clustering task. To address this issue, in this paper we propose Deep Embedded Multi-view Clustering via Jointly Learning Latent Representations and Graphs (DMVCJ), which utilizes the latent graphs to promote the performance of deep embedded MVC models from two aspects. Firstly, by learning the latent graphs and feature representations jointly, the graph convolution network (GCN) technique becomes available for our model. With the capability of GCN in exploiting the information from both graphs and features, the clustering performance of our model is significantly promoted. Secondly, based on the adjacency relations of nodes shown in the latent graphs, we design a sample-weighting strategy to alleviate the noisy issue, and further improve the effectiveness and robustness of the model. Experimental results on different types of real-world multi-view datasets demonstrate the effectiveness of DMVCJ.

Zhenqian Wu, Xiaoyuan Li, Yazhou Ren et al.

The accuracy of facial expression recognition is typically affected by the following factors: high similarities across different expressions, disturbing factors, and micro-facial movement of rapid and subtle changes. One potentially viable solution for addressing these barriers is to exploit the neutral information concealed in neutral expression images. To this end, in this paper we propose a self-Paced Neutral Expression-Disentangled Learning (SPNDL) model. SPNDL disentangles neutral information from facial expressions, making it easier to extract key and deviation features. Specifically, it allows to capture discriminative information among similar expressions and perceive micro-facial movements. In order to better learn these neutral expression-disentangled features (NDFs) and to alleviate the non-convex optimization problem, a self-paced learning (SPL) strategy based on NDFs is proposed in the training stage. SPL learns samples from easy to complex by increasing the number of samples selected into the training process, which enables to effectively suppress the negative impacts introduced by low-quality samples and inconsistently distributed NDFs. Experiments on three popular databases (i.e., CK+, Oulu-CASIA, and RAF-DB) show the effectiveness of our proposed method.

Zhengqing Yuan, Yixin Liu, Yihan Cao et al.

Text-to-video generation has made significant strides, but replicating the capabilities of advanced systems like OpenAI Sora remains challenging due to their closed-source nature. Existing open-source methods struggle to achieve comparable performance, often hindered by ineffective agent collaboration and inadequate training data quality. In this paper, we introduce Mora, a novel multi-agent framework that leverages existing open-source modules to replicate Sora functionalities. We address these fundamental limitations by proposing three key techniques: (1) multi-agent fine-tuning with a self-modulation factor to enhance inter-agent coordination, (2) a data-free training strategy that uses large models to synthesize training data, and (3) a human-in-the-loop mechanism combined with multimodal large language models for data filtering to ensure high-quality training datasets. Our comprehensive experiments on six video generation tasks demonstrate that Mora achieves performance comparable to Sora on VBench, outperforming existing open-source methods across various tasks. Specifically, in the text-to-video generation task, Mora achieved a Video Quality score of 0.800, surpassing Sora 0.797 and outperforming all other baseline models across six key metrics. Additionally, in the image-to-video generation task, Mora achieved a perfect Dynamic Degree score of 1.00, demonstrating exceptional capability in enhancing motion realism and achieving higher Imaging Quality than Sora. These results highlight the potential of collaborative multi-agent systems and human-in-the-loop mechanisms in advancing text-to-video generation. Our code is available at \url{https://github.com/lichao-sun/Mora}.

Cheng Wang, Yu Jiang, Zhihao Peng et al.

Functional Magnetic Resonance Imaging (fMRI) is essential for studying brain function and diagnosing neurological disorders, but current analysis methods face reproducibility and transferability issues due to complex pre-processing and task-specific models. We introduce NeuroSTORM (Neuroimaging Foundation Model with Spatial-Temporal Optimized Representation Modeling), a generalizable framework that directly learns from 4D fMRI volumes and enables efficient knowledge transfer across diverse applications. NeuroSTORM is pre-trained on 28.65 million fMRI frames (>9,000 hours) from over 50,000 subjects across multiple centers and ages 5 to 100. Using a Mamba backbone and a shifted scanning strategy, it efficiently processes full 4D volumes. We also propose a spatial-temporal optimized pre-training approach and task-specific prompt tuning to improve transferability. NeuroSTORM outperforms existing methods across five tasks: age/gender prediction, phenotype prediction, disease diagnosis, fMRI-to-image retrieval, and task-based fMRI classification. It demonstrates strong clinical utility on datasets from hospitals in the U.S., South Korea, and Australia, achieving top performance in disease diagnosis and cognitive phenotype prediction. NeuroSTORM provides a standardized, open-source foundation model to improve reproducibility and transferability in fMRI-based clinical research.

Xinxu Wei, Kanhao Zhao, Yong Jiao et al.

As large language models (LLMs) continue to revolutionize AI research, there is a growing interest in building large-scale brain foundation models to advance neuroscience. While most existing brain foundation models are pre-trained on time-series signals or connectome features, we propose a novel graph-based pre-training paradigm for constructing a brain graph foundation model. In this paper, we introduce the Brain Graph Foundation Model, termed BrainGFM, a unified framework that leverages graph contrastive learning and graph masked autoencoders for large-scale fMRI-based pre-training. BrainGFM is pre-trained on a diverse mixture of brain atlases with varying parcellations, significantly expanding the pre-training corpus and enhancing the model's ability to generalize across heterogeneous fMRI-derived brain representations. To support efficient and versatile downstream transfer, we integrate both graph prompts and language prompts into the model design, enabling BrainGFM to flexibly adapt to a wide range of atlases, neurological and psychiatric disorders, and task settings. Furthermore, we employ meta-learning to optimize the graph prompts, facilitating strong generalization to previously unseen disorders under both few-shot and zero-shot learning conditions via language-guided prompting. BrainGFM is pre-trained on 27 neuroimaging datasets spanning 25 common neurological and psychiatric disorders, encompassing 2 types of brain atlases (functional and anatomical) across 8 widely-used parcellations, and covering over 25,000 subjects, 60,000 fMRI scans, and a total of 400,000 graph samples aggregated across all atlases and parcellations. The code is available at: https://github.com/weixinxu666/BrainGFM

Xinwei Luo, Songlin Zhao, Yun Zong et al.

Retinal image plays a crucial role in diagnosing various diseases, as retinal structures provide essential diagnostic information. However, effectively capturing structural features while integrating them with contextual information from retinal images remains a challenge. In this work, we propose segmentation-guided dual-branch network for retinal disease diagnosis using retinal images and their segmentation maps, named SegImgNet. SegImgNet incorporates a segmentation module to generate multi-scale retinal structural feature maps from retinal images. The classification module employs two encoders to independently extract features from segmented images and retinal images for disease classification. To further enhance feature extraction, we introduce the Segmentation-Guided Attention (SGA) block, which leverages feature maps from the segmentation module to refine the classification process. We evaluate SegImgNet on the public AIROGS dataset and the private e-ROP dataset. Experimental results demonstrate that SegImgNet consistently outperforms existing methods, underscoring its effectiveness in retinal disease diagnosis. The code is publicly available at https://github.com/hawk-sudo/SegImgNet.

Songlin Zhao, Rong Zhou, Yu Zhang et al.

In this paper, we introduce a novel normative modeling approach that incorporates focal loss and adversarial autoencoders (FAAE) for Alzheimer's Disease (AD) diagnosis and biomarker identification. Our method is an end-to-end approach that embeds an adversarial focal loss discriminator within the autoencoder structure, specifically designed to effectively target and capture more complex and challenging cases. We first use the enhanced autoencoder to create a normative model based on data from healthy control (HC) individuals. We then apply this model to estimate total and regional neuroanatomical deviation in AD patients. Through extensive experiments on the OASIS-3 and ADNI datasets, our approach significantly outperforms previous state-of-the-art methods. This advancement not only streamlines the detection process but also provides a greater insight into the biomarker potential for AD. Our code can be found at \url{https://github.com/soz223/FAAE}.

Kai Zhang, Rong Zhou, Eashan Adhikarla et al.

Traditional biomedical artificial intelligence (AI) models, designed for specific tasks or modalities, often exhibit limited flexibility in real-world deployment and struggle to utilize holistic information. Generalist AI holds the potential to address these limitations due to its versatility in interpreting different data types and generating tailored outputs for diverse needs. However, existing biomedical generalist AI solutions are typically heavyweight and closed source to researchers, practitioners, and patients. Here, we propose BiomedGPT, the first open-source and lightweight vision-language foundation model, designed as a generalist capable of performing various biomedical tasks. BiomedGPT achieved state-of-the-art results in 16 out of 25 experiments while maintaining a computing-friendly model scale. We also conducted human evaluations to assess the capabilities of BiomedGPT in radiology visual question answering, report generation, and summarization. BiomedGPT exhibits robust prediction ability with a low error rate of 3.8% in question answering, satisfactory performance with an error rate of 8.3% in writing complex radiology reports, and competitive summarization ability with a nearly equivalent preference score to human experts. Our method demonstrates that effective training with diverse data can lead to more practical biomedical AI for improving diagnosis and workflow efficiency.

Zhaoming Kong, Lichao Sun, Hao Peng et al.

In this paper, we propose MGNet, a simple and effective multiplex graph convolutional network (GCN) model for multimodal brain network analysis. The proposed method integrates tensor representation into the multiplex GCN model to extract the latent structures of a set of multimodal brain networks, which allows an intuitive 'grasping' of the common space for multimodal data. Multimodal representations are then generated with multiplex GCNs to capture specific graph structures. We conduct classification task on two challenging real-world datasets (HIV and Bipolar disorder), and the proposed MGNet demonstrates state-of-the-art performance compared to competitive benchmark methods. Apart from objective evaluations, this study may bear special significance upon network theory to the understanding of human connectome in different modalities. The code is available at https://github.com/ZhaomingKong/MGNets.

Zhaoming Kong, Xiaowei Yang, Lifang He

Filtering multi-dimensional images such as color images, color videos, multispectral images and magnetic resonance images is challenging in terms of both effectiveness and efficiency. Leveraging the nonlocal self-similarity (NLSS) characteristic of images and sparse representation in the transform domain, the block-matching and 3D filtering (BM3D) based methods show powerful denoising performance. Recently, numerous new approaches with different regularization terms, transforms and advanced deep neural network (DNN) architectures are proposed to improve denoising quality. In this paper, we extensively compare over 60 methods on both synthetic and real-world datasets. We also introduce a new color image and video dataset for benchmarking, and our evaluations are performed from four different perspectives including quantitative metrics, visual effects, human ratings and computational cost. Comprehensive experiments demonstrate: (i) the effectiveness and efficiency of the BM3D family for various denoising tasks, (ii) a simple matrix-based algorithm could produce similar results compared with its tensor counterparts, and (iii) several DNN models trained with synthetic Gaussian noise show state-of-the-art performance on real-world color image and video datasets. Despite the progress in recent years, we discuss shortcomings and possible extensions of existing techniques. Datasets and codes for evaluation are made publicly available at https://github.com/ZhaomingKong/Denoising-Comparison.

Chen Li, Xutan Peng, Hao Peng et al.

Recently, graph-based algorithms have drawn much attention because of their impressive success in semi-supervised setups. For better model performance, previous studies learn to transform the topology of the input graph. However, these works only focus on optimizing the original nodes and edges, leaving the direction of augmenting existing data unexplored. In this paper, by simulating the generation process of graph signals, we propose a novel heuristic pre-processing technique, namely ELectoral COllege (ELCO), which automatically expands new nodes and edges to refine the label similarity within a dense subgraph. Substantially enlarging the original training set with high-quality generated labeled data, our framework can effectively benefit downstream models. To justify the generality and practicality of ELCO, we couple it with the popular Graph Convolution Network and Graph Attention Network to perform extensive evaluations on three standard datasets. In all setups tested, our method boosts the average score of base models by a large margin of 4.7 points, as well as consistently outperforms the state-of-the-art. We release our code and data on https://github.com/RingBDStack/ELCO to guarantee reproducibility.

Zichen Wen, Yawen Ling, Yazhou Ren et al.

Recently there is a growing focus on graph data, and multi-view graph clustering has become a popular area of research interest. Most of the existing methods are only applicable to homophilous graphs, yet the extensive real-world graph data can hardly fulfill the homophily assumption, where the connected nodes tend to belong to the same class. Several studies have pointed out that the poor performance on heterophilous graphs is actually due to the fact that conventional graph neural networks (GNNs), which are essentially low-pass filters, discard information other than the low-frequency information on the graph. Nevertheless, on certain graphs, particularly heterophilous ones, neglecting high-frequency information and focusing solely on low-frequency information impedes the learning of node representations. To break this limitation, our motivation is to perform graph filtering that is closely related to the homophily degree of the given graph, with the aim of fully leveraging both low-frequency and high-frequency signals to learn distinguishable node embedding. In this work, we propose Adaptive Hybrid Graph Filter for Multi-View Graph Clustering (AHGFC). Specifically, a graph joint process and graph joint aggregation matrix are first designed by using the intrinsic node features and adjacency relationship, which makes the low and high-frequency signals on the graph more distinguishable. Then we design an adaptive hybrid graph filter that is related to the homophily degree, which learns the node embedding based on the graph joint aggregation matrix. After that, the node embedding of each view is weighted and fused into a consensus embedding for the downstream task. Experimental results show that our proposed model performs well on six datasets containing homophilous and heterophilous graphs.

Kaiqiao Han, Yi Yang, Zijie Huang et al.

Brain network analysis is vital for understanding the neural interactions regarding brain structures and functions, and identifying potential biomarkers for clinical phenotypes. However, widely used brain signals such as Blood Oxygen Level Dependent (BOLD) time series generated from functional Magnetic Resonance Imaging (fMRI) often manifest three challenges: (1) missing values, (2) irregular samples, and (3) sampling misalignment, due to instrumental limitations, impacting downstream brain network analysis and clinical outcome predictions. In this work, we propose a novel model called BrainODE to achieve continuous modeling of dynamic brain signals using Ordinary Differential Equations (ODE). By learning latent initial values and neural ODE functions from irregular time series, BrainODE effectively reconstructs brain signals at any time point, mitigating the aforementioned three data challenges of brain signals altogether. Comprehensive experimental results on real-world neuroimaging datasets demonstrate the superior performance of BrainODE and its capability of addressing the three data challenges.

Xinpeng Wang, Rong Zhou, Han Xie et al.

Multimodal Federated Learning (MFL) has emerged as a promising approach for collaboratively training multimodal models across distributed clients, particularly in healthcare domains. In the context of brain imaging analysis, modality incompleteness presents a significant challenge, where some institutions may lack specific imaging modalities (e.g., PET, MRI, or CT) due to privacy concerns, device limitations, or data availability issues. While existing work typically assumes modality completeness or oversimplifies missing-modality scenarios, we simulate a more realistic setting by considering both client-level and instance-level modality incompleteness in this study. Building on this realistic simulation, we propose ClusMFL, a novel MFL framework that leverages feature clustering for cross-institutional brain imaging analysis under modality incompleteness. Specifically, ClusMFL utilizes the FINCH algorithm to construct a pool of cluster centers for the feature embeddings of each modality-label pair, effectively capturing fine-grained data distributions. These cluster centers are then used for feature alignment within each modality through supervised contrastive learning, while also acting as proxies for missing modalities, allowing cross-modal knowledge transfer. Furthermore, ClusMFL employs a modality-aware aggregation strategy, further enhancing the model's performance in scenarios with severe modality incompleteness. We evaluate the proposed framework on the ADNI dataset, utilizing structural MRI and PET scans. Extensive experimental results demonstrate that ClusMFL achieves state-of-the-art performance compared to various baseline methods across varying levels of modality incompleteness, providing a scalable solution for cross-institutional brain imaging analysis.

Zichen Wen, Tianyi Wu, Yazhou Ren et al.

Multi-view clustering is an important machine learning task for multi-media data, encompassing various domains such as images, videos, and texts. Moreover, with the growing abundance of graph data, the significance of multi-view graph clustering (MVGC) has become evident. Most existing methods focus on graph neural networks (GNNs) to extract information from both graph structure and feature data to learn distinguishable node representations. However, traditional GNNs are designed with the assumption of homophilous graphs, making them unsuitable for widely prevalent heterophilous graphs. Several techniques have been introduced to enhance GNNs for heterophilous graphs. While these methods partially mitigate the heterophilous graph issue, they often neglect the advantages of traditional GNNs, such as their simplicity, interpretability, and efficiency. In this paper, we propose a novel multi-view graph clustering method based on dual-optimized adaptive graph reconstruction, named DOAGC. It mainly aims to reconstruct the graph structure adapted to traditional GNNs to deal with heterophilous graph issues while maintaining the advantages of traditional GNNs. Specifically, we first develop an adaptive graph reconstruction mechanism that accounts for node correlation and original structural information. To further optimize the reconstruction graph, we design a dual optimization strategy and demonstrate the feasibility of our optimization strategy through mutual information theory. Numerous experiments demonstrate that DOAGC effectively mitigates the heterophilous graph problem.

Guangjie Zeng, Hao Peng, Angsheng Li et al. · salesforce

Semi-supervised clustering techniques have emerged as valuable tools for leveraging prior information in the form of constraints to improve the quality of clustering outcomes. Despite the proliferation of such methods, the ability to seamlessly integrate various types of constraints remains limited. While structural entropy has proven to be a powerful clustering approach with wide-ranging applications, it has lacked a variant capable of accommodating these constraints. In this work, we present Semi-supervised clustering via Structural Entropy (SSE), a novel method that can incorporate different types of constraints from diverse sources to perform both partitioning and hierarchical clustering. Specifically, we formulate a uniform view for the commonly used pairwise and label constraints for both types of clustering. Then, we design objectives that incorporate these constraints into structural entropy and develop tailored algorithms for their optimization. We evaluate SSE on nine clustering datasets and compare it with eleven semi-supervised partitioning and hierarchical clustering methods. Experimental results demonstrate the superiority of SSE on clustering accuracy with different types of constraints. Additionally, the functionality of SSE for biological data analysis is demonstrated by cell clustering experiments conducted on four single-cell RNAseq datasets.

Haoteng Tang, Guodong Liu, Siyuan Dai et al.

The MRI-derived brain network serves as a pivotal instrument in elucidating both the structural and functional aspects of the brain, encompassing the ramifications of diseases and developmental processes. However, prevailing methodologies, often focusing on synchronous BOLD signals from functional MRI (fMRI), may not capture directional influences among brain regions and rarely tackle temporal functional dynamics. In this study, we first construct the brain-effective network via the dynamic causal model. Subsequently, we introduce an interpretable graph learning framework termed Spatio-Temporal Embedding ODE (STE-ODE). This framework incorporates specifically designed directed node embedding layers, aiming at capturing the dynamic interplay between structural and effective networks via an ordinary differential equation (ODE) model, which characterizes spatial-temporal brain dynamics. Our framework is validated on several clinical phenotype prediction tasks using two independent publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.

Keqi Han, Yao Su, Lifang He et al.

Functional brain connectome is crucial for deciphering the neural mechanisms underlying cognitive functions and neurological disorders. Graph deep learning models have recently gained tremendous popularity in this field. However, their actual effectiveness in modeling the brain connectome remains unclear. In this study, we re-examine graph deep learning models based on four large-scale neuroimaging studies encompassing diverse cognitive and clinical outcomes. Surprisingly, we find that the message aggregation mechanism, a hallmark of graph deep learning models, does not help with predictive performance as typically assumed, but rather consistently degrades it. To address this issue, we propose a hybrid model combining a linear model with a graph attention network through dual pathways, achieving robust predictions and enhanced interpretability by revealing both localized and global neural connectivity patterns. Our findings urge caution in adopting complex deep learning models for functional brain connectome analysis, emphasizing the need for rigorous experimental designs to establish tangible performance gains and perhaps more importantly, to pursue improvements in model interpretability.

Chenhang Cui, Yazhou Ren, Jingyu Pu et al.

Deep multi-view subspace clustering (DMVSC) has recently attracted increasing attention due to its promising performance. However, existing DMVSC methods still have two issues: (1) they mainly focus on using autoencoders to nonlinearly embed the data, while the embedding may be suboptimal for clustering because the clustering objective is rarely considered in autoencoders, and (2) existing methods typically have a quadratic or even cubic complexity, which makes it challenging to deal with large-scale data. To address these issues, in this paper we propose a novel deep multi-view subspace clustering method with anchor graph (DMCAG). To be specific, DMCAG firstly learns the embedded features for each view independently, which are used to obtain the subspace representations. To significantly reduce the complexity, we construct an anchor graph with small size for each view. Then, spectral clustering is performed on an integrated anchor graph to obtain pseudo-labels. To overcome the negative impact caused by suboptimal embedded features, we use pseudo-labels to refine the embedding process to make it more suitable for the clustering task. Pseudo-labels and embedded features are updated alternately. Furthermore, we design a strategy to keep the consistency of the labels based on contrastive learning to enhance the clustering performance. Empirical studies on real-world datasets show that our method achieves superior clustering performance over other state-of-the-art methods.

Weihang Yuan, Hector Munoz-Avila, Venkatsampath Raja Gogineni et al.

The ability of an agent to change its objectives in response to unexpected events is desirable in dynamic environments. In order to provide this capability to hierarchical task network (HTN) planning, we propose an extension of the paradigm called task modifiers, which are functions that receive a task list and a state and produce a new task list. We focus on a particular type of problems in which planning and execution are interleaved and the ability to handle exogenous events is crucial. To determine the efficacy of this approach, we evaluate the performance of our task modifier implementation in two environments, one of which is a simulation that differs substantially from traditional HTN domains.

Xiaoqin Pan, Xuan Lin, Dongsheng Cao et al.

Drug development is time-consuming and expensive. Repurposing existing drugs for new therapies is an attractive solution that accelerates drug development at reduced experimental costs, specifically for Coronavirus Disease 2019 (COVID-19), an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, comprehensively obtaining and productively integrating available knowledge and big biomedical data to effectively advance deep learning models is still challenging for drug repurposing in other complex diseases. In this review, we introduce guidelines on how to utilize deep learning methodologies and tools for drug repurposing. We first summarized the commonly used bioinformatics and pharmacogenomics databases for drug repurposing. Next, we discuss recently developed sequence-based and graph-based representation approaches as well as state-of-the-art deep learning-based methods. Finally, we present applications of drug repurposing to fight the COVID-19 pandemic, and outline its future challenges.

Jun Yu, Zhaoming Kong, Aditya Kendre et al.

This paper presents a novel graph-based kernel learning approach for connectome analysis. Specifically, we demonstrate how to leverage the naturally available structure within the graph representation to encode prior knowledge in the kernel. We first proposed a matrix factorization to directly extract structural features from natural symmetric graph representations of connectome data. We then used them to derive a structure-persevering graph kernel to be fed into the support vector machine. The proposed approach has the advantage of being clinically interpretable. Quantitative evaluations on challenging HIV disease classification (DTI- and fMRI-derived connectome data) and emotion recognition (EEG-derived connectome data) tasks demonstrate the superior performance of our proposed methods against the state-of-the-art. Results showed that relevant EEG-connectome information is primarily encoded in the alpha band during the emotion regulation task.

Ye Liu, Jian-Guo Zhang, Yao Wan et al.

To capture the semantic graph structure from raw text, most existing summarization approaches are built on GNNs with a pre-trained model. However, these methods suffer from cumbersome procedures and inefficient computations for long-text documents. To mitigate these issues, this paper proposes HETFORMER, a Transformer-based pre-trained model with multi-granularity sparse attentions for long-text extractive summarization. Specifically, we model different types of semantic nodes in raw text as a potential heterogeneous graph and directly learn heterogeneous relationships (edges) among nodes by Transformer. Extensive experiments on both single- and multi-document summarization tasks show that HETFORMER achieves state-of-the-art performance in Rouge F1 while using less memory and fewer parameters.

Hejie Cui, Wei Dai, Yanqiao Zhu et al.

Interpretable brain network models for disease prediction are of great value for the advancement of neuroscience. GNNs are promising to model complicated network data, but they are prone to overfitting and suffer from poor interpretability, which prevents their usage in decision-critical scenarios like healthcare. To bridge this gap, we propose BrainNNExplainer, an interpretable GNN framework for brain network analysis. It is mainly composed of two jointly learned modules: a backbone prediction model that is specifically designed for brain networks and an explanation generator that highlights disease-specific prominent brain network connections. Extensive experimental results with visualizations on two challenging disease prediction datasets demonstrate the unique interpretability and outstanding performance of BrainNNExplainer.

Yanqiao Zhu, Hejie Cui, Lifang He et al.

Multimodal brain networks characterize complex connectivities among different brain regions from both structural and functional aspects and provide a new means for mental disease analysis. Recently, Graph Neural Networks (GNNs) have become a de facto model for analyzing graph-structured data. However, how to employ GNNs to extract effective representations from brain networks in multiple modalities remains rarely explored. Moreover, as brain networks provide no initial node features, how to design informative node attributes and leverage edge weights for GNNs to learn is left unsolved. To this end, we develop a novel multiview GNN for multimodal brain networks. In particular, we regard each modality as a view for brain networks and employ contrastive learning for multimodal fusion. Then, we propose a GNN model which takes advantage of the message passing scheme by propagating messages based on degree statistics and brain region connectivities. Extensive experiments on two real-world disease datasets (HIV and Bipolar) demonstrate the effectiveness of our proposed method over state-of-the-art baselines.

Jie Xu, Yazhou Ren, Huayi Tang et al.

Multi-view clustering, a long-standing and important research problem, focuses on mining complementary information from diverse views. However, existing works often fuse multiple views' representations or handle clustering in a common feature space, which may result in their entanglement especially for visual representations. To address this issue, we present a novel VAE-based multi-view clustering framework (Multi-VAE) by learning disentangled visual representations. Concretely, we define a view-common variable and multiple view-peculiar variables in the generative model. The prior of view-common variable obeys approximately discrete Gumbel Softmax distribution, which is introduced to extract the common cluster factor of multiple views. Meanwhile, the prior of view-peculiar variable follows continuous Gaussian distribution, which is used to represent each view's peculiar visual factors. By controlling the mutual information capacity to disentangle the view-common and view-peculiar representations, continuous visual information of multiple views can be separated so that their common discrete cluster information can be effectively mined. Experimental results demonstrate that Multi-VAE enjoys the disentangled and explainable visual representations, while obtaining superior clustering performance compared with state-of-the-art methods.

Jie Xu, Huayi Tang, Yazhou Ren et al.

Multi-view clustering can explore common semantics from multiple views and has attracted increasing attention. However, existing works punish multiple objectives in the same feature space, where they ignore the conflict between learning consistent common semantics and reconstructing inconsistent view-private information. In this paper, we propose a new framework of multi-level feature learning for contrastive multi-view clustering to address the aforementioned issue. Our method learns different levels of features from the raw features, including low-level features, high-level features, and semantic labels/features in a fusion-free manner, so that it can effectively achieve the reconstruction objective and the consistency objectives in different feature spaces. Specifically, the reconstruction objective is conducted on the low-level features. Two consistency objectives based on contrastive learning are conducted on the high-level features and the semantic labels, respectively. They make the high-level features effectively explore the common semantics and the semantic labels achieve the multi-view clustering. As a result, the proposed framework can reduce the adverse influence of view-private information. Extensive experiments on public datasets demonstrate that our method achieves state-of-the-art clustering effectiveness.

Jianxin Li, Xingcheng Fu, Hao Peng et al.

Graph embedding is essential for graph mining tasks. With the prevalence of graph data in real-world applications, many methods have been proposed in recent years to learn high-quality graph embedding vectors various types of graphs. However, most existing methods usually randomly select the negative samples from the original graph to enhance the training data without considering the noise. In addition, most of these methods only focus on the explicit graph structures and cannot fully capture complex semantics of edges such as various relationships or asymmetry. In order to address these issues, we propose a robust and generalized framework for adversarial graph embedding based on generative adversarial networks. Inspired by generative adversarial network, we propose a robust and generalized framework for adversarial graph embedding, named AGE. AGE generates the fake neighbor nodes as the enhanced negative samples from the implicit distribution, and enables the discriminator and generator to jointly learn each node's robust and generalized representation. Based on this framework, we propose three models to handle three types of graph data and derive the corresponding optimization algorithms, i.e., UG-AGE and DG-AGE for undirected and directed homogeneous graphs, respectively, and HIN-AGE for heterogeneous information networks. Extensive experiments show that our methods consistently and significantly outperform existing state-of-the-art methods across multiple graph mining tasks, including link prediction, node classification, and graph reconstruction.

Gongxu Luo, Jianxin Li, Jianlin Su et al.

Graph representation learning has achieved great success in many areas, including e-commerce, chemistry, biology, etc. However, the fundamental problem of choosing the appropriate dimension of node embedding for a given graph still remains unsolved. The commonly used strategies for Node Embedding Dimension Selection (NEDS) based on grid search or empirical knowledge suffer from heavy computation and poor model performance. In this paper, we revisit NEDS from the perspective of minimum entropy principle. Subsequently, we propose a novel Minimum Graph Entropy (MinGE) algorithm for NEDS with graph data. To be specific, MinGE considers both feature entropy and structure entropy on graphs, which are carefully designed according to the characteristics of the rich information in them. The feature entropy, which assumes the embeddings of adjacent nodes to be more similar, connects node features and link topology on graphs. The structure entropy takes the normalized degree as basic unit to further measure the higher-order structure of graphs. Based on them, we design MinGE to directly calculate the ideal node embedding dimension for any graph. Finally, comprehensive experiments with popular Graph Neural Networks (GNNs) on benchmark datasets demonstrate the effectiveness and generalizability of our proposed MinGE.

Mehrnaz Najafi, Lifang He, Philip S. Yu

With recent advances in data collection from multiple sources, multi-view data has received significant attention. In multi-view data, each view represents a different perspective of data. Since label information is often expensive to acquire, multi-view clustering has gained growing interest, which aims to obtain better clustering solution by exploiting complementary and consistent information across all views rather than only using an individual view. Due to inevitable sensor failures, data in each view may contain error. Error often exhibits as noise or feature-specific corruptions or outliers. Multi-view data may contain any or combination of these error types. Blindly clustering multi-view data i.e., without considering possible error in view(s) could significantly degrade the performance. The goal of error-robust multi-view clustering is to obtain useful outcome even if the multi-view data is corrupted. Existing error-robust multi-view clustering approaches with explicit error removal formulation can be structured into five broad research categories - sparsity norm based approaches, graph based methods, subspace based learning approaches, deep learning based methods and hybrid approaches, this survey summarizes and reviews recent advances in error-robust clustering for multi-view data. Finally, we highlight the challenges and provide future research opportunities.

Sicong Che, Hao Peng, Lichao Sun et al.

Along with the rapid expansion of information technology and digitalization of health data, there is an increasing concern on maintaining data privacy while garnering the benefits in medical field. Two critical challenges are identified: Firstly, medical data is naturally distributed across multiple local sites, making it difficult to collectively train machine learning models without data leakage. Secondly, in medical applications, data are often collected from different sources and views, resulting in heterogeneity and complexity that requires reconciliation. This paper aims to provide a generic Federated Multi-View Learning (FedMV) framework for multi-view data leakage prevention, which is based on different types of local data availability and enables to accommodate two types of problems: Vertical Federated Multi-View Learning (V-FedMV) and Horizontal Federated Multi-View Learning (H-FedMV). We experimented with real-world keyboard data collected from BiAffect study. The results demonstrated that the proposed FedMV approach can make full use of multi-view data in a privacy-preserving way, and both V-FedMV and H-FedMV methods perform better than their single-view and pairwise counterparts. Besides, the proposed model can be easily adapted to deal with multi-view sequential data in a federated environment, which has been modeled and experimentally studied. To the best of our knowledge, this framework is the first to consider both vertical and horizontal diversification in the multi-view setting, as well as their sequential federated learning.