arXiv subjects

Lifang He

Publications and source records attributed to Lifang He.

At least 73 records · Page 4Linked to original sources

arXiv2023

A Comprehensive Survey on Pretrained Foundation Models: A History from BERT to ChatGPT

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.

cs.AI↗

arXiv2023

Hierarchical State Abstraction Based on Structural Information Principles

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.

cs.AI↗

arXiv2023

Self-Paced Neutral Expression-Disentangled Learning for Facial Expression Recognition

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.

cs.CV↗

arXiv2022

ABN: Anti-Blur Neural Networks for Multi-Stage Deformable Image Registration

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

cs.CV↗

arXiv2022

ERNet: Unsupervised Collective Extraction and Registration in Neuroimaging Data

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

cs.CV↗

arXiv2022

BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks

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.

q-bio.NC↗

arXiv2022

Normative Modeling via Conditional Variational Autoencoder and Adversarial Learning to Identify Brain Dysfunction in Alzheimer's Disease

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.

cs.LG↗

arXiv2022

Deep Clustering: A Comprehensive Survey

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.

cs.LG↗

arXiv2022

Adversarial Attack and Defense on Graph Data: A Survey

Deep neural networks (DNNs) have been widely applied to various applications, including image classification, text generation, audio recognition, and graph data analysis. However, recent studies have shown that DNNs are vulnerable to adversarial attacks. Though there are several works about adversarial attack and defense strategies on domains such as images and natural language processing, it is still difficult to directly transfer the learned knowledge to graph data due to its representation structure. Given the importance of graph analysis, an increasing number of studies over the past few years have attempted to analyze the robustness of machine learning models on graph data. Nevertheless, existing research considering adversarial behaviors on graph data often focuses on specific types of attacks with certain assumptions. In addition, each work proposes its own mathematical formulation, which makes the comparison among different methods difficult. Therefore, this review is intended to provide an overall landscape of more than 100 papers on adversarial attack and defense strategies for graph data, and establish a unified formulation encompassing most graph adversarial learning models. Moreover, we also compare different graph attacks and defenses along with their contributions and limitations, as well as summarize the evaluation metrics, datasets and future trends. We hope this survey can help fill the gap in the literature and facilitate further development of this promising new field.

cs.CR↗

arXiv2022

Tensor-Based Multi-Modality Feature Selection and Regression for Alzheimer's Disease Diagnosis

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.

cs.LG↗

arXiv2022

From Known to Unknown: Quality-aware Self-improving Graph Neural Network for Open Set Social Event Detection

State-of-the-art Graph Neural Networks (GNNs) have achieved tremendous success in social event detection tasks when restricted to a closed set of events. However, considering the large amount of data needed for training a neural network and the limited ability of a neural network in handling previously unknown data, it remains a challenge for existing GNN-based methods to operate in an open set setting. To address this problem, we design a Quality-aware Self-improving Graph Neural Network (QSGNN) which extends the knowledge from known to unknown by leveraging the best of known samples and reliable knowledge transfer. Specifically, to fully exploit the labeled data, we propose a novel supervised pairwise loss with an additional orthogonal inter-class relation constraint to train the backbone GNN encoder. The learnt, already-known events further serve as strong reference bases for the unknown ones, which greatly prompts knowledge acquisition and transfer. When the model is generalized to unknown data, to ensure the effectiveness and reliability, we further leverage the reference similarity distribution vectors for pseudo pairwise label generation, selection and quality assessment. Following the diversity principle of active learning, our method selects diverse pair samples with the generated pseudo labels to fine-tune the GNN encoder. Besides, we propose a novel quality-guided optimization in which the contributions of pseudo labels are weighted based on consistency. We thoroughly evaluate our model on two large real-world social event datasets. Experiments demonstrate that our model achieves state-of-the-art results and extends well to unknown events.

cs.SI↗

arXiv2022

Deep reinforcement learning guided graph neural networks for brain network analysis

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.

cs.LG↗

arXiv2022

Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis

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.

q-bio.NC↗

arXiv2022

Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learning

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.

cs.LG↗

arXiv2022

Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis

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.

q-bio.NC↗

arXiv2022

Deep Embedded Multi-View Clustering via Jointly Learning Latent Representations and Graphs

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.

cs.LG↗

arXiv2022

Interpretable Graph Convolutional Network of Multi-Modality Brain Imaging for Alzheimer's Disease Diagnosis

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.

cs.LG↗

arXiv2022

Multi-level Feature Learning for Contrastive Multi-view Clustering

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.

cs.LG↗