arXiv subjects

Lifang He

Publications and source records attributed to Lifang He.

At least 91 records · Page 5Linked to original sources

arXiv2022

Structure-Preserving Graph Kernel for Brain Network Classification

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.

eess.IV↗

arXiv2022

Task Modifiers for HTN Planning and Acting

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.

cs.AI↗

arXiv2022

Deep learning for drug repurposing: methods, databases, and applications

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.

q-bio.BM↗

arXiv2021

A Survey on Text Classification: From Shallow to Deep Learning

Text classification is the most fundamental and essential task in natural language processing. The last decade has seen a surge of research in this area due to the unprecedented success of deep learning. Numerous methods, datasets, and evaluation metrics have been proposed in the literature, raising the need for a comprehensive and updated survey. This paper fills the gap by reviewing the state-of-the-art approaches from 1961 to 2021, focusing on models from traditional models to deep learning. We create a taxonomy for text classification according to the text involved and the models used for feature extraction and classification. We then discuss each of these categories in detail, dealing with both the technical developments and benchmark datasets that support tests of predictions. A comprehensive comparison between different techniques, as well as identifying the pros and cons of various evaluation metrics are also provided in this survey. Finally, we conclude by summarizing key implications, future research directions, and the challenges facing the research area.

cs.CL↗

arXiv2021

HETFORMER: Heterogeneous Transformer with Sparse Attention for Long-Text Extractive Summarization

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.

cs.CL↗

arXiv2021

FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks

Graph Neural Network (GNN) research is rapidly growing thanks to the capacity of GNNs in learning distributed representations from graph-structured data. However, centralizing a massive amount of real-world graph data for GNN training is prohibitive due to privacy concerns, regulation restrictions, and commercial competitions. Federated learning (FL), a trending distributed learning paradigm, provides possibilities to solve this challenge while preserving data privacy. Despite recent advances in vision and language domains, there is no suitable platform for the FL of GNNs. To this end, we introduce FedGraphNN, an open FL benchmark system that can facilitate research on federated GNNs. FedGraphNN is built on a unified formulation of graph FL and contains a wide range of datasets from different domains, popular GNN models, and FL algorithms, with secure and efficient system support. Particularly for the datasets, we collect, preprocess, and partition 36 datasets from 7 domains, including both publicly available ones and specifically obtained ones such as hERG and Tencent. Our empirical analysis showcases the utility of our benchmark system, while exposing significant challenges in graph FL: federated GNNs perform worse in most datasets with a non-IID split than centralized GNNs; the GNN model that attains the best result in the centralized setting may not maintain its advantage in the FL setting. These results imply that more research efforts are needed to unravel the mystery behind federated GNNs. Moreover, our system performance analysis demonstrates that the FedGraphNN system is computationally efficient and secure to large-scale graphs datasets. We maintain the source code at https://github.com/FedML-AI/FedGraphNN.

cs.LG↗

arXiv2021

Graph Entropy Guided Node Embedding Dimension Selection for Graph Neural Networks

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.

cs.LG↗

arXiv2021

Multiplex Graph Networks for Multimodal Brain Network Analysis

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.

cs.CV↗

arXiv2021

BrainNNExplainer: An Interpretable Graph Neural Network Framework for Brain Network based Disease Analysis

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.

cs.LG↗

arXiv2021

Multi-VAE: Learning Disentangled View-common and View-peculiar Visual Representations for Multi-view Clustering

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.

cs.CV↗

arXiv2021

Adversarial Directed Graph Embedding

Node representation learning for directed graphs is critically important to facilitate many graph mining tasks. To capture the directed edges between nodes, existing methods mostly learn two embedding vectors for each node, source vector and target vector. However, these methods learn the source and target vectors separately. For the node with very low indegree or outdegree, the corresponding target vector or source vector cannot be effectively learned. In this paper, we propose a novel Directed Graph embedding framework based on Generative Adversarial Network, called DGGAN. The main idea is to use adversarial mechanisms to deploy a discriminator and two generators that jointly learn each node's source and target vectors. For a given node, the two generators are trained to generate its fake target and source neighbor nodes from the same underlying distribution, and the discriminator aims to distinguish whether a neighbor node is real or fake. The two generators are formulated into a unified framework and could mutually reinforce each other to learn more robust source and target vectors. Extensive experiments show that DGGAN consistently and significantly outperforms existing state-of-the-art methods across multiple graph mining tasks on directed graphs.

cs.SI↗

arXiv2021

SUGAR: Subgraph Neural Network with Reinforcement Pooling and Self-Supervised Mutual Information Mechanism

Graph representation learning has attracted increasing research attention. However, most existing studies fuse all structural features and node attributes to provide an overarching view of graphs, neglecting finer substructures' semantics, and suffering from interpretation enigmas. This paper presents a novel hierarchical subgraph-level selection and embedding based graph neural network for graph classification, namely SUGAR, to learn more discriminative subgraph representations and respond in an explanatory way. SUGAR reconstructs a sketched graph by extracting striking subgraphs as the representative part of the original graph to reveal subgraph-level patterns. To adaptively select striking subgraphs without prior knowledge, we develop a reinforcement pooling mechanism, which improves the generalization ability of the model. To differentiate subgraph representations among graphs, we present a self-supervised mutual information mechanism to encourage subgraph embedding to be mindful of the global graph structural properties by maximizing their mutual information. Extensive experiments on six typical bioinformatics datasets demonstrate a significant and consistent improvement in model quality with competitive performance and interpretability.

cs.LG↗

arXiv2021

A Robust and Generalized Framework for Adversarial Graph Embedding

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.

cs.LG↗

arXiv2021

FedMood: Federated Learning on Mobile Health Data for Mood Detection

Depression is one of the most common mental illness problems, and the symptoms shown by patients are not consistent, making it difficult to diagnose in the process of clinical practice and pathological research. Although researchers hope that artificial intelligence can contribute to the diagnosis and treatment of depression, the traditional centralized machine learning needs to aggregate patient data, and the data privacy of patients with mental illness needs to be strictly confidential, which hinders machine learning algorithms clinical application. To solve the problem of privacy of the medical history of patients with depression, we implement federated learning to analyze and diagnose depression. First, we propose a general multi-view federated learning framework using multi-source data, which can extend any traditional machine learning model to support federated learning across different institutions or parties. Secondly, we adopt late fusion methods to solve the problem of inconsistent time series of multi-view data. Finally, we compare the federated framework with other cooperative learning frameworks in performance and discuss the related results.

cs.CY↗

arXiv2021

Error-Robust Multi-View Clustering: Progress, Challenges and Opportunities

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.

cs.LG↗

arXiv2021

Federated Multi-View Learning for Private Medical Data Integration and Analysis

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.

cs.AI↗

arXiv2021

Non-Linear Fusion for Self-Paced Multi-View Clustering

With the advance of the multi-media and multi-modal data, multi-view clustering (MVC) has drawn increasing attentions recently. In this field, one of the most crucial challenges is that the characteristics and qualities of different views usually vary extensively. Therefore, it is essential for MVC methods to find an effective approach that handles the diversity of multiple views appropriately. To this end, a series of MVC methods focusing on how to integrate the loss from each view have been proposed in the past few years. Among these methods, the mainstream idea is assigning weights to each view and then combining them linearly. In this paper, inspired by the effectiveness of non-linear combination in instance learning and the auto-weighted approaches, we propose Non-Linear Fusion for Self-Paced Multi-View Clustering (NSMVC), which is totally different from the the conventional linear-weighting algorithms. In NSMVC, we directly assign different exponents to different views according to their qualities. By this way, the negative impact from the corrupt views can be significantly reduced. Meanwhile, to address the non-convex issue of the MVC model, we further define a novel regularizer-free modality of Self-Paced Learning (SPL), which fits the proposed non-linear model perfectly. Experimental results on various real-world data sets demonstrate the effectiveness of the proposed method.

cs.LG↗

arXiv2021

Higher-Order Attribute-Enhancing Heterogeneous Graph Neural Networks

Graph neural networks (GNNs) have been widely used in deep learning on graphs. They can learn effective node representations that achieve superior performances in graph analysis tasks such as node classification and node clustering. However, most methods ignore the heterogeneity in real-world graphs. Methods designed for heterogeneous graphs, on the other hand, fail to learn complex semantic representations because they only use meta-paths instead of meta-graphs. Furthermore, they cannot fully capture the content-based correlations between nodes, as they either do not use the self-attention mechanism or only use it to consider the immediate neighbors of each node, ignoring the higher-order neighbors. We propose a novel Higher-order Attribute-Enhancing (HAE) framework that enhances node embedding in a layer-by-layer manner. Under the HAE framework, we propose a Higher-order Attribute-Enhancing Graph Neural Network (HAEGNN) for heterogeneous network representation learning. HAEGNN simultaneously incorporates meta-paths and meta-graphs for rich, heterogeneous semantics, and leverages the self-attention mechanism to explore content-based nodes interactions. The unique higher-order architecture of HAEGNN allows examining the first-order as well as higher-order neighborhoods. Moreover, HAEGNN shows good explainability as it learns the importances of different meta-paths and meta-graphs. HAEGNN is also memory-efficient, for it avoids per meta-path based matrix calculation. Experimental results not only show HAEGNN superior performance against the state-of-the-art methods in node classification, node clustering, and visualization, but also demonstrate its superiorities in terms of memory efficiency and explainability.

cs.LG↗