arXiv subjects

Hejie Cui

Publications and source records attributed to Hejie Cui.

48 records · Page 3Linked to original sources

arXiv2022

Brain Network Transformer

Human brains are commonly modeled as networks of Regions of Interest (ROIs) and their connections for the understanding of brain functions and mental disorders. Recently, Transformer-based models have been studied over different types of data, including graphs, shown to bring performance gains widely. In this work, we study Transformer-based models for brain network analysis. Driven by the unique properties of data, we model brain networks as graphs with nodes of fixed size and order, which allows us to (1) use connection profiles as node features to provide natural and low-cost positional information and (2) learn pair-wise connection strengths among ROIs with efficient attention weights across individuals that are predictive towards downstream analysis tasks. Moreover, we propose an Orthonormal Clustering Readout operation based on self-supervised soft clustering and orthonormal projection. This design accounts for the underlying functional modules that determine similar behaviors among groups of ROIs, leading to distinguishable cluster-aware node embeddings and informative graph embeddings. Finally, we re-standardize the evaluation pipeline on the only one publicly available large-scale brain network dataset of ABIDE, to enable meaningful comparison of different models. Experiment results show clear improvements of our proposed Brain Network Transformer on both the public ABIDE and our restricted ABCD datasets. The implementation is available at https://github.com/Wayfear/BrainNetworkTransformer.

cs.LG↗

arXiv2022

On Positional and Structural Node Features for Graph Neural Networks on Non-attributed Graphs

Graph neural networks (GNNs) have been widely used in various graph-related problems such as node classification and graph classification, where superior performance is mainly established when natural node features are available. However, it is not well understood how GNNs work without natural node features, especially regarding the various ways to construct artificial ones. In this paper, we point out the two types of artificial node features, i.e., positional and structural node features, and provide insights on why each of them is more appropriate for certain tasks, i.e., positional node classification, structural node classification, and graph classification. Extensive experimental results on 10 benchmark datasets validate our insights, thus leading to a practical guideline on the choices between different artificial node features for GNNs on non-attributed graphs. The code is available at https://github.com/zjzijielu/gnn-positional-structural-node-features.

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

FBNETGEN: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation

Functional magnetic resonance imaging (fMRI) is one of the most common imaging modalities to investigate brain functions. Recent studies in neuroscience stress the great potential of functional brain networks constructed from fMRI data for clinical predictions. Traditional functional brain networks, however, are noisy and unaware of downstream prediction tasks, while also incompatible with the deep graph neural network (GNN) models. In order to fully unleash the power of GNNs in network-based fMRI analysis, we develop FBNETGEN, a task-aware and interpretable fMRI analysis framework via deep brain network generation. In particular, we formulate (1) prominent region of interest (ROI) features extraction, (2) brain networks generation, and (3) clinical predictions with GNNs, in an end-to-end trainable model under the guidance of particular prediction tasks. Along with the process, the key novel component is the graph generator which learns to transform raw time-series features into task-oriented brain networks. Our learnable graphs also provide unique interpretations by highlighting prediction-related brain regions. Comprehensive experiments on two datasets, i.e., the recently released and currently largest publicly available fMRI dataset Adolescent Brain Cognitive Development (ABCD), and the widely-used fMRI dataset PNC, prove the superior effectiveness and interpretability of FBNETGEN. The implementation is available at https://github.com/Wayfear/FBNETGEN.

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.

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arXiv2022

How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map Generation

Graph neural networks (GNNs), as a group of powerful tools for representation learning on irregular data, have manifested superiority in various downstream tasks. With unstructured texts represented as concept maps, GNNs can be exploited for tasks like document retrieval. Intrigued by how can GNNs help document retrieval, we conduct an empirical study on a large-scale multi-discipline dataset CORD-19. Results show that instead of the complex structure-oriented GNNs such as GINs and GATs, our proposed semantics-oriented graph functions achieve better and more stable performance based on the BM25 retrieved candidates. Our insights in this case study can serve as a guideline for future work to develop effective GNNs with appropriate semantics-oriented inductive biases for textual reasoning tasks like document retrieval and classification. All code for this case study is available at https://github.com/HennyJie/GNN-DocRetrieval.

cs.IR↗

arXiv2021

Structure-Aware Hard Negative Mining for Heterogeneous Graph Contrastive Learning

Recently, heterogeneous Graph Neural Networks (GNNs) have become a de facto model for analyzing HGs, while most of them rely on a relative large number of labeled data. In this work, we investigate Contrastive Learning (CL), a key component in self-supervised approaches, on HGs to alleviate the label scarcity problem. We first generate multiple semantic views according to metapaths and network schemas. Then, by pushing node embeddings corresponding to different semantic views close to each other (positives) and pulling other embeddings apart (negatives), one can obtain informative representations without human annotations. However, this CL approach ignores the relative hardness of negative samples, which may lead to suboptimal performance. Considering the complex graph structure and the smoothing nature of GNNs, we propose a structure-aware hard negative mining scheme that measures hardness by structural characteristics for HGs. By synthesizing more negative nodes, we give larger weights to harder negatives with limited computational overhead to further boost the performance. Empirical studies on three real-world datasets show the effectiveness of our proposed method. The proposed method consistently outperforms existing state-of-the-art methods and notably, even surpasses several supervised counterparts.

cs.LG↗

arXiv2021

Effective and Interpretable fMRI Analysis via Functional Brain Network Generation

Recent studies in neuroscience show great potential of functional brain networks constructed from fMRI data for popularity modeling and clinical predictions. However, existing functional brain networks are noisy and unaware of downstream prediction tasks, while also incompatible with recent powerful machine learning models of GNNs. In this work, we develop an end-to-end trainable pipeline to extract prominent fMRI features, generate brain networks, and make predictions with GNNs, all under the guidance of downstream prediction tasks. Preliminary experiments on the PNC fMRI data show the superior effectiveness and unique interpretability of our framework.

cs.LG↗

arXiv2021

Zero-Shot Scene Graph Relation Prediction through Commonsense Knowledge Integration

Relation prediction among entities in images is an important step in scene graph generation (SGG), which further impacts various visual understanding and reasoning tasks. Existing SGG frameworks, however, require heavy training yet are incapable of modeling unseen (i.e.,zero-shot) triplets. In this work, we stress that such incapability is due to the lack of commonsense reasoning,i.e., the ability to associate similar entities and infer similar relations based on general understanding of the world. To fill this gap, we propose CommOnsense-integrAted sCenegrapHrElation pRediction (COACHER), a framework to integrate commonsense knowledge for SGG, especially for zero-shot relation prediction. Specifically, we develop novel graph mining pipelines to model the neighborhoods and paths around entities in an external commonsense knowledge graph, and integrate them on top of state-of-the-art SGG frameworks. Extensive quantitative evaluations and qualitative case studies on both original and manipulated datasets from Visual Genome demonstrate the effectiveness of our proposed approach.

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

Pulmonary Vessel Segmentation based on Orthogonal Fused U-Net++ of Chest CT Images

Pulmonary vessel segmentation is important for clinical diagnosis of pulmonary diseases, while is also challenging due to the complicated structure. In this work, we present an effective framework and refinement process of pulmonary vessel segmentation from chest computed tomographic (CT) images. The key to our approach is a 2.5D segmentation network applied from three orthogonal axes, which presents a robust and fully automated pulmonary vessel segmentation result with lower network complexity and memory usage compared to 3D networks. The slice radius is introduced to convolve the adjacent information of the center slice and the multi-planar fusion optimizes the presentation of intra- and inter- slice features. Besides, the tree-like structure of the pulmonary vessel is extracted in the post-processing process, which is used for segmentation refining and pruning. In the evaluation experiments, three fusion methods are tested and the most promising one is compared with the state-of-the-art 2D and 3D structures on 300 cases of lung images randomly selected from LIDC dataset. Our method outperforms other network structures by a large margin and achieves by far the highest average DICE score of 0.9272 and precision of 0.9310, as per our knowledge from the pulmonary vessel segmentation models available in the literature.

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