Training deep neural networks (DNNs) with limited supervision has been a popular research topic as it can significantly alleviate the annotation burden. Self-training has been successfully applied in semi-supervised learning tasks, but one drawback of self-training is that it is vulnerable to the label noise from incorrect pseudo labels. Inspired by the fact that samples with similar labels tend to share similar representations, we develop a neighborhood-based sample selection approach to tackle the issue of noisy pseudo labels. We further stabilize self-training via aggregating the predictions from different rounds during sample selection. Experiments on eight tasks show that our proposed method outperforms the strongest self-training baseline with 1.83% and 2.51% performance gain for text and graph datasets on average. Our further analysis demonstrates that our proposed data selection strategy reduces the noise of pseudo labels by 36.8% and saves 57.3% of the time when compared with the best baseline. Our code and appendices will be uploaded to https://github.com/ritaranx/NeST.

Biological networks are commonly used in biomedical and healthcare domains to effectively model the structure of complex biological systems with interactions linking biological entities. However, due to their characteristics of high dimensionality and low sample size, directly applying deep learning models on biological networks usually faces severe overfitting. In this work, we propose R-MIXUP, a Mixup-based data augmentation technique that suits the symmetric positive definite (SPD) property of adjacency matrices from biological networks with optimized training efficiency. The interpolation process in R-MIXUP leverages the log-Euclidean distance metrics from the Riemannian manifold, effectively addressing the swelling effect and arbitrarily incorrect label issues of vanilla Mixup. We demonstrate the effectiveness of R-MIXUP with five real-world biological network datasets on both regression and classification tasks. Besides, we derive a commonly ignored necessary condition for identifying the SPD matrices of biological networks and empirically study its influence on the model performance. The code implementation can be found in Appendix E.

Images contain rich relational knowledge that can help machines understand the world. Existing methods on visual knowledge extraction often rely on the pre-defined format (e.g., sub-verb-obj tuples) or vocabulary (e.g., relation types), restricting the expressiveness of the extracted knowledge. In this work, we take a first exploration to a new paradigm of open visual knowledge extraction. To achieve this, we present OpenVik which consists of an open relational region detector to detect regions potentially containing relational knowledge and a visual knowledge generator that generates format-free knowledge by prompting the large multimodality model with the detected region of interest. We also explore two data enhancement techniques for diversifying the generated format-free visual knowledge. Extensive knowledge quality evaluations highlight the correctness and uniqueness of the extracted open visual knowledge by OpenVik. Moreover, integrating our extracted knowledge across various visual reasoning applications shows consistent improvements, indicating the real-world applicability of OpenVik.

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.

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 BrainGBwebsite 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.

Brain networks, graphical models such as those constructed from MRI, have been widely used in pathological prediction and analysis of brain functions. Within the complex brain system, differences in neuronal connection strengths parcellate the brain into various functional modules (network communities), which are critical for brain analysis. However, identifying such communities within the brain has been a nontrivial issue due to the complexity of neuronal interactions. In this work, we propose a novel interpretable transformer-based model for joint hierarchical cluster identification and brain network classification with three main contributions. First, we offer an end-to-end transformer-based approach to learning clustering assignments. Through pairwise attention, a clustering layer, BCluster, and a transformer encoder collaboratively learn a globally shared clustering assignment that is continuously tuned to downstream tasks. BCluster enhances the model’s performance and reduces run time complexity while also providing clinical insights. Second, we propose a hierarchical structure for the clustering model, enabling the model to learn more abstract, higher-level cluster representations by combining lower-level modules. Each clustering layer is attached to a distinct readout module, which allows the model to utilize the cluster embeddings of every layer effectively. Last but not least, we redesign the attention mechanism of the transformer with stochastic noise, which enhances its cluster learning capability. We compare our model’s performance with SOTA models and perform clustering analysis with the ground truth community labels. Extensive experimental results show that with the help of hierarchical clustering, the model achieves increased accuracy and reduced runtime complexity while providing plausible insight into the functional organization of brain regions.

Multimodal brain networks extracted from functional magnetic resonance imaging (fMRI) characterize complex connectivities among brain regions from both structural and functional, showing great potential for mental health analysis. Deep neural network models have led a tremendous success in various downstream tasks. However, common property in brain network data, the small number of samples compared with the huge amount of features, hinders the application of deep learning techniques for brain network analysis. This work presents a graph-embedding method by leveraging the unique characteristics of brain networks to unleash the power of deep neural networks and achieve outstanding prediction performance with proper explainability. Experiment results show clear advancements in our proposed braceNet on both real and synthetic datasets.

Functional magnetic resonance imaging (fMRI) has become one of the most common imaging modalities for brain function analysis. Recently, graph neural networks (GNN) have been adopted for fMRI analysis with superior performance. Unfortunately, traditional functional brain networks are mainly constructed based on similarities among region of interests (ROI), which are noisy and agnostic to the downstream prediction tasks and can lead to inferior results for GNN-based models. To better adapt GNNs for fMRI analysis, we propose TBDS, an end-to-end framework based on Task-aware Brain connectivity DAG (short for Directed Acyclic Graph) Structure generation for fMRI analysis. The key component of TBDS is the brain network generator which adopts a DAG learning approach to transform the raw time-series into task-aware brain connectivities. Besides, we design an additional contrastive regularization to inject task-specific knowledge during the brain network generation process. Comprehensive experiments on two fMRI datasets, namely Adolescent Brain Cognitive Development (ABCD) and Philadelphia Neuroimaging Cohort (PNC) datasets demonstrate the efficacy of TBDS. In addition, the generated brain networks also highlight the prediction-related brain regions and thus provide unique interpretations of the prediction results. Our implementation will be published upon acceptance.

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 collection, 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 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.

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.

Facial recognition is a key enabling component for emerging Internet of Things (IoT) services such as smart homes or responsive offices. Through the use of deep neural networks, facial recognition has achieved excellent performance. However, this is only possibly when trained with hundreds of images of each user in different viewing and lighting conditions. Clearly, this level of effort in enrolment and labelling is impossible for wide-spread deployment and adoption. Inspired by the fact that most people carry smart wireless devices with them, e.g. smartphones, we propose to use this wireless identifier as a supervisory label. This allows us to curate a dataset of facial images that are unique to a certain domain e.g. a set of people in a particular office. This custom corpus can then be used to finetune existing pre-trained models e.g. FaceNet. However, due to the vagaries of wireless propagation in buildings, the supervisory labels are noisy and weak. We propose a novel technique, AutoTune, which learns and refines the association between a face and wireless identifier over time, by increasing the inter-cluster separation and minimizing the intra-cluster distance. Through extensive experiments with multiple users on two sites, we demonstrate the ability of AutoTune to design an environment-specific, continually evolving facial recognition system with entirely no user effort.

Face recognition has become the de facto authentication solution in a broad spectrum of applications, from smart buildings, to industrial monitoring and security services. However, in many of those real-world scenarios, tracking or identifying people with facial recognition is extremely challenging due to the variations in the environment such as lighting conditions, camera viewing angles and subject motion. For most of the state-of-the-art face recognition systems, they need to be trained on a large dataset containing a good variety of labelled face images to work well. However, collecting and manually labelling such datasets is difficult and time consuming, probably more so than developing the algorithms. In this paper, we propose a novel framework to automatically label user identities with their face images in smart spaces, exploiting the fact that the users tend to carry their smart devices while seen by the surveillance cameras. We evaluate our method on 10 users in a smart building setting, and the experimental results show that our method can achieve > 0.9 f1 score on average.