Multi-task Heterogeneous Graph Learning on Electronic Health Records

Learning electronic health records (EHRs) has received emerging attention because of its capability to facilitate accurate medical diagnosis. Since the EHRs contain enriched information specifying complex interactions between entities, modeling EHRs with graphs is shown to be effective in practice. The EHRs, however, present a great degree of heterogeneity, sparsity, and complexity, which hamper the performance of most of the models applied to them. Moreover, existing approaches modeling EHRs often focus on learning the representations for a single task, overlooking the multi-task nature of EHR analysis problems and resulting in limited generalizability across different tasks. In view of these limitations, we propose a novel framework for EHR modeling, namely MulT-EHR (Multi-Task EHR), which leverages a heterogeneous graph to mine the complex relations and model the heterogeneity in the EHRs. To mitigate the large degree of noise, we introduce a denoising module based on the causal inference framework to adjust for severe confounding effects and reduce noise in the EHR data. Additionally, since our model adopts a single graph neural network for simultaneous multi-task prediction, we design a multi-task learning module to leverage the inter-task knowledge to regularize the training process. Extensive empirical studies on MIMIC-III and MIMIC-IV datasets validate that the proposed method consistently outperforms the state-of-the-art designs in four popular EHR analysis tasks -- drug recommendation, and predictions of the length of stay, mortality, and readmission. Thorough ablation studies demonstrate the robustness of our method upon variations to key components and hyperparameters.

cDP-MIL: Robust Multiple Instance Learning via Cascaded Dirichlet Process

Multiple instance learning (MIL) has been extensively applied to whole slide histopathology image (WSI) analysis. The existing aggregation strategy in MIL, which primarily relies on the first-order distance (e.g., mean difference) between instances, fails to accurately approximate the true feature distribution of each instance, leading to biased slide-level representations. Moreover, the scarcity of WSI observations easily leads to model overfitting, resulting in unstable testing performance and limited generalizability. To tackle these challenges, we propose a new Bayesian nonparametric framework for multiple instance learning, which adopts a cascade of Dirichlet processes (cDP) to incorporate the instance-to-bag characteristic of the WSIs. We perform feature aggregation based on the latent clusters formed by the Dirichlet process, which incorporates the covariances of the patch features and forms more representative clusters. We then perform bag-level prediction with another Dirichlet process model on the bags, which imposes a natural regularization on learning to prevent overfitting and enhance generalizability. Moreover, as a Bayesian nonparametric method, the cDP model can accurately generate posterior uncertainty, which allows for the detection of outlier samples and tumor localization. Extensive experiments on five WSI benchmarks validate the superior performance of our method, as well as its generalizability and ability to estimate uncertainties. Codes are available at https://github.com/HKU-MedAI/cDPMIL.

Adaptive Uncertainty Estimation via High-Dimensional Testing on Latent Representations

Uncertainty estimation aims to evaluate the confidence of a trained deep neural network. However, existing uncertainty estimation approaches rely on low-dimensional distributional assumptions and thus suffer from the high dimensionality of latent features. Existing approaches tend to focus on uncertainty on discrete classification probabilities, which leads to poor generalizability to uncertainty estimation for other tasks. Moreover, most of the literature requires seeing the out-of-distribution (OOD) data in the training for better estimation of uncertainty, which limits the uncertainty estimation performance in practice because the OOD data are typically unseen. To overcome these limitations, we propose a new framework using data-adaptive high-dimensional hypothesis testing for uncertainty estimation, which leverages the statistical properties of the feature representations. Our method directly operates on latent representations and thus does not require retraining the feature encoder under a modified objective. The test statistic relaxes the feature distribution assumptions to high dimensionality, and it is more discriminative to uncertainties in the latent representations. We demonstrate that encoding features with Bayesian neural networks can enhance testing performance and lead to more accurate uncertainty estimation. We further introduce a family-wise testing procedure to determine the optimal threshold of OOD detection, which minimizes the false discovery rate (FDR). Extensive experiments validate the satisfactory performance of our framework on uncertainty estimation and task-specific prediction over a variety of competitors. The experiments on the OOD detection task also show satisfactory performance of our method when the OOD data are unseen in the training. Codes are available at https://github.com/HKU-MedAI/bnn_uncertainty.

Source-Aware Embedding Training on Heterogeneous Information Networks

Heterogeneous information networks (HINs) have been extensively applied to real-world tasks, such as recommendation systems, social networks, and citation networks. While existing HIN representation learning methods can effectively learn the semantic and structural features in the network, little awareness was given to the distribution discrepancy of subgraphs within a single HIN. However, we find that ignoring such distribution discrepancy among subgraphs from multiple sources would hinder the effectiveness of graph embedding learning algorithms. This motivates us to propose SUMSHINE (Scalable Unsupervised Multi-Source Heterogeneous Information Network Embedding) -- a scalable unsupervised framework to align the embedding distributions among multiple sources of an HIN. Experimental results on real-world datasets in a variety of downstream tasks validate the performance of our method over the state-of-the-art heterogeneous information network embedding algorithms.

Histopathology Whole Slide Image Analysis with Heterogeneous Graph Representation Learning

Graph-based methods have been extensively applied to whole-slide histopathology image (WSI) analysis due to the advantage of modeling the spatial relationships among different entities. However, most of the existing methods focus on modeling WSIs with homogeneous graphs (e.g., with homogeneous node type). Despite their successes, these works are incapable of mining the complex structural relations between biological entities (e.g., the diverse interaction among different cell types) in the WSI. We propose a novel heterogeneous graph-based framework to leverage the inter-relationships among different types of nuclei for WSI analysis. Specifically, we formulate the WSI as a heterogeneous graph with "nucleus-type" attribute to each node and a semantic similarity attribute to each edge. We then present a new heterogeneous-graph edge attribute transformer (HEAT) to take advantage of the edge and node heterogeneity during massage aggregating. Further, we design a new pseudo-label-based semantic-consistent pooling mechanism to obtain graph-level features, which can mitigate the over-parameterization issue of conventional cluster-based pooling. Additionally, observing the limitations of existing association-based localization methods, we propose a causal-driven approach attributing the contribution of each node to improve the interpretability of our framework. Extensive experiments on three public TCGA benchmark datasets demonstrate that our framework outperforms the state-of-the-art methods with considerable margins on various tasks. Our codes are available at https://github.com/HKU-MedAI/WSI-HGNN.

Asymmetric Graph Representation Learning

Despite the enormous success of graph neural networks (GNNs), most existing GNNs can only be applicable to undirected graphs where relationships among connected nodes are two-way symmetric (i.e., information can be passed back and forth). However, there is a vast amount of applications where the information flow is asymmetric, leading to directed graphs where information can only be passed in one direction. For example, a directed edge indicates that the information can only be conveyed forwardly from the start node to the end node, but not backwardly. To accommodate such an asymmetric structure of directed graphs within the framework of GNNs, we propose a simple yet remarkably effective framework for directed graph analysis to incorporate such one-way information passing. We define an incoming embedding and an outgoing embedding for each node to model its sending and receiving features respectively. We further develop two steps in our directed GNN model with the first one to aggregate/update the incoming features of nodes and the second one to aggregate/update the outgoing features. By imposing the two roles for each node, the likelihood of a directed edge can be calculated based on the outgoing embedding of the start node and the incoming embedding of the end node. The log-likelihood of all edges plays a natural role of regularization for the proposed model, which can alleviate the over-smoothing problem of the deep GNNs. Extensive experiments on multiple real-world directed graphs demonstrate outstanding performances of the proposed model in both node-level and graph-level tasks.

Efficient Unpaired Image Dehazing with Cyclic Perceptual-Depth Supervision

Image dehazing without paired haze-free images is of immense importance, as acquiring paired images often entails significant cost. However, we observe that previous unpaired image dehazing approaches tend to suffer from performance degradation near depth borders, where depth tends to vary abruptly. Hence, we propose to anneal the depth border degradation in unpaired image dehazing with cyclic perceptual-depth supervision. Coupled with the dual-path feature re-using backbones of the generators and discriminators, our model achieves $\mathbf{20.36}$ Peak Signal-to-Noise Ratio (PSNR) on NYU Depth V2 dataset, significantly outperforming its predecessors with reduced Floating Point Operations (FLOPs).

Text classification with pixel embedding

We propose a novel framework to understand the text by converting sentences or articles into video-like 3-dimensional tensors. Each frame, corresponding to a slice of the tensor, is a word image that is rendered by the word's shape. The length of the tensor equals to the number of words in the sentence or article. The proposed transformation from the text to a 3-dimensional tensor makes it very convenient to implement an $n$-gram model with convolutional neural networks for text analysis. Concretely, we impose a 3-dimensional convolutional kernel on the 3-dimensional text tensor. The first two dimensions of the convolutional kernel size equal the size of the word image and the last dimension of the kernel size is $n$. That is, every time when we slide the 3-dimensional kernel over a word sequence, the convolution covers $n$ word images and outputs a scalar. By iterating this process continuously for each $n$-gram along with the sentence or article with multiple kernels, we obtain a 2-dimensional feature map. A subsequent 1-dimensional max-over-time pooling is applied to this feature map, and three fully-connected layers are used for conducting text classification finally. Experiments of several text classification datasets demonstrate surprisingly superior performances using the proposed model in comparison with existing methods.

Nonparametric Functional Approximation with Delaunay Triangulation

We propose a differentiable nonparametric algorithm, the Delaunay triangulation learner (DTL), to solve the functional approximation problem on the basis of a $p$-dimensional feature space. By conducting the Delaunay triangulation algorithm on the data points, the DTL partitions the feature space into a series of $p$-dimensional simplices in a geometrically optimal way, and fits a linear model within each simplex. We study its theoretical properties by exploring the geometric properties of the Delaunay triangulation, and compare its performance with other statistical learners in numerical studies.

Adaptive Iterative Hessian Sketch via A-Optimal Subsampling

Iterative Hessian sketch (IHS) is an effective sketching method for modeling large-scale data. It was originally proposed by Pilanci and Wainwright (2016; JMLR) based on randomized sketching matrices. However, it is computationally intensive due to the iterative sketch process. In this paper, we analyze the IHS algorithm under the unconstrained least squares problem setting, then propose a deterministic approach for improving IHS via A-optimal subsampling. Our contributions are three-fold: (1) a good initial estimator based on the $A$-optimal design is suggested; (2) a novel ridged preconditioner is developed for repeated sketching; and (3) an exact line search method is proposed for determining the optimal step length adaptively. Extensive experimental results demonstrate that our proposed A-optimal IHS algorithm outperforms the existing accelerated IHS methods.