Unsupervised graph-level representation learning with hierarchical contrasts

A retrospective prognostic evaluation using unsupervised learning in the treatment of COVID-19 patients with hypertension treated with ACEI/ARB drugs

Introduction

This study aimed to evaluate the prognosis of patients with COVID-19 and hypertension who were treated with angiotensin-converting enzyme inhibitor (ACEI)/angiotensin receptor B (ARB) drugs and to identify key features affecting patient prognosis using an unsupervised learning method.

Methods

A large-scale clinical dataset, including patient information, medical history, and laboratory test results, was collected. Two hundred patients with COVID-19 and hypertension were included. After cluster analysis, patients were divided into good and poor prognosis groups. The unsupervised learning method was used to evaluate clinical characteristics and prognosis, and patients were divided into different prognosis groups. The improved wild dog optimization algorithm (IDOA) was used for feature selection and cluster analysis, followed by the IDOA-k-means algorithm. The impact of ACEI/ARB drugs on patient prognosis and key characteristics affecting patient prognosis were also analysed.

Results

Key features related to prognosis included baseline information and laboratory test results, while clinical symptoms and imaging results had low predictive power. The top six important features were age, hypertension grade, MuLBSTA, ACEI/ARB, NT-proBNP, and high-sensitivity troponin I. These features were consistent with the results of the unsupervised prediction model. A visualization system was developed based on these key features.

Conclusion

Using unsupervised learning and the improved k-means algorithm, this study accurately analysed the prognosis of patients with COVID-19 and hypertension. The use of ACEI/ARB drugs was found to be a protective factor for poor clinical prognosis. Unsupervised learning methods can be used to differentiate patient populations and assess treatment effects. This study identified important features affecting patient prognosis and developed a visualization system with clinical significance for prognosis assessment and treatment decision-making.

A Comprehensive Survey on Deep Graph Representation Learning

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

Towards generalizable Graph Contrastive Learning: An information theory perspective

Graph Contrastive Learning (GCL) is increasingly employed in graph representation learning with the primary aim of learning node/graph representations from a predefined pretext task that can generalize to various downstream tasks. Meanwhile, the transition from a specific pretext task to diverse and unpredictable downstream tasks poses a significant challenge for GCL's generalization ability. Most existing GCL approaches maximize mutual information between two views derived from the original graph, either randomly or heuristically. However, the generalization ability of GCL and its theoretical principles are still less studied. In this paper, we introduce a novel metric GCL-GE, to quantify the generalization gap between predefined pretext and agnostic downstream tasks. Given the inherent intractability of GCL-GE, we leverage concepts from information theory to derive a mutual information upper bound that is independent of the downstream tasks, thus enabling the metric's optimization despite the variability in downstream tasks. Based on the theoretical insight, we propose InfoAdv, a GCL framework to directly enhance generalization by jointly optimizing GCL-GE and InfoMax. Extensive experiments validate the capability of InfoAdv to enhance performance across a wide variety of downstream tasks, demonstrating its effectiveness in improving the generalizability of GCL.

Object-stable unsupervised dual contrastive learning image-to-image translation with query-selected attention and convolutional block attention module

Recently, contrastive learning has gained popularity in the field of unsupervised image-to-image (I2I) translation. In a previous study, a query-selected attention (QS-Attn) module, which employed an attention matrix with a probability distribution, was used to maximize the mutual information between the source and translated images. This module selected significant queries using an entropy metric computed from the attention matrix. However, it often selected many queries with equal significance measures, leading to an excessive focus on the background. In this study, we proposed a dual-learning framework with QS-Attn and convolutional block attention module (CBAM) called object-stable dual contrastive learning generative adversarial network (OS-DCLGAN). In this paper, we utilize a CBAM, which learns what and where to emphasize or suppress, thereby refining intermediate features effectively. This CBAM was integrated before the QS-Attn module to capture significant domain information for I2I translation tasks. The proposed framework outperformed recently introduced approaches in various I2I translation tasks, showing its effectiveness and versatility. The code is available at https://github.com/RedPotatoChip/OSUDL.

Self-supervised contrastive graph representation with node and graph augmentation

Graph representation is a critical technology in the field of knowledge engineering and knowledge-based applications since most knowledge bases are represented in the graph structure. Nowadays, contrastive learning has become a prominent way for graph representation by contrasting positive-positive and positive-negative node pairs between two augmentation graphs. It has achieved new state-of-the-art in the field of self-supervised graph representation. However, existing contrastive graph representation methods mainly focus on modifying (normally removing some edges/nodes) the original graph structure to generate the augmentation graph for the contrastive. It inevitably changes the original graph structures, meaning the generated augmentation graph is no longer equivalent to the original graph. This harms the performance of the representation in many structure-sensitive graphs such as protein graphs, chemical graphs, molecular graphs, etc. Moreover, there is only one positive-positive node pair but relatively massive positive-negative node pairs in the self-supervised graph contrastive learning. This can lead to the same class, or very similar samples are considered negative samples. To this end, in this work, we propose a Virtual Masking Augmentation (VMA) to generate an augmentation graph without changing any structures from the original graph. Meanwhile, a node augmentation method is proposed to augment the positive node pairs by discovering the most similar nodes in the same graph. Then, two different augmentation graphs are generated and put into a contrastive learning model to learn the graph representation. Extensive experiments on massive datasets demonstrate that our method achieves new state-of-the-art results on self-supervised graph representation. The source code of the proposed method is available at https://github.com/DuanhaoranCC/CGRA.

3D graph neural network with few-shot learning for predicting drug-drug interactions in scaffold-based cold start scenario

Understanding drug-drug interactions (DDI) of new drugs is critical for minimizing unexpected adverse drug reactions. The modeling of new drugs is called a cold start scenario. In this scenario, Only a few structural information or physicochemical information about new drug is available. The 3D conformation of drug molecules usually plays a crucial role in chemical properties compared to the 2D structure. 3D graph network with few-shot learning is a promising solution. However, the 3D heterogeneity of drug molecules and the discretization of atomic distributions lead to spatial confusion in few-shot learning. Here, we propose a 3D graph neural network with few-shot learning, Meta3D-DDI, to predict DDI events in cold start scenario. The 3DGNN ensures rotation and translation invariance by calculating atomic pairwise distances, and incorporates 3D structure and distance information in the information aggregation stage. The continuous filter interaction module can continuously simulate the filter to obtain the interaction between the target atom and other atoms. Meta3D-DDI further develops a FSL strategy based on bilevel optimization to transfer meta-knowledge for DDI prediction tasks from existing drugs to new drugs. In addition, the existing cold start setting may cause the scaffold structure information in the training set to leak into the test set. We design scaffold-based cold start scenario to ensure that the drug scaffolds in the training set and test set do not overlap. The extensive experiments demonstrate that our architecture achieves the SOTA performance for DDI prediction under scaffold-based cold start scenario on two real-world datasets. The visual experiment shows that Meta3D-DDI significantly improves the learning for DDI prediction of new drugs. We also demonstrate how Meta3D-DDI can reduce the amount of data required to make meaningful DDI predictions.