Recent years have witnessed the emergence and flourishing of hierarchical graph pooling neural networks (HGPNNs) which are effective graph representation learning approaches for graph level tasks such as graph classification. However, current HGPNNs do not take full advantage of the graph's intrinsic structures (e.g., community structure). Moreover, the pooling operations in existing HGPNNs are difficult to be interpreted. In this paper, we propose a new interpretable graph pooling framework - CommPOOL, that can capture and preserve the hierarchical community structure of graphs in the graph representation learning process. Specifically, the proposed community pooling mechanism in CommPOOL utilizes an unsupervised approach for capturing the inherent community structure of graphs in an interpretable manner. CommPOOL is a general and flexible framework for hierarchical graph representation learning that can further facilitate various graph-level tasks. Evaluations on five public benchmark datasets and one synthetic dataset demonstrate the superior performance of CommPOOL in graph representation learning for graph classification compared to the state-of-the-art baseline methods, and its effectiveness in capturing and preserving the community structure of graphs.
Recent work in graph neural networks (GNNs) has led to improvements in molecular activity and property prediction tasks. Unfortunately, GNNs often fail to capture the relative importance of interactions between molecular substructures, in part due to the absence of efficient intermediate pooling steps. To address these issues, we propose LaPool (Laplacian Pooling), a novel, data-driven, and interpretable hierarchical graph pooling method that takes into account both node features and graph structure to improve molecular representation. We benchmark LaPool on molecular graph prediction and unde…
GALUX inc.（GALUX公司）；Seoul National University（首尔国立大学）
In drug discovery, aqueous solubility is an important pharmacokinetic property which affects absorption and assay availability of drug. Thus, in silico prediction of solubility has been studied for its utility in virtual screening and lead optimization. Recently, machine learning (ML) methods using experimental data has been popular because physics-based methods like quantum mechanics and molecular dynamics are not suitable for high-throughput tasks due to its computational costs. However, ML method can exhibit over-fitting problem in a data-deficient condition, and this is the case for most c…
Towards Interpretable Drug-Drug Interaction Prediction: A Graph-Based Approach with Molecular and Network-Level Explanations
Data Science Institute, School of Mathematics, Shandong University（数据科学研究院、数学学院、山东大学）；Academy of Mathematics and Systems Science, Chinese Academy of Sciences（数学与系统科学研究院、中国科学院）；Data Science Institute, Shandong University（数据科学研究院、山东大学）
University of Pittsburgh（匹兹堡大学）；University of Illinois at Chicago（伊利诺伊大学芝加哥分校）
Recently brain networks have been widely adopted to study brain dynamics, brain development and brain diseases. Graph representation learning techniques on brain functional networks can facilitate the discovery of novel biomarkers for clinical phenotypes and neurodegenerative diseases. However, current graph learning techniques have several issues on brain network mining. Firstly, most current graph learning models are designed for unsigned graph, which hinders the analysis of many signed network data (e.g., brain functional networks). Meanwhile, the insufficiency of brain network data limits …
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）；Facebook AI Research（Facebook人工智能研究院）
Understanding how certain brain regions relate to a specific neurological disorder has been an important area of neuroimaging research. A promising approach to identify the salient regions is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, e.g. brain networks constructed by functional magnetic resonance imaging (fMRI). We propose an interpretable GNN framework with a novel salient region selection mechanism to determine neurological brain biomarkers associated with disorders. Specifically, we design novel regularized pooling layers that highlight salient…
Hierarchical Pooling and Explainability in Graph Neural Networks for Tumor and Tissue-of-Origin Classification Using RNA-seq Data
Institute of Informatics（信息学院）；Universidade Federal do Rio Grande do Sul（鲁汶联邦大学）；Bioinformatics Core（生物信息学核心）；Hospital de Clínicas de Porto Alegre（波多利亚临床医院）
University of Science and Technology of China（中国科学技术大学）；Sea AI Lab（Sea人工智能实验室）；National University of Singapore（新加坡国立大学）
In graph classification, attention and pooling-based graph neural networks (GNNs) prevail to extract the critical features from the input graph and support the prediction. They mostly follow the paradigm of learning to attend, which maximizes the mutual information between the attended graph and the ground-truth label. However, this paradigm makes GNN classifiers recklessly absorb all the statistical correlations between input features and labels in the training data, without distinguishing the causal and noncausal effects of features. Instead of underscoring the causal features, the attended …
We propose a combination of a variational autoencoder and a transformer based model which fully utilises graph convolutional and graph pooling layers to operate directly on graphs. The transformer model implements a novel node encoding layer, replacing the position encoding typically used in transformers, to create a transformer with no position information that operates on graphs, encoding adjacent node properties into the edge generation process. The proposed model builds on graph generative work operating on graphs with edge features, creating a model that offers improved scalability with t…
Department of Computing, Imperial College London, UK（伦敦帝国学院计算机系）；Department of Mathematics, Imperial College London, UK（伦敦帝国学院数学系）；London School of Geometry（几何与数论研究所）
Sea-Net: A Small and Inherently Interpretable Neural Network for Time Series Classification
Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL)（里尔信息、信号与自动化研究中心）；University of Lille（里尔大学）；CNRS（法国国家科学研究中心）；Centrale Lille（里尔中央理工学院）
We propose a novel graph pooling operation using cliques as the unit pool. As this approach is purely topological, rather than featural, it is more readily interpretable, a better analogue to image coarsening than filtering or pruning techniques, and entirely nonparametric. The operation is implemented within graph convolution network (GCN) and GraphSAGE architectures and tested against standard graph classification benchmarks. In addition, we explore the backwards compatibility of the pooling to regular graphs, demonstrating competitive performance when replacing two-by-two pooling in standar…
Graduate School of Science and Technology（科技研究生院）；Nara Institute of Science and Technology（奈良先端科学技术大学院大学）
Graphs are a highly expressive data structure, but it is often difficult for humans to find patterns from a complex graph. Hence, generating human-interpretable sequences from graphs have gained interest, called graph2seq learning. It is expected that the compositionality in a graph can be associated to the compositionality in the output sequence in many graph2seq tasks. Therefore, applying compositionality-aware GNN architecture would improve the model performance. In this study, we adopt the multi-level attention pooling (MLAP) architecture, that can aggregate graph representations from mult…
FIGNN: Feature-Specific Interpretability for Graph Neural Network Surrogate Models
Department of Mechanical Engineering, Pennsylvania State University, University Park, 16802, PA, USA（宾夕法尼亚州立大学机械工程系）；College of Information Sciences and Technology, Pennsylvania State University, University Park, 16802, PA, USA（宾夕法尼亚州立大学信息科学与技术学院）；Power Systems Division, Argonne National Laboratory, Lemont, 60439, IL, USA（阿贡国家实验室电力系统分部）
Temple University（天普大学）；East China Normal University（华东师范大学）；Fudan University（复旦大学）；Georgia Institute of Technology（佐治亚理工学院）
Graph neural networks are promising architecture for learning and inference with graph-structured data. Yet difficulties in modelling the ``parts'' and their ``interactions'' still persist in terms of graph classification, where graph-level representations are usually obtained by squeezing the whole graph into a single vector through graph pooling. From complex systems point of view, mixing all the parts of a system together can affect both model interpretability and predictive performance, because properties of a complex system arise largely from the interaction among its components. We analy…
Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the utilization and exploration of tiered molecular latent spaces, either individually - the node (atom) tier, the group tier, or the graph (molecule) tier - or jointly, as well as navigation across the tiers. In this paper, we discuss the use of tiered graph autoencoders together with graph prediction for molecular graphs. We show features of molecular graphs used…
GRACE: Generative Representation Learning via Contrastive Policy Optimization
University of Illinois Urbana–Champaign（伊利诺伊大学厄巴纳-香槟分校）；Australian National University（澳大利亚国立大学）；Hong Kong University of Science and Technology（香港科学与技术大学）；University of Wisconsin–Madison（威斯康星大学麦迪逊分校）；University of Washington（华盛顿大学）
Hierarchical Multiscale Structure-Function Coupling for Brain Connectome Integration
School of Medicine, University of Dundee, UK（邓迪大学医学院）；School of Science and Engineering, University of Dundee, UK（邓迪大学科学与工程学院）；College of Medicine and Biological Information Engineering, Northeastern University, China（东北大学医学院与生物信息工程学院）；College of Medical Informatics, Chongqing Medical University, China（重庆医科大学医学信息学院）；School of Airspace Science and Engineering, Shandong University, China（山东大学航空航天科学与工程学院）；Chinese Institute for Brain Research, China（中国脑科学研究院）；Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK（剑桥大学应用数学与理论物理系）；Department of Clinical Neurosciences, University of Cambridge, UK（剑桥大学临床神经科学系）
