Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userMolecular structure prediction based on graph convolutional networks
36
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Due to the important application of molecular structure in many fields, calculation by experimental means or traditional density functional theory is often time consuming. In view of this, a new Model Structure based on Graph Convolutional Neural network (MSGCN) is proposed, which can determine the molecular structure by predicting the distance between two atoms. In order to verify the effect of MSGCN model, the model is compared with the method of calculating molecular three-dimensional conformation in RDKit, and the result is better than it. In addition, the distance predicted by the MSGCN model and the distance calculated by the QM9 dataset were used to predict the molecular properties, thus proving the effectiveness of the distance predicted by the MSGCN model.
rate research
Read More
Spectral graph convolutional networks (SGCNs) have been attracting increasing attention in graph representation learning partly due to their interpretability through the prism of the established graph signal processing framework. However, existing SGCNs are limited in implementing graph convolutions with rigid transforms that could not adapt to signals residing on graphs and tasks at hand. In this paper, we propose a novel class of spectral graph convolutional networks that implement graph convolutions with adaptive graph wavelets. Specifically, the adaptive graph wavelets are learned with neural network-parameterized lifting structures, where structure-aware attention-based lifting operations are developed to jointly consider graph structures and node features. We propose to lift based on diffusion wavelets to alleviate the structural information loss induced by partitioning non-bipartite graphs. By design, the locality and sparsity of the resulting wavelet transform as well as the scalability of the lifting structure for large and varying-size graphs are guaranteed. We further derive a soft-thresholding filtering operation by learning sparse graph representations in terms of the learned wavelets, which improves the scalability and interpretablity, and yield a localized, efficient and scalable spectral graph convolution. To ensure that the learned graph representations are invariant to node permutations, a layer is employed at the input of the networks to reorder the nodes according to their local topology information. We evaluate the proposed networks in both node-level and graph-level representation learning tasks on benchmark citation and bioinformatics graph datasets. Extensive experiments demonstrate the superiority of the proposed networks over existing SGCNs in terms of accuracy, efficiency and scalability.
Interference between pharmacological substances can cause serious medical injuries. Correctly predicting so-called drug-drug interactions (DDI) does not only reduce these cases but can also result in a reduction of drug development cost. Presently, most drug-related knowledge is the result of clinical evaluations and post-marketing surveillance; resulting in a limited amount of information. Existing data-driven prediction approaches for DDIs typically rely on a single source of information, while using information from multiple sources would help improve predictions. Machine learning (ML) techniques are used, but the techniques are often unable to deal with skewness in the data. Hence, we propose a new ML approach for predicting DDIs based on multiple data sources. For this task, we use 12,000 drug features from DrugBank, PharmGKB, and KEGG drugs, which are integrated using Knowledge Graphs (KGs). To train our prediction model, we first embed the nodes in the graph using various embedding approaches. We found that the best performing combination was a ComplEx embedding method creating using PyTorch-BigGraph (PBG) with a Convolutional-LSTM network and classic machine learning-based prediction models. The model averaging ensemble method of three best classifiers yields up to 0.94, 0.92, 0.80 for AUPR, F1-score, and MCC, respectively during 5-fold cross-validation tests.
Graphs have been widely adopted to denote structural connections between entities. The relations are in many cases heterogeneous, but entangled together and denoted merely as a single edge between a pair of nodes. For example, in a social network graph, users in different latent relationships like friends and colleagues, are usually connected via a bare edge that conceals such intrinsic connections. In this paper, we introduce a novel graph convolutional network (GCN), termed as factorizable graph convolutional network(FactorGCN), that explicitly disentangles such intertwined relations encoded in a graph. FactorGCN takes a simple graph as input, and disentangles it into several factorized graphs, each of which represents a latent and disentangled relation among nodes. The features of the nodes are then aggregated separately in each factorized latent space to produce disentangled features, which further leads to better performances for downstream tasks. We evaluate the proposed FactorGCN both qualitatively and quantitatively on the synthetic and real-world datasets, and demonstrate that it yields truly encouraging results in terms of both disentangling and feature aggregation. Code is publicly available at https://github.com/ihollywhy/FactorGCN.PyTorch.
Action recognition with skeleton data has recently attracted much attention in computer vision. Previous studies are mostly based on fixed skeleton graphs, only capturing local physical dependencies among joints, which may miss implicit joint correlations. To capture richer dependencies, we introduce an encoder-decoder structure, called A-link inference module, to capture action-specific latent dependencies, i.e. actional links, directly from actions. We also extend the existing skeleton graphs to represent higher-order dependencies, i.e. structural links. Combing the two types of links into a generalized skeleton graph, we further propose the actional-structural graph convolution network (AS-GCN), which stacks actional-structural graph convolution and temporal convolution as a basic building block, to learn both spatial and temporal features for action recognition. A future pose prediction head is added in parallel to the recognition head to help capture more detailed action patterns through self-supervision. We validate AS-GCN in action recognition using two skeleton data sets, NTU-RGB+D and Kinetics. The proposed AS-GCN achieves consistently large improvement compared to the state-of-the-art methods. As a side product, AS-GCN also shows promising results for future pose prediction.
Skeleton-based human action recognition has attracted much attention with the prevalence of accessible depth sensors. Recently, graph convolutional networks (GCNs) have been widely used for this task due to their powerful capability to model graph data. The topology of the adjacency graph is a key factor for modeling the correlations of the input skeletons. Thus, previous methods mainly focus on the design/learning of the graph topology. But once the topology is learned, only a single-scale feature and one transformation exist in each layer of the networks. Many insights, such as multi-scale information and multiple sets of transformations, that have been proven to be very effective in convolutional neural networks (CNNs), have not been investigated in GCNs. The reason is that, due to the gap between graph-structured skeleton data and conventional image/video data, it is very challenging to embed these insights into GCNs. To overcome this gap, we reinvent the split-transform-merge strategy in GCNs for skeleton sequence processing. Specifically, we design a simple and highly modularized graph convolutional network architecture for skeleton-based action recognition. Our network is constructed by repeating a building block that aggregates multi-granularity information from both the spatial and temporal paths. Extensive experiments demonstrate that our network outperforms state-of-the-art methods by a significant margin with only 1/5 of the parameters and 1/10 of the FLOPs. Code is available at https://github.com/yellowtownhz/STIGCN.
suggested questions
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
