Transformers have become methods of choice in many applications thanks to their ability to represent complex interaction between elements. However, extending the Transformer architecture to non-sequential data such as molecules and enabling its training on small datasets remain a challenge. In this work, we introduce a Transformer-based architecture for molecule property prediction, which is able to capture the geometry of the molecule. We modify the classical positional encoder by an initial encoding of the molecule geometry, as well as a learned gated self-attention mechanism. We further suggest an augmentation scheme for molecular data capable of avoiding the overfitting induced by the overparameterized architecture. The proposed framework outperforms the state-of-the-art methods while being based on pure machine learning solely, i.e. the method does not incorporate domain knowledge from quantum chemistry and does not use extended geometric inputs beside the pairwise atomic distances.
相關內容
Geometric deep learning (GDL), which is based on neural network architectures that incorporate and process symmetry information, has emerged as a recent paradigm in artificial intelligence. GDL bears particular promise in molecular modeling applications, in which various molecular representations with different symmetry properties and levels of abstraction exist. This review provides a structured and harmonized overview of molecular GDL, highlighting its applications in drug discovery, chemical synthesis prediction, and quantum chemistry. Emphasis is placed on the relevance of the learned molecular features and their complementarity to well-established molecular descriptors. This review provides an overview of current challenges and opportunities, and presents a forecast of the future of GDL for molecular sciences.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction, MIRACLE for brevity, to capture inter-view molecule structure and intra-view interactions between molecules simultaneously. MIRACLE treats a DDI network as a multi-view graph where each node in the interaction graph itself is a drug molecular graph instance. We use GCNs and bond-aware attentive message passing networks to encode DDI relationships and drug molecular graphs in the MIRACLE learning stage, respectively. Also, we propose a novel unsupervised contrastive learning component to balance and integrate the multi-view information. Comprehensive experiments on multiple real datasets show that MIRACLE outperforms the state-of-the-art DDI prediction models consistently.
Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.
End-to-end speech translation poses a heavy burden on the encoder, because it has to transcribe, understand, and learn cross-lingual semantics simultaneously. To obtain a powerful encoder, traditional methods pre-train it on ASR data to capture speech features. However, we argue that pre-training the encoder only through simple speech recognition is not enough and high-level linguistic knowledge should be considered. Inspired by this, we propose a curriculum pre-training method that includes an elementary course for transcription learning and two advanced courses for understanding the utterance and mapping words in two languages. The difficulty of these courses is gradually increasing. Experiments show that our curriculum pre-training method leads to significant improvements on En-De and En-Fr speech translation benchmarks.
Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn node representations on the fixed and homogeneous graphs. The limitations especially become problematic when learning representations on a misspecified graph or a heterogeneous graph that consists of various types of nodes and edges. In this paper, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which involve identifying useful connections between unconnected nodes on the original graph, while learning effective node representation on the new graphs in an end-to-end fashion. Graph Transformer layer, a core layer of GTNs, learns a soft selection of edge types and composite relations for generating useful multi-hop connections so-called meta-paths. Our experiments show that GTNs learn new graph structures, based on data and tasks without domain knowledge, and yield powerful node representation via convolution on the new graphs. Without domain-specific graph preprocessing, GTNs achieved the best performance in all three benchmark node classification tasks against the state-of-the-art methods that require pre-defined meta-paths from domain knowledge.
Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the ordering of node neighbors, even when there is a geometric interpretation of the graph vertices that provides an order based on their spatial positions. To remedy this issue, we propose Geometric Graph Convolutional Network (geo-GCN) which uses spatial features to efficiently learn from graphs that can be naturally located in space. Our contribution is threefold: we propose a GCN-inspired architecture which (i) leverages node positions, (ii) is a proper generalisation of both GCNs and Convolutional Neural Networks (CNNs), (iii) benefits from augmentation which further improves the performance and assures invariance with respect to the desired properties. Empirically, geo-GCN outperforms state-of-the-art graph-based methods on image classification and chemical tasks.
Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.
Deep distance metric learning (DDML), which is proposed to learn image similarity metrics in an end-to-end manner based on the convolution neural network, has achieved encouraging results in many computer vision tasks.$L2$-normalization in the embedding space has been used to improve the performance of several DDML methods. However, the commonly used Euclidean distance is no longer an accurate metric for $L2$-normalized embedding space, i.e., a hyper-sphere. Another challenge of current DDML methods is that their loss functions are usually based on rigid data formats, such as the triplet tuple. Thus, an extra process is needed to prepare data in specific formats. In addition, their losses are obtained from a limited number of samples, which leads to a lack of the global view of the embedding space. In this paper, we replace the Euclidean distance with the cosine similarity to better utilize the $L2$-normalization, which is able to attenuate the curse of dimensionality. More specifically, a novel loss function based on the von Mises-Fisher distribution is proposed to learn a compact hyper-spherical embedding space. Moreover, a new efficient learning algorithm is developed to better capture the global structure of the embedding space. Experiments for both classification and retrieval tasks on several standard datasets show that our method achieves state-of-the-art performance with a simpler training procedure. Furthermore, we demonstrate that, even with a small number of convolutional layers, our model can still obtain significantly better classification performance than the widely used softmax loss.
The Fisher information metric is an important foundation of information geometry, wherein it allows us to approximate the local geometry of a probability distribution. Recurrent neural networks such as the Sequence-to-Sequence (Seq2Seq) networks that have lately been used to yield state-of-the-art performance on speech translation or image captioning have so far ignored the geometry of the latent embedding, that they iteratively learn. We propose the information geometric Seq2Seq (GeoSeq2Seq) network which abridges the gap between deep recurrent neural networks and information geometry. Specifically, the latent embedding offered by a recurrent network is encoded as a Fisher kernel of a parametric Gaussian Mixture Model, a formalism common in computer vision. We utilise such a network to predict the shortest routes between two nodes of a graph by learning the adjacency matrix using the GeoSeq2Seq formalism; our results show that for such a problem the probabilistic representation of the latent embedding supersedes the non-probabilistic embedding by 10-15\%.
小貼士
登錄享
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191