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Register a new userFew-Shot Graph Learning for Molecular Property Prediction
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Added by
Zhichun Guo
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The recent success of graph neural networks has significantly boosted molecular property prediction, advancing activities such as drug discovery. The existing deep neural network methods usually require large training dataset for each property, impairing their performances in cases (especially for new molecular properties) with a limited amount of experimental data, which are common in real situations. To this end, we propose Meta-MGNN, a novel model for few-shot molecular property prediction. Meta-MGNN applies molecular graph neural network to learn molecular representation and builds a meta-learning framework for model optimization. To exploit unlabeled molecular information and address task heterogeneity of different molecular properties, Meta-MGNN further incorporates molecular structure, attribute based self-supervised modules and self-attentive task weights into the former framework, strengthening the whole learning model. Extensive experiments on two public multi-property datasets demonstrate that Meta-MGNN outperforms a variety of state-of-the-art methods.
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Attributed networks nowadays are ubiquitous in a myriad of high-impact applications, such as social network analysis, financial fraud detection, and drug discovery. As a central analytical task on attributed networks, node classification has received much attention in the research community. In real-world attributed networks, a large portion of node classes only contain limited labeled instances, rendering a long-tail node class distribution. Existing node classification algorithms are unequipped to handle the textit{few-shot} node classes. As a remedy, few-shot learning has attracted a surge of attention in the research community. Yet, few-shot node classification remains a challenging problem as we need to address the following questions: (i) How to extract meta-knowledge from an attributed network for few-shot node classification? (ii) How to identify the informativeness of each labeled instance for building a robust and effective model? To answer these questions, in this paper, we propose a graph meta-learning framework -- Graph Prototypical Networks (GPN). By constructing a pool of semi-supervised node classification tasks to mimic the real test environment, GPN is able to perform textit{meta-learning} on an attributed network and derive a highly generalizable model for handling the target classification task. Extensive experiments demonstrate the superior capability of GPN in few-shot node classification.
Link prediction for knowledge graphs aims to predict missing connections between entities. Prevailing methods are limited to a transductive setting and hard to process unseen entities. The recent proposed subgraph-based models provided alternatives to predict links from the subgraph structure surrounding a candidate triplet. However, these methods require abundant known facts of training triplets and perform poorly on relationships that only have a few triplets. In this paper, we propose Meta-iKG, a novel subgraph-based meta-learner for few-shot inductive relation reasoning. Meta-iKG utilizes local subgraphs to transfer subgraph-specific information and learn transferable patterns faster via meta gradients. In this way, we find the model can quickly adapt to few-shot relationships using only a handful of known facts with inductive settings. Moreover, we introduce a large-shot relation update procedure to traditional meta-learning to ensure that our model can generalize well both on few-shot and large-shot relations. We evaluate Meta-iKG on inductive benchmarks sampled from NELL and Freebase, and the results show that Meta-iKG outperforms the current state-of-the-art methods both in few-shot scenarios and standard inductive settings.
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a huge number of potential chemical compounds. Machine learning methods for molecular modeling are attractive alternatives, however, the development of expressive, accurate, and scalable graph neural networks for learning molecular representations is still challenging. In this work, we propose a simple and powerful graph neural networks for molecular property prediction. We model a molecular as a directed complete graph in which each atom has a spatial position, and introduce a recursive neural network with simple gating function. We also feed input embeddings for every layers as skip connections to accelerate the training. Experimental results show that our model achieves the state-of-the-art performance on the standard benchmark dataset for molecular property prediction.
Zero-shot and few-shot learning aim to improve generalization to unseen concepts, which are promising in many realistic scenarios. Due to the lack of data in unseen domain, relation modeling between seen and unseen domains is vital for knowledge transfer in these tasks. Most existing methods capture seen-unseen relation implicitly via semantic embedding or feature generation, resulting in inadequate use of relation and some issues remain (e.g. domain shift). To tackle these challenges, we propose a Transferable Graph Generation (TGG) approach, in which the relation is modeled and utilized explicitly via graph generation. Specifically, our proposed TGG contains two main components: (1) Graph generation for relation modeling. An attention-based aggregate network and a relation kernel are proposed, which generate instance-level graph based on a class-level prototype graph and visual features. Proximity information aggregating is guided by a multi-head graph attention mechanism, where seen and unseen features synthesized by GAN are revised as node embeddings. The relation kernel further generates edges with GCN and graph kernel method, to capture instance-level topological structure while tackling data imbalance and noise. (2) Relation propagation for relation utilization. A dual relation propagation approach is proposed, where relations captured by the generated graph are separately propagated from the seen and unseen subgraphs. The two propagations learn from each other in a dual learning fashion, which performs as an adaptation way for mitigating domain shift. All components are jointly optimized with a meta-learning strategy, and our TGG acts as an end-to-end framework unifying conventional zero-shot, generalized zero-shot and few-shot learning. Extensive experiments demonstrate that it consistently surpasses existing methods of the above three fields by a significant margin.
The arc of drug discovery entails a multiparameter optimization problem spanning vast length scales. They key parameters range from solubility (angstroms) to protein-ligand binding (nanometers) to in vivo toxicity (meters). Through feature learning---instead of feature engineering---deep neural networks promise to outperform both traditional physics-based and knowledge-based machine learning models for predicting molecular properties pertinent to drug discovery. To this end, we present the PotentialNet family of graph convolutions. These models are specifically designed for and achieve state-of-the-art performance for protein-ligand binding affinity. We further validate these deep neural networks by setting new standards of performance in several ligand-based tasks. In parallel, we introduce a new metric, the Regression Enrichment Factor $EF_chi^{(R)}$, to measure the early enrichment of computational models for chemical data. Finally, we introduce a cross-validation strategy based on structural homology clustering that can more accurately measure model generalizability, which crucially distinguishes the aims of machine learning for drug discovery from standard machine learning tasks.
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