A Graph to Graphs Framework for Retrosynthesis Prediction

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive and also suffer from the problem of coverage. In this paper, we propose a novel template-free approach called G2Gs by transforming a target molecular graph into a set of reactant molecular graphs. G2Gs first splits the target molecular graph into a set of synthons by identifying the reaction centers, and then translates the synthons to the final reactant graphs via a variational graph translation framework. Experimental results show that G2Gs significantly outperforms existing template-free approaches by up to 63% in terms of the top-1 accuracy and achieves a performance close to that of state-of-the-art template based approaches, but does not require domain knowledge and is much more scalable.

GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation

Molecular graph generation is a fundamental problem for drug discovery and has been attracting growing attention. The problem is challenging since it requires not only generating chemically valid molecular structures but also optimizing their chemical properties in the meantime. Inspired by the recent progress in deep generative models, in this paper we propose a flow-based autoregressive model for graph generation called GraphAF. GraphAF combines the advantages of both autoregressive and flow-based approaches and enjoys: (1) high model flexibility for data density estimation; (2) efficient parallel computation for training; (3) an iterative sampling process, which allows leveraging chemical domain knowledge for valency checking. Experimental results show that GraphAF is able to generate 68% chemically valid molecules even without chemical knowledge rules and 100% valid molecules with chemical rules. The training process of GraphAF is two times faster than the existing state-of-the-art approach GCPN. After fine-tuning the model for goal-directed property optimization with reinforcement learning, GraphAF achieves state-of-the-art performance on both chemical property optimization and constrained property optimization.

BLK-REW: A Unified Block-based DNN Pruning Framework using Reweighted Regularization Method

Accelerating DNN execution on various resource-limited computing platforms has been a long-standing problem. Prior works utilize l1-based group lasso or dynamic regularization such as ADMM to perform structured pruning on DNN models to leverage the parallel computing architectures. However, both of the pruning dimensions and pruning methods lack universality, which leads to degraded performance and limited applicability. To solve the problem, we propose a new block-based pruning framework that comprises a general and flexible structured pruning dimension as well as a powerful and efficient reweighted regularization method. Our framework is universal, which can be applied to both CNNs and RNNs, implying complete support for the two major kinds of computation-intensive layers (i.e., CONV and FC layers). To complete all aspects of the pruning-for-acceleration task, we also integrate compiler-based code optimization into our framework that can perform DNN inference in a real-time manner. To the best of our knowledge, it is the first time that the weight pruning framework achieves universal coverage for both CNNs and RNNs with real-time mobile acceleration and no accuracy compromise.

An Image Enhancing Pattern-based Sparsity for Real-time Inference on Mobile Devices

Weight pruning has been widely acknowledged as a straightforward and effective method to eliminate redundancy in Deep Neural Networks (DNN), thereby achieving acceleration on various platforms. However, most of the pruning techniques are essentially trade-offs between model accuracy and regularity which lead to impaired inference accuracy and limited on-device acceleration performance. To solve the problem, we introduce a new sparsity dimension, namely pattern-based sparsity that comprises pattern and connectivity sparsity, and becoming both highly accurate and hardware friendly. With carefully designed patterns, the proposed pruning unprecedentedly and consistently achieves accuracy enhancement and better feature extraction ability on different DNN structures and datasets, and our pattern-aware pruning framework also achieves pattern library extraction, pattern selection, pattern and connectivity pruning and weight training simultaneously. Our approach on the new pattern-based sparsity naturally fits into compiler optimization for highly efficient DNN execution on mobile platforms. To the best of our knowledge, it is the first time that mobile devices achieve real-time inference for the large-scale DNN models thanks to the unique spatial property of pattern-based sparsity and the help of the code generation capability of compilers.

Learning Dynamic Knowledge Graphs to Generalize on Text-Based Games

Playing text-based games requires skill in processing natural language and in planning. Although a key goal for agents solving this task is to generalize across multiple games, most previous work has either focused on solving a single game or has tackled generalization with rule-based heuristics. In this work, we investigate how structured information in the form of a knowledge graph (KG) can facilitate effective planning and generalization. We introduce a novel transformer-based sequence-to-sequence model that constructs a "belief" KG from raw text observations of the environment, dynamically updating this belief graph at every game step as it receives new observations. To train this model to build useful graph representations, we introduce and analyze a set of graph-related pre-training tasks. We demonstrate empirically that KG-based representations from our model help agents to converge faster to better policies for multiple text-based games, and further, enable stronger zero-shot performance on unseen games. Experiments on unseen games show that our best agent outperforms text-based baselines by 21.6%.

Continuous Graph Neural Networks

This paper builds the connection between graph neural networks and traditional dynamical systems. Existing graph neural networks essentially define a discrete dynamic on node representations with multiple graph convolution layers. We propose continuous graph neural networks (CGNN), which generalise existing graph neural networks into the continuous-time dynamic setting. The key idea is how to characterise the continuous dynamics of node representations, i.e. the derivatives of node representations w.r.t. time. Inspired by existing diffusion-based methods on graphs (e.g. PageRank and epidemic models on social networks), we define the derivatives as a combination of the current node representations, the representations of neighbors, and the initial values of the nodes. We propose and analyse different possible dynamics on graphs---including each dimension of node representations (a.k.a. the feature channel) change independently or interact with each other---both with theoretical justification. The proposed continuous graph neural networks are robust to over-smoothing and hence capture the long-range dependencies between nodes. Experimental results on the task of node classification prove the effectiveness of our proposed approach over competitive baselines.

KEPLER: A Unified Model for Knowledge Embedding and Pre-trained Language Representation

Pre-trained language representation models (PLMs) learn effective language representations from large-scale unlabeled corpora. Knowledge embedding (KE) algorithms encode the entities and relations in knowledge graphs into informative embeddings to do knowledge graph completion and provide external knowledge for various NLP applications. In this paper, we propose a unified model for Knowledge Embedding and Pre-trained LanguagE Representation (KEPLER), which not only better integrates factual knowledge into PLMs but also effectively learns knowledge graph embeddings. Our KEPLER utilizes a PLM to encode textual descriptions of entities as their entity embeddings, and then jointly learn the knowledge embeddings and language representations. Experimental results on various NLP tasks such as the relation extraction and the entity typing show that our KEPLER can achieve comparable results to the state-of-the-art knowledge-enhanced PLMs without any additional inference overhead. Furthermore, we construct Wikidata5m, a new large-scale knowledge graph dataset with aligned text descriptions, to evaluate KE embedding methods in both the traditional transductive setting and the challenging inductive setting, which needs the models to predict entity embeddings for unseen entities. Experiments demonstrate our KEPLER can achieve good results in both settings.