Hongyu Guo

Shengchao Liu, Hanchen Wang, Weiyang Liu et al.

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functionalities. However, the lack of 3D information in real-world scenarios has significantly impeded the learning of geometric graph representation. To cope with this challenge, we propose the Graph Multi-View Pre-training (GraphMVP) framework where self-supervised learning (SSL) is performed by leveraging the correspondence and consistency between 2D topological structures and 3D geometric views. GraphMVP effectively learns a 2D molecular graph encoder that is enhanced by richer and more discriminative 3D geometry. We further provide theoretical insights to justify the effectiveness of GraphMVP. Finally, comprehensive experiments show that GraphMVP can consistently outperform existing graph SSL methods.

Sun Sun, Hongyu Guo

Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the observed data and the latent representation induced by the encoder and the decoder. The resulting algorithm jointly optimizes the modelling losses in both the data and the latent spaces with the loss in the data space leading to the denoising effect. With the symmetric treatment of the data and the latent representation, the algorithm implicitly preserves the local structure of the data in the latent space. To further improve the quality of the latent representation, we incorporate a reconstruction loss into the objective, which significantly benefits both the generation and reconstruction. We empirically show the superior performance of SWAEs over the state-of-the-art generative autoencoders in terms of classification, reconstruction, and generation.

Minghao Xu, Hang Wang, Bingbing Ni et al.

This paper studies unsupervised/self-supervised whole-graph representation learning, which is critical in many tasks such as molecule properties prediction in drug and material discovery. Existing methods mainly focus on preserving the local similarity structure between different graph instances but fail to discover the global semantic structure of the entire data set. In this paper, we propose a unified framework called Local-instance and Global-semantic Learning (GraphLoG) for self-supervised whole-graph representation learning. Specifically, besides preserving the local similarities, GraphLoG introduces the hierarchical prototypes to capture the global semantic clusters. An efficient online expectation-maximization (EM) algorithm is further developed for learning the model. We evaluate GraphLoG by pre-training it on massive unlabeled graphs followed by fine-tuning on downstream tasks. Extensive experiments on both chemical and biological benchmark data sets demonstrate the effectiveness of the proposed approach.

Hongyu Guo

Label Smoothing (LS) is an effective regularizer to improve the generalization of state-of-the-art deep models. For each training sample the LS strategy smooths the one-hot encoded training signal by distributing its distribution mass over the non ground-truth classes, aiming to penalize the networks from generating overconfident output distributions. This paper introduces a novel label smoothing technique called Pairwise Label Smoothing (PLS). The PLS takes a pair of samples as input. Smoothing with a pair of ground-truth labels enables the PLS to preserve the relative distance between the two truth labels while further soften that between the truth labels and the other targets, resulting in models producing much less confident predictions than the LS strategy. Also, unlike current LS methods, which typically require to find a global smoothing distribution mass through cross-validation search, PLS automatically learns the distribution mass for each input pair during training. We empirically show that PLS significantly outperforms LS and the baseline models, achieving up to 30% of relative classification error reduction. We also visually show that when achieving such accuracy gains the PLS tends to produce very low winning softmax scores.

Chence Shi, Minkai Xu, Hongyu Guo et al.

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.

Masoumeh Soflaei, Hongyu Guo, Ali Al-Bashabsheh et al.

We consider the problem of learning a neural network classifier. Under the information bottleneck (IB) principle, we associate with this classification problem a representation learning problem, which we call "IB learning". We show that IB learning is, in fact, equivalent to a special class of the quantization problem. The classical results in rate-distortion theory then suggest that IB learning can benefit from a "vector quantization" approach, namely, simultaneously learning the representations of multiple input objects. Such an approach assisted with some variational techniques, result in a novel learning framework, "Aggregated Learning", for classification with neural network models. In this framework, several objects are jointly classified by a single neural network. The effectiveness of this framework is verified through extensive experiments on standard image recognition and text classification tasks.

Junfan Chen, Richong Zhang, Yongyi Mao et al.

Distant supervision for relation extraction enables one to effectively acquire structured relations out of very large text corpora with less human efforts. Nevertheless, most of the prior-art models for such tasks assume that the given text can be noisy, but their corresponding labels are clean. Such unrealistic assumption is contradictory with the fact that the given labels are often noisy as well, thus leading to significant performance degradation of those models on real-world data. To cope with this challenge, we propose a novel label-denoising framework that combines neural network with probabilistic modelling, which naturally takes into account the noisy labels during learning. We empirically demonstrate that our approach significantly improves the current art in uncovering the ground-truth relation labels.

Guillaume P. Archambault, Yongyi Mao, Hongyu Guo et al.

In this work, we explain the working mechanism of MixUp in terms of adversarial training. We introduce a new class of adversarial training schemes, which we refer to as directional adversarial training, or DAT. In a nutshell, a DAT scheme perturbs a training example in the direction of another example but keeps its original label as the training target. We prove that MixUp is equivalent to a special subclass of DAT, in that it has the same expected loss function and corresponds to the same optimization problem asymptotically. This understanding not only serves to explain the effectiveness of MixUp, but also reveals a more general family of MixUp schemes, which we call Untied MixUp. We prove that the family of Untied MixUp schemes is equivalent to the entire class of DAT schemes. We establish empirically the existence of Untied Mixup schemes which improve upon MixUp.

Hongyu Guo, Yongyi Mao, Richong Zhang

Mixup, a recent proposed data augmentation method through linearly interpolating inputs and modeling targets of random samples, has demonstrated its capability of significantly improving the predictive accuracy of the state-of-the-art networks for image classification. However, how this technique can be applied to and what is its effectiveness on natural language processing (NLP) tasks have not been investigated. In this paper, we propose two strategies for the adaption of Mixup on sentence classification: one performs interpolation on word embeddings and another on sentence embeddings. We conduct experiments to evaluate our methods using several benchmark datasets. Our studies show that such interpolation strategies serve as an effective, domain independent data augmentation approach for sentence classification, and can result in significant accuracy improvement for both CNN and LSTM models.

Hongyu Guo, Yongyi Mao, Richong Zhang

MixUp is a recently proposed data-augmentation scheme, which linearly interpolates a random pair of training examples and correspondingly the one-hot representations of their labels. Training deep neural networks with such additional data is shown capable of significantly improving the predictive accuracy of the current art. The power of MixUp, however, is primarily established empirically and its working and effectiveness have not been explained in any depth. In this paper, we develop an understanding for MixUp as a form of "out-of-manifold regularization", which imposes certain "local linearity" constraints on the model's input space beyond the data manifold. This analysis enables us to identify a limitation of MixUp, which we call "manifold intrusion". In a nutshell, manifold intrusion in MixUp is a form of under-fitting resulting from conflicts between the synthetic labels of the mixed-up examples and the labels of original training data. Such a phenomenon usually happens when the parameters controlling the generation of mixing policies are not sufficiently fine-tuned on the training data. To address this issue, we propose a novel adaptive version of MixUp, where the mixing policies are automatically learned from the data using an additional network and objective function designed to avoid manifold intrusion. The proposed regularizer, AdaMixUp, is empirically evaluated on several benchmark datasets. Extensive experiments demonstrate that AdaMixUp improves upon MixUp when applied to the current art of deep classification models.

Martin Renqiang Min, Hongyu Guo, Dinghan Shen

Parametric embedding methods such as parametric t-SNE (pt-SNE) have been widely adopted for data visualization and out-of-sample data embedding without further computationally expensive optimization or approximation. However, the performance of pt-SNE is highly sensitive to the hyper-parameter batch size due to conflicting optimization goals, and often produces dramatically different embeddings with different choices of user-defined perplexities. To effectively solve these issues, we present parametric t-distributed stochastic exemplar-centered embedding methods. Our strategy learns embedding parameters by comparing given data only with precomputed exemplars, resulting in a cost function with linear computational and memory complexity, which is further reduced by noise contrastive samples. Moreover, we propose a shallow embedding network with high-order feature interactions for data visualization, which is much easier to tune but produces comparable performance in contrast to a deep neural network employed by pt-SNE. We empirically demonstrate, using several benchmark datasets, that our proposed methods significantly outperform pt-SNE in terms of robustness, visual effects, and quantitative evaluations.

Hongyu Guo

While natural languages are compositional, how state-of-the-art neural models achieve compositionality is still unclear. We propose a deep network, which not only achieves competitive accuracy for text classification, but also exhibits compositional behavior. That is, while creating hierarchical representations of a piece of text, such as a sentence, the lower layers of the network distribute their layer-specific attention weights to individual words. In contrast, the higher layers compose meaningful phrases and clauses, whose lengths increase as the networks get deeper until fully composing the sentence.

Hongyu Guo, Colin Cherry, Jiang Su

We propose a multi-view network for text classification. Our method automatically creates various views of its input text, each taking the form of soft attention weights that distribute the classifier's focus among a set of base features. For a bag-of-words representation, each view focuses on a different subset of the text's words. Aggregating many such views results in a more discriminative and robust representation. Through a novel architecture that both stacks and concatenates views, we produce a network that emphasizes both depth and width, allowing training to converge quickly. Using our multi-view architecture, we establish new state-of-the-art accuracies on two benchmark tasks.

Martin Renqiang Min, Hongyu Guo, Dongjin Song

Explicit high-order feature interactions efficiently capture essential structural knowledge about the data of interest and have been used for constructing generative models. We present a supervised discriminative High-Order Parametric Embedding (HOPE) approach to data visualization and compression. Compared to deep embedding models with complicated deep architectures, HOPE generates more effective high-order feature mapping through an embarrassingly simple shallow model. Furthermore, two approaches to generating a small number of exemplars conveying high-order interactions to represent large-scale data sets are proposed. These exemplars in combination with the feature mapping learned by HOPE effectively capture essential data variations. Moreover, through HOPE, these exemplars are employed to increase the computational efficiency of kNN classification for fast information retrieval by thousands of times. For classification in two-dimensional embedding space on MNIST and USPS datasets, our shallow method HOPE with simple Sigmoid transformations significantly outperforms state-of-the-art supervised deep embedding models based on deep neural networks, and even achieved historically low test error rate of 0.65% in two-dimensional space on MNIST, which demonstrates the representational efficiency and power of supervised shallow models with high-order feature interactions.