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Drug discovery often relies on the successful prediction of protein-ligand binding affinity. Recent advances have shown great promise in applying graph neural networks (GNNs) for better affinity prediction by learning the representations of protein-ligand complexes. However, existing solutions usually treat protein-ligand complexes as topological graph data, thus the biomolecular structural information is not fully utilized. The essential long-range interactions among atoms are also neglected in GNN models. To this end, we propose a structure-aware interactive graph neural network (SIGN) which consists of two components: polar-inspired graph attention layers (PGAL) and pairwise interactive pooling (PiPool). Specifically, PGAL iteratively performs the node-edge aggregation process to update embeddings of nodes and edges while preserving the distance and angle information among atoms. Then, PiPool is adopted to gather interactive edges with a subsequent reconstruction loss to reflect the global interactions. Exhaustive experimental study on two benchmarks verifies the superiority of SIGN.

While many existing graph neural networks (GNNs) have been proven to perform $\ell_2$-based graph smoothing that enforces smoothness globally, in this work we aim to further enhance the local smoothness adaptivity of GNNs via $\ell_1$-based graph smoothing. As a result, we introduce a family of GNNs (Elastic GNNs) based on $\ell_1$ and $\ell_2$-based graph smoothing. In particular, we propose a novel and general message passing scheme into GNNs. This message passing algorithm is not only friendly to back-propagation training but also achieves the desired smoothing properties with a theoretical convergence guarantee. Experiments on semi-supervised learning tasks demonstrate that the proposed Elastic GNNs obtain better adaptivity on benchmark datasets and are significantly robust to graph adversarial attacks. The implementation of Elastic GNNs is available at \url{//github.com/lxiaorui/ElasticGNN}.

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine learning methods are ideal for the design of large amounts of potential new candidate molecules, which are naturally represented as graphs. Graph generation is being revolutionized by deep learning methods, and molecular generation is one of its most promising applications. In this paper, we introduce a sequential molecular graph generator based on a set of graph neural network modules, which we call MG^2N^2. At each step, a node or a group of nodes is added to the graph, along with its connections. The modular architecture simplifies the training procedure, also allowing an independent retraining of a single module. Sequentiality and modularity make the generation process interpretable. The use of graph neural networks maximizes the information in input at each generative step, which consists of the subgraph produced during the previous steps. Experiments of unconditional generation on the QM9 and Zinc datasets show that our model is capable of generalizing molecular patterns seen during the training phase, without overfitting. The results indicate that our method is competitive, and outperforms challenging baselines for unconditional generation.

We propose a new STAcked and Reconstructed Graph Convolutional Networks (STAR-GCN) architecture to learn node representations for boosting the performance in recommender systems, especially in the cold start scenario. STAR-GCN employs a stack of GCN encoder-decoders combined with intermediate supervision to improve the final prediction performance. Unlike the graph convolutional matrix completion model with one-hot encoding node inputs, our STAR-GCN learns low-dimensional user and item latent factors as the input to restrain the model space complexity. Moreover, our STAR-GCN can produce node embeddings for new nodes by reconstructing masked input node embeddings, which essentially tackles the cold start problem. Furthermore, we discover a label leakage issue when training GCN-based models for link prediction tasks and propose a training strategy to avoid the issue. Empirical results on multiple rating prediction benchmarks demonstrate our model achieves state-of-the-art performance in four out of five real-world datasets and significant improvements in predicting ratings in the cold start scenario. The code implementation is available in //github.com/jennyzhang0215/STAR-GCN.

Medical image segmentation is a primary task in many applications, and the accuracy of the segmentation is a necessity. Recently, many deep learning networks derived from U-Net have been extensively used and have achieved notable results. To further improve and refine the performance of U-Net, parallel decoders along with mask prediction decoder have been carried out and have shown significant improvement with additional advantages. In our work, we utilize the advantages of using a combination of contour and distance map as regularizers. In turn, we propose a novel architecture Psi-Net with a single encoder and three parallel decoders, one decoder to learn the mask and other two to learn the auxiliary tasks of contour detection and distance map estimation. The learning of these auxiliary tasks helps in capturing the shape and boundary. We also propose a new joint loss function for the proposed architecture. The loss function consists of a weighted combination of Negative likelihood and Mean Square Error loss. We have used two publicly available datasets: 1) Origa dataset for the task of optic cup and disc segmentation and 2) Endovis segment dataset for the task of polyp segmentation to evaluate our model. We have conducted extensive experiments using our network to show our model gives better results in terms of segmentation, boundary and shape metrics.

Although end-to-end neural text-to-speech (TTS) methods (such as Tacotron2) are proposed and achieve state-of-the-art performance, they still suffer from two problems: 1) low efficiency during training and inference; 2) hard to model long dependency using current recurrent neural networks (RNNs). Inspired by the success of Transformer network in neural machine translation (NMT), in this paper, we introduce and adapt the multi-head attention mechanism to replace the RNN structures and also the original attention mechanism in Tacotron2. With the help of multi-head self-attention, the hidden states in the encoder and decoder are constructed in parallel, which improves the training efficiency. Meanwhile, any two inputs at different times are connected directly by self-attention mechanism, which solves the long range dependency problem effectively. Using phoneme sequences as input, our Transformer TTS network generates mel spectrograms, followed by a WaveNet vocoder to output the final audio results. Experiments are conducted to test the efficiency and performance of our new network. For the efficiency, our Transformer TTS network can speed up the training about 4.25 times faster compared with Tacotron2. For the performance, rigorous human tests show that our proposed model achieves state-of-the-art performance (outperforms Tacotron2 with a gap of 0.048) and is very close to human quality (4.39 vs 4.44 in MOS).

Deep Convolutional Neural Networks (CNNs) are a special type of Neural Networks, which have shown state-of-the-art results on various competitive benchmarks. The powerful learning ability of deep CNN is largely achieved with the use of multiple non-linear feature extraction stages that can automatically learn hierarchical representation from the data. Availability of a large amount of data and improvements in the hardware processing units have accelerated the research in CNNs and recently very interesting deep CNN architectures are reported. The recent race in deep CNN architectures for achieving high performance on the challenging benchmarks has shown that the innovative architectural ideas, as well as parameter optimization, can improve the CNN performance on various vision-related tasks. In this regard, different ideas in the CNN design have been explored such as use of different activation and loss functions, parameter optimization, regularization, and restructuring of processing units. However, the major improvement in representational capacity is achieved by the restructuring of the processing units. Especially, the idea of using a block as a structural unit instead of a layer is gaining substantial appreciation. This survey thus focuses on the intrinsic taxonomy present in the recently reported CNN architectures and consequently, classifies the recent innovations in CNN architectures into seven different categories. These seven categories are based on spatial exploitation, depth, multi-path, width, feature map exploitation, channel boosting and attention. Additionally, it covers the elementary understanding of the CNN components and sheds light on the current challenges and applications of CNNs.

Recently, much advance has been made in image captioning, and an encoder-decoder framework has achieved outstanding performance for this task. In this paper, we propose an extension of the encoder-decoder framework by adding a component called guiding network. The guiding network models the attribute properties of input images, and its output is leveraged to compose the input of the decoder at each time step. The guiding network can be plugged into the current encoder-decoder framework and trained in an end-to-end manner. Hence, the guiding vector can be adaptively learned according to the signal from the decoder, making itself to embed information from both image and language. Additionally, discriminative supervision can be employed to further improve the quality of guidance. The advantages of our proposed approach are verified by experiments carried out on the MS COCO dataset.

Despite of the success of Generative Adversarial Networks (GANs) for image generation tasks, the trade-off between image diversity and visual quality are an well-known issue. Conventional techniques achieve either visual quality or image diversity; the improvement in one side is often the result of sacrificing the degradation in the other side. In this paper, we aim to achieve both simultaneously by improving the stability of training GANs. A key idea of the proposed approach is to implicitly regularizing the discriminator using a representative feature. For that, this representative feature is extracted from the data distribution, and then transferred to the discriminator for enforcing slow updates of the gradient. Consequently, the entire training process is stabilized because the learning curve of discriminator varies slowly. Based on extensive evaluation, we demonstrate that our approach improves the visual quality and diversity of state-of-the art GANs.

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.