Potential Drug-Drug Interaction(DDI) occurring while treating complex or co-existing diseases with drug combinations may cause changes in drugs' pharmacological activity. Therefore, DDI prediction has been an important task in the medical healthy machine learning community. Graph-based learning methods have recently aroused widespread interest and are proved to be a priority for this task. However, these methods are often limited to exploiting the inter-view drug molecular structure and ignoring the drug's intra-view interaction relationship, vital to capturing the complex DDI patterns. 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 GCN to encode DDI relationships and a bond-aware attentive message propagating method to capture drug molecular structure information in the MIRACLE learning stage. 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.
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Self-supervised learning based on instance discrimination has shown remarkable progress. In particular, contrastive learning, which regards each image as well as its augmentations as a separate class, and pushes all other images away, has been proved effective for pretraining. However, contrasting two images that are de facto similar in semantic space is hard for optimization and not applicable for general representations. In this paper, we tackle the representation inefficiency of contrastive learning and propose a hierarchical training strategy to explicitly model the invariance to semantic similar images in a bottom-up way. This is achieved by extending the contrastive loss to allow for multiple positives per anchor, and explicitly pulling semantically similar images/patches together at the earlier layers as well as the last embedding space. In this way, we are able to learn feature representation that is more discriminative throughout different layers, which we find is beneficial for fast convergence. The hierarchical semantic aggregation strategy produces more discriminative representation on several unsupervised benchmarks. Notably, on ImageNet with ResNet-50 as backbone, we reach $76.4\%$ top-1 accuracy with linear evaluation, and $75.1\%$ top-1 accuracy with only $10\%$ labels.
The 2019 novel coronavirus (SARS-CoV-2) pandemic has resulted in more than a million deaths, high morbidities, and economic distress worldwide. There is an urgent need to identify medications that would treat and prevent novel diseases like the 2019 coronavirus disease (COVID-19). Drug repurposing is a promising strategy to discover new medical indications of the existing approved drugs due to several advantages in terms of the costs, safety factors, and quick results compared to new drug design and discovery. In this work, we explore computational data-driven methods for drug repurposing and propose a dedicated graph neural network (GNN) based drug repurposing model, called Dr-COVID. Although we analyze the predicted drugs in detail for COVID-19, the model is generic and can be used for any novel diseases. We construct a four-layered heterogeneous graph to model the complex interactions between drugs, diseases, genes, and anatomies. We pose drug repurposing as a link prediction problem. Specifically, we design an encoder based on the scalable inceptive graph neural network (SIGN) to generate embeddings for all the nodes in the four-layered graph and propose a quadratic norm scorer as a decoder to predict treatment for a disease. We provide a detailed analysis of the 150 potential drugs (such as Dexamethasone, Ivermectin) predicted by Dr-COVID for COVID-19 from different pharmacological classes (e.g., corticosteroids, antivirals, antiparasitic). Out of these 150 drugs, 46 drugs are currently in clinical trials. Dr-COVID is evaluated in terms of its prediction performance and its ability to rank the known treatment drugs for diseases as high as possible. For a majority of the diseases, Dr-COVID ranks the actual treatment drug in the top 15.
Click-through rate (CTR) prediction is an essential task in web applications such as online advertising and recommender systems, whose features are usually in multi-field form. The key of this task is to model feature interactions among different feature fields. Recently proposed deep learning based models follow a general paradigm: raw sparse input multi-filed features are first mapped into dense field embedding vectors, and then simply concatenated together to feed into deep neural networks (DNN) or other specifically designed networks to learn high-order feature interactions. However, the simple \emph{unstructured combination} of feature fields will inevitably limit the capability to model sophisticated interactions among different fields in a sufficiently flexible and explicit fashion. In this work, we propose to represent the multi-field features in a graph structure intuitively, where each node corresponds to a feature field and different fields can interact through edges. The task of modeling feature interactions can be thus converted to modeling node interactions on the corresponding graph. To this end, we design a novel model Feature Interaction Graph Neural Networks (Fi-GNN). Taking advantage of the strong representative power of graphs, our proposed model can not only model sophisticated feature interactions in a flexible and explicit fashion, but also provide good model explanations for CTR prediction. Experimental results on two real-world datasets show its superiority over the state-of-the-arts.
Knowledge graph embedding aims to learn distributed representations for entities and relations, and is proven to be effective in many applications. Crossover interactions --- bi-directional effects between entities and relations --- help select related information when predicting a new triple, but haven't been formally discussed before. In this paper, we propose CrossE, a novel knowledge graph embedding which explicitly simulates crossover interactions. It not only learns one general embedding for each entity and relation as most previous methods do, but also generates multiple triple specific embeddings for both of them, named interaction embeddings. We evaluate embeddings on typical link prediction tasks and find that CrossE achieves state-of-the-art results on complex and more challenging datasets. Furthermore, we evaluate embeddings from a new perspective --- giving explanations for predicted triples, which is important for real applications. In this work, an explanation for a triple is regarded as a reliable closed-path between the head and the tail entity. Compared to other baselines, we show experimentally that CrossE, benefiting from interaction embeddings, is more capable of generating reliable explanations to support its predictions.
Predicting properties of nodes in a graph is an important problem with applications in a variety of domains. Graph-based Semi-Supervised Learning (SSL) methods aim to address this problem by labeling a small subset of the nodes as seeds and then utilizing the graph structure to predict label scores for the rest of the nodes in the graph. Recently, Graph Convolutional Networks (GCNs) have achieved impressive performance on the graph-based SSL task. In addition to label scores, it is also desirable to have confidence scores associated with them. Unfortunately, confidence estimation in the context of GCN has not been previously explored. We fill this important gap in this paper and propose ConfGCN, which estimates labels scores along with their confidences jointly in GCN-based setting. ConfGCN uses these estimated confidences to determine the influence of one node on another during neighborhood aggregation, thereby acquiring anisotropic capabilities. Through extensive analysis and experiments on standard benchmarks, we find that ConfGCN is able to outperform state-of-the-art baselines. We have made ConfGCN's source code available to encourage reproducible research.
While supervised learning has enabled great progress in many applications, unsupervised learning has not seen such widespread adoption, and remains an important and challenging endeavor for artificial intelligence. In this work, we propose a universal unsupervised learning approach to extract useful representations from high-dimensional data, which we call Contrastive Predictive Coding. The key insight of our model is to learn such representations by predicting the future in latent space by using powerful autoregressive models. We use a probabilistic contrastive loss which induces the latent space to capture information that is maximally useful to predict future samples. It also makes the model tractable by using negative sampling. While most prior work has focused on evaluating representations for a particular modality, we demonstrate that our approach is able to learn useful representations achieving strong performance on four distinct domains: speech, images, text and reinforcement learning in 3D environments.
We present Deep Graph Infomax (DGI), a general approach for learning node representations within graph-structured data in an unsupervised manner. DGI relies on maximizing mutual information between patch representations and corresponding high-level summaries of graphs---both derived using established graph convolutional network architectures. The learnt patch representations summarize subgraphs centered around nodes of interest, and can thus be reused for downstream node-wise learning tasks. In contrast to most prior approaches to unsupervised learning with GCNs, DGI does not rely on random walk objectives, and is readily applicable to both transductive and inductive learning setups. We demonstrate competitive performance on a variety of node classification benchmarks, which at times even exceeds the performance of supervised learning.
The potential of graph convolutional neural networks for the task of zero-shot learning has been demonstrated recently. 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, knowledge from distant nodes can get diluted when propagating through intermediate nodes, because current approaches to zero-shot learning use graph propagation schemes that perform Laplacian smoothing at each layer. We show that extensive smoothing does not help the task of regressing classifier weights in zero-shot learning. In order to still incorporate information from distant nodes and utilize the graph structure, we propose an Attentive Dense Graph Propagation Module (ADGPM). ADGPM 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 and an attention scheme is further used to weigh their contribution depending on the distance to the node. Finally, we illustrate that finetuning of the feature representation after training the ADGPM leads to considerable improvements. Our method achieves competitive results, outperforming previous zero-shot learning approaches.
There has been much recent work on training neural attention models at the sequence-level using either reinforcement learning-style methods or by optimizing the beam. In this paper, we survey a range of classical objective functions that have been widely used to train linear models for structured prediction and apply them to neural sequence to sequence models. Our experiments show that these losses can perform surprisingly well by slightly outperforming beam search optimization in a like for like setup. We also report new state of the art results on both IWSLT'14 German-English translation as well as Gigaword abstractive summarization. On the larger WMT'14 English-French translation task, sequence-level training achieves 41.5 BLEU which is on par with the state of the art.
Options in reinforcement learning allow agents to hierarchically decompose a task into subtasks, having the potential to speed up learning and planning. However, autonomously learning effective sets of options is still a major challenge in the field. In this paper we focus on the recently introduced idea of using representation learning methods to guide the option discovery process. Specifically, we look at eigenoptions, options obtained from representations that encode diffusive information flow in the environment. We extend the existing algorithms for eigenoption discovery to settings with stochastic transitions and in which handcrafted features are not available. We propose an algorithm that discovers eigenoptions while learning non-linear state representations from raw pixels. It exploits recent successes in the deep reinforcement learning literature and the equivalence between proto-value functions and the successor representation. We use traditional tabular domains to provide intuition about our approach and Atari 2600 games to demonstrate its potential.
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