The development of new drugs is costly, time consuming, and often accompanied with safety issues. Drug repurposing can avoid the expensive and lengthy process of drug development by finding new uses for already approved drugs. In order to repurpose drugs effectively, it is useful to know which proteins are targeted by which drugs. Computational models that estimate the interaction strength of new drug–target pairs have the potential to expedite drug repurposing. Several models have been proposed for this task. However, these models represent the drugs as strings, which is not a natural way to represent molecules. We propose a new model called GraphDTA that represents drugs as graphs and uses graph neural networks to predict drug–target affinity. We show that graph neural networks not only predict drug–target affinity better than non-deep learning models, but also outperform competing deep learning methods. Our results confirm that deep learning models are appropriate for drug–target binding affinity prediction, and that representing drugs as graphs can lead to further improvements. Availability of data and materials The proposed models are implemented in Python. Related data, pre-trained models, and source code are publicly available at https://github.com/thinng/GraphDTA. All scripts and data needed to reproduce the post-hoc statistical analysis are available from https://doi.org/10.5281/zenodo.3603523.

Background: While the development of new drugs is costly, time consuming, and often accompanied with safety issues, drug repurposing, where old drugs with established safety are used for medical conditions other than originally developed, is an attractive alternative. Then, how the old drugs work on new targets becomes a crucial part of drug repurposing and gains much of interest. Several statistical and machine learning models have been proposed to estimate drug-target binding affinity and deep learning approaches have been shown to be among state-of-the-art methods. However, drugs and targets in these models have been commonly represented in 1D strings, regardless the fact that molecules are by nature formed by the chemical bonding of atoms. Method: In this work, we propose GraphDTA to capture the structural information of drugs, possibly enhancing the predictive power of the affinity. In particular, unlike competing methods, drugs are represented as graphs and graph convolutional networks are used to learn drug-target binding affinity. We trial our method on two benchmark datasets of drug-target binding affinity and compare the performance with state-of-the-art models in the research field. Results: The results show that our proposed method can not only predict the affinity better than non-deep learning models, but also outperform competing deep learning approaches. This demonstrates the practical advantages of graph-based representation for molecules in providing accurate prediction of drug-target binding affinity. The application may also include any recommendation systems where either or both of the user-and product-like sides can be represented in graphs. Availability and implementation: The proposed models are implemented in Python. Related data, pre-trained models, and source code are publicly available at https://github.com/thinng/GraphDTA.

We introduce dual-decoder Transformer, a new model architecture that jointly performs automatic speech recognition (ASR) and multilingual speech translation (ST). Our models are based on the original Transformer architecture (Vaswani et al., 2017) but consist of two decoders, each responsible for one task (ASR or ST). Our major contribution lies in how these decoders interact with each other: one decoder can attend to different information sources from the other via a dual-attention mechanism. We propose two variants of these architectures corresponding to two different levels of dependencies between the decoders, called the parallel and cross dual-decoder Transformers, respectively. Extensive experiments on the MuST-C dataset show that our models outperform the previously-reported highest translation performance in the multilingual settings, and outperform as well bilingual one-to-one results. Furthermore, our parallel models demonstrate no trade-off between ASR and ST compared to the vanilla multi-task architecture. Our code and pre-trained models are available at https://github.com/formiel/speech-translation.

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Adapter modules were recently introduced as an efficient alternative to fine-tuning in NLP. Adapter tuning consists in freezing pretrained parameters of a model and injecting lightweight modules between layers, resulting in the addition of only a small number of taskspecific trainable parameters. While adapter tuning was investigated for multilingual neural machine translation, this paper proposes a comprehensive analysis of adapters for multilingual speech translation (ST). Starting from different pre-trained models (a multilingual ST trained on parallel data or a multilingual BART (mBART) trained on non-parallel multilingual data), we show that adapters can be used to: (a) efficiently specialize ST to specific language pairs with a low extra cost in terms of parameters, and (b) transfer from an automatic speech recognition (ASR) task and an mBART pretrained model to a multilingual ST task. Experiments show that adapter tuning offer competitive results to full fine-tuning, while being much more parameter-efficient.