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At the early stages of the drug discovery, molecule toxicity prediction is crucial to excluding drug candidates that are likely to fail in clinical trials. In this paper, we presented a novel molecular representation method and developed a corresponding deep learning-based framework called TOP (the abbreviation of TOxicity Prediction). TOP integrates specifically designed data preprocessing methods, an RNN based on bidirectional gated recurrent unit (BiGRU), and fully connected neural networks for end-to-end molecular representation learning and chemical toxicity prediction. TOP can automatically learn a mixed molecular representation from not only SMILES contextual information that describes the molecule structure, but also physiochemical properties. Therefore, TOP can overcome the drawbacks of existing methods that use either of them, thus greatly promotes toxicity prediction accuracy. We conducted extensive experiments over 14 classic toxicity prediction tasks on three different benchmark datasets, including balanced and imbalanced ones. The results show that, with the help of the novel molecular representation method, TOP significantly outperforms not only three baseline machine learning methods, but also five state-of-the-art methods., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Anomalies (or outliers) indicate a minority of data items that are quite different from the majority (inliers) of a dataset in a certain aspect. Unsupervised anomaly detection (UAD) is an important but not yet extensively studied research topic. Recent deep learning based methods exploit the reconstruction gap between inliers and outliers to discriminate them. However, it is observed that the reconstruction gap often decreases rapidly as the training process goes. And there is no reasonable way to set the training stop point. To support effective UAD, we propose a new UAD framework by introducing a Latent Feature Reconstruction (LFR) layer that can be applied to recent UAD methods. The LFR layer acts as a regularizer to constrain the latent features in a low-rank subspace from which inliers can be reconstructed well while outliers cannot. We develop two new UAD methods by implementing the proposed framework with autoencoder architecture and geometric transformation scheme. Experiments on five benchmarks show that our proposed methods can achieve state-of-the-art performance in most cases. [ABSTRACT FROM AUTHOR]

Sea Surface Temperature (SST) prediction is a hot topic that has received tremendous popularity in recent years. Existing methods for SST prediction usually select one sea area of interest and conduct SST prediction by learning the spatial and temporal dependencies and patterns in historical SST data. However, global SST is a unified system of high regionality, and the SST in different sea areas shows different changing patterns due to the influence of various factors, e.g., geographic location, ocean currents and sea depth. Without a good understanding of such regionality of SST, we cannot quantitatively integrate the regionality information of SST into SST prediction models to make them adaptive to different SST patterns around the world and improve the prediction accuracy. To address this issue, we proposed the Multi-Stage Spatio–Temporal Clustering (MuSTC) method to quantitatively identify sea areas with similar SST patterns. First, MuSTC sequentially learns the representation of long-term SST with a deep temporal encoder and calculates the spatial correlation scores between grid ocean regions with self-attention. Then, MuSTC clusters grid ocean regions based on the original SST data, encoded long-term SST representation and spatial correlation scores, respectively, to obtain the sea areas with similar SST patterns from different perspectives. According to the experiments in three ocean areas, i.e., the North Pacific Ocean (NPO), the South Atlantic Ocean (SAO) and the North Atlantic Ocean (NAO), the clustering results generally match the distribution of ocean currents, which demonstrates the effectiveness of our MuSTC method. In addition, we integrate the clustering results into two representative spatio–temporal prediction models, i.e., Spatio–Temporal Graph Convolutional Networks (STGCN) and Adaptive Graph Convolutional Recurrent Network (AGCRN), to conduct SST prediction. According to the results of experiments, the integration of regionality information leads to the reduction of Root Mean Square Error (RMSE) by 1.95%, 1.39% and 1.28% in NPO, SAO and NAO, respectively, using the STGCN model, and the reduction of RMSE by 4.94%, 0.74% and 1.43% by using the AGCRN model. Such results indicate that the integration of regionality information could notably improve the prediction accuracy of SST. [ABSTRACT FROM AUTHOR]

Molecular property prediction (MPP) is a crucial and fundamental task for AI-aided drug discovery (AIDD). Recent studies have shown great promise of applying self-supervised learning (SSL) to producing molecular representations to cope with the widely-concerned data scarcity problem in AIDD. As some specific substructures of molecules play important roles in determining molecular properties, molecular representations learned by deep learning models are expected to attach more importance to such substructures implicitly or explicitly to achieve better predictive performance. However, few SSL pre-trained models for MPP in the literature have ever focused on such substructures. To challenge this situation, this paper presents a C hemistry- A ware F ragmentation for E ffective MPP (CAFE-MPP in short) under the self-supervised contrastive learning framework. First, a novel fragment-based molecular graph (FMG) is designed to represent the topological relationship between chemistry-aware substructures that constitute a molecule. Then, with well-designed hard negative pairs, a is pre-trained on fragment-level by contrastive learning to extract representations for the nodes in FMGs. Finally, a Graphormer model is leveraged to produce molecular representations for MPP based on the embeddings of fragments. Experiments on 11 benchmark datasets show that the proposed CAFE-MPP method achieves state-of-the-art performance on 7 of the 11 datasets and the second-best performance on 3 datasets, compared with six remarkable self-supervised methods. Further investigations also demonstrate that CAFE-MPP can learn to embed molecules into representations implicitly containing the information of fragments highly correlated to molecular properties, and can alleviate the over-smoothing problem of graph neural networks. [ABSTRACT FROM AUTHOR]

Sea surface temperature (SST) has important impacts on the global ecology, and having a good understanding of the predictability, i.e., the possibility of achieving accurate prediction, of SST can help us monitor the marine environment and climate change, and guide the selection and design of SST prediction methods. However, existing studies for analyzing SST mostly measure the rising or falling trends of SST. To address this issue, we introduce a temporal-correlated entropy to quantify the predictability of SST series from both global coarse-grained and local fine-grained aspects, and make SST prediction with multiple deep learning models to prove the effectiveness of such predictability evaluation method. In addition, we explore the dynamics of SST predictability by dividing the time range of interest into consecutive time periods, evaluating the corresponding predictability of SST for each time period, and analyzing the stability of the predictability of SST over time. According to the experiments, the SST predictability values near the poles and equator are really high. The average SST predictability values of the East China Sea, Bohai Sea, and Antarctic Ocean are 0.719, 0.706, and 0.886, respectively, and the size relationship of the SST predictability in the three local sea areas is consistent with our prediction results using multiple representative SST prediction methods, which corroborates the reliability of the predictability evaluation method. In addition, we found that the SST predictability in the Antarctic Ocean changes more dramatically over time than in the East China Sea and the Bohai Sea. The results of SST predictability and its dynamic analysis indicate that global warming, ocean currents, and human activities all have significant impacts on the predictability of SST. [ABSTRACT FROM AUTHOR]

Motivation Accurately predicting drug–target interaction (DTI) is a crucial step to drug discovery. Recently, deep learning techniques have been widely used for DTI prediction and achieved significant performance improvement. One challenge in building deep learning models for DTI prediction is how to appropriately represent drugs and targets. Target distance map and molecular graph are low dimensional and informative representations, which however have not been jointly used in DTI prediction. Another challenge is how to effectively model the mutual impact between drugs and targets. Though attention mechanism has been used to capture the one-way impact of targets on drugs or vice versa, the mutual impact between drugs and targets has not yet been explored, which is very important in predicting their interactions. Results Therefore, in this article we propose MINN-DTI, a new model for DTI prediction. MINN-DTI combines an interacting-transformer module (called Interformer) with an improved Communicative Message Passing Neural Network (CMPNN) (called Inter-CMPNN) to better capture the two-way impact between drugs and targets, which are represented by molecular graph and distance map, respectively. The proposed method obtains better performance than the state-of-the-art methods on three benchmark datasets: DUD-E, human and BindingDB. MINN-DTI also provides good interpretability by assigning larger weights to the amino acids and atoms that contribute more to the interactions between drugs and targets. Availability and implementation The data and code of this study are available at https://github.com/admislf/MINN-DTI. [ABSTRACT FROM AUTHOR]

Background: Protein protein interactions (PPIs) are essential to most of the biological processes. The prediction of PPIs is beneficial to the understanding of protein functions and thus is helpful to pathological analysis, disease diagnosis and drug design etc. As the amount of protein data is growing fast in the post genomic era, high-throughput experimental methods are expensive and time-consuming for the prediction of PPIs. Thus, computational methods have attracted researcher's attention in recent years. A large number of computational methods have been proposed based on different protein sequence encoders. Results: Notably, the confidence score of a protein sequence pair could be regarded as a kind of measurement to PPIs. The higher the confidence score for one protein pair is, the more likely the protein pair interacts. Thus in this paper, a deep learning framework, called ordinal regression and recurrent convolutional neural network (OR-RCNN) method, is introduced to predict PPIs from the perspective of confidence score. It mainly contains two parts: the encoder part of protein sequence pair and the prediction part of PPIs by confidence score. In the first part, two recurrent convolutional neural networks (RCNNs) with shared parameters are applied to construct two protein sequence embedding vectors, which can automatically extract robust local features and sequential information from the protein pairs. Based on it, the two embedding vectors are encoded into one novel embedding vector by element-wise multiplication. By taking the ordinal information behind confidence score into consideration, ordinal regression is used to construct multiple sub-classifiers in the second part. The results of multiple sub-classifiers are aggregated to obtain the final confidence score. Following that, the existence of PPIs is determined by the confidence score. We set a threshold θ , and say the interaction exists between the protein pair if its confidence score is bigger than θ . Conclusions: We applied our method to predict PPIs on data sets S. cerevisiae and Homo sapiens. Through experimental verification, our method outperforms state-of-the-art PPI prediction models. [ABSTRACT FROM AUTHOR]

The identification of interactions between compounds and proteins plays an important role in network pharmacology and drug discovery. However, experimentally identifying compound-protein interactions (CPIs) is generally expensive and time-consuming, computational approaches are thus introduced. Among these, machine-learning based methods have achieved a considerable success. However, due to the nonlinear and imbalanced nature of biological data, many machine learning approaches have their own limitations. Recently, deep learning techniques show advantages over many state-of-the-art machine learning methods in some applications. In this study, we aim at improving the performance of CPI prediction based on deep learning, and propose a method called DL-CPI (the abbreviation of D eep L earning for C ompound- P rotein I nteractions prediction), which employs deep neural network (DNN) to effectively learn the representations of compound-protein pairs. Extensive experiments show that DL-CPI can learn useful features of compound-protein pairs by a layerwise abstraction, and thus achieves better prediction performance than existing methods on both balanced and imbalanced datasets. [ABSTRACT FROM AUTHOR]

Sea surface temperature (SST) plays an important role in various oceanic applications, including climate prediction, ocean environment monitoring and marine disaster warning. Although many approaches have been developed for predicting SST, most of them conduct the prediction only based on historical SST data. However, SST is essentially affected by many external factors, e.g. , the short-wave radiation from the sun and the long-wave radiation from the atmosphere and ground, which are ignored by existing approaches. In this work, we proposed a Multi-source Spatio-Temporal data fusion model (MUST) to fuse multi-source data, including SST data and external factors, to improve the accuracy of short-term SST prediction. Concretely, MUST first introduces Bicubic Convolutional Interpolation (BCI) to address the issue of inconsistent spatial resolutions of multi-source data, then employs the Spatio-Temporal Dilated ConvLSTM (ST-DC) to learn the spatio-temporal features of SST and external factors, and finally fuses the learned features from multi-source data to predict SST with a Cross Data Fusion (CDF) component. As validated on two real datasets, MUST achieves much better performance than existing SST prediction approaches. • Multiple sources of data improve the prediction of short-term SST. • A MUST model was proposed to predict the SST for future seven days. • A case study was conducted in the regions of Nino3.4 and East China Sea. • The proposed MUST model outperforms CNN, LeNet and ConvLSTM. [ABSTRACT FROM AUTHOR]