Interference between pharmacological substances can cause serious medical injuries. Correctly predicting so-called drug-drug interactions (DDI) does not only reduce these cases but can also result in a reduction of drug development cost. Presently, most drug-related knowledge is the result of clinical evaluations and post-marketing surveillance; resulting in a limited amount of information. Existing data-driven prediction approaches for DDIs typically rely on a single source of information, while using information from multiple sources would help improve predictions. Machine learning (ML) techniques are used, but the techniques are often unable to deal with skewness in the data. Hence, we propose a new ML approach for predicting DDIs based on multiple data sources. For this task, we use 12,000 drug features from DrugBank, PharmGKB, and KEGG drugs, which are integrated using Knowledge Graphs (KGs). To train our prediction model, we first embed the nodes in the graph using various embedding approaches. We found that the best performing combination was a ComplEx embedding method creating using PyTorch-BigGraph (PBG) with a Convolutional-LSTM network and classic machine learning-based prediction models. The model averaging ensemble method of three best classifiers yields up to 0.94, 0.92, 0.80 for AUPR, F1-score, and MCC, respectively during 5-fold cross-validation tests.
College of Artificial Intelligence, Nankai University（南开大学人工智能学院）；Shenzhen Research Institute, Nankai University（南开大学深圳研究院）；Ji Hua Laboratory（季华实验室）；State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University（南开大学药学院药物化学生物学国家重点实验室）
This paper focuses on three critical problems on protein classification. Firstly, Carbohydrate-active enzyme (CAZyme) classification can help people to understand the properties of enzymes. However, one CAZyme may belong to several classes. This leads to Multi-label CAZyme classification. Secondly, to capture information from the secondary structure of protein, protein classification is modeled as graph classification problem. Thirdly, compound-protein interactions prediction employs graph learning for compound with sequential embedding for protein. This can be seen as classification task for …
Rochester Institute of Technology（罗切斯特理工学院）；Thomas H. Gosnell School of Life Sciences（托马斯·H·戈斯内尔生命科学学院）
Biomedical interaction networks have incredible potential to be useful in the prediction of biologically meaningful interactions, identification of network biomarkers of disease, and the discovery of putative drug targets. Recently, graph neural networks have been proposed to effectively learn representations for biomedical entities and achieved state-of-the-art results in biomedical interaction prediction. These methods only consider information from immediate neighbors but cannot learn a general mixing of features from neighbors at various distances. In this paper, we present a higher-order …
Research on Adverse Drug Reaction Prediction Model Combining Knowledge Graph Embedding and Deep Learning
University of Southampton（南安普顿大学）；University of Science and Technology of China（中国科学技术大学）；San Francisco Bay University（旧金山湾大学）；Trine University（特莱恩大学）；The Hong Kong University of Science and Technology（香港科技大学）；SouthWest JiaoTong University（西南交通大学）
Indian Association for the Cultivation of Science（印度科学培育协会）
Development of new drugs is an expensive and time-consuming process. Due to the world-wide SARS-CoV-2 outbreak, it is essential that new drugs for SARS-CoV-2 are developed as soon as possible. Drug repurposing techniques can reduce the time span needed to develop new drugs by probing the list of existing FDA-approved drugs and their properties to reuse them for combating the new disease. We propose a novel architecture DeepGLSTM, which is a Graph Convolutional network and LSTM based method that predicts binding affinity values between the FDA-approved drugs and the viral proteins of SARS-CoV-2…
Novartis Institutes for BioMedical Research（诺华生物医学研究所）
The exploration of novel chemical spaces is one of the most important tasks of cheminformatics when supporting the drug discovery process. Properly designed and trained deep neural networks can provide a viable alternative to brute-force de novo approaches or various other machine-learning techniques for generating novel drug-like molecules. In this article we present a method to generate molecules using a long short-term memory (LSTM) neural network and provide an analysis of the results, including a virtual screening test. Using the network one million drug-like molecules were generated in 2…
DRExplainer: Quantifiable Interpretability in Drug Response Prediction with Directed Graph Convolutional Network
University of Science and Technology of China（中国科学技术大学）；School of Information and Artificial Intelligence, Anhui Agricultural University（安徽农业大学信息与人工智能学院）；Institutes of Physical Science and Information Technology, Anhui University（安徽大学物理科学与信息技术研究院）
Action recognition greatly benefits motion understanding in video analysis. Recurrent networks such as long short-term memory (LSTM) networks are a popular choice for motion-aware sequence learning tasks. Recently, a convolutional extension of LSTM was proposed, in which input-to-hidden and hidden-to-hidden transitions are modeled through convolution with a single kernel. This implies an unavoidable trade-off between effectiveness and efficiency. Herein, we propose a new enhancement to convolutional LSTM networks that supports accommodation of multiple convolutional kernels and layers. This re…
Fully convolutional neural networks (FCN) have been shown to achieve state-of-the-art performance on the task of classifying time series sequences. We propose the augmentation of fully convolutional networks with long short term memory recurrent neural network (LSTM RNN) sub-modules for time series classification. Our proposed models significantly enhance the performance of fully convolutional networks with a nominal increase in model size and require minimal preprocessing of the dataset. The proposed Long Short Term Memory Fully Convolutional Network (LSTM-FCN) achieves state-of-the-art perfo…
Long Short Term Memory Fully Convolutional Neural Networks (LSTM-FCN) and Attention LSTM-FCN (ALSTM-FCN) have shown to achieve state-of-the-art performance on the task of classifying time series signals on the old University of California-Riverside (UCR) time series repository. However, there has been no study on why LSTM-FCN and ALSTM-FCN perform well. In this paper, we perform a series of ablation tests (3627 experiments) on LSTM-FCN and ALSTM-FCN to provide a better understanding of the model and each of its sub-module. Results from the ablation tests on ALSTM-FCN and LSTM-FCN show that the…
The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）
Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico predictions based on machine learning have proved to be a cost-efficient way to complement the in vitro and in vivo methods. However, the performance of the established models has been limited by their incapability of dealing with the interactions between drugs and proteins, which play an important role in the mechanism behind the BBB penetrating behaviors. To addres…
United International University（联合国际大学）；University of Tehran（德黑兰大学）
The task of drug-target interaction prediction holds significant importance in pharmacology and therapeutic drug design. In this paper, we present FRnet-DTI, an auto encoder and a convolutional classifier for feature manipulation and drug target interaction prediction. Two convolutional neural neworks are proposed where one model is used for feature manipulation and the other one for classification. Using the first method FRnet-1, we generate 4096 features for each of the instances in each of the datasets and use the second method, FRnet-2, to identify interaction probability employing those f…
This paper explores the use of convolution LSTMs to simultaneously learn spatial- and temporal-information in videos. A deep network of convolutional LSTMs allows the model to access the entire range of temporal information at all spatial scales of the data. We describe our experiments involving convolution LSTMs for lipreading that demonstrate the model is capable of selectively choosing which spatiotemporal scales are most relevant for a particular dataset. The proposed deep architecture also holds promise in other applications where spatiotemporal features play a vital role without having t…
We consider the problem of predicting semantic segmentation of future frames in a video. Given several observed frames in a video, our goal is to predict the semantic segmentation map of future frames that are not yet observed. A reliable solution to this problem is useful in many applications that require real-time decision making, such as autonomous driving. We propose a novel model that uses convolutional LSTM (ConvLSTM) to encode the spatiotemporal information of observed frames for future prediction. We also extend our model to use bidirectional ConvLSTM to capture temporal information in…
Hybrid LSTM-fully convolutional networks (LSTM-FCN) for time series classification have produced state-of-the-art classification results on univariate time series. We show that replacing the LSTM with a gated recurrent unit (GRU) to create a GRU-fully convolutional network hybrid model (GRU-FCN) can offer even better performance on many time series datasets. The proposed GRU-FCN model outperforms state-of-the-art classification performance in many univariate and multivariate time series datasets. In addition, since the GRU uses a simpler architecture than the LSTM, it has fewer training parame…
An essential task in predictive maintenance is the prediction of the Remaining Useful Life (RUL) through the analysis of multivariate time series. Using the sliding window method, Convolutional Neural Network (CNN) and conventional Recurrent Neural Network (RNN) approaches have produced impressive results on this matter, due to their ability to learn optimized features. However, sequence information is only partially modeled by CNN approaches. Due to the flatten mechanism in conventional RNNs, like Long Short Term Memories (LSTM), the temporal information within the window is not fully preserv…
Deep convolutional neural networks comprise a subclass of deep neural networks (DNN) with a constrained architecture that leverages the spatial and temporal structure of the domain they model. Convolutional networks achieve the best predictive performance in areas such as speech and image recognition by hierarchically composing simple local features into complex models. Although DNNs have been used in drug discovery for QSAR and ligand-based bioactivity predictions, none of these models have benefited from this powerful convolutional architecture. This paper introduces AtomNet, the first struc…
Phase unwrapping is a classical ill-posed problem which aims to recover the true phase from wrapped phase. In this paper, we introduce a novel Convolutional Neural Network (CNN) that incorporates a Spatial Quad-Directional Long Short Term Memory (SQD-LSTM) for phase unwrapping, by formulating it as a regression problem. Incorporating SQD-LSTM can circumvent the typical CNNs' inherent difficulty of learning global spatial dependencies which are vital when recovering the true phase. Furthermore, we employ a problem specific composite loss function to train this network. The proposed network is f…
Absorption, distribution, metabolism, and excretion (ADME) studies are critical for drug discovery. Conventionally, these tasks, together with other chemical property predictions, rely on domain-specific feature descriptors, or fingerprints. Following the recent success of neural networks, we developed Chemi-Net, a completely data-driven, domain knowledge-free, deep learning method for ADME property prediction. To compare the relative performance of Chemi-Net with Cubist, one of the popular machine learning programs used by Amgen, a large-scale ADME property prediction study was performed on-s…
COMSATS University Islamabad（COMSATS伊斯兰堡大学）；Tsinghua University（清华大学）；Arab Open University-Palestine（阿拉伯开放大学巴勒斯坦分校）；Jashore University of Science and Technology（杰索尔科技大学）
Approximately, 50 million people in the world are affected by epilepsy. For patients, the anti-epileptic drugs are not always useful and these drugs may have undesired side effects on a patient's health. If the seizure is predicted the patients will have enough time to take preventive measures. The purpose of this work is to investigate the application of bidirectional LSTM for seizure prediction. In this paper, we trained EEG data from canines on a double Bidirectional LSTM layer followed by a fully connected layer. The data was provided in the form of a Kaggle competition by American Epileps…
Microsoft Corporation（微软公司）；Microsoft Turing（微软图灵）
We present the encoder-forecaster convolutional long short-term memory (LSTM) deep-learning model that powers Microsoft Weather's operational precipitation nowcasting product. This model takes as input a sequence of weather radar mosaics and deterministically predicts future radar reflectivity at lead times up to 6 hours. By stacking a large input receptive field along the feature dimension and conditioning the model's forecaster with predictions from the physics-based High Resolution Rapid Refresh (HRRR) model, we are able to outperform optical flow and HRRR baselines by 20-25% on multiple me…
Univ. Politècnica de Catalunya（加泰罗尼亚理工大学）；UPC BarcelonaTech（UPC巴塞罗那技术学院）；Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center（智能数据科学与人工智能（IDEAI-UPC）研究中心）
G-Protein Coupled Receptors (GPCRs) are a big family of eukaryotic cell transmembrane proteins, responsible for numerous biological processes. From a practical viewpoint around 34\% of the drugs approved by the US Food and Drug Administration target these receptors. They can be analyzed from their simulated molecular dynamics, including the prediction of their behavior in the presence of drugs. In this paper, the capability of Long Short-Term Memory Networks (LSTMs) are evaluated to learn and predict the molecular dynamic trajectories of a receptor. Several models were trained with the 3D posi…
School of Information Technology, University of Cincinnati（辛辛那提大学信息技术学院）；School of Computing and Informatics, University of Louisiana at Lafayette（路易斯安那大学拉法叶分校计算与信息学院）
Spatiotemporal sequence prediction is an important problem in deep learning. We study next-frame(s) video prediction using a deep-learning-based predictive coding framework that uses convolutional, long short-term memory (convLSTM) modules. We introduce a novel reduced-gate convolutional LSTM(rgcLSTM) architecture that requires a significantly lower parameter budget than a comparable convLSTM. By using a single multi-function gate, our reduced-gate model achieves equal or better next-frame(s) prediction accuracy than the original convolutional LSTM while using a smaller parameter budget, there…
Baylor College of Medicine（贝勒医学院）；Michael E. DeBakey VA Medical Center（迈克尔·E·德贝基退伍军人事务医疗中心）
The Early diagnosis and treatment of depression is essential for effective treatment. Depression, while being one of the most common mental illnesses, is still poorly understood in both research and clinical practice. Among different treatments, drug prescription is widely used, however the drug treatment is not effective for many patients. In this work, we propose a method for major depressive disorder (MDD) diagnosis as well as a method for predicting the drug response in patient with MDD using EEG signals. Method: We employ transformers, which are modified recursive neural networks with nov…
Deep learning models utilizing convolution layers have achieved state-of-the-art performance on univariate time series classification tasks. In this work, we propose improving CNN based time series classifiers by utilizing Octave Convolutions (OctConv) to outperform themselves. These network architectures include Fully Convolutional Networks (FCN), Residual Neural Networks (ResNets), LSTM-Fully Convolutional Networks (LSTM-FCN), and Attention LSTM-Fully Convolutional Networks (ALSTM-FCN). The proposed layers significantly improve each of these models with minimally increased network parameters…
Financial markets are a complex dynamical system. The complexity comes from the interaction between a market and its participants, in other words, the integrated outcome of activities of the entire participants determines the markets trend, while the markets trend affects activities of participants. These interwoven interactions make financial markets keep evolving. Inspired by stochastic recurrent models that successfully capture variability observed in natural sequential data such as speech and video, we propose CLVSA, a hybrid model that consists of stochastic recurrent networks, the sequen…
Monitoring the biomedical literature for cases of Adverse Drug Reactions (ADRs) is a critically important and time consuming task in pharmacovigilance. The development of computer assisted approaches to aid this process in different forms has been the subject of many recent works. One particular area that has shown promise is the use of Deep Neural Networks, in particular, Convolutional Neural Networks (CNNs), for the detection of ADR relevant sentences. Using token-level convolutions and general purpose word embeddings, this architecture has shown good performance relative to more traditional…
The use of drug combinations, termed polypharmacy, is common to treat patients with complex diseases and co-existing conditions. However, a major consequence of polypharmacy is a much higher risk of adverse side effects for the patient. Polypharmacy side effects emerge because of drug-drug interactions, in which activity of one drug may change if taken with another drug. The knowledge of drug interactions is limited because these complex relationships are rare, and are usually not observed in relatively small clinical testing. Discovering polypharmacy side effects thus remains an important cha…
University of Maryland（马里兰大学）；NVIDIA Research（英伟达研究院）
Learning from spatio-temporal data has numerous applications such as human-behavior analysis, object tracking, video compression, and physics simulation.However, existing methods still perform poorly on challenging video tasks such as long-term forecasting. This is because these kinds of challenging tasks require learning long-term spatio-temporal correlations in the video sequence. In this paper, we propose a higher-order convolutional LSTM model that can efficiently learn these correlations, along with a succinct representations of the history. This is accomplished through a novel tensor tra…
Tsinghua University（清华大学）；University of Science and Technology of China（中国科学技术大学）；University of Michigan（密歇根大学）；Columbia University in the City of New York（纽约哥伦比亚大学）；National University of Defense Technology（国防科技大学）
A challenge in speech production research is to predict future tongue movements based on a short period of past tongue movements. This study tackles speaker-dependent tongue motion prediction problem in unlabeled ultrasound videos with convolutional long short-term memory (ConvLSTM) networks. The model has been tested on two different ultrasound corpora. ConvLSTM outperforms 3-dimensional convolutional neural network (3DCNN) in predicting the 9\textsuperscript{th} frames based on 8 preceding frames, and also demonstrates good capacity to predict only the tongue contours in future frames. Furth…
As the climate changes, the severity of wildland fires is expected to worsen. Models that accurately capture fire propagation dynamics greatly help efforts for understanding, responding to and mitigating the damages caused by these fires. Machine learning techniques provide a potential approach for developing such models. The objective of this study is to evaluate the feasibility of using a Convolutional Long Short-Term Memory (ConvLSTM) recurrent neural network to model the dynamics of wildland fire propagation. The machine learning model is trained on simulated wildfire data generated by a m…
In this work, we present a machine learning approach for reducing the error when numerically solving time-dependent partial differential equations (PDE). We use a fully convolutional LSTM network to exploit the spatiotemporal dynamics of PDEs. The neural network serves to enhance finite-difference and finite-volume methods (FDM/FVM) that are commonly used to solve PDEs, allowing us to maintain guarantees on the order of convergence of our method. We train the network on simulation data, and show that our network can reduce error by a factor of 2 to 3 compared to the baseline algorithms. We dem…
Massachusetts Institute of Technology（麻省理工学院）；Stanford University（斯坦福大学）
Recent advances in machine learning have made significant contributions to drug discovery. Deep neural networks in particular have been demonstrated to provide significant boosts in predictive power when inferring the properties and activities of small-molecule compounds. However, the applicability of these techniques has been limited by the requirement for large amounts of training data. In this work, we demonstrate how one-shot learning can be used to significantly lower the amounts of data required to make meaningful predictions in drug discovery applications. We introduce a new architectur…
The University of Arizona（亚利桑那大学）；Massachusetts Institute of Technology（麻省理工学院）
This study presents a novel unsupervised convolutional Neural Network (NN) architecture with nonlocal interactions for solving Partial Differential Equations (PDEs). The nonlocal Peridynamic Differential Operator (PDDO) is employed as a convolutional filter for evaluating derivatives the field variable. The NN captures the time-dynamics in smaller latent space through encoder-decoder layers with a Convolutional Long-short Term Memory (ConvLSTM) layer between them. The ConvLSTM architecture is modified by employing a novel activation function to improve the predictive capability of the learning…
Hong Kong University of Science and Technology（香港科技大学）
Tactile sensing is essential to the human perception system, so as to robot. In this paper, we develop a novel optical-based tactile sensor "FingerVision" with effective signal processing algorithms. This sensor is composed of soft skin with embedded marker array bonded to rigid frame, and a web camera with a fisheye lens. While being excited with contact force, the camera tracks the movements of markers and deformation field is obtained. Compared to existing tactile sensors, our sensor features compact footprint, high resolution, and ease of fabrication. Besides, utilizing the deformation fie…
University of Louisiana at Lafayette（路易斯安那大学拉斐特分校）
The problem of video frame prediction has received much interest due to its relevance to many computer vision applications such as autonomous vehicles or robotics. Supervised methods for video frame prediction rely on labeled data, which may not always be available. In this paper, we provide a novel unsupervised deep-learning method called Inception-based LSTM for video frame prediction. The general idea of inception networks is to implement wider networks instead of deeper networks. This network design was shown to improve the performance of image classification. The proposed method is evalua…
IBM Research Zurich（IBM苏黎世研究院）；ETH Zurich（苏黎世联邦理工学院）；University of Zurich（苏黎世大学）；RWTH Aachen University（亚琛工业大学）；Heidelberg University（海德堡大学）
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure in the form of a SMILES sequence, gene expression profiles of tumors and prior knowledge on intracellular interactions from protein-protein interaction networks. We demonstrate that our multiscale convolutional attention-based (MCA) encoder significantly outperforms a baseline mod…
Case Western Reserve University（凯斯西储大学）；IBM Almaden Research Center（IBM阿尔马登研究中心）
We explore a solution for learning disease signatures from weakly, yet easily obtainable, annotated volumetric medical imaging data by analyzing 3D volumes as a sequence of 2D images. We demonstrate the performance of our solution in the detection of emphysema in lung cancer screening low-dose CT images. Our approach utilizes convolutional long short-term memory (LSTM) to "scan" sequentially through an imaging volume for the presence of disease in a portion of scanned region. This framework allowed effective learning given only volumetric images and binary disease labels, thus enabling trainin…
University of Edinburgh（爱丁堡大学）；Microsoft Research（微软研究院）；UC Irvine（加州大学尔湾分校）；University of Washington（华盛顿大学）；University of Alberta（阿尔伯塔大学）
We consider whether deep convolutional networks (CNNs) can represent decision functions with similar accuracy as recurrent networks such as LSTMs. First, we show that a deep CNN with an architecture inspired by the models recently introduced in image recognition can yield better accuracy than previous convolutional and LSTM networks on the standard 309h Switchboard automatic speech recognition task. Then we show that even more accurate CNNs can be trained under the guidance of LSTMs using a variant of model compression, which we call model blending because the teacher and student models are si…
The Long Short-Term Memory (LSTM) layer is an important advancement in the field of neural networks and machine learning, allowing for effective training and impressive inference performance. LSTM-based neural networks have been successfully employed in various applications such as speech processing and language translation. The LSTM layer can be simplified by removing certain components, potentially speeding up training and runtime with limited change in performance. In particular, the recently introduced variants, called SLIM LSTMs, have shown success in initial experiments to support this v…
The prevalent approaches of Chinese word segmentation task almost rely on the Bi-LSTM neural network. However, the methods based the Bi-LSTM have some inherent drawbacks: hard to parallel computing, little efficient in applying the Dropout method to inhibit the Overfitting and little efficient in capturing the character information at the more distant site of a long sentence for the word segmentation task. In this work, we propose a sequence-to-sequence transformer model for Chinese word segmentation, which is premised a type of convolutional neural network named temporal convolutional network…
Risk Analysis in Customer Relationship Management via Quantile Region Convolutional Neural Network-Long Short-Term Memory and Cross-Attention Mechanism
Longyan University（龙岩学院）；National Central University（中央大学）；University of Portsmouth（朴茨茅斯大学）；Institute of Semiconductors, Chinese Academy of Sciences（中国科学院半导体研究所）；Northeastern University（东北大学）
Predicting Drug Solubility Using Different Machine Learning Methods -- Linear Regression Model with Extracted Chemical Features vs Graph Convolutional Neural Network
Harvard University（哈佛大学）；University of California, Berkeley（加州大学伯克利分校）；Carlmont High School（卡尔蒙特高中）；Lawrence Berkeley National Laboratory（劳伦斯伯克利国家实验室）
The University of Texas at Dallas（德克萨斯大学达拉斯分校）；Verisk Analytics, Inc.（韦里斯科分析公司）；Duke University（杜克大学）
Predicting and discovering drug-drug interactions (DDIs) is an important problem and has been studied extensively both from medical and machine learning point of view. Almost all of the machine learning approaches have focused on text data or textual representation of the structural data of drugs. We present the first work that uses drug structure images as the input and utilizes a Siamese convolutional network architecture to predict DDIs.
University of Amsterdam（阿姆斯特丹大学）；University of Edinburgh（爱丁堡大学）
Semantic role labeling (SRL) is the task of identifying the predicate-argument structure of a sentence. It is typically regarded as an important step in the standard NLP pipeline. As the semantic representations are closely related to syntactic ones, we exploit syntactic information in our model. We propose a version of graph convolutional networks (GCNs), a recent class of neural networks operating on graphs, suited to model syntactic dependency graphs. GCNs over syntactic dependency trees are used as sentence encoders, producing latent feature representations of words in a sentence. We obser…
ADVA Optical Networking SE（ADVA光网络公司）；Christian-Albrechts-Universität zu Kiel（基尔大学）
A hybrid prognostic model based on convolutional neural networks (CNN) and long short-term memory (LSTM) is proposed to predict the laser remaining useful life (RUL). The experimental results show that it outperforms the conventional methods.
