Deep-DRM: a computational method for identifying disease-related metabolites based on graph deep learning approaches

2020 ◽  
Author(s):  
Tianyi Zhao ◽  
Yang Hu ◽  
Liang Cheng
Keyword(s):  
Deep Learning ◽  
Chemical Structure ◽  
Computational Method ◽  
Learning Approaches ◽  
Convolutional Network ◽  
Functional Changes ◽  
Chemical Structures ◽  
Association Pattern ◽  
Semantic Associations ◽  
Components Analysis

Abstract Motivation: The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with our knowledge about genes, RNAs, and proteins, we still know few about diseases-related metabolites. All the few existed methods for identifying diseases-related metabolites ignore the chemical structure of metabolites, fail to recognize the association pattern between metabolites and diseases, and fail to apply to isolated diseases and metabolites. Results: In this study, we present a graph deep learning based method, named Deep-DRM, for identifying diseases-related metabolites. First, chemical structures of metabolites were used to calculate similarities of metabolites. The similarities of diseases were obtained based on their functional gene network and semantic associations. Therefore, both metabolites and diseases network could be built. Next, Graph Convolutional Network (GCN) was applied to encode the features of metabolites and diseases, respectively. Then, the dimension of these features was reduced by Principal components analysis (PCA) with retainment 99% information. Finally, Deep neural network was built for identifying true metabolite-disease pairs (MDPs) based on these features. The 10-cross validations on three testing setups showed outstanding AUC (0.952) and AUPR (0.939) of Deep-DRM compared with previous methods and similar approaches. Ten of top 15 predicted associations between diseases and metabolites got support by other studies, which suggests that Deep-DRM is an efficient method to identify MDPs. Contact: [email protected]. Availability and implementation: https://github.com/zty2009/GPDNN-for-Identify-ing-Disease-related-Metabolites.

scholarly journals DECIMER 1.0: deep learning for chemical image recognition using transformers

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Kohulan Rajan ◽  
Achim Zielesny ◽  
Christoph Steinbeck
Keyword(s):  
Deep Learning ◽  
Image Recognition ◽  
Chemical Structure ◽  
Learning Approaches ◽  
Chemical Structures ◽  
Structure Recognition ◽  
Best Fitting ◽  
Preliminary Communication ◽  
Computational Intelligence Methods ◽  
Chemical Image

AbstractThe amount of data available on chemical structures and their properties has increased steadily over the past decades. In particular, articles published before the mid-1990 are available only in printed or scanned form. The extraction and storage of data from those articles in a publicly accessible database are desirable, but doing this manually is a slow and error-prone process. In order to extract chemical structure depictions and convert them into a computer-readable format, Optical Chemical Structure Recognition (OCSR) tools were developed where the best performing OCSR tools are mostly rule-based. The DECIMER (Deep lEarning for Chemical ImagE Recognition) project was launched to address the OCSR problem with the latest computational intelligence methods to provide an automated open-source software solution. Various current deep learning approaches were explored to seek a best-fitting solution to the problem. In a preliminary communication, we outlined the prospect of being able to predict SMILES encodings of chemical structure depictions with about 90% accuracy using a dataset of 50–100 million molecules. In this article, the new DECIMER model is presented, a transformer-based network, which can predict SMILES with above 96% accuracy from depictions of chemical structures without stereochemical information and above 89% accuracy for depictions with stereochemical information.

scholarly journals DECIMER 1.0: Deep Learning for Chemical Image Recognition using Transformers

2021 ◽  
Author(s):  
Kohulan Rajan ◽  
Achim Zielesny ◽  
Christoph Steinbeck
Keyword(s):  
Deep Learning ◽  
Image Recognition ◽  
Chemical Structure ◽  
Learning Approaches ◽  
Chemical Structures ◽  
Structure Recognition ◽  
Best Fitting ◽  
Preliminary Communication ◽  
Computational Intelligence Methods ◽  
Chemical Image

<p>The amount of data available on chemical structures and their properties has increased exponentially over the past decades. In particular, articles published before the mid-1990 are available only in printed or scanned form. The extraction and storage of data from those articles in a publicly accessible database are desirable, but doing this manually is a slow and error-prone process. In order to extract chemical structure depictions and convert them into a computer-readable format, optical chemical structure recognition (OCSR) tools were developed where the best performing OCSR tools are mostly rule-based.</p><p> </p><p>The DECIMER (Deep lEarning for Chemical ImagE Recognition) project was launched to address the OCSR problem with the latest computational intelligence methods to provide an automated open-source software solution. Various current deep learning approaches were explored to seek a best-fitting solution to the problem. In a preliminary communication, we outlined the prospect of being able to predict SMILES encodings of chemical structure depictions with about 90% accuracy using a dataset of 50-100 million molecules. In this article, the new DECIMER model is presented, a transformer-based network, which can predict SMILES with above 96% accuracy from depictions of chemical structures without stereochemical information and above 89% accuracy for depictions with stereochemical information.</p><p><br></p>

scholarly journals DECIMER 1.0: Deep Learning for Chemical Image Recognition using Transformers

2021 ◽  
Author(s):  
Kohulan Rajan ◽  
Achim Zielesny ◽  
Christoph Steinbeck
Keyword(s):  
Deep Learning ◽  
Image Recognition ◽  
Chemical Structure ◽  
Learning Approaches ◽  
Chemical Structures ◽  
Structure Recognition ◽  
Best Fitting ◽  
Preliminary Communication ◽  
Computational Intelligence Methods ◽  
Chemical Image

<p>The amount of data available on chemical structures and their properties has increased exponentially over the past decades. In particular, articles published before the mid-1990 are available only in printed or scanned form. The extraction and storage of data from those articles in a publicly accessible database are desirable, but doing this manually is a slow and error-prone process. In order to extract chemical structure depictions and convert them into a computer-readable format, optical chemical structure recognition (OCSR) tools were developed where the best performing OCSR tools are mostly rule-based.</p><p> </p><p>The DECIMER (Deep lEarning for Chemical ImagE Recognition) project was launched to address the OCSR problem with the latest computational intelligence methods to provide an automated open-source software solution. Various current deep learning approaches were explored to seek a best-fitting solution to the problem. In a preliminary communication, we outlined the prospect of being able to predict SMILES encodings of chemical structure depictions with about 90% accuracy using a dataset of 50-100 million molecules. In this article, the new DECIMER model is presented, a transformer-based network, which can predict SMILES with above 96% accuracy from depictions of chemical structures without stereochemical information and above 89% accuracy for depictions with stereochemical information.</p><p><br></p>

scholarly journals Time Series Classification with InceptionFCN

Sensors ◽  
2021 ◽  
Vol 22 (1) ◽  
pp. 157
Author(s):  
Saidrasul Usmankhujaev ◽  
Bunyodbek Ibrokhimov ◽  
Shokhrukh Baydadaev ◽  
Jangwoo Kwon
Keyword(s):  
Time Series ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Learning Approaches ◽  
Time Series Classification ◽  
Convolutional Network ◽  
Training Time ◽  
Learning Techniques ◽  
Significant Research ◽  
Previous State

Deep neural networks (DNN) have proven to be efficient in computer vision and data classification with an increasing number of successful applications. Time series classification (TSC) has been one of the challenging problems in data mining in the last decade, and significant research has been proposed with various solutions, including algorithm-based approaches as well as machine and deep learning approaches. This paper focuses on combining the two well-known deep learning techniques, namely the Inception module and the Fully Convolutional Network. The proposed method proved to be more efficient than the previous state-of-the-art InceptionTime method. We tested our model on the univariate TSC benchmark (the UCR/UEA archive), which includes 85 time-series datasets, and proved that our network outperforms the InceptionTime in terms of the training time and overall accuracy on the UCR archive.

scholarly journals On Training Targets for Deep Learning Approaches to Clean Speech Magnitude Spectrum Estimation

2020 ◽  
Author(s):  
Aaron Nicolson ◽  
Kuldip K. Paliwal
Keyword(s):  
Deep Learning ◽  
Minimum Mean Square Error ◽  
Auditory Scene Analysis ◽  
Spectrum Estimation ◽  
Learning Approaches ◽  
Computational Auditory Scene Analysis ◽  
Convolutional Network ◽  
Magnitude Spectrum ◽  
Front End ◽  
Asr System

The estimation of the clean speech short-time magnitude spectrum (MS) is key for speech enhancement and separation. Moreover, an automatic speech recognition (ASR) system that employs a front-end relies on clean speech MS estimation to remain robust. Training targets for deep learning approaches to clean speech MS estimation fall into three main categories: computational auditory scene analysis (CASA), MS, and minimum mean-square error (MMSE) training targets. In this study, we aim to determine which training target produces enhanced/separated speech at the highest quality and intelligibility, and which is most suitable as a front-end for robust ASR. The training targets were evaluated using a temporal convolutional network (TCN) on the DEMAND Voice Bank and Deep Xi datasets---which include real-world non-stationary and coloured noise sources at multiple SNR levels. Seven objective measures were used, including the word error rate (WER) of the Deep Speech ASR system. We find that MMSE training targets produce the highest objective quality scores. We also find that CASA training targets, in particular the ideal ratio mask (IRM), produce the highest intelligibility scores and perform best as a front-end for robust ASR.

scholarly journals On Training Targets for Deep Learning Approaches to Clean Speech Magnitude Spectrum Estimation

2020 ◽  
Author(s):  
Aaron Nicolson ◽  
Kuldip K. Paliwal
Keyword(s):  
Deep Learning ◽  
Minimum Mean Square Error ◽  
Auditory Scene Analysis ◽  
Spectrum Estimation ◽  
Learning Approaches ◽  
Computational Auditory Scene Analysis ◽  
Convolutional Network ◽  
Magnitude Spectrum ◽  
Front End ◽  
Asr System

The estimation of the clean speech short-time magnitude spectrum (MS) is key for speech enhancement and separation. Moreover, an automatic speech recognition (ASR) system that employs a front-end relies on clean speech MS estimation to remain robust. Training targets for deep learning approaches to clean speech MS estimation fall into three main categories: computational auditory scene analysis (CASA), MS, and minimum mean-square error (MMSE) training targets. In this study, we aim to determine which training target produces enhanced/separated speech at the highest quality and intelligibility, and which is most suitable as a front-end for robust ASR. The training targets were evaluated using a temporal convolutional network (TCN) on the DEMAND Voice Bank and Deep Xi datasets---which include real-world non-stationary and coloured noise sources at multiple SNR levels. Seven objective measures were used, including the word error rate (WER) of the Deep Speech ASR system. We find that MMSE training targets produce the highest objective quality scores. We also find that CASA training targets, in particular the ideal ratio mask (IRM), produce the highest intelligibility scores and perform best as a front-end for robust ASR.

scholarly journals Towards Inferring Nanopore Sequencing Ionic Currents from Nucleotide Chemical Structures

2020 ◽  
Author(s):  
Hongxu Ding ◽  
Ioannis Anastopoulos ◽  
Andrew D. Bailey ◽  
Joshua Stuart ◽  
Benedict Paten
Keyword(s):  
Deep Learning ◽  
De Novo ◽  
Ionic Currents ◽  
Chemical Information ◽  
Nanopore Sequencing ◽  
Convolutional Network ◽  
Methyl Group ◽  
Learning Framework ◽  
Chemical Structures

ABSTRACTThe characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework can generalize the chemical information of the 5-methyl group from thymine to cytosine by correctly predicting 5-methylcytosine-containing DNA 6mers, thus shedding light on the de novo detection of nucleotide modifications.

scholarly journals DeepLPC-MHANet: Multi-Head Self-Attention for Augmented Kalman Filter-based Speech Enhancement

2021 ◽  
Author(s):  
Sujan Kumar Roy ◽  
Aaron Nicolson ◽  
Kuldip K. Paliwal
Keyword(s):  
Deep Learning ◽  
Kalman Filter ◽  
Speech Enhancement ◽  
Linear Prediction ◽  
Power Spectra ◽  
Previous Method ◽  
Learning Approaches ◽  
Convolutional Network ◽  
Listening Tests ◽  
Prediction Coefficient

Current augmented Kalman filter (AKF)-based speech enhancement algorithms utilise a temporal convolutional network (TCN) to estimate the clean speech and noise linear prediction coefficient (LPC). However, the multi-head attention network (MHANet) has demonstrated the ability to more efficiently model the long-term dependencies of noisy speech than TCNs. Motivated by this, we investigate the MHANet for LPC estimation. We aim to produce clean speech and noise LPC parameters with the least bias to date. With this, we also aim to produce higher quality and more intelligible enhanced speech than any current KF or AKF-based SEA. Here, we investigate MHANet within the DeepLPC framework. DeepLPC is a deep learning framework for jointly estimating the clean speech and noise LPC power spectra. DeepLPC is selected as it exhibits significantly less bias than other frameworks, by avoiding the use of whitening filters and post-processing. DeepLPC-MHANet is evaluated on the NOIZEUS corpus using subjective AB listening tests, as well as seven different objective measures (CSIG, CBAK, COVL, PESQ, STOI, SegSNR, and SI-SDR). DeepLPC-MHANet is compared to five existing deep learning-based methods. Compared to other deep learning approaches, DeepLPC-MHANet produced clean speech LPC estimates with the least amount of bias. DeepLPC-MHANet-AKF also produced higher objective scores than any of the competing methods (with an improvement of 0.17 for CSIG, 0.15 for CBAK, 0.19 for COVL, 0.24 for PESQ, 3.70\% for STOI, 1.03 dB for SegSNR, and 1.04 dB for SI-SDR over the next best method). The enhanced speech produced by DeepLPC-MHANet-AKF was also the most preferred amongst ten listeners. By producing LPC estimates with the least amount of bias to date, DeepLPC-MHANet enables the AKF to produce enhanced speech at a higher quality and intelligibility than any previous method.

scholarly journals DECIMER Segmentation - Automated Extraction of Chemical Structure Depictions from Scientific Literature

2021 ◽  
Author(s):  
Kohulan Rajan ◽  
Henning Otto brinkhaus ◽  
Maria Sorokina ◽  
Achim Zielesny ◽  
Christoph Steinbeck
Keyword(s):  
Deep Learning ◽  
Web Application ◽  
Chemical Structure ◽  
Scientific Literature ◽  
Data Extraction ◽  
Scientific Publications ◽  
Automated Recognition ◽  
Chemical Structures ◽  
Machine Readable ◽  
Chemical Image

<p>Chemistry looks back at many decades of publications on chemical compounds, their structures and properties, in scientific articles. Liberating this knowledge (semi-)automatically and making it available to the world in open-access databases is a current challenge. Apart from mining textual information, Optical Chemical Structure Recognition (OCSR), the translation of an image of a chemical structure into a machine-readable representation, is part of this workflow. As the OCSR process requires an image containing a chemical structure, there is a need for a publicly available tool that automatically recognizes and segments chemical structure depictions from scientific publications. This is especially important for older documents which are only available as scanned pages. Here, we present DECIMER (Deep lEarning for Chemical IMagE Recognition) Segmentation, the first open-source, deep learning-based tool for automated recognition and segmentation of chemical structures from the scientific literature.</p><br><p>The workflow is divided into two main stages. During the detection step, a deep learning model recognizes chemical structure depictions and creates masks which define their positions on the input page. Subsequently, potentially incomplete masks are expanded in a post-processing workflow. The performance of DECIMER Segmentation has been manually evaluated on three sets of publications from different publishers. The approach operates on bitmap images of journal pages to be applicable also to older articles before the introduction of vector images in PDFs. </p><br><p>By making the source code and the trained model publicly available, we hope to contribute to the development of comprehensive chemical data extraction workflows. In order to facilitate access to DECIMER Segmentation, we also developed a web application. The web application, available at <a href="https://decimer.ai">https://decimer.ai</a>, lets the user upload a pdf file and retrieve the segmented structure depictions.</p><div><br></div>

scholarly journals Motif-Matching Based Subgraph-Level Attentional Convolutional Network for Graph Classification

2020 ◽  
Vol 34 (04) ◽  
pp. 5387-5394
Author(s):  
Hao Peng ◽  
Jianxin Li ◽  
Qiran Gong ◽  
Yuanxin Ning ◽  
Senzhang Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Social Network ◽  
Spatial Information ◽  
Structural Information ◽  
Feature Learning ◽  
Drug Analysis ◽  
Classification Performance ◽  
Learning Approaches ◽  
Graph Classification ◽  
Convolutional Network

Graph classification is critically important to many real-world applications that are associated with graph data such as chemical drug analysis and social network mining. Traditional methods usually require feature engineering to extract the graph features that can help discriminate the graphs of different classes. Although recently deep learning based graph embedding approaches are proposed to automatically learn graph features, they mostly use a few vertex arrangements extracted from the graph for feature learning, which may lose some structural information. In this work, we present a novel motif-based attentional graph convolution neural network for graph classification, which can learn more discriminative and richer graph features. Specifically, a motif-matching guided subgraph normalization method is developed to better preserve the spatial information. A novel subgraph-level self-attention network is also proposed to capture the different impacts or weights of different subgraphs. Experimental results on both bioinformatics and social network datasets show that the proposed models significantly improve graph classification performance over both traditional graph kernel methods and recent deep learning approaches.

Sign in / Sign up

Export Citation Format

Share Document