scholarly journals Biological sequence modeling with convolutional kernel networks

2019 ◽  
Vol 35 (18) ◽  
pp. 3294-3302 ◽  
Author(s):  
Dexiong Chen ◽  
Laurent Jacob ◽  
Julien Mairal
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Hybrid Approach ◽  
Training Data ◽  
Supplementary Information ◽  
Small Scale ◽  
Biological Sequences ◽  
Homology Detection ◽  
Binding Prediction ◽  
Sequence Modeling

Abstract Motivation The growing number of annotated biological sequences available makes it possible to learn genotype-phenotype relationships from data with increasingly high accuracy. When large quantities of labeled samples are available for training a model, convolutional neural networks can be used to predict the phenotype of unannotated sequences with good accuracy. Unfortunately, their performance with medium- or small-scale datasets is mitigated, which requires inventing new data-efficient approaches. Results We introduce a hybrid approach between convolutional neural networks and kernel methods to model biological sequences. Our method enjoys the ability of convolutional neural networks to learn data representations that are adapted to a specific task, while the kernel point of view yields algorithms that perform significantly better when the amount of training data is small. We illustrate these advantages for transcription factor binding prediction and protein homology detection, and we demonstrate that our model is also simple to interpret, which is crucial for discovering predictive motifs in sequences. Availability and implementation Source code is freely available at https://gitlab.inria.fr/dchen/CKN-seq. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Biological Sequence Modeling with Convolutional Kernel Networks

2017 ◽  
Author(s):  
Dexiong Chen ◽  
Laurent Jacob ◽  
Julien Mairal
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Hybrid Approach ◽  
Training Data ◽  
Small Scale ◽  
Biological Sequences ◽  
Biological Sequence ◽  
Homology Detection ◽  
Binding Prediction ◽  
Sequence Modeling

AbstractThe growing number of annotated biological sequences available makes it possible to learn genotype-phenotype relationships from data with increasingly high accuracy. When large quantities of labeled samples are available for training a model, convolutional neural networks can be used to predict the phenotype of unannotated sequences with good accuracy. Unfortunately, their performance with medium- or small-scale datasets is mitigated, which requires inventing new data-efficient approaches. In this paper, we introduce a hybrid approach between convolutional neural networks and kernel methods to model biological sequences. Our method enjoys the ability of convolutional neural networks to learn data representations that are adapted to a specific task, while the kernel point of view yields algorithms that perform significantly better when the amount of training data is small. We illustrate these advantages for transcription factor binding prediction and protein homology detection, and we demonstrate that our model is also simple to interpret, which is crucial for discovering predictive motifs in sequences. The source code is freely available at https://gitlab.inria.fr/dchen/CKN-seq.

scholarly journals CNN-PepPred: An open-source tool to create convolutional NN models for the discovery of patterns in peptide sets. Application to peptide-MHC class II binding prediction

2021 ◽  
Author(s):  
Valentin Junet ◽  
Xavier Daura
Keyword(s):  
Neural Networks ◽  
Open Source ◽  
Mhc Class Ii ◽  
Convolutional Neural Networks ◽  
Operating Systems ◽  
Class Ii ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Binding Prediction ◽  
Open Source Tool

Abstract Summary The ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to discover such patterns, along with its application to peptide-HLA class II binding prediction. The tool can be used locally on different operating systems, with CPUs or GPUs, to train, evaluate, apply and visualize models. Availability and Implementation CNN-PepPred is freely available as a Python tool with a detailed User’s Guide at: https://github.com/ComputBiol-IBB/CNN-PepPred Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ACME: pan-specific peptide–MHC class I binding prediction through attention-based deep neural networks

2019 ◽  
Vol 35 (23) ◽  
pp. 4946-4954 ◽  
Author(s):  
Yan Hu ◽  
Ziqiang Wang ◽  
Hailin Hu ◽  
Fangping Wan ◽  
Lin Chen ◽  
...  
Keyword(s):  
Neural Networks ◽  
Mhc Class I ◽  
Pearson Correlation ◽  
Vital Role ◽  
Training Data ◽  
Class I ◽  
Supplementary Information ◽  
Binding Affinities ◽  
Binding Prediction ◽  
Therapeutic Vaccines

Abstract Motivation Prediction of peptide binding to the major histocompatibility complex (MHC) plays a vital role in the development of therapeutic vaccines for the treatment of cancer. Algorithms with improved correlations between predicted and actual binding affinities are needed to increase precision and reduce the number of false positive predictions. Results We present ACME (Attention-based Convolutional neural networks for MHC Epitope binding prediction), a new pan-specific algorithm to accurately predict the binding affinities between peptides and MHC class I molecules, even for those new alleles that are not seen in the training data. Extensive tests have demonstrated that ACME can significantly outperform other state-of-the-art prediction methods with an increase of the Pearson correlation coefficient between predicted and measured binding affinities by up to 23 percentage points. In addition, its ability to identify strong-binding peptides has been experimentally validated. Moreover, by integrating the convolutional neural network with attention mechanism, ACME is able to extract interpretable patterns that can provide useful and detailed insights into the binding preferences between peptides and their MHC partners. All these results have demonstrated that ACME can provide a powerful and practically useful tool for the studies of peptide–MHC class I interactions. Availability and implementation ACME is available as an open source software at https://github.com/HYsxe/ACME. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SATELLITE-DERIVED BATHYMETRY USING CONVOLUTIONAL NEURAL NETWORKS AND MULTISPECTRAL SENTINEL-2 IMAGES

2021 ◽  
Vol XLIII-B3-2021 ◽  
pp. 201-207
Author(s):  
Y. A. Lumban-Gaol ◽  
K. A. Ohori ◽  
R. Y. Peters
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Window Size ◽  
Short Wave ◽  
Training Data ◽  
Coefficient Of Determination ◽  
Linear Transform ◽  
Band Combinations ◽  
Sentinel 2

Abstract. Satellite-Derived Bathymetry (SDB) has been used in many applications related to coastal management. SDB can efficiently fill data gaps obtained from traditional measurements with echo sounding. However, it still requires numerous training data, which is not available in many areas. Furthermore, the accuracy problem still arises considering the linear model could not address the non-relationship between reflectance and depth due to bottom variations and noise. Convolutional Neural Networks (CNN) offers the ability to capture the connection between neighbouring pixels and the non-linear relationship. These CNN characteristics make it compelling to be used for shallow water depth extraction. We investigate the accuracy of different architectures using different window sizes and band combinations. We use Sentinel-2 Level 2A images to provide reflectance values, and Lidar and Multi Beam Echo Sounder (MBES) datasets are used as depth references to train and test the model. A set of Sentinel-2 and in-situ depth subimage pairs are extracted to perform CNN training. The model is compared to the linear transform and applied to two other study areas. Resulting accuracy ranges from 1.3 m to 1.94 m, and the coefficient of determination reaches 0.94. The SDB model generated using a window size of 9x9 indicates compatibility with the reference depths, especially at areas deeper than 15 m. The addition of both short wave infrared bands to the four visible bands in training improves the overall accuracy of SDB. The implementation of the pre-trained model to other study areas provides similar results depending on the water conditions.

Uncertainty quantification in fault detection using convolutional neural networks

Geophysics ◽  
2021 ◽  
pp. 1-45
Author(s):  
Runhai Feng ◽  
Dario Grana ◽  
Niels Balling
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Reservoir Characterization ◽  
Epistemic Uncertainty ◽  
Confidence Regions ◽  
Training Data ◽  
Model Parameters ◽  
Sigmoid Function ◽  
Learning Tools

Segmentation of faults based on seismic images is an important step in reservoir characterization. With the recent developments of deep-learning methods and the availability of massive computing power, automatic interpretation of seismic faults has become possible. The likelihood of occurrence for a fault can be quantified using a sigmoid function. Our goal is to quantify the fault model uncertainty that is generally not captured by deep-learning tools. We propose to use the dropout approach, a regularization technique to prevent overfitting and co-adaptation in hidden units, to approximate the Bayesian inference and estimate the principled uncertainty over functions. Particularly, the variance of the learned model has been decomposed into aleatoric and epistemic parts. The proposed method is applied to a real dataset from the Netherlands F3 block with two different dropout ratios in convolutional neural networks. The aleatoric uncertainty is irreducible since it relates to the stochastic dependency within the input observations. As the number of Monte-Carlo realizations increases, the epistemic uncertainty asymptotically converges and the model standard deviation decreases, because the variability of model parameters is better simulated or explained with a larger sample size. This analysis can quantify the confidence to use fault predictions with less uncertainty. Additionally, the analysis suggests where more training data are needed to reduce the uncertainty in low confidence regions.

scholarly journals Land Cover Classification from fused DSM and UAV Images Using Convolutional Neural Networks

2019 ◽  
Vol 11 (12) ◽  
pp. 1461 ◽  
Author(s):  
Husam A. H. Al-Najjar ◽  
Bahareh Kalantar ◽  
Biswajeet Pradhan ◽  
Vahideh Saeidi ◽  
Alfian Abdul Halin ◽  
...  
Keyword(s):  
Neural Networks ◽  
Land Cover ◽  
Convolutional Neural Networks ◽  
Land Cover Classification ◽  
Training Data ◽  
Surface Model ◽  
Kappa Index ◽  
Diverse Range ◽  
Average Accuracy ◽  
Uav Images

In recent years, remote sensing researchers have investigated the use of different modalities (or combinations of modalities) for classification tasks. Such modalities can be extracted via a diverse range of sensors and images. Currently, there are no (or only a few) studies that have been done to increase the land cover classification accuracy via unmanned aerial vehicle (UAV)–digital surface model (DSM) fused datasets. Therefore, this study looks at improving the accuracy of these datasets by exploiting convolutional neural networks (CNNs). In this work, we focus on the fusion of DSM and UAV images for land use/land cover mapping via classification into seven classes: bare land, buildings, dense vegetation/trees, grassland, paved roads, shadows, and water bodies. Specifically, we investigated the effectiveness of the two datasets with the aim of inspecting whether the fused DSM yields remarkable outcomes for land cover classification. The datasets were: (i) only orthomosaic image data (Red, Green and Blue channel data), and (ii) a fusion of the orthomosaic image and DSM data, where the final classification was performed using a CNN. CNN, as a classification method, is promising due to hierarchical learning structure, regulating and weight sharing with respect to training data, generalization, optimization and parameters reduction, automatic feature extraction and robust discrimination ability with high performance. The experimental results show that a CNN trained on the fused dataset obtains better results with Kappa index of ~0.98, an average accuracy of 0.97 and final overall accuracy of 0.98. Comparing accuracies between the CNN with DSM result and the CNN without DSM result for the overall accuracy, average accuracy and Kappa index revealed an improvement of 1.2%, 1.8% and 1.5%, respectively. Accordingly, adding the heights of features such as buildings and trees improved the differentiation between vegetation specifically where plants were dense.

scholarly journals Beach State Recognition Using Argus Imagery and Convolutional Neural Networks

2020 ◽  
Vol 12 (23) ◽  
pp. 3953
Author(s):  
Ashley N. Ellenson ◽  
Joshua A. Simmons ◽  
Greg W. Wilson ◽  
Tyler J. Hesser ◽  
Kristen D. Splinter
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
New South ◽  
Equilibrium States ◽  
The Self ◽  
Training Data ◽  
Local Data ◽  
State Recognition ◽  
South Wales ◽  
Key Driver

Nearshore morphology is a key driver in wave breaking and the resulting nearshore circulation, recreational safety, and nutrient dispersion. Morphology persists within the nearshore in specific shapes that can be classified into equilibrium states. Equilibrium states convey qualitative information about bathymetry and relevant physical processes. While nearshore bathymetry is a challenge to collect, much information about the underlying bathymetry can be gained from remote sensing of the surfzone. This study presents a new method to automatically classify beach state from Argus daytimexposure imagery using a machine learning technique called convolutional neural networks (CNNs). The CNN processed imagery from two locations: Narrabeen, New South Wales, Australia and Duck, North Carolina, USA. Three different CNN models are examined, one trained at Narrabeen, one at Duck, and one trained at both locations. Each model was tested at the location where it was trained in a self-test, and the single-beach models were tested at the location where it was not trained in a transfer-test. For the self-tests, skill (as measured by the F-score) was comparable to expert agreement (CNN F-values at Duck = 0.80 and Narrabeen = 0.59). For the transfer-tests, the CNN model skill was reduced by 24–48%, suggesting the algorithm requires additional local data to improve transferability performance. Transferability tests showed that comparable F-scores (within 10%) to the self-trained cases can be achieved at both locations when at least 25% of the training data is from each site. This suggests that if applied to additional locations, a CNN model trained at one location may be skillful at new sites with limited new imagery data needed. Finally, a CNN visualization technique (Guided-Grad-CAM) confirmed that the CNN determined classifications using image regions (e.g., incised rip channels, terraces) that were consistent with beach state labelling rules.

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