DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network

AbstractMotivationIt is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence, they are expected to produce divergent outputs.ResultsTo overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially-oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidences. Moreover, DeepSSV incorporates the mapping information of both reference-allele-supporting and variant-allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts, and alleviates the need of post-call filters that heavily depend on prior knowledge. We fitted the model on ground truth somatic mutations, and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1score.Availability and Implementationhttps://github.com/jingmeng-bioinformatics/[email protected] informationSupplementary data are available at online.

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DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network

Briefings in Bioinformatics ◽

10.1093/bib/bbaa272 ◽

2020 ◽

Author(s):

Jing Meng ◽

Brandon Victor ◽

Zhen He ◽

Hongde Liu ◽

Taijiao Jiang

Keyword(s):

Neural Network ◽

Convolutional Neural Network ◽

Somatic Mutations ◽

Ground Truth ◽

Variant Allele ◽

Learning Approaches ◽

Limited Information ◽

Sequencing Data ◽

Reference Allele ◽

Feature Representations

Abstract It is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, they take into consideration only limited information about the reference and potential variant allele in both tumor and normal samples at a candidate somatic site. Also, they differ in how biological and technological noises are addressed. Hence, they are expected to produce divergent outputs. To overcome the drawbacks of existing somatic callers, we develop a deep learning-based tool called DeepSSV, which employs a convolutional neural network (CNN) model to learn increasingly abstract feature representations from the raw data in higher feature layers. DeepSSV creates a spatially oriented representation of read alignments around the candidate somatic sites adapted for the convolutional architecture, which enables it to expand to effectively gather scattered evidence. Moreover, DeepSSV incorporates the mapping information of both reference allele-supporting and variant allele-supporting reads in the tumor and normal samples at a genomic site that are readily available in the pileup format file. Together, the CNN model can process the whole alignment information. Such representational richness allows the model to capture the dependencies in the sequence and identify context-based sequencing artifacts. We fitted the model on ground truth somatic mutations and did benchmarking experiments on simulated and real tumors. The benchmarking results demonstrate that DeepSSV outperforms its state-of-the-art competitors in overall F1 score.

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A simple convolutional neural network for prediction of enhancer–promoter interactions with DNA sequence data

Bioinformatics ◽

10.1093/bioinformatics/bty1050 ◽

2019 ◽

Vol 35 (17) ◽

pp. 2899-2906 ◽

Cited By ~ 11

Author(s):

Zhong Zhuang ◽

Xiaotong Shen ◽

Wei Pan

Keyword(s):

Neural Network ◽

Convolutional Neural Network ◽

Cell Line ◽

Dna Sequence ◽

Statistical Power ◽

Sequence Data ◽

Association Studies ◽

Supplementary Information ◽

Genome Wide Association Studies ◽

Learning Approaches

Abstract Motivation Enhancer–promoter interactions (EPIs) in the genome play an important role in transcriptional regulation. EPIs can be useful in boosting statistical power and enhancing mechanistic interpretation for disease- or trait-associated genetic variants in genome-wide association studies. Instead of expensive and time-consuming biological experiments, computational prediction of EPIs with DNA sequence and other genomic data is a fast and viable alternative. In particular, deep learning and other machine learning methods have been demonstrated with promising performance. Results First, using a published human cell line dataset, we demonstrate that a simple convolutional neural network (CNN) performs as well as, if no better than, a more complicated and state-of-the-art architecture, a hybrid of a CNN and a recurrent neural network. More importantly, in spite of the well-known cell line-specific EPIs (and corresponding gene expression), in contrast to the standard practice of training and predicting for each cell line separately, we propose two transfer learning approaches to training a model using all cell lines to various extents, leading to substantially improved predictive performance. Availability and implementation Computer code is available at https://github.com/zzUMN/Combine-CNN-Enhancer-and-Promoters. Supplementary information Supplementary data are available at Bioinformatics online.

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Carpal Bone Segmentation Using Fully Convolutional Neural Network

Current Medical Imaging Formerly Current Medical Imaging Reviews ◽

10.2174/1573405615666190724101600 ◽

2019 ◽

Vol 15 (10) ◽

pp. 983-989

Author(s):

Liang Kim Meng ◽

Azira Khalil ◽

Muhamad Hanif Ahmad Nizar ◽

Maryam Kamarun Nisham ◽

Belinda Pingguan-Murphy ◽

...

Keyword(s):

Neural Network ◽

Convolutional Neural Network ◽

Automatic Segmentation ◽

Ground Truth ◽

Bone Age ◽

Image Feature ◽

Qualitative Assessment ◽

Carpal Bone ◽

Radiographic Images ◽

Accurate Quantitative Analysis

Background: Bone Age Assessment (BAA) refers to a clinical procedure that aims to identify a discrepancy between biological and chronological age of an individual by assessing the bone age growth. Currently, there are two main methods of executing BAA which are known as Greulich-Pyle and Tanner-Whitehouse techniques. Both techniques involve a manual and qualitative assessment of hand and wrist radiographs, resulting in intra and inter-operator variability accuracy and time-consuming. An automatic segmentation can be applied to the radiographs, providing the physician with more accurate delineation of the carpal bone and accurate quantitative analysis. Methods: In this study, we proposed an image feature extraction technique based on image segmentation with the fully convolutional neural network with eight stride pixel (FCN-8). A total of 290 radiographic images including both female and the male subject of age ranging from 0 to 18 were manually segmented and trained using FCN-8. Results and Conclusion: The results exhibit a high training accuracy value of 99.68% and a loss rate of 0.008619 for 50 epochs of training. The experiments compared 58 images against the gold standard ground truth images. The accuracy of our fully automated segmentation technique is 0.78 ± 0.06, 1.56 ±0.30 mm and 98.02% in terms of Dice Coefficient, Hausdorff Distance, and overall qualitative carpal recognition accuracy, respectively.

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Geometric property-based convolutional neural network for indoor object detection

International Journal of Advanced Robotic Systems ◽

10.1177/1729881421993323 ◽

2021 ◽

Vol 18 (1) ◽

pp. 172988142199332

Author(s):

Xintao Ding ◽

Boquan Li ◽

Jinbao Wang

Keyword(s):

Neural Network ◽

Object Detection ◽

Convolutional Neural Network ◽

Geometric Property ◽

Ground Truth ◽

Geometric Constraints ◽

Depth Information ◽

Training Set ◽

Object Knowledge ◽

The Mean

Indoor object detection is a very demanding and important task for robot applications. Object knowledge, such as two-dimensional (2D) shape and depth information, may be helpful for detection. In this article, we focus on region-based convolutional neural network (CNN) detector and propose a geometric property-based Faster R-CNN method (GP-Faster) for indoor object detection. GP-Faster incorporates geometric property in Faster R-CNN to improve the detection performance. In detail, we first use mesh grids that are the intersections of direct and inverse proportion functions to generate appropriate anchors for indoor objects. After the anchors are regressed to the regions of interest produced by a region proposal network (RPN-RoIs), we then use 2D geometric constraints to refine the RPN-RoIs, in which the 2D constraint of every classification is a convex hull region enclosing the width and height coordinates of the ground-truth boxes on the training set. Comparison experiments are implemented on two indoor datasets SUN2012 and NYUv2. Since the depth information is available in NYUv2, we involve depth constraints in GP-Faster and propose 3D geometric property-based Faster R-CNN (DGP-Faster) on NYUv2. The experimental results show that both GP-Faster and DGP-Faster increase the performance of the mean average precision.

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Unraveling the deep learning gearbox in optical coherence tomography image segmentation towards explainable artificial intelligence

Communications Biology ◽

10.1038/s42003-021-01697-y ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Peter M. Maloca ◽

Philipp L. Müller ◽

Aaron Y. Lee ◽

Adnan Tufail ◽

Konstantinos Balaskas ◽

...

Keyword(s):

Neural Network ◽

Machine Learning ◽

Optical Coherence Tomography ◽

Image Segmentation ◽

Convolutional Neural Network ◽

Learning Algorithm ◽

Ground Truth ◽

Optical Coherence Tomography Image ◽

Optical Coherence ◽

Tomography Image

AbstractMachine learning has greatly facilitated the analysis of medical data, while the internal operations usually remain intransparent. To better comprehend these opaque procedures, a convolutional neural network for optical coherence tomography image segmentation was enhanced with a Traceable Relevance Explainability (T-REX) technique. The proposed application was based on three components: ground truth generation by multiple graders, calculation of Hamming distances among graders and the machine learning algorithm, as well as a smart data visualization (‘neural recording’). An overall average variability of 1.75% between the human graders and the algorithm was found, slightly minor to 2.02% among human graders. The ambiguity in ground truth had noteworthy impact on machine learning results, which could be visualized. The convolutional neural network balanced between graders and allowed for modifiable predictions dependent on the compartment. Using the proposed T-REX setup, machine learning processes could be rendered more transparent and understandable, possibly leading to optimized applications.

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Real-Time Automated Classification of Sky Conditions Using Deep Learning and Edge Computing

Remote Sensing ◽

10.3390/rs13193859 ◽

2021 ◽

Vol 13 (19) ◽

pp. 3859

Author(s):

Joby M. Prince Czarnecki ◽

Sathishkumar Samiappan ◽

Meilun Zhou ◽

Cary Daniel McCraine ◽

Louis L. Wasson

Keyword(s):

Neural Network ◽

Deep Learning ◽

Image Quality ◽

Convolutional Neural Network ◽

Precision Agriculture ◽

Edge Computing ◽

Training Data ◽

Learning Approaches ◽

Sky Conditions

The radiometric quality of remotely sensed imagery is crucial for precision agriculture applications because estimations of plant health rely on the underlying quality. Sky conditions, and specifically shadowing from clouds, are critical determinants in the quality of images that can be obtained from low-altitude sensing platforms. In this work, we first compare common deep learning approaches to classify sky conditions with regard to cloud shadows in agricultural fields using a visible spectrum camera. We then develop an artificial-intelligence-based edge computing system to fully automate the classification process. Training data consisting of 100 oblique angle images of the sky were provided to a convolutional neural network and two deep residual neural networks (ResNet18 and ResNet34) to facilitate learning two classes, namely (1) good image quality expected, and (2) degraded image quality expected. The expectation of quality stemmed from the sky condition (i.e., density, coverage, and thickness of clouds) present at the time of the image capture. These networks were tested using a set of 13,000 images. Our results demonstrated that ResNet18 and ResNet34 classifiers produced better classification accuracy when compared to a convolutional neural network classifier. The best overall accuracy was obtained by ResNet34, which was 92% accurate, with a Kappa statistic of 0.77. These results demonstrate a low-cost solution to quality control for future autonomous farming systems that will operate without human intervention and supervision.

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A Deep Siamese Convolution Neural Network for Multi-Class Classification of Alzheimer Disease

Brain Sciences ◽

10.3390/brainsci10020084 ◽

2020 ◽

Vol 10 (2) ◽

pp. 84 ◽

Cited By ~ 6

Author(s):

Atif Mehmood ◽

Muazzam Maqsood ◽

Muzaffar Bashir ◽

Yang Shuyuan

Keyword(s):

Neural Network ◽

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Convolutional Neural Network ◽

State Of The Art ◽

Early Stage ◽

The State ◽

Test Accuracy ◽

Learning Approaches

Alzheimer’s disease (AD) may cause damage to the memory cells permanently, which results in the form of dementia. The diagnosis of Alzheimer’s disease at an early stage is a problematic task for researchers. For this, machine learning and deep convolutional neural network (CNN) based approaches are readily available to solve various problems related to brain image data analysis. In clinical research, magnetic resonance imaging (MRI) is used to diagnose AD. For accurate classification of dementia stages, we need highly discriminative features obtained from MRI images. Recently advanced deep CNN-based models successfully proved their accuracy. However, due to a smaller number of image samples available in the datasets, there exist problems of over-fitting hindering the performance of deep learning approaches. In this research, we developed a Siamese convolutional neural network (SCNN) model inspired by VGG-16 (also called Oxford Net) to classify dementia stages. In our approach, we extend the insufficient and imbalanced data by using augmentation approaches. Experiments are performed on a publicly available dataset open access series of imaging studies (OASIS), by using the proposed approach, an excellent test accuracy of 99.05% is achieved for the classification of dementia stages. We compared our model with the state-of-the-art models and discovered that the proposed model outperformed the state-of-the-art models in terms of performance, efficiency, and accuracy.

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Deep learning for glioblastoma segmentation using preoperative magnetic resonance imaging identifies volumetric features associated with survival

Acta Neurochirurgica ◽

10.1007/s00701-020-04483-7 ◽

2020 ◽

Vol 162 (12) ◽

pp. 3067-3080

Author(s):

Yizhou Wan ◽

Roushanak Rahmat ◽

Stephen J. Price

Keyword(s):

Neural Network ◽

Overall Survival ◽

Convolutional Neural Network ◽

Multiple Testing ◽

Network Performance ◽

Cox Regression ◽

Prognostic Significance ◽

Ground Truth ◽

Cox Regression Analysis ◽

Volumetric Features

Abstract Background Measurement of volumetric features is challenging in glioblastoma. We investigate whether volumetric features derived from preoperative MRI using a convolutional neural network–assisted segmentation is correlated with survival. Methods Preoperative MRI of 120 patients were scored using Visually Accessible Rembrandt Images (VASARI) features. We trained and tested a multilayer, multi-scale convolutional neural network on multimodal brain tumour segmentation challenge (BRATS) data, prior to testing on our dataset. The automated labels were manually edited to generate ground truth segmentations. Network performance for our data and BRATS data was compared. Multivariable Cox regression analysis corrected for multiple testing using the false discovery rate was performed to correlate clinical and imaging variables with overall survival. Results Median Dice coefficients in our sample were (1) whole tumour 0.94 (IQR, 0.82–0.98) compared to 0.91 (IQR, 0.83–0.94 p = 0.012), (2) FLAIR region 0.84 (IQR, 0.63–0.95) compared to 0.81 (IQR, 0.69–0.8 p = 0.170), (3) contrast-enhancing region 0.91 (IQR, 0.74–0.98) compared to 0.83 (IQR, 0.78–0.89 p = 0.003) and (4) necrosis region were 0.82 (IQR, 0.47–0.97) compared to 0.67 (IQR, 0.42–0.81 p = 0.005). Contrast-enhancing region/tumour core ratio (HR 4.73 [95% CI, 1.67–13.40], corrected p = 0.017) and necrotic core/tumour core ratio (HR 8.13 [95% CI, 2.06–32.12], corrected p = 0.011) were independently associated with overall survival. Conclusion Semi-automated segmentation of glioblastoma using a convolutional neural network trained on independent data is robust when applied to routine clinical data. The segmented volumes have prognostic significance.

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A Recurrent Neural Network Approach for Automated Neural Tracing in Multispectral 3D Images

10.1101/230441 ◽

2018 ◽

Author(s):

Yan Yan ◽

Douglas H. Roossien ◽

Benjamin V. Sadis ◽

Jason J. Corso ◽

Dawen Cai

Keyword(s):

Neural Network ◽

Deep Learning ◽

Neuronal Cell ◽

Ground Truth ◽

Neuronal Morphology ◽

Spectral Information ◽

Neural Net ◽

Learning Approaches ◽

3D Images ◽

Neural Tracing

AbstractNeuronal morphology reconstruction in fluorescence microscopy 3D images is essential for analyzing neuronal cell type and connectivity. Manual tracing of neurons in these images is time consuming and subjective. Automated tracing is highly desired yet is one of the foremost challenges in computational neuroscience. The multispectral labeling technique, Brainbow utilizes high dimensional spectral information to distinguish intermingled neuronal processes. It is particular interesting to develop new algorithms to include the spectral information into the tracing process. Recently, deep learning approaches achieved state-of-the-art in different computer vision and medical imaging applications. To benefit from the power of deep learning, in this paper, we propose an automated neural tracing approach in multispectral 3D Brainbow images based on recurrent neural net-work. We first adopt VBM4D approach to denoise multispectral 3D images. Then we generate cubes as training samples along the ground truth, manually traced paths. These cubes are the input to the recur-rent neural network. The proposed approach is simple and effective. The approach can be implemented with the deep learning toolbox ‘Keras’ in 100 lines. Finally, to evaluate our approach, we computed the average and standard deviation of DIADEM metric from the ground truth results to our tracing results, and from our tracing results to the ground truth results. Extensive experimental results on the collected dataset demonstrate that the proposed approach performs well in Brainbow labeled mouse brain images.

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Domain Randomization for Detection and Position Estimation of Multiples of a Single Object With Applications to Localizing Bolts on Structures

Volume 1: 39th Computers and Information in Engineering Conference ◽

10.1115/detc2019-97393 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ezra Ameperosa ◽

Pranav A. Bhounsule

Keyword(s):

Neural Network ◽

Convolutional Neural Network ◽

Position Estimation ◽

Learning Approaches ◽

Single Object ◽

Automated Method ◽

The Neural Network ◽

Periodic Maintenance ◽

Camera Position ◽

Periodic Replacement

Abstract Periodic replacement of fasteners such as bolts are an integral part of many structures (e.g., airplanes, cars, ships) and require periodic maintenance that may involve either their tightening or replacement. Current manual practices are time consuming and costly especially due to the large number of bolts. Thus, an automated method that is able to visually detect and localize bolt positions would be highly beneficial. In this paper, we demonstrate the use of deep neural network using domain randomization for detecting and localizing multiple bolts on a workpiece. In contrast to previous deep learning approaches that require training on real images, the use of domain randomization allows for all training to be done in simulation. The key idea here is to create a wide variety of computer generated synthetic images by varying the texture, color, camera position and orientation, distractor objects, and noise, and train the neural network on these images such that the neural network is robust to scene variability and hence provides accurate results when deployed on real images. Using domain randomization, we train two neural networks, a faster regional convolutional neural network for detecting the bolt and predicting a bounding box, and a regression convolutional neural network for estimating the x- and y-position of the bolt relative to the coordinates fixed to the workpiece. Our results indicate that in the best case we are able to detect bolts with 85% accuracy and are able to predict the position of 75% of bolts within 1.27 cm. The novelty of this work is in the use of domain randomization to detect and localize: (1) multiples of a single object, and (2) small sized objects (0.6 cm × 2.5 cm).

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