scholarly journals Designing and Implementing a Method of Data Augmentation Using Machine Learning

2021 ◽  
Vol 55 ◽  
pp. 54-61
Author(s):  
Aren Mayilyan ◽  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Image Segmentation ◽  
Environmental Conditions ◽  
Input Data ◽  
Data Augmentation ◽  
Small Set ◽  
Problem Data

Efficiency of neural network (NN) models depend on the parameters given and the input data. Due to the complexity of environmental conditions and limitations the data for NN models, especially for the case of images, can be insufficient. To overcome this problem data augmentation has been used to enlarge the dataset. The task is to generate diverse set of images from a small set of images for NN training. Due to data augmentation transformation, 3105 new images out of 345 input data were created for classification, detection and image segmentation.

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

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.

scholarly journals Robust Approach to Supervised Deep Neural Network Training for Real-Time Object Classification in Cluttered Indoor Environment

2021 ◽  
Vol 11 (15) ◽  
pp. 7148
Author(s):  
Bedada Endale ◽  
Abera Tullu ◽  
Hayoung Shi ◽  
Beom-Soo Kang
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Real Time ◽  
Network Architecture ◽  
Input Data ◽  
Deep Neural Network ◽  
Data Augmentation ◽  
Object Classification ◽  
Training Data ◽  
Gradient Descent Algorithm

Unmanned aerial vehicles (UAVs) are being widely utilized for various missions: in both civilian and military sectors. Many of these missions demand UAVs to acquire artificial intelligence about the environments they are navigating in. This perception can be realized by training a computing machine to classify objects in the environment. One of the well known machine training approaches is supervised deep learning, which enables a machine to classify objects. However, supervised deep learning comes with huge sacrifice in terms of time and computational resources. Collecting big input data, pre-training processes, such as labeling training data, and the need for a high performance computer for training are some of the challenges that supervised deep learning poses. To address these setbacks, this study proposes mission specific input data augmentation techniques and the design of light-weight deep neural network architecture that is capable of real-time object classification. Semi-direct visual odometry (SVO) data of augmented images are used to train the network for object classification. Ten classes of 10,000 different images in each class were used as input data where 80% were for training the network and the remaining 20% were used for network validation. For the optimization of the designed deep neural network, a sequential gradient descent algorithm was implemented. This algorithm has the advantage of handling redundancy in the data more efficiently than other algorithms.

SCONES: Self-Consistent Neural Network for Protein Stability Prediction Upon Mutation

2021 ◽  
Author(s):  
Yashas Samaga B L ◽  
Shampa Raghunathan ◽  
U. Deva Priyakumar
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Protein Stability ◽  
Data Augmentation ◽  
Stability Prediction ◽  
Structural Environment ◽  
Self Consistent ◽  
The Difference ◽  
Protein Sequence Space ◽  
New Machine

<div>Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protein sequence space thoroughly are laborious. To this end, many machine learning based methods have been developed to predict thermodynamic stability changes upon mutation. These methods have been evaluated for symmetric consistency by testing with hypothetical reverse mutations. In this work, we propose transitive data augmentation, evaluating transitive consistency, and a new machine learning based method, first of its kind, that incorporates both symmetric and transitive properties into the architecture. Our method, called SCONES, is an interpretable neural network that estimates a residue's contributions towards protein stability dG in its local structural environment. The difference between independently predicted contributions of the reference and mutant residues in a missense mutation is reported as dG. We show that this self-consistent machine learning architecture is immune to many common biases in datasets, relies less on data than existing methods, and is robust to overfitting.</div><div><br></div>

scholarly journals A mechanism-aware and multiomic machine-learning pipeline characterizes yeast cell growth

2020 ◽  
Vol 117 (31) ◽  
pp. 18869-18879 ◽  
Author(s):  
Christopher Culley ◽  
Supreeta Vijayakumar ◽  
Guido Zampieri ◽  
Claudio Angione
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Machine Learning ◽  
Cell Growth ◽  
Yeast Cell ◽  
Metabolic Flux ◽  
Data Augmentation ◽  
Predictive Accuracy ◽  
Expression Profiles ◽  
Metabolic Reconstruction

Metabolic modeling and machine learning are key components in the emerging next generation of systems and synthetic biology tools, targeting the genotype–phenotype–environment relationship. Rather than being used in isolation, it is becoming clear that their value is maximized when they are combined. However, the potential of integrating these two frameworks for omic data augmentation and integration is largely unexplored. We propose, rigorously assess, and compare machine-learning–based data integration techniques, combining gene expression profiles with computationally generated metabolic flux data to predict yeast cell growth. To this end, we create strain-specific metabolic models for 1,143Saccharomyces cerevisiaemutants and we test 27 machine-learning methods, incorporating state-of-the-art feature selection and multiview learning approaches. We propose a multiview neural network using fluxomic and transcriptomic data, showing that the former increases the predictive accuracy of the latter and reveals functional patterns that are not directly deducible from gene expression alone. We test the proposed neural network on a further 86 strains generated in a different experiment, therefore verifying its robustness to an additional independent dataset. Finally, we show that introducing mechanistic flux features improves the predictions also for knockout strains whose genes were not modeled in the metabolic reconstruction. Our results thus demonstrate that fusing experimental cues with in silico models, based on known biochemistry, can contribute with disjoint information toward biologically informed and interpretable machine learning. Overall, this study provides tools for understanding and manipulating complex phenotypes, increasing both the prediction accuracy and the extent of discernible mechanistic biological insights.

scholarly journals DMCNN: A Deep Multiscale Convolutional Neural Network Model for Medical Image Segmentation

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Lin Teng ◽  
Hang Li ◽  
Shahid Karim
Keyword(s):  
Neural Network ◽  
Feature Extraction ◽  
Image Segmentation ◽  
Convolutional Neural Network ◽  
Medical Image ◽  
Data Augmentation ◽  
Medical Images ◽  
Medical Image Segmentation ◽  
Related Area ◽  
Segmentation Accuracy

Medical image segmentation is one of the hot issues in the related area of image processing. Precise segmentation for medical images is a vital guarantee for follow-up treatment. At present, however, low gray contrast and blurred tissue boundaries are common in medical images, and the segmentation accuracy of medical images cannot be effectively improved. Especially, deep learning methods need more training samples, which lead to time-consuming process. Therefore, we propose a novelty model for medical image segmentation based on deep multiscale convolutional neural network (CNN) in this article. First, we extract the region of interest from the raw medical images. Then, data augmentation is operated to acquire more training datasets. Our proposed method contains three models: encoder, U-net, and decoder. Encoder is mainly responsible for feature extraction of 2D image slice. The U-net cascades the features of each block of the encoder with those obtained by deconvolution in the decoder under different scales. The decoding is mainly responsible for the upsampling of the feature graph after feature extraction of each group. Simulation results show that the new method can boost the segmentation accuracy. And, it has strong robustness compared with other segmentation methods.

scholarly journals Interpretation of Neural Networks Is Fragile

2019 ◽  
Vol 33 ◽  
pp. 3681-3688 ◽  
Author(s):  
Amirata Ghorbani ◽  
Abubakar Abid ◽  
James Zou
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Input Data ◽  
Learning Algorithm ◽  
Hessian Matrix ◽  
Machine Learning Algorithm ◽  
Feature Importance ◽  
Adversarial Attack ◽  
Measurement Biases

In order for machine learning to be trusted in many applications, it is critical to be able to reliably explain why the machine learning algorithm makes certain predictions. For this reason, a variety of methods have been developed recently to interpret neural network predictions by providing, for example, feature importance maps. For both scientific robustness and security reasons, it is important to know to what extent can the interpretations be altered by small systematic perturbations to the input data, which might be generated by adversaries or by measurement biases. In this paper, we demonstrate how to generate adversarial perturbations that produce perceptively indistinguishable inputs that are assigned the same predicted label, yet have very different interpretations. We systematically characterize the robustness of interpretations generated by several widely-used feature importance interpretation methods (feature importance maps, integrated gradients, and DeepLIFT) on ImageNet and CIFAR-10. In all cases, our experiments show that systematic perturbations can lead to dramatically different interpretations without changing the label. We extend these results to show that interpretations based on exemplars (e.g. influence functions) are similarly susceptible to adversarial attack. Our analysis of the geometry of the Hessian matrix gives insight on why robustness is a general challenge to current interpretation approaches.

scholarly journals Acoustic Classification of Surface and Underwater Vessels in the Ocean Using Supervised Machine Learning

Sensors ◽  
2019 ◽  
Vol 19 (16) ◽  
pp. 3492 ◽  
Author(s):  
Jongkwon Choi ◽  
Youngmin Choo ◽  
Keunhwa Lee
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Density Matrix ◽  
Spectral Density ◽  
Input Data ◽  
Supervised Machine Learning ◽  
Data Driven ◽  
Matrix Elements ◽  
Spectral Density Matrix ◽  
Cross Spectral Density

Four data-driven methods—random forest (RF), support vector machine (SVM), feed-forward neural network (FNN), and convolutional neural network (CNN)—are applied to discriminate surface and underwater vessels in the ocean using low-frequency acoustic pressure data. Acoustic data are modeled considering a vertical line array by a Monte Carlo simulation using the underwater acoustic propagation model, KRAKEN, in the ocean environment of East Sea in Korea. The raw data are preprocessed and reorganized into the phone-space cross-spectral density matrix (pCSDM) and mode-space cross-spectral density matrix (mCSDM). Two additional matrices are generated using the absolute values of matrix elements in each CSDM. Each of these four matrices is used as input data for supervised machine learning. Binary classification is performed by using RF, SVM, FNN, and CNN, and the obtained results are compared. All machine-learning algorithms show an accuracy of >95% for three types of input data—the pCSDM, mCSDM, and mCSDM with the absolute matrix elements. The CNN is the best in terms of low percent error. In particular, the result using the complex pCSDM is encouraging because these data-driven methods inherently do not require environmental information. This work demonstrates the potential of machine learning to discriminate between surface and underwater vessels in the ocean.

scholarly journals Combined In-silico and Machine Learning Approaches Toward Predicting Arrhythmic Risk in Post-infarction Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Mary M. Maleckar ◽  
Lena Myklebust ◽  
Julie Uv ◽  
Per Magne Florvaag ◽  
Vilde Strøm ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
In Silico ◽  
Data Augmentation ◽  
Nearest Neighbors ◽  
Patient Data ◽  
Patient Specific ◽  
Support Vector ◽  
Geometric Features ◽  
K Nearest Neighbors

Background: Remodeling due to myocardial infarction (MI) significantly increases patient arrhythmic risk. Simulations using patient-specific models have shown promise in predicting personalized risk for arrhythmia. However, these are computationally- and time- intensive, hindering translation to clinical practice. Classical machine learning (ML) algorithms (such as K-nearest neighbors, Gaussian support vector machines, and decision trees) as well as neural network techniques, shown to increase prediction accuracy, can be used to predict occurrence of arrhythmia as predicted by simulations based solely on infarct and ventricular geometry. We present an initial combined image-based patient-specific in silico and machine learning methodology to assess risk for dangerous arrhythmia in post-infarct patients. Furthermore, we aim to demonstrate that simulation-supported data augmentation improves prediction models, combining patient data, computational simulation, and advanced statistical modeling, improving overall accuracy for arrhythmia risk assessment.Methods: MRI-based computational models were constructed from 30 patients 5 days post-MI (the “baseline” population). In order to assess the utility biophysical model-supported data augmentation for improving arrhythmia prediction, we augmented the virtual baseline patient population. Each patient ventricular and ischemic geometry in the baseline population was used to create a subfamily of geometric models, resulting in an expanded set of patient models (the “augmented” population). Arrhythmia induction was attempted via programmed stimulation at 17 sites for each virtual patient corresponding to AHA LV segments and simulation outcome, “arrhythmia,” or “no-arrhythmia,” were used as ground truth for subsequent statistical prediction (machine learning, ML) models. For each patient geometric model, we measured and used choice data features: the myocardial volume and ischemic volume, as well as the segment-specific myocardial volume and ischemia percentage, as input to ML algorithms. For classical ML techniques (ML), we trained k-nearest neighbors, support vector machine, logistic regression, xgboost, and decision tree models to predict the simulation outcome from these geometric features alone. To explore neural network ML techniques, we trained both a three - and a four-hidden layer multilayer perceptron feed forward neural networks (NN), again predicting simulation outcomes from these geometric features alone. ML and NN models were trained on 70% of randomly selected segments and the remaining 30% was used for validation for both baseline and augmented populations.Results: Stimulation in the baseline population (30 patient models) resulted in reentry in 21.8% of sites tested; in the augmented population (129 total patient models) reentry occurred in 13.0% of sites tested. ML and NN models ranged in mean accuracy from 0.83 to 0.86 for the baseline population, improving to 0.88 to 0.89 in all cases.Conclusion: Machine learning techniques, combined with patient-specific, image-based computational simulations, can provide key clinical insights with high accuracy rapidly and efficiently. In the case of sparse or missing patient data, simulation-supported data augmentation can be employed to further improve predictive results for patient benefit. This work paves the way for using data-driven simulations for prediction of dangerous arrhythmia in MI patients.

Machine learning approaches for ELNES/XANES

Microscopy ◽  
2020 ◽  
Vol 69 (2) ◽  
pp. 92-109 ◽  
Author(s):  
Teruyasu Mizoguchi ◽  
Shin Kiyohara
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Decision Tree ◽  
Hierarchical Clustering ◽  
Data Augmentation ◽  
Xanes Spectrum ◽  
Feedforward Neural Network ◽  
Material Structure ◽  
Learning Approaches ◽  
Edge Structure

Abstract Materials characterization is indispensable for materials development. In particular, spectroscopy provides atomic configuration, chemical bonding and vibrational information, which are crucial for understanding the mechanism underlying the functions of a material. Despite its importance, the interpretation of spectra using human-driven methods, such as manual comparison of experimental spectra with reference/simulated spectra, is becoming difficult owing to the rapid increase in experimental spectral data. To overcome the limitations of such methods, we develop new data-driven approaches based on machine learning. Specifically, we use hierarchical clustering, a decision tree and a feedforward neural network to investigate the electron energy loss near edge structures (ELNES) spectrum, which is identical to the X-ray absorption near edge structure (XANES) spectrum. Hierarchical clustering and the decision tree are used to interpret and predict ELNES/XANES, while the feedforward neural network is used to obtain hidden information about the material structure and properties from the spectra. Further, we construct a prediction model that is robust against noise by data augmentation. Finally, we apply our method to noisy spectra and predict six properties accurately. In summary, the proposed approaches can pave the way for fast and accurate spectrum interpretation/prediction as well as local measurement of material functions.

scholarly journals Data Augmentation and Pretraining for Template-Based Retrosynthetic Prediction in Computer-Aided Synthesis Planning

2020 ◽  
Author(s):  
Michael Fortunato ◽  
Connor W. Coley ◽  
Brian Barnes ◽  
Klavs F. Jensen
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Data Augmentation ◽  
Machine Learning Algorithms ◽  
Learning Models ◽  
The Neural Network ◽  
Computer Aided ◽  
Synthesis Planning ◽  
The One ◽  
Machine Learning Models

This work presents efforts to augment the performance of data-driven machine learning algorithms for reaction template recommendation used in computer-aided synthesis planning software. Often, machine learning models designed to perform the task of prioritizing reaction templates or molecular transformations are focused on reporting high accuracy metrics for the one-to-one mapping of product molecules in reaction databases to the template extracted from the recorded reaction. The available templates that get selected for inclusion in these machine learning models have been previously limited to those that appear frequently in the reaction databases and exclude potentially useful transformations. By augmenting open-access datasets of organic reactions with artificially calculated template applicability and pretraining a template relevance neural network on this augmented applicability dataset, we report an increase in the template applicability recall and an increase in the diversity of predicted precursors. The augmentation and pretraining effectively teaches the neural network an increased set of templates that could theoretically lead to successful reactions for a given target. Even on a small dataset of well curated reactions, the data augmentation and pretraining methods resulted in an increase in top-1 accuracy, especially for rare templates, indicating these strategies can be very useful for small datasets.

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