massNet: integrated processing and classification of spatially resolved mass spectrometry data using deep learning for rapid tumor delineation

2021 ◽  
Author(s):  
Walid M. Abdelmoula ◽  
Sylwia Stopka ◽  
Elizabeth C. Randall ◽  
Michael Regan ◽  
Jeffrey N. Agar ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Deep Learning ◽  
Disease Diagnosis ◽  
Learning Model ◽  
Mass Spectrometry Data ◽  
Support Vector ◽  
Complex Nature ◽  
Peak Picking ◽  
Tumor Delineation ◽  
Deep Learning Model

Motivation: Mass spectrometry imaging (MSI) provides rich biochemical information in a label-free manner and therefore holds promise to substantially impact current practice in disease diagnosis. However, the complex nature of MSI data poses computational challenges in its analysis. The complexity of the data arises from its large size, high dimensionality, and spectral non-linearity. Preprocessing, including peak picking, has been used to reduce raw data complexity, however peak picking is sensitive to parameter selection that, perhaps prematurely, shapes the downstream analysis for tissue classification and ensuing biological interpretation. Results: We propose a deep learning model, massNet, that provides the desired qualities of scalability, non-linearity, and speed in MSI data analysis. This deep learning model was used, without prior preprocessing and peak picking, to classify MSI data from a mouse brain harboring a patient-derived tumor. The massNet architecture established automatically learning of predictive features, and automated methods were incorporated to identify peaks with potential for tumor delineation. The model's performance was assessed using cross-validation, and the results demonstrate higher accuracy and a 174-fold gain in speed compared to the established classical machine learning method, support vector machine. Availability and Implementation: The code is publicly available on GitHub.

scholarly journals A Hybrid Prognostics Deep Learning Model for Remaining Useful Life Prediction

Electronics ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 39
Author(s):  
Zhiyuan Xie ◽  
Shichang Du ◽  
Jun Lv ◽  
Yafei Deng ◽  
Shiyao Jia
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Learning Model ◽  
Recurrent Network ◽  
Remaining Useful Life ◽  
Support Vector ◽  
Second Phase ◽  
Learning Methods ◽  
Useful Life ◽  
Deep Learning Model

Remaining Useful Life (RUL) prediction is significant in indicating the health status of the sophisticated equipment, and it requires historical data because of its complexity. The number and complexity of such environmental parameters as vibration and temperature can cause non-linear states of data, making prediction tremendously difficult. Conventional machine learning models such as support vector machine (SVM), random forest, and back propagation neural network (BPNN), however, have limited capacity to predict accurately. In this paper, a two-phase deep-learning-model attention-convolutional forget-gate recurrent network (AM-ConvFGRNET) for RUL prediction is proposed. The first phase, forget-gate convolutional recurrent network (ConvFGRNET) is proposed based on a one-dimensional analog long short-term memory (LSTM), which removes all the gates except the forget gate and uses chrono-initialized biases. The second phase is the attention mechanism, which ensures the model to extract more specific features for generating an output, compensating the drawbacks of the FGRNET that it is a black box model and improving the interpretability. The performance and effectiveness of AM-ConvFGRNET for RUL prediction is validated by comparing it with other machine learning methods and deep learning methods on the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) dataset and a dataset of ball screw experiment.

scholarly journals Precision Measurement for Industry 4.0 Standards towards Solid Waste Classification through Enhanced Imaging Sensors and Deep Learning Model

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Leow Wei Qin ◽  
Muneer Ahmad ◽  
Ihsan Ali ◽  
Rafia Mumtaz ◽  
Syed Mohammad Hassan Zaidi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Solid Waste ◽  
Precision Measurement ◽  
Mobile Applications ◽  
Industry 4.0 ◽  
Learning Model ◽  
Edge Computing ◽  
Support Vector ◽  
Waste Classification ◽  
Deep Learning Model

Achievement of precision measurement is highly desired in a current industrial revolution where a significant increase in living standards increased municipal solid waste. The current industry 4.0 standards require accurate and efficient edge computing sensors towards solid waste classification. Thus, if waste is not managed properly, it would bring about an adverse impact on health, the economy, and the global environment. All stakeholders need to realize their roles and responsibilities for solid waste generation and recycling. To ensure recycling can be successful, the waste should be correctly and efficiently separated. The performance of edge computing devices is directly proportional to computational complexity in the context of nonorganic waste classification. Existing research on waste classification was done using CNN architecture, e.g., AlexNet, which contains about 62,378,344 parameters, and over 729 million floating operations (FLOPs) are required to classify a single image. As a result, it is too heavy and not suitable for computing applications that require inexpensive computational complexities. This research proposes an enhanced lightweight deep learning model for solid waste classification developed using MobileNetV2, efficient for lightweight applications including edge computing devices and other mobile applications. The proposed model outperforms the existing similar models achieving an accuracy of 82.48% and 83.46% with Softmax and support vector machine (SVM) classifiers, respectively. Although MobileNetV2 may provide a lower accuracy if compared to CNN architecture which is larger and heavier, the accuracy is still comparable, and it is more practical for edge computing devices and mobile applications.

scholarly journals A Mobile-Based Deep Learning Model for Cassava Disease Diagnosis

2019 ◽  
Vol 10 ◽  
Author(s):  
Amanda Ramcharan ◽  
Peter McCloskey ◽  
Kelsee Baranowski ◽  
Neema Mbilinyi ◽  
Latifa Mrisho ◽  
...  
Keyword(s):  
Deep Learning ◽  
Disease Diagnosis ◽  
Learning Model ◽  
Deep Learning Model

scholarly journals Improved Deep Feature Learning by Synchronization Measurements for Multi-Channel EEG Emotion Recognition

Complexity ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-15 ◽  
Author(s):  
Hao Chao ◽  
Liang Dong ◽  
Yongli Liu ◽  
Baoyun Lu
Keyword(s):  
Deep Learning ◽  
Emotion Recognition ◽  
Affective Computing ◽  
Learning Model ◽  
Support Vector ◽  
Eeg Signals ◽  
Global Synchronization ◽  
Spatial Characteristics ◽  
Maximal Information Coefficient ◽  
Deep Learning Model

Emotion recognition based on multichannel electroencephalogram (EEG) signals is a key research area in the field of affective computing. Traditional methods extract EEG features from each channel based on extensive domain knowledge and ignore the spatial characteristics and global synchronization information across all channels. This paper proposes a global feature extraction method that encapsulates the multichannel EEG signals into gray images. The maximal information coefficient (MIC) for all channels was first measured. Subsequently, an MIC matrix was constructed according to the electrode arrangement rules and represented by an MIC gray image. Finally, a deep learning model designed with two principal component analysis convolutional layers and a nonlinear transformation operation extracted the spatial characteristics and global interchannel synchronization features from the constructed feature images, which were then input to support vector machines to perform the emotion recognition tasks. Experiments were conducted on the benchmark dataset for emotion analysis using EEG, physiological, and video signals. The experimental results demonstrated that the global synchronization features and spatial characteristics are beneficial for recognizing emotions and the proposed deep learning model effectively mines and utilizes the two salient features.

scholarly journals The Impact of Emotional Music on Active ROI in Patients with Depression Based on Deep Learning: A Task-State fMRI Study

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Renzhou Gui ◽  
Tongjie Chen ◽  
Han Nie
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Correlation Matrix ◽  
Nearest Neighbor ◽  
Learning Model ◽  
Fmri Data ◽  
Support Vector ◽  
K Nearest Neighbor ◽  
The Impact ◽  
Deep Learning Model

With the continuous development of science, more and more research results have proved that machine learning is capable of diagnosing and studying the major depressive disorder (MDD) in the brain. We propose a deep learning network with multibranch and local residual feedback, for four different types of functional magnetic resonance imaging (fMRI) data produced by depressed patients and control people under the condition of listening to positive- and negative-emotions music. We use the large convolution kernel of the same size as the correlation matrix to match the features and obtain the results of feature matching of 264 regions of interest (ROIs). Firstly, four-dimensional fMRI data are used to generate the two-dimensional correlation matrix of one person’s brain based on ROIs and then processed by the threshold value which is selected according to the characteristics of complex network and small-world network. After that, the deep learning model in this paper is compared with support vector machine (SVM), logistic regression (LR), k-nearest neighbor (kNN), a common deep neural network (DNN), and a deep convolutional neural network (CNN) for classification. Finally, we further calculate the matched ROIs from the intermediate results of our deep learning model which can help related fields further explore the pathogeny of depression patients.

scholarly journals Personalized deep learning of individual immunopeptidomes to identify neoantigens for cancer vaccines

2019 ◽  
Author(s):  
Ngoc Hieu Tran ◽  
Rui Qiao ◽  
Lei Xin ◽  
Xin Chen ◽  
Baozhen Shan ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Deep Learning ◽  
De Novo ◽  
Mass Spectrometry Data ◽  
Main Role ◽  
Accurate Identification ◽  
Identification Rate ◽  
Cell Responses ◽  
First Time ◽  
Deep Learning Model

AbstractTumor-specific neoantigens play the main role for developing personal vaccines in cancer immunotherapy. We propose, for the first time, a personalized de novo sequencing workflow to identify HLA-I and HLA-II neoantigens directly and solely from mass spectrometry data. Our workflow trains a personal deep learning model on the immunopeptidome of an individual patient and then uses it to predict mutated neoantigens of that patient. This personalized learning and mass spectrometry-based approach enables comprehensive and accurate identification of neoantigens. We applied the workflow to datasets of five melanoma patients and substantially improved the accuracy and identification rate of de novo HLA peptides by 14.3% and 38.9%, respectively. This subsequently led to the identification of 10,440 HLA-I and 1,585 HLA-II new peptides that were not presented in existing databases. Most importantly, our workflow successfully discovered 17 neoantigens of both HLA-I and HLA-II, including those with validated T cell responses and those novel neoantigens that had not been reported in previous studies.

scholarly journals SmartFall: A Smartwatch-Based Fall Detection System Using Deep Learning

Sensors ◽  
2018 ◽  
Vol 18 (10) ◽  
pp. 3363 ◽  
Author(s):  
Taylor Mauldin ◽  
Marc Canby ◽  
Vangelis Metsis ◽  
Anne Ngu ◽  
Coralys Rivera
Keyword(s):  
Support Vector Machine ◽  
Deep Learning ◽  
Naive Bayes ◽  
Fall Detection ◽  
Learning Model ◽  
Naïve Bayes ◽  
Sensor Data ◽  
Support Vector ◽  
Accelerometer Data ◽  
Deep Learning Model

This paper presents SmartFall, an Android app that uses accelerometer data collected from a commodity-based smartwatch Internet of Things (IoT) device to detect falls. The smartwatch is paired with a smartphone that runs the SmartFall application, which performs the computation necessary for the prediction of falls in real time without incurring latency in communicating with a cloud server, while also preserving data privacy. We experimented with both traditional (Support Vector Machine and Naive Bayes) and non-traditional (Deep Learning) machine learning algorithms for the creation of fall detection models using three different fall datasets (Smartwatch, Notch, Farseeing). Our results show that a Deep Learning model for fall detection generally outperforms more traditional models across the three datasets. This is attributed to the Deep Learning model’s ability to automatically learn subtle features from the raw accelerometer data that are not available to Naive Bayes and Support Vector Machine, which are restricted to learning from a small set of extracted features manually specified. Furthermore, the Deep Learning model exhibits a better ability to generalize to new users when predicting falls, an important quality of any model that is to be successful in the real world. We also present a three-layer open IoT system architecture used in SmartFall, which can be easily adapted for the collection and analysis of other sensor data modalities (e.g., heart rate, skin temperature, walking patterns) that enables remote monitoring of a subject’s wellbeing.

Automatic Lumen Border Detection in IVUS Images Using Deep Learning Model and Handcrafted Features

2021 ◽  
Vol 43 (2) ◽  
pp. 59-73
Author(s):  
Kai Li ◽  
Jijun Tong ◽  
Xinjian Zhu ◽  
Shudong Xia
Keyword(s):  
Deep Learning ◽  
Cuckoo Search ◽  
Disease Diagnosis ◽  
Learning Model ◽  
Clinical Analysis ◽  
Interventional Treatment ◽  
Feature Subset ◽  
Border Detection ◽  
Important Indicator ◽  
Deep Learning Model

In the clinical analysis of Intravascular ultrasound (IVUS) images, the lumen size is an important indicator of coronary atherosclerosis, and is also the premise of coronary artery disease diagnosis and interventional treatment. In this study, a fully automatic method based on deep learning model and handcrafted features is presented for the detection of the lumen borders in IVUS images. First, 193 handcrafted features are extracted from the IVUS images. Then hybrid feature vectors are constructed by combining handcrafted features with 64 high-level features extracted from U-Net. In order to obtain the feature subsets with larger contribution, we employ the extended binary cuckoo search for feature selection. Finally, the selected 36-dimensional hybrid feature subset is used to classify the test images using dictionary learning based on kernel sparse coding. The proposed algorithm is tested on the publicly available dataset and evaluated using three indicators. Through ablation experiments, mean value of the experimental results (Jaccard: 0.88, Hausdorff distance: 0.36, Percentage of the area difference: 0.06) prove to be effective improving lumen border detection. Furthermore, compared with the recent methods used on the same dataset, the proposed method shows good performance and high accuracy.

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