scholarly journals MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Yang-Ming Lin ◽  
Ching-Tai Chen ◽  
Jia-Ming Chang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Large Scale ◽  
Learning Algorithm ◽  
Pearson Correlation ◽  
Tandem Mass ◽  
Spectral Library ◽  
Deep Convolutional Neural Networks ◽  
Library Search

Abstract Background Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An accurate tandem mass spectrum prediction tool is thus crucial in expanding the peptide space and increasing the coverage of spectral library search. Results We propose MS2CNN, a non-linear regression model based on deep convolutional neural networks, a deep learning algorithm. The features for our model are amino acid composition, predicted secondary structure, and physical-chemical features such as isoelectric point, aromaticity, helicity, hydrophobicity, and basicity. MS2CNN was trained with five-fold cross validation on a three-way data split on the large-scale human HCD MS2 dataset of Orbitrap LC-MS/MS downloaded from the National Institute of Standards and Technology. It was then evaluated on a publicly available independent test dataset of human HeLa cell lysate from LC-MS experiments. On average, our model shows better cosine similarity and Pearson correlation coefficient (0.690 and 0.632) than MS2PIP (0.647 and 0.601) and is comparable with pDeep (0.692 and 0.642). Notably, for the more complex MS2 spectra of 3+ peptides, MS2PIP is significantly better than both MS2PIP and pDeep. Conclusions We showed that MS2CNN outperforms MS2PIP for 2+ and 3+ peptides and pDeep for 3+ peptides. This implies that MS2CNN, the proposed convolutional neural network model, generates highly accurate MS2 spectra for LC-MS/MS experiments using Orbitrap machines, which can be of great help in protein and peptide identifications. The results suggest that incorporating more data for deep learning model may improve performance.

Soil properties: their prediction and feature extraction from the LUCAS spectral library using deep convolutional neural networks

2021 ◽  
Author(s):  
Liang Zhong ◽  
Xi Guo ◽  
Zhe Xu ◽  
Meng Ding
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Soil Properties ◽  
Convolutional Neural Networks ◽  
Soil Texture ◽  
Precision Agriculture ◽  
Organic Carbon Content ◽  
Spectral Library ◽  
Deep Convolutional Neural Networks ◽  
Large Soil

<p>Soil, as a non-renewable resource, should be monitored continuously to prevent its degradation and promote sustainable agricultural management. Soil spectroscopy in the visible-near infrared range is a fast and cost-effective analytical technique to predict soil properties. The use of large soil spectral libraries can reduce the work needed to reliably estimate soil properties and obtain robust models capable of widespread applicability. Deep learning is apt for big data analysis, and this approach could herald a profound change in the way we model soil spectral data generally. Accordingly, we explored the modeling potential of deep convolutional neural networks (DCNNs) for soil properties based on a large soil spectral library. The European topsoil dataset provided by the Land Use/Cover Area frame Survey (LUCAS) was used without any pre-processing of spectra or covariates added. Two 16-layer DCNN models (ResNet-16 and VGGNet-16) were successfully used to make regression predictions of seven soil properties and classification predictions of soil texture into four groups and 12 levels. Our results showed that the ResNet-16 and VGGNet-16 models produced highly accurate predictions for most soil properties, being superior to either a shallow convolutional neural network and traditional machine learning approaches. Soil organic carbon content, nitrogen content, cation exchange capacity, pH, and calcium carbonate content were well predicted, having a ratio of performance to deviation (RPD) > 2.0. Soil potassium content was adequately predicted (1.4 ≤ RPD ≤ 2.0) and phosphorous content was poorly predicted (RPD < 1.4). The overall classification accuracy of soil texture was 0.749 (four groups) and 0.566 (12 levels). The position of feature wavelengths differed among the soil properties, for which multiple characteristic peaks were common. This study fully demonstrates the modeling potential of deep learning with soil hyperspectral data, which could bring us closer to achieving precision agriculture.</p>

scholarly journals Deep convolutional neural networks for cardiovascular vulnerable plaque detection

2019 ◽  
Vol 277 ◽  
pp. 02024 ◽  
Author(s):  
Lincan Li ◽  
Tong Jia ◽  
Tianqi Meng ◽  
Yizhe Liu
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Vulnerable Plaque ◽  
Recall Rate ◽  
Superior Performance ◽  
Learning Approaches ◽  
Deep Convolutional Neural Networks ◽  
Vulnerable Plaques ◽  
Plaque Detection

In this paper, an accurate two-stage deep learning method is proposed to detect vulnerable plaques in ultrasonic images of cardiovascular. Firstly, a Fully Convonutional Neural Network (FCN) named U-Net is used to segment the original Intravascular Optical Coherence Tomography (IVOCT) cardiovascular images. We experiment on different threshold values to find the best threshold for removing noise and background in the original images. Secondly, a modified Faster RCNN is adopted to do precise detection. The modified Faster R-CNN utilize six-scale anchors (122,162,322,642,1282,2562) instead of the conventional one scale or three scale approaches. First, we present three problems in cardiovascular vulnerable plaque diagnosis, then we demonstrate how our method solve these problems. The proposed method in this paper apply deep convolutional neural networks to the whole diagnostic procedure. Test results show the Recall rate, Precision rate, IoU (Intersection-over-Union) rate and Total score are 0.94, 0.885, 0.913 and 0.913 respectively, higher than the 1st team of CCCV2017 Cardiovascular OCT Vulnerable Plaque Detection Challenge. AP of the designed Faster RCNN is 83.4%, higher than conventional approaches which use one-scale or three-scale anchors. These results demonstrate the superior performance of our proposed method and the power of deep learning approaches in diagnose cardiovascular vulnerable plaques.

Online Estimation of Lithium-Ion Battery Capacity Using Deep Convolutional Neural Networks

2018 ◽  
Author(s):  
Sheng Shen ◽  
M. K. Sadoughi ◽  
Xiangyi Chen ◽  
Mingyi Hong ◽  
Chao Hu
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Lithium Ion ◽  
Relevance Vector Machine ◽  
Rechargeable Batteries ◽  
Li Ion Battery ◽  
Deep Convolutional Neural Networks ◽  
Battery Capacity ◽  
Li Ion

Over the past two decades, safety and reliability of lithium-ion (Li-ion) rechargeable batteries have been receiving a considerable amount of attention from both industry and academia. To guarantee safe and reliable operation of a Li-ion battery pack and build failure resilience in the pack, battery management systems (BMSs) should possess the capability to monitor, in real time, the state of health (SOH) of the individual cells in the pack. This paper presents a deep learning method, named deep convolutional neural networks, for cell-level SOH assessment based on the capacity, voltage, and current measurements during a charge cycle. The unique features of deep convolutional neural networks include the local connectivity and shared weights, which enable the model to estimate battery capacity accurately using the measurements during charge. To our knowledge, this is the first attempt to apply deep learning to online SOH assessment of Li-ion battery. 10-year daily cycling data from implantable Li-ion cells are used to verify the performance of the proposed method. Compared with traditional machine learning methods such as relevance vector machine and shallow neural networks, the proposed method is demonstrated to produce higher accuracy and robustness in capacity estimation.

scholarly journals Deep learning networks reflect cytoarchitectonic features used in brain mapping

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kai Kiwitz ◽  
Christian Schiffer ◽  
Hannah Spitzer ◽  
Timo Dickscheid ◽  
Katrin Amunts
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Brain Mapping ◽  
Learning Approaches ◽  
Deep Convolutional Neural Networks ◽  
Promising Alternative ◽  
Cortical Areas ◽  
Cytoarchitectonic Mapping ◽  
Profile Approach

AbstractThe distribution of neurons in the cortex (cytoarchitecture) differs between cortical areas and constitutes the basis for structural maps of the human brain. Deep learning approaches provide a promising alternative to overcome throughput limitations of currently used cytoarchitectonic mapping methods, but typically lack insight as to what extent they follow cytoarchitectonic principles. We therefore investigated in how far the internal structure of deep convolutional neural networks trained for cytoarchitectonic brain mapping reflect traditional cytoarchitectonic features, and compared them to features of the current grey level index (GLI) profile approach. The networks consisted of a 10-block deep convolutional architecture trained to segment the primary and secondary visual cortex. Filter activations of the networks served to analyse resemblances to traditional cytoarchitectonic features and comparisons to the GLI profile approach. Our analysis revealed resemblances to cellular, laminar- as well as cortical area related cytoarchitectonic features. The networks learned filter activations that reflect the distinct cytoarchitecture of the segmented cortical areas with special regard to their laminar organization and compared well to statistical criteria of the GLI profile approach. These results confirm an incorporation of relevant cytoarchitectonic features in the deep convolutional neural networks and mark them as a valid support for high-throughput cytoarchitectonic mapping workflows.

scholarly journals Fusion High-Resolution Network for Diagnosing ChestX-ray Images

Electronics ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 190 ◽  
Author(s):  
Zhiwei Huang ◽  
Jinzhao Lin ◽  
Liming Xu ◽  
Huiqian Wang ◽  
Tong Bai ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Resolution ◽  
Convolutional Neural Networks ◽  
Characteristic Curve ◽  
Area Under The Curve ◽  
Disease Classification ◽  
Deep Convolutional Neural Networks ◽  
Learning Methods ◽  
Global And Local

The application of deep convolutional neural networks (CNN) in the field of medical image processing has attracted extensive attention and demonstrated remarkable progress. An increasing number of deep learning methods have been devoted to classifying ChestX-ray (CXR) images, and most of the existing deep learning methods are based on classic pretrained models, trained by global ChestX-ray images. In this paper, we are interested in diagnosing ChestX-ray images using our proposed Fusion High-Resolution Network (FHRNet). The FHRNet concatenates the global average pooling layers of the global and local feature extractors—it consists of three branch convolutional neural networks and is fine-tuned for thorax disease classification. Compared with the results of other available methods, our experimental results showed that the proposed model yields a better disease classification performance for the ChestX-ray 14 dataset, according to the receiver operating characteristic curve and area-under-the-curve score. An ablation study further confirmed the effectiveness of the global and local branch networks in improving the classification accuracy of thorax diseases.

Sign in / Sign up

Export Citation Format

Share Document