scholarly journals SpeCollate: Deep cross-modal similarity network for mass spectrometry data based peptide deductions

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259349
Author(s):  
Muhammad Usman Tariq ◽  
Fahad Saeed
Keyword(s):  
Mass Spectrometry ◽  
Deep Learning ◽  
Mass Spectra ◽  
Search Algorithms ◽  
Database Search ◽  
Theoretical Spectrum ◽  
Scoring Functions ◽  
Similarity Network ◽  
Learning Network ◽  
Deep Learning Network

Historically, the database search algorithms have been the de facto standard for inferring peptides from mass spectrometry (MS) data. Database search algorithms deduce peptides by transforming theoretical peptides into theoretical spectra and matching them to the experimental spectra. Heuristic similarity-scoring functions are used to match an experimental spectrum to a theoretical spectrum. However, the heuristic nature of the scoring functions and the simple transformation of the peptides into theoretical spectra, along with noisy mass spectra for the less abundant peptides, can introduce a cascade of inaccuracies. In this paper, we design and implement a Deep Cross-Modal Similarity Network called SpeCollate, which overcomes these inaccuracies by learning the similarity function between experimental spectra and peptides directly from the labeled MS data. SpeCollate transforms spectra and peptides into a shared Euclidean subspace by learning fixed size embeddings for both. Our proposed deep-learning network trains on sextuplets of positive and negative examples coupled with our custom-designed SNAP-loss function. Online hardest negative mining is used to select the appropriate negative examples for optimal training performance. We use 4.8 million sextuplets obtained from the NIST and MassIVE peptide libraries to train the network and demonstrate that for closed search, SpeCollate is able to perform better than Crux and MSFragger in terms of the number of peptide-spectrum matches (PSMs) and unique peptides identified under 1% FDR for real-world data. SpeCollate also identifies a large number of peptides not reported by either Crux or MSFragger. To the best of our knowledge, our proposed SpeCollate is the first deep-learning network that can determine the cross-modal similarity between peptides and mass-spectra for MS-based proteomics. We believe SpeCollate is significant progress towards developing machine-learning solutions for MS-based omics data analysis. SpeCollate is available at https://deepspecs.github.io/.

scholarly journals UAVs in rail damage image diagnostics supported by deep-learning networks

2021 ◽  
Vol 11 (1) ◽  
pp. 339-348
Author(s):  
Piotr Bojarczak ◽  
Piotr Lesiak
Keyword(s):  
Deep Learning ◽  
Head Width ◽  
Learning Networks ◽  
Image Brightness ◽  
Learning Network ◽  
Rail Head ◽  
Image Recording ◽  
Python Language ◽  
Deep Learning Network ◽  
Efficiency Rate

Abstract The article uses images from Unmanned Aerial Vehicles (UAVs) for rail diagnostics. The main advantage of such a solution compared to traditional surveys performed with measuring vehicles is the elimination of decreased train traffic. The authors, in the study, limited themselves to the diagnosis of hazardous split defects in rails. An algorithm has been proposed to detect them with an efficiency rate of about 81% for defects not less than 6.9% of the rail head width. It uses the FCN-8 deep-learning network, implemented in the Tensorflow environment, to extract the rail head by image segmentation. Using this type of network for segmentation increases the resistance of the algorithm to changes in the recorded rail image brightness. This is of fundamental importance in the case of variable conditions for image recording by UAVs. The detection of these defects in the rail head is performed using an algorithm in the Python language and the OpenCV library. To locate the defect, it uses the contour of a separate rail head together with a rectangle circumscribed around it. The use of UAVs together with artificial intelligence to detect split defects is an important element of novelty presented in this work.

scholarly journals BioECG: Improving ECG Biometrics with Deep Learning and Enhanced Datasets

2021 ◽  
Vol 11 (13) ◽  
pp. 5880
Author(s):  
Paloma Tirado-Martin ◽  
Raul Sanchez-Reillo
Keyword(s):  
Deep Learning ◽  
Temporal Variations ◽  
Physical Activities ◽  
Learning Tools ◽  
Biometric Recognition ◽  
Learning Network ◽  
Deep Learning Network ◽  
Electrocardiogram Ecg

Nowadays, Deep Learning tools have been widely applied in biometrics. Electrocardiogram (ECG) biometrics is not the exception. However, the algorithm performances rely heavily on a representative dataset for training. ECGs suffer constant temporal variations, and it is even more relevant to collect databases that can represent these conditions. Nonetheless, the restriction in database publications obstructs further research on this topic. This work was developed with the help of a database that represents potential scenarios in biometric recognition as data was acquired in different days, physical activities and positions. The classification was implemented with a Deep Learning network, BioECG, avoiding complex and time-consuming signal transformations. An exhaustive tuning was completed including variations in enrollment length, improving ECG verification for more complex and realistic biometric conditions. Finally, this work studied one-day and two-days enrollments and their effects. Two-days enrollments resulted in huge general improvements even when verification was accomplished with more unstable signals. EER was improved in 63% when including a change of position, up to almost 99% when visits were in a different day and up to 91% if the user experienced a heartbeat increase after exercise.

scholarly journals Method for Diagnosing the Bone Marrow Edema of Sacroiliac Joint in Patients with Axial Spondyloarthritis Using Magnetic Resonance Image Analysis Based on Deep Learning

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1156
Author(s):  
Kang Hee Lee ◽  
Sang Tae Choi ◽  
Guen Young Lee ◽  
You Jung Ha ◽  
Sang-Il Choi
Keyword(s):  
Bone Marrow ◽  
Deep Learning ◽  
Bone Marrow Edema ◽  
Axial Spondyloarthritis ◽  
Mr Images ◽  
Sacroiliac Joints ◽  
Learning Network ◽  
Active Sacroiliitis ◽  
Deep Learning Network ◽  
Marrow Edema

Axial spondyloarthritis (axSpA) is a chronic inflammatory disease of the sacroiliac joints. In this study, we develop a method for detecting bone marrow edema by magnetic resonance (MR) imaging of the sacroiliac joints and a deep-learning network. A total of 815 MR images of the sacroiliac joints were obtained from 60 patients diagnosed with axSpA and 19 healthy subjects. Gadolinium-enhanced fat-suppressed T1-weighted oblique coronal images were used for deep learning. Active sacroiliitis was defined as bone marrow edema, and the following processes were performed: setting the region of interest (ROI) and normalizing it to a size suitable for input to a deep-learning network, determining bone marrow edema using a convolutional-neural-network-based deep-learning network for individual MR images, and determining sacroiliac arthritis in subject examinations based on the classification results of individual MR images. About 70% of the patients and normal subjects were randomly selected for the training dataset, and the remaining 30% formed the test dataset. This process was repeated five times to calculate the average classification rate of the five-fold sets. The gradient-weighted class activation mapping method was used to validate the classification results. In the performance analysis of the ResNet18-based classification network for individual MR images, use of the ROI showed excellent detection performance of bone marrow edema with 93.55 ± 2.19% accuracy, 92.87 ± 1.27% recall, and 94.69 ± 3.03% precision. The overall performance was additionally improved using a median filter to reflect the context information. Finally, active sacroiliitis was diagnosed in individual subjects with 96.06 ± 2.83% accuracy, 100% recall, and 94.84 ± 3.73% precision. This is a pilot study to diagnose bone marrow edema by deep learning based on MR images, and the results suggest that MR analysis using deep learning can be a useful complementary means for clinicians to diagnose bone marrow edema.

Automated ECG Classification Based on 1D Deep Learning Network

Methods ◽  
2021 ◽  
Author(s):  
Chun-Yen Chen ◽  
Yan-Ting Lin ◽  
Shie-Jue Lee ◽  
Wei-Chung Tsai ◽  
Tien-Chi Huang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Learning Network ◽  
Deep Learning Network
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