scholarly journals BreakNet: detecting deletions using long reads and a deep learning approach

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junwei Luo ◽  
Hongyu Ding ◽  
Jiquan Shen ◽  
Haixia Zhai ◽  
Zhengjiang Wu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Genetic Diseases ◽  
Structural Variations ◽  
Short Term ◽  
New Approach ◽  
Feature Vectors ◽  
Long Reads ◽  
Long Read ◽  
Long Short Term Memory

Abstract Background Structural variations (SVs) occupy a prominent position in human genetic diversity, and deletions form an important type of SV that has been suggested to be associated with genetic diseases. Although various deletion calling methods based on long reads have been proposed, a new approach is still needed to mine features in long-read alignment information. Recently, deep learning has attracted much attention in genome analysis, and it is a promising technique for calling SVs. Results In this paper, we propose BreakNet, a deep learning method that detects deletions by using long reads. BreakNet first extracts feature matrices from long-read alignments. Second, it uses a time-distributed convolutional neural network (CNN) to integrate and map the feature matrices to feature vectors. Third, BreakNet employs a bidirectional long short-term memory (BLSTM) model to analyse the produced set of continuous feature vectors in both the forward and backward directions. Finally, a classification module determines whether a region refers to a deletion. On real long-read sequencing datasets, we demonstrate that BreakNet outperforms Sniffles, SVIM and cuteSV in terms of their F1 scores. The source code for the proposed method is available from GitHub at https://github.com/luojunwei/BreakNet. Conclusions Our work shows that deep learning can be combined with long reads to call deletions more effectively than existing methods.

scholarly journals Application of Rough and Fuzzy Set Theory for Prediction of Stochastic Wind Speed Data Using Long Short-Term Memory

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 924
Author(s):  
Moslem Imani ◽  
Hoda Fakour ◽  
Wen-Hau Lan ◽  
Huan-Chin Kao ◽  
Chi Ming Lee ◽  
...  
Keyword(s):  
Deep Learning ◽  
Wind Speed ◽  
Set Theory ◽  
Rough Set ◽  
Fuzzy Set Theory ◽  
Short Term Memory ◽  
Learning Model ◽  
Short Term ◽  
Long Short Term Memory ◽  
Deep Learning Model

Despite the great significance of precisely forecasting the wind speed for development of the new and clean energy technology and stable grid operators, the stochasticity of wind speed makes the prediction a complex and challenging task. For improving the security and economic performance of power grids, accurate short-term wind power forecasting is crucial. In this paper, a deep learning model (Long Short-term Memory (LSTM)) has been proposed for wind speed prediction. Knowing that wind speed time series is nonlinear stochastic, the mutual information (MI) approach was used to find the best subset from the data by maximizing the joint MI between subset and target output. To enhance the accuracy and reduce input characteristics and data uncertainties, rough set and interval type-2 fuzzy set theory are combined in the proposed deep learning model. Wind speed data from an international airport station in the southern coast of Iran Bandar-Abbas City was used as the original input dataset for the optimized deep learning model. Based on the statistical results, the rough set LSTM (RST-LSTM) model showed better prediction accuracy than fuzzy and original LSTM, as well as traditional neural networks, with the lowest error for training and testing datasets in different time horizons. The suggested model can support the optimization of the control approach and the smooth procedure of power system. The results confirm the superior capabilities of deep learning techniques for wind speed forecasting, which could also inspire new applications in meteorology assessment.

scholarly journals Schätzung der Verdunstung mithilfe von Machine- und Deep Learning-Methoden

2021 ◽  
Author(s):  
Claire Brenner ◽  
Jonathan Frame ◽  
Grey Nearing ◽  
Karsten Schulz
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Sich Eine ◽  
Short Term ◽  
Term Memory ◽  
Neuronales Netzwerk ◽  
Long Short Term Memory

ZusammenfassungDie Verdunstung ist ein entscheidender Prozess im globalen Wasser‑, Energie- sowie Kohlenstoffkreislauf. Daten zur räumlich-zeitlichen Dynamik der Verdunstung sind daher von großer Bedeutung für Klimamodellierungen, zur Abschätzung der Auswirkungen der Klimakrise sowie nicht zuletzt für die Landwirtschaft.In dieser Arbeit wenden wir zwei Machine- und Deep Learning-Methoden für die Vorhersage der Verdunstung mit täglicher und halbstündlicher Auflösung für Standorte des FLUXNET-Datensatzes an. Das Long Short-Term Memory Netzwerk ist ein rekurrentes neuronales Netzwerk, welchen explizit Speichereffekte berücksichtigt und Zeitreihen der Eingangsgrößen analysiert (entsprechend physikalisch-basierten Wasserbilanzmodellen). Dem gegenüber gestellt werden Modellierungen mit XGBoost, einer Entscheidungsbaum-Methode, die in diesem Fall nur Informationen für den zu bestimmenden Zeitschritt erhält (entsprechend physikalisch-basierten Energiebilanzmodellen). Durch diesen Vergleich der beiden Modellansätze soll untersucht werden, inwieweit sich durch die Berücksichtigung von Speichereffekten Vorteile für die Modellierung ergeben.Die Analysen zeigen, dass beide Modellansätze gute Ergebnisse erzielen und im Vergleich zu einem ausgewerteten Referenzdatensatz eine höhere Modellgüte aufweisen. Vergleicht man beide Modelle, weist das LSTM im Mittel über alle 153 untersuchten Standorte eine bessere Übereinstimmung mit den Beobachtungen auf. Allerdings zeigt sich eine Abhängigkeit der Güte der Verdunstungsvorhersage von der Vegetationsklasse des Standorts; vor allem wärmere, trockene Standorte mit kurzer Vegetation werden durch das LSTM besser repräsentiert, wohingegen beispielsweise in Feuchtgebieten XGBoost eine bessere Übereinstimmung mit den Beobachtung liefert. Die Relevanz von Speichereffekten scheint daher zwischen Ökosystemen und Standorten zu variieren.Die präsentierten Ergebnisse unterstreichen das Potenzial von Methoden der künstlichen Intelligenz für die Beschreibung der Verdunstung.

scholarly journals Multiple Pedestrians and Vehicles Tracking in Aerial Imagery Using a Convolutional Neural Network

2021 ◽  
Vol 13 (10) ◽  
pp. 1953
Author(s):  
Seyed Majid Azimi ◽  
Maximilian Kraus ◽  
Reza Bahmanyar ◽  
Peter Reinartz
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Object Tracking ◽  
Short Term Memory ◽  
Aerial Imagery ◽  
Future Research ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

In this paper, we address various challenges in multi-pedestrian and vehicle tracking in high-resolution aerial imagery by intensive evaluation of a number of traditional and Deep Learning based Single- and Multi-Object Tracking methods. We also describe our proposed Deep Learning based Multi-Object Tracking method AerialMPTNet that fuses appearance, temporal, and graphical information using a Siamese Neural Network, a Long Short-Term Memory, and a Graph Convolutional Neural Network module for more accurate and stable tracking. Moreover, we investigate the influence of the Squeeze-and-Excitation layers and Online Hard Example Mining on the performance of AerialMPTNet. To the best of our knowledge, we are the first to use these two for regression-based Multi-Object Tracking. Additionally, we studied and compared the L1 and Huber loss functions. In our experiments, we extensively evaluate AerialMPTNet on three aerial Multi-Object Tracking datasets, namely AerialMPT and KIT AIS pedestrian and vehicle datasets. Qualitative and quantitative results show that AerialMPTNet outperforms all previous methods for the pedestrian datasets and achieves competitive results for the vehicle dataset. In addition, Long Short-Term Memory and Graph Convolutional Neural Network modules enhance the tracking performance. Moreover, using Squeeze-and-Excitation and Online Hard Example Mining significantly helps for some cases while degrades the results for other cases. In addition, according to the results, L1 yields better results with respect to Huber loss for most of the scenarios. The presented results provide a deep insight into challenges and opportunities of the aerial Multi-Object Tracking domain, paving the way for future research.

Ionospheric TEC prediction using Long Short-Term Memory deep learning network

2021 ◽  
Vol 366 (1) ◽  
Author(s):  
Zhichao Wen ◽  
Shuhui Li ◽  
Lihua Li ◽  
Bowen Wu ◽  
Jianqiang Fu
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Short Term ◽  
Term Memory ◽  
Learning Network ◽  
Long Short Term Memory ◽  
Deep Learning Network

scholarly journals Near Real-Time Global Solar Radiation Forecasting at Multiple Time-Step Horizons Using the Long Short-Term Memory Network

Energies ◽  
2020 ◽  
Vol 13 (14) ◽  
pp. 3517 ◽  
Author(s):  
Anh Ngoc-Lan Huynh ◽  
Ravinesh C. Deo ◽  
Duc-Anh An-Vo ◽  
Mumtaz Ali ◽  
Nawin Raj ◽  
...  
Keyword(s):  
Deep Learning ◽  
Solar Radiation ◽  
Short Term Memory ◽  
Global Solar Radiation ◽  
Multiple Time ◽  
Short Term ◽  
Time Step ◽  
Term Memory ◽  
Multiple Time Step ◽  
Long Short Term Memory

This paper aims to develop the long short-term memory (LSTM) network modelling strategy based on deep learning principles, tailored for the very short-term, near-real-time global solar radiation (GSR) forecasting. To build the prescribed LSTM model, the partial autocorrelation function is applied to the high resolution, 1 min scaled solar radiation dataset that generates statistically significant lagged predictor variables describing the antecedent behaviour of GSR. The LSTM algorithm is adopted to capture the short- and the long-term dependencies within the GSR data series patterns to accurately predict the future GSR at 1, 5, 10, 15, and 30 min forecasting horizons. This objective model is benchmarked at a solar energy resource rich study site (Bac-Ninh, Vietnam) against the competing counterpart methods employing other deep learning, a statistical model, a single hidden layer and a machine learning-based model. The LSTM model generates satisfactory predictions at multiple-time step horizons, achieving a correlation coefficient exceeding 0.90, outperforming all of the counterparts. In accordance with robust statistical metrics and visual analysis of all tested data, the study ascertains the practicality of the proposed LSTM approach to generate reliable GSR forecasts. The Diebold–Mariano statistic test also shows LSTM outperforms the counterparts in most cases. The study confirms the practical utility of LSTM in renewable energy studies, and broadly in energy-monitoring devices tailored for other energy variables (e.g., hydro and wind energy).

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