A Deep Learning and Ontology Based Framework for Textual Requirements Analysis and Conceptual Model Generation

Author(s):  
Yongjun Qie ◽  
Huanhuan Shen ◽  
Aishan Liu
2018 ◽  
Vol 35 (4) ◽  
pp. 691-693 ◽  
Author(s):  
Sheng Wang ◽  
Shiyang Fei ◽  
Zongan Wang ◽  
Yu Li ◽  
Jinbo Xu ◽  
...  

Abstract Motivation PredMP is the first web service, to our knowledge, that aims at de novo prediction of the membrane protein (MP) 3D structure followed by the embedding of the MP into the lipid bilayer for visualization. Our approach is based on a high-throughput Deep Transfer Learning (DTL) method that first predicts MP contacts by learning from non-MPs and then predicts the 3D model of the MP using the predicted contacts as distance restraints. This algorithm is derived from our previous Deep Learning (DL) method originally developed for soluble protein contact prediction, which has been officially ranked No. 1 in CASP12. The DTL framework in our approach overcomes the challenge that there are only a limited number of solved MP structures for training the deep learning model. There are three modules in the PredMP server: (i) The DTL framework followed by the contact-assisted folding protocol has already been implemented in RaptorX-Contact, which serves as the key module for 3D model generation; (ii) The 1D annotation module, implemented in RaptorX-Property, is used to predict the secondary structure and disordered regions; and (iii) the visualization module to display the predicted MPs embedded in the lipid bilayer guided by the predicted transmembrane topology. Results Tested on 510 non-redundant MPs, our server predicts correct folds for ∼290 MPs, which significantly outperforms existing methods. Tested on a blind and live benchmark CAMEO from September 2016 to January 2018, PredMP can successfully model all 10 MPs belonging to the hard category. Availability and implementation PredMP is freely accessed on the web at http://www.predmp.com. Supplementary information Supplementary data are available at Bioinformatics online.


IEEE Access ◽  
2019 ◽  
Vol 7 ◽  
pp. 62734-62749 ◽  
Author(s):  
Kyi Thar ◽  
Thant Zin Oo ◽  
Yan Kyaw Tun ◽  
Do Hyeon Kim ◽  
Ki Tae Kim ◽  
...  

2020 ◽  
Author(s):  
Basil Kraft ◽  
Martin Jung ◽  
Marco Körner ◽  
Markus Reichstein

<p>Deep (recurrent) neural networks have proven very useful to model multivariate sequential data streams of complex dynamic natural systems and have already been successfully applied to model hydrological processes. Compared to physically based models, however, the internal representation of a neural network is not directly interpretable and model predictions often lack physical consistency. Hybrid modeling is a promising approach that synergizes the advantage of process-based modeling (interpretability, theoretical foundations) and deep learning (data adaptivity, less prior knowledge required): By combining these two approaches, flexible and partially interpretable models can be created that have the potential to advance the understanding and predictability of environmental systems.</p><p>Here, we implement such a hybrid hydrological model on a global scale. The model consists of three main blocks: 1) A Long-Short-Term Memory (LSTM) model, which extracts temporal features from the meteorological forcing time-series. 2) A multi-branch neural network comprising of independent, fully connected layers, taking the LSTM state as input and yielding a set of latent, interpretable variables (e.g. soil moisture recharge). 3) A conceptual model block that implements hydrological balance equations, driven by the above interpretable variables. The model is trained simultaneously on global observation-based products of total water storage, snow water equivalent, evapotranspiration and runoff. To combine the different loss terms, we use self-paced task uncertainty weighing as done in state-of-the-art multi-task learning.</p><p>Preliminary results suggest that the hybrid modeling approach captures global patterns of the hydrological cycle’s variability that are consistent with observations and our process understanding. The approach opens doors to novel data-driven simulations, attribution and diagnostic assessments of water cycle variations globally. The presented approach is—to our knowledge—the first application of the hybrid approach to model environmental systems.</p>


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