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      Accelerating Flash Calculation through Deep Learning Methods

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          Abstract

          In the past two decades, researchers have made remarkable progress in accelerating flash calculation, which is very useful in a variety of engineering processes. In this paper, general phase splitting problem statements and flash calculation procedures using the Successive Substitution Method are reviewed, while the main shortages are pointed out. Two acceleration methods, Newton's method and the Sparse Grids Method are presented afterwards as a comparison with the deep learning model proposed in this paper. A detailed introduction from artificial neural networks to deep learning methods is provided here with the authors' own remarks. Factors in the deep learning model are investigated to show their effect on the final result. A selected model based on that has been used in a flash calculation predictor with comparison with other methods mentioned above. It is shown that results from the optimized deep learning model meet the experimental data well with the shortest CPU time. More comparison with experimental data has been conducted to show the robustness of our model.

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          DEEPre: sequence-based enzyme EC number prediction by deep learning

          Yu Li, Sheng WANG, Ramzan Umarov … (2017)
          Abstract Motivation Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive to experimentally determine the function of every enzyme. Therefore, computational enzyme function prediction has become increasingly important. In this paper, we develop such an approach, determining the enzyme function by predicting the Enzyme Commission number. Results We propose an end-to-end feature selection and classification model training approach, as well as an automatic and robust feature dimensionality uniformization method, DEEPre, in the field of enzyme function prediction. Instead of extracting manually crafted features from enzyme sequences, our model takes the raw sequence encoding as inputs, extracting convolutional and sequential features from the raw encoding based on the classification result to directly improve the prediction performance. The thorough cross-fold validation experiments conducted on two large-scale datasets show that DEEPre improves the prediction performance over the previous state-of-the-art methods. In addition, our server outperforms five other servers in determining the main class of enzymes on a separate low-homology dataset. Two case studies demonstrate DEEPre’s ability to capture the functional difference of enzyme isoforms. Availability and implementation The server could be accessed freely at http://www.cbrc.kaust.edu.sa/DEEPre. Supplementary information Supplementary data are available at Bioinformatics online.
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            Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape

            Hanjun Dai, Ramzan Umarov, Hiroyuki Kuwahara … (2017)
            Abstract Motivation An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods. Availability and implementation Our program is freely available at https://github.com/ramzan1990/sequence2vec. Contact xin.gao@kaust.edu.sa or lsong@cc.gatech.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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              DLBI: deep learning guided Bayesian inference for structure reconstruction of super-resolution fluorescence microscopy

              Yu Li, Fan Xu, Fa Zhang … (2018)
              Abstract Motivation Super-resolution fluorescence microscopy with a resolution beyond the diffraction limit of light, has become an indispensable tool to directly visualize biological structures in living cells at a nanometer-scale resolution. Despite advances in high-density super-resolution fluorescent techniques, existing methods still have bottlenecks, including extremely long execution time, artificial thinning and thickening of structures, and lack of ability to capture latent structures. Results Here, we propose a novel deep learning guided Bayesian inference (DLBI) approach, for the time-series analysis of high-density fluorescent images. Our method combines the strength of deep learning and statistical inference, where deep learning captures the underlying distribution of the fluorophores that are consistent with the observed time-series fluorescent images by exploring local features and correlation along time-axis, and statistical inference further refines the ultrastructure extracted by deep learning and endues physical meaning to the final image. In particular, our method contains three main components. The first one is a simulator that takes a high-resolution image as the input, and simulates time-series low-resolution fluorescent images based on experimentally calibrated parameters, which provides supervised training data to the deep learning model. The second one is a multi-scale deep learning module to capture both spatial information in each input low-resolution image as well as temporal information among the time-series images. And the third one is a Bayesian inference module that takes the image from the deep learning module as the initial localization of fluorophores and removes artifacts by statistical inference. Comprehensive experimental results on both real and simulated datasets demonstrate that our method provides more accurate and realistic local patch and large-field reconstruction than the state-of-the-art method, the 3B analysis, while our method is more than two orders of magnitude faster. Availability and implementation The main program is available at https://github.com/lykaust15/DLBI Supplementary information Supplementary data are available at Bioinformatics online.
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                Author and article information

                Journal
                Publication date Created: 19 September 2018
                Article
                ArXiV ID: 1809.07311
                SO-VID: d505e97c-a71c-40d6-be22-30ce1af53256
                License:

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

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                Categories cs.CE physics.chem-ph physics.comp-ph

                ScienceOpen disciplines: Applied computer science,Mathematical & Computational physics,Physical chemistry
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                ScienceOpen disciplines: Applied computer science, Mathematical & Computational physics, Physical chemistry

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