Cheminformatics in MS-based environmental exposomics: Current achievements and future directions

Compound annotation using MS/MS data is the major bottleneck in interpretation of mass spectrometry data during non-targeted screening and suspect screening exposomics studies. Apart from compound identification using available databases or mass spectral libraries, the true challenge comes when completely new compounds have to be identified. Along with recent advances in MS instrumentation that set grounds to a new revolutionary age in environmental exposomics, a multitude of cheminformatics annotation approaches has been developed. Herein, we review the basic principles of the cutting-edge cheminformatics MS-based approaches employed in eco-exposome annotation.We give a solid background discussing the eco-exposome concept in relation to the advances in MS instrumentation, and define the three crucial cheminformatics tasks used in the eco-exposome annotation: molecular formula assignment, compound prioritization and compound annotation. The basic principles of compound annotation are discussed, which are based on three approaches of utilizing structural information inherent to MS data. These involve direct, indirect and joint annotation approaches. We assess their performance through the ability to annotate eco-exposome constituents. We discuss future perspectives and give directions to new annotation strategies and performance evaluation protocols aiming to solve current issues hampering the incorporation of cheminformatics annotation approaches in regular eco-exposome annotation workflows.     

Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning

Nuclear magnetic resonance (NMR) spectroscopy serves as an indispensable tool in chemistry and biology but often suffers from long experimental times. We present a proof‐of‐concept of the application of deep learning and neural networks for high‐quality, reliable, and very fast NMR spectra reconstruction from limited experimental data. We show that the neural network training can be achieved using solely synthetic NMR signals, which lifts the prohibiting demand for a large volume of realistic training data usually required for a deep learning approach.     

Prediction of 5-hydroxytryptamine transporter inhibitors based on machine learning

In patients with depression, the use of 5-HT reuptake inhibitors can improve the condition. Machine learning methods can be used in ligand-based activity prediction processes. In order to predict SERT inhibitors, the SERT inhibitor data from the ChEMBL database was screened and pre-processed. Then 4 machine learning methods (LR, SVM, RF, and KNN) and 4 molecular fingerprints (CDK, Graph, MACCS, and PubChem) were used to build 16 prediction models. The top 5 models of accuracy (Q) in the cross-validation of training set were used to build three different ensemble learning models. In the test1 set, the VOT_CLF3 model had the largest SP (0.871), Q (0.869), AUC (0.919), and MCC (0.728). In the unbalanced test2 set, VOT_CLF3 had the largest SE (0.857), SP (0.867), Q (0.865) and MCC (0.639). VOT_CLF3 was recommended for the virtual screening process of SERT inhibitors. In addition, 12 molecular structural alerts that frequently appear in SERT inhibitors were found (P < 0.05), which provided important reference value for the design work of SERT inhibitors.     

Density Functional Theory as a Data Science

The development of density functional theory (DFT) functionals and physical corrections are reviewed focusing on the physical meanings and the semiempirical parameters from the viewpoint of data science. This review shows that DFT exchange‐correlation functionals have been developed under many strict physical conditions with minimizing the number of the semiempirical parameters, except for some recent functionals. Major physical corrections for exchange‐correlation function‐ als are also shown to have clear physical meanings independent of the functionals, though they inevitably require minimum semiempirical parameters dependent on the functionals combined. We, therefore, interpret that DFT functionals with physical corrections are the most sophisticated target functions that are physically legitimated, even from the viewpoint of data science.     

Combining convolutional neural networks and in‐line near‐infrared spectroscopy for real‐time monitoring of the chromatographic elution process in commercial production of notoginseng total saponins

The chromatographic elution process is a key step in the production of notoginseng total saponins. Due to quality variability of loading samples and resin capacity decreasing over cycle time, saponins, especially the five main saponins of notoginseng total saponins, need to be monitored in real time during the elution process. In this study, convolutional neural networks, one of the most popular deep learning methods, were used to develop quantitative calibration models based on in‐line near‐infrared spectroscopy for notoginsenoside R₁, ginsenosides Rg₁, Re, Rb₁ and Rd, and their sum concentration, with root mean square error of prediction values of 0.87, 2.76, 0.60, 1.57, 0.28, and 4.99 mg/mL, respectively. Partial least squares calibration models were also developed for model performance comparison. Results show predicted concentration profiles outputted by both the convolutional neural network models and partial least squares models show agreements with the real trends defined by reference measurements, and can be used for elution process monitoring and endpoint determination. To the best of our knowledge, this is the first reported case study of combining convolutional neural networks and in‐line near‐infrared spectroscopy for monitoring of the chromatographic elution process in commercial production of botanical drug products.     

Machine-Learning Adsorption on Binary Alloy Surfaces for Catalyst Screening

Over the last few years, machine learning is gradually becoming an essential approach for the investigation of heterogeneous catalysis. As one of the important catalysts, binary alloys have attracted extensive attention for the screening of bifunctional catalysts. Here we present a holistic framework for machine learning approach to rapidly predict adsorption energies on the surfaces of metals and binary alloys. We evaluate different machine-learning methods to understand their applicability to the problem and combine a tree-ensemble method with a compressed-sensing method to construct decision trees for about 60000 adsorption data. Compared to linear scaling relations, our approach enables to make more accurate predictions lowering predictive root-mean-square error by a factor of two and more general to predict adsorption energies of various adsorbates on thousands of binary alloys surfaces, thus paving the way for the discovery of novel bimetallic catalysts.     

固相萃取-离子色谱-积分脉冲安培法测定人血清中游离氨基酸

比较了磺基水杨酸和无水甲醇沉淀人血清中蛋白质的效果,优化了国产732型阳离子交换树脂进行固相萃取净化的条件和Dionex-600离子色谱分析系统的梯度淋洗条件。用该离子色谱仪检测了谷氨酰胺等14种氨基酸,结果表明,峰面积-浓度的校正曲线的相关系数为0.9900~0.9995,检出限为0.02~0.59mg/L;峰面积的相对标准偏差为1.9%~10.4%;回收率为80.6%~114.8%。     

An Edge Server Placement Method Based on Reinforcement Learning

In mobile edge computing systems, the edge server placement problem is mainly tackled as a multi-objective optimization problem and solved with mixed integer programming, heuristic or meta-heuristic algorithms, etc. These methods, however, have profound defect implications such as poor scalability, local optimal solutions, and parameter tuning difficulties. To overcome these defects, we propose a novel edge server placement algorithm based on deep q-network and reinforcement learning, dubbed DQN-ESPA, which can achieve optimal placements without relying on previous placement experience. In DQN-ESPA, the edge server placement problem is modeled as a Markov decision process, which is formalized with the state space, action space and reward function, and it is subsequently solved using a reinforcement learning algorithm. Experimental results using real datasets from Shanghai Telecom show that DQN-ESPA outperforms state-of-the-art algorithms such as simulated annealing placement algorithm (SAPA), Top-K placement algorithm (TKPA), K-Means placement algorithm (KMPA), and random placement algorithm (RPA). In particular, with a comprehensive consideration of access delay and workload balance, DQN-ESPA achieves up to 13.40% and 15.54% better placement performance for 100 and 300 edge servers respectively.     

A Banking Platform to Leverage Data Driven Marketing with Machine Learning

Payment data is one of the most valuable assets that retail banks can leverage as the major competitive advantage with respect to new entrants such as Fintech companies or giant internet companies. In marketing, the value behind data relates to the power of encoding customer preferences: the better you know your customer, the better your marketing strategy. In this paper, we present a B2B2C lead generation application based on payment transaction data within the online banking system. In this approach, the bank is an intermediary between its private customers and merchants. The bank uses its competence in Machine Learning driven marketing to build a lead generation application that helps merchants run data driven campaigns through the banking channels to reach retail customers. The bank’s retail customers trade the utility hidden in its payment transaction data for special offers and discounts offered by merchants. During the entire process banks protects the privacy of the retail customer.     

A Hybrid Method Using HAVOK Analysis and Machine Learning for Predicting Chaotic Time Series

The prediction of chaotic time series systems has remained a challenging problem in recent decades. A hybrid method using Hankel Alternative View Of Koopman (HAVOK) analysis and machine learning (HAVOK-ML) is developed to predict chaotic time series. HAVOK-ML simulates the time series by reconstructing a closed linear model so as to achieve the purpose of prediction. It decomposes chaotic dynamics into intermittently forced linear systems by HAVOK analysis and estimates the external intermittently forcing term using machine learning. The prediction performance evaluations confirm that the proposed method has superior forecasting skills compared with existing prediction methods.