Large scale prediction of groundwater nitrate concentrations from spatial data using machine learning

2019 ◽  
Vol 668 ◽  
pp. 1317-1327 ◽  
Author(s):  
Lukas Knoll ◽  
Lutz Breuer ◽  
Martin Bach
2019 ◽  
Vol 1 ◽  
pp. 1-2 ◽  
Author(s):  
Izabela Karsznia ◽  
Karolina Sielicka

<p><strong>Abstract.</strong> The decision about removing or maintaining an object while changing detail level requires taking into account many features of the object itself and its surrounding. Automatic generalization is the optimal way to obtain maps at various scales, based on a single spatial database, storing up-to-date information with a high level of spatial accuracy. Researchers agree on the need for fully automating the generalization process (Stoter et al., 2016). Numerous research centres, cartographic agencies as well as commercial companies have undertaken successful attempts of implementing certain generalization solutions (Stoter et al., 2009, 2014, 2016; Regnauld, 2015; Burghardt et al., 2008; Chaundhry and Mackaness, 2008). Nevertheless, an effective and consistent methodology for generalizing small-scale maps has not gained enough attention so far, as most of the conducted research has focused on the acquisition of large-scale maps (Stoter et al., 2016). The presented research aims to fulfil this gap by exploring new variables, which are of the key importance in the automatic settlement selection process at small scales. Addressing this issue is an essential step to propose new algorithms for effective and automatic settlement selection that will contribute to enriching, the sparsely filled small-scale generalization toolbox.</p><p>The main idea behind this research is using machine learning (ML) for the new variable exploration which can be important in the automatic settlement generalization in small-scales. For automation of the generalization process, cartographic knowledge has to be collected and formalized. So far, a few approaches based on the use of ML have already been proposed. One of the first attempts to determine generalization parameters with the use of ML was performed by Weibel et al. (1995). The learning material was the observation of cartographers manual work. Also, Mustière tried to identify the optimal sequence of the generalization operators for the roads using ML (1998). A different approach was presented by Sester (2000). The goal was to extract the cartographic knowledge from spatial data characteristics, especially from the attributes and geometric properties of objects, regularities and repetitive patterns that govern object selection with the use of decision trees. Lagrange et al. (2000), Balboa and López (2008) also used ML techniques, namely neural networks to generalize line objects. Recently, Sester et al. (2018) proposed the application of deep learning for the task of building generalization. As noticed by Sester et al. (2018), these ideas, although interesting, remained proofs of concepts only. Moreover, they concerned topographic databases and large-scale maps. Promising results of automatic settlement selection in small scales was reported by Karsznia and Weibel (2018). To improve the settlement selection process, they have used data enrichment and ML. Thanks to classification models based on the decision trees, they explored new variables that are decisive in the settlement selection process. However, they have also concluded that there is probably still more “deep knowledge” to be discovered, possibly linked to further variables that were not included in their research. Thus the motivation for this research is to fulfil this research gap and look for additional, essential variables governing settlement selection in small scales.</p>


2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.


2021 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
Jose L. Medina-Franco

<p>Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.</p>


2019 ◽  
Author(s):  
Ryther Anderson ◽  
Achay Biong ◽  
Diego Gómez-Gualdrón

<div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div>


2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.


Author(s):  
Mark Endrei ◽  
Chao Jin ◽  
Minh Ngoc Dinh ◽  
David Abramson ◽  
Heidi Poxon ◽  
...  

Rising power costs and constraints are driving a growing focus on the energy efficiency of high performance computing systems. The unique characteristics of a particular system and workload and their effect on performance and energy efficiency are typically difficult for application users to assess and to control. Settings for optimum performance and energy efficiency can also diverge, so we need to identify trade-off options that guide a suitable balance between energy use and performance. We present statistical and machine learning models that only require a small number of runs to make accurate Pareto-optimal trade-off predictions using parameters that users can control. We study model training and validation using several parallel kernels and more complex workloads, including Algebraic Multigrid (AMG), Large-scale Atomic Molecular Massively Parallel Simulator, and Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics. We demonstrate that we can train the models using as few as 12 runs, with prediction error of less than 10%. Our AMG results identify trade-off options that provide up to 45% improvement in energy efficiency for around 10% performance loss. We reduce the sample measurement time required for AMG by 90%, from 13 h to 74 min.


Author(s):  
Yexuan Shi ◽  
Yongxin Tong ◽  
Yuxiang Zeng ◽  
Zimu Zhou ◽  
Bolin Ding ◽  
...  

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