scholarly journals The relevant range of scales for multi-scale contextual spatial modelling

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Thorsten Behrens ◽  
Raphael A. Viscarra Rossel ◽  
Ruth Kerry ◽  
Robert MacMillan ◽  
Karsten Schmidt ◽  
...  
Keyword(s):  
Machine Learning ◽  
Spatial Autocorrelation ◽  
Multiple Scales ◽  
A Priori ◽  
Computational Cost ◽  
Scale Space ◽  
Spatial Modelling ◽  
Environmental Models ◽  
Covariate Information ◽  
Relevant Range

Abstract Spatial autocorrelation in the residuals of spatial environmental models can be due to missing covariate information. In many cases, this spatial autocorrelation can be accounted for by using covariates from multiple scales. Here, we propose a data-driven, objective and systematic method for deriving the relevant range of scales, with distinct upper and lower scale limits, for spatial modelling with machine learning and evaluated its effect on modelling accuracy. We also tested an approach that uses the variogram to see whether such an effective scale space can be approximated a priori and at smaller computational cost. Results showed that modelling with an effective scale space can improve spatial modelling with machine learning and that there is a strong correlation between properties of the variogram and the relevant range of scales. Hence, the variogram of a soil property can be used for a priori approximations of the effective scale space for contextual spatial modelling and is therefore an important analytical tool not only in geostatistics, but also for analyzing structural dependencies in contextual spatial modelling.

An Automated Machine Learning-Genetic Algorithm Framework With Active Learning for Design Optimization

2021 ◽  
Vol 143 (8) ◽  
Author(s):  
Opeoluwa Owoyele ◽  
Pinaki Pal ◽  
Alvaro Vidal Torreira
Keyword(s):  
Machine Learning ◽  
Active Learning ◽  
Design Optimization ◽  
Fuel Injection ◽  
A Priori ◽  
Computational Cost ◽  
Learning Approach ◽  
Data Generation ◽  
Compression Ignition Engine ◽  
Hyperparameter Selection

AbstractThe use of machine learning (ML)-based surrogate models is a promising technique to significantly accelerate simulation-driven design optimization of internal combustion (IC) engines, due to the high computational cost of running computational fluid dynamics (CFD) simulations. However, training the ML models requires hyperparameter selection, which is often done using trial-and-error and domain expertise. Another challenge is that the data required to train these models are often unknown a priori. In this work, we present an automated hyperparameter selection technique coupled with an active learning approach to address these challenges. The technique presented in this study involves the use of a Bayesian approach to optimize the hyperparameters of the base learners that make up a super learner model. In addition to performing hyperparameter optimization (HPO), an active learning approach is employed, where the process of data generation using simulations, ML training, and surrogate optimization is performed repeatedly to refine the solution in the vicinity of the predicted optimum. The proposed approach is applied to the optimization of a compression ignition engine with control parameters relating to fuel injection, in-cylinder flow, and thermodynamic conditions. It is demonstrated that by automatically selecting the best values of the hyperparameters, a 1.6% improvement in merit value is obtained, compared to an improvement of 1.0% with default hyperparameters. Overall, the framework introduced in this study reduces the need for technical expertise in training ML models for optimization while also reducing the number of simulations needed for performing surrogate-based design optimization.

Nanosecond Photodynamics Simulations of a Cis-Trans Isomerization Are Enabled by Machine Learning

2020 ◽  
Author(s):  
Jingbai Li ◽  
Patrick Reiser ◽  
André Eberhard ◽  
Pascal Friederich ◽  
Steven Lopez
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Excited State ◽  
Adaptive Sampling ◽  
Computational Cost ◽  
Ground Truth ◽  
Absolute Error ◽  
Photochemical Reactions ◽  
Computational Techniques ◽  
Full Potential

<p>Photochemical reactions are being increasingly used to construct complex molecular architectures with mild and straightforward reaction conditions. Computational techniques are increasingly important to understand the reactivities and chemoselectivities of photochemical isomerization reactions because they offer molecular bonding information along the excited-state(s) of photodynamics. These photodynamics simulations are resource-intensive and are typically limited to 1–10 picoseconds and 1,000 trajectories due to high computational cost. Most organic photochemical reactions have excited-state lifetimes exceeding 1 picosecond, which places them outside possible computational studies. Westermeyr <i>et al.</i> demonstrated that a machine learning approach could significantly lengthen photodynamics simulation times for a model system, methylenimmonium cation (CH<sub>2</sub>NH<sub>2</sub><sup>+</sup>).</p><p>We have developed a Python-based code, Python Rapid Artificial Intelligence <i>Ab Initio</i> Molecular Dynamics (PyRAI<sup>2</sup>MD), to accomplish the unprecedented 10 ns <i>cis-trans</i> photodynamics of <i>trans</i>-hexafluoro-2-butene (CF<sub>3</sub>–CH=CH–CF<sub>3</sub>) in 3.5 days. The same simulation would take approximately 58 years with ground-truth multiconfigurational dynamics. We proposed an innovative scheme combining Wigner sampling, geometrical interpolations, and short-time quantum chemical trajectories to effectively sample the initial data, facilitating the adaptive sampling to generate an informative and data-efficient training set with 6,232 data points. Our neural networks achieved chemical accuracy (mean absolute error of 0.032 eV). Our 4,814 trajectories reproduced the S<sub>1</sub> half-life (60.5 fs), the photochemical product ratio (<i>trans</i>: <i>cis</i> = 2.3: 1), and autonomously discovered a pathway towards a carbene. The neural networks have also shown the capability of generalizing the full potential energy surface with chemically incomplete data (<i>trans</i> → <i>cis</i> but not <i>cis</i> → <i>trans</i> pathways) that may offer future automated photochemical reaction discoveries.</p>

BAND NN: A Deep Learning Framework For Energy Prediction and Geometry Optimization of Organic Small Molecules

2019 ◽  
Author(s):  
Siddhartha Laghuvarapu ◽  
Yashaswi Pathak ◽  
U. Deva Priyakumar
Keyword(s):  
Machine Learning ◽  
Density Functional ◽  
Computational Cost ◽  
Geometry Optimization ◽  
Dft Methods ◽  
Energy Prediction ◽  
Machine Learning Model ◽  
Equilibrium Structures ◽  
High Level ◽  
Non Equilibrium

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations that span over the conformational, configurational and reaction space. The transferability of this model on systems larger than the ones in the dataset is demonstrated by performing calculations on select large molecules. Importantly, employing the BAND NN model, it is possible to perform geometry optimizations starting from non-equilibrium structures along with predicting their energies.

scholarly journals The Role of Global Appearance of Omnidirectional Images in Relative Distance and Orientation Retrieval

Sensors ◽  
2021 ◽  
Vol 21 (10) ◽  
pp. 3327
Author(s):  
Vicente Román ◽  
Luis Payá ◽  
Adrián Peidró ◽  
Mónica Ballesta ◽  
Oscar Reinoso
Keyword(s):  
Mobile Robotics ◽  
A Priori ◽  
Computational Cost ◽  
Relevant Information ◽  
Local Features ◽  
New Family ◽  
Lighting Conditions ◽  
Omnidirectional Images ◽  
Great Development

Over the last few years, mobile robotics has experienced a great development thanks to the wide variety of problems that can be solved with this technology. An autonomous mobile robot must be able to operate in a priori unknown environments, planning its trajectory and navigating to the required target points. With this aim, it is crucial solving the mapping and localization problems with accuracy and acceptable computational cost. The use of omnidirectional vision systems has emerged as a robust choice thanks to the big quantity of information they can extract from the environment. The images must be processed to obtain relevant information that permits solving robustly the mapping and localization problems. The classical frameworks to address this problem are based on the extraction, description and tracking of local features or landmarks. However, more recently, a new family of methods has emerged as a robust alternative in mobile robotics. It consists of describing each image as a whole, what leads to conceptually simpler algorithms. While methods based on local features have been extensively studied and compared in the literature, those based on global appearance still merit a deep study to uncover their performance. In this work, a comparative evaluation of six global-appearance description techniques in localization tasks is carried out, both in terms of accuracy and computational cost. Some sets of images captured in a real environment are used with this aim, including some typical phenomena such as changes in lighting conditions, visual aliasing, partial occlusions and noise.

scholarly journals Multirate Processing with Selective Subbands and Machine Learning for Efficient Arrhythmia Classification

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1511
Author(s):  
Saeed Mian Qaisar ◽  
Alaeddine Mihoub ◽  
Moez Krichen ◽  
Humaira Nisar
Keyword(s):  
Machine Learning ◽  
Signal Reconstruction ◽  
Computational Cost ◽  
Machine Learning Techniques ◽  
Features Selection ◽  
Frequency Content ◽  
Fixed Rate ◽  
Ecg Signals ◽  
Learning Techniques ◽  
Multirate Processing

The usage of wearable gadgets is growing in the cloud-based health monitoring systems. The signal compression, computational and power efficiencies play an imperative part in this scenario. In this context, we propose an efficient method for the diagnosis of cardiovascular diseases based on electrocardiogram (ECG) signals. The method combines multirate processing, wavelet decomposition and frequency content-based subband coefficient selection and machine learning techniques. Multirate processing and features selection is used to reduce the amount of information processed thus reducing the computational complexity of the proposed system relative to the equivalent fixed-rate solutions. Frequency content-dependent subband coefficient selection enhances the compression gain and reduces the transmission activity and computational cost of the post cloud-based classification. We have used MIT-BIH dataset for our experiments. To avoid overfitting and biasness, the performance of considered classifiers is studied by using five-fold cross validation (5CV) and a novel proposed partial blind protocol. The designed method achieves more than 12-fold computational gain while assuring an appropriate signal reconstruction. The compression gain is 13 times compared to fixed-rate counterparts and the highest classification accuracies are 97.06% and 92.08% for the 5CV and partial blind cases, respectively. Results suggest the feasibility of detecting cardiac arrhythmias using the proposed approach.

scholarly journals Predicting optimal deep brain stimulation parameters for Parkinson’s disease using functional MRI and machine learning

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexandre Boutet ◽  
Radhika Madhavan ◽  
Gavin J. B. Elias ◽  
Suresh E. Joel ◽  
Robert Gramer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Deep Brain Stimulation ◽  
Brain Stimulation ◽  
A Priori ◽  
Brain Response ◽  
Brain Responses ◽  
Clinical Benefits ◽  
Deep Brain

AbstractCommonly used for Parkinson’s disease (PD), deep brain stimulation (DBS) produces marked clinical benefits when optimized. However, assessing the large number of possible stimulation settings (i.e., programming) requires numerous clinic visits. Here, we examine whether functional magnetic resonance imaging (fMRI) can be used to predict optimal stimulation settings for individual patients. We analyze 3 T fMRI data prospectively acquired as part of an observational trial in 67 PD patients using optimal and non-optimal stimulation settings. Clinically optimal stimulation produces a characteristic fMRI brain response pattern marked by preferential engagement of the motor circuit. Then, we build a machine learning model predicting optimal vs. non-optimal settings using the fMRI patterns of 39 PD patients with a priori clinically optimized DBS (88% accuracy). The model predicts optimal stimulation settings in unseen datasets: a priori clinically optimized and stimulation-naïve PD patients. We propose that fMRI brain responses to DBS stimulation in PD patients could represent an objective biomarker of clinical response. Upon further validation with additional studies, these findings may open the door to functional imaging-assisted DBS programming.

scholarly journals Machine Learning for Statistical Modeling

2021 ◽  
Vol 26 (3) ◽  
pp. 1-17
Author(s):  
Urmimala Roy ◽  
Tanmoy Pramanik ◽  
Subhendu Roy ◽  
Avhishek Chatterjee ◽  
Leonard F. Register ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Distribution ◽  
Switching Time ◽  
A Priori ◽  
Random Access ◽  
Spin Transfer Torque ◽  
Support Vector ◽  
Micromagnetic Simulations ◽  
Physical Systems ◽  
Computational Resources

We propose a methodology to perform process variation-aware device and circuit design using fully physics-based simulations within limited computational resources, without developing a compact model. Machine learning (ML), specifically a support vector regression (SVR) model, has been used. The SVR model has been trained using a dataset of devices simulated a priori, and the accuracy of prediction by the trained SVR model has been demonstrated. To produce a switching time distribution from the trained ML model, we only had to generate the dataset to train and validate the model, which needed ∼500 hours of computation. On the other hand, if 10 6 samples were to be simulated using the same computation resources to generate a switching time distribution from micromagnetic simulations, it would have taken ∼250 days. Spin-transfer-torque random access memory (STTRAM) has been used to demonstrate the method. However, different physical systems may be considered, different ML models can be used for different physical systems and/or different device parameter sets, and similar ends could be achieved by training the ML model using measured device data.

scholarly journals Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Annachiara Tinivella ◽  
Luca Pinzi ◽  
Giulio Rastelli
Keyword(s):  
Machine Learning ◽  
Carbonic Anhydrase ◽  
A Priori ◽  
Selective Inhibition ◽  
Great Promise ◽  
Classification Models ◽  
Machine Learning Classification ◽  
Central Interest ◽  
Human Carbonic Anhydrase ◽  
In Silico Models

AbstractThe development of selective inhibitors of the clinically relevant human Carbonic Anhydrase (hCA) isoforms IX and XII has become a major topic in drug research, due to their deregulation in several types of cancer. Indeed, the selective inhibition of these two isoforms, especially with respect to the homeostatic isoform II, holds great promise to develop anticancer drugs with limited side effects. Therefore, the development of in silico models able to predict the activity and selectivity against the desired isoform(s) is of central interest. In this work, we have developed a series of machine learning classification models, trained on high confidence data extracted from ChEMBL, able to predict the activity and selectivity profiles of ligands for human Carbonic Anhydrase isoforms II, IX and XII. The training datasets were built with a procedure that made use of flexible bioactivity thresholds to obtain well-balanced active and inactive classes. We used multiple algorithms and sampling sizes to finally select activity models able to classify active or inactive molecules with excellent performances. Remarkably, the results herein reported turned out to be better than those obtained by models built with the classic approach of selecting an a priori activity threshold. The sequential application of such validated models enables virtual screening to be performed in a fast and more reliable way to predict the activity and selectivity profiles against the investigated isoforms.

scholarly journals On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn’t

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 527
Author(s):  
Eran Elhaik ◽  
Dan Graur
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
A Priori ◽  
Neutral Theory ◽  
Dominant Mode ◽  
Supervised Machine Learning ◽  
Training Dataset ◽  
Selective Sweeps ◽  
Two Factors ◽  
Negative Controls

In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transformation was aided by a series of articles by Daniel Schrider and Andrew Kern. Within this series, a paper entitled “Soft sweeps are the dominant mode of adaptation in the human genome” (Schrider and Kern, Mol. Biol. Evolut. 2017, 34(8), 1863–1877) attracted a great deal of attention, in particular in conjunction with another paper (Kern and Hahn, Mol. Biol. Evolut. 2018, 35(6), 1366–1371), for purporting to discredit the Neutral Theory of Molecular Evolution (Kimura 1968). Here, we address an alleged novelty in Schrider and Kern’s paper, i.e., the claim that their study involved an artificial intelligence technique called supervised machine learning (SML). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known empirically to be true. Curiously, Schrider and Kern did not possess a training dataset of genomic segments known a priori to have evolved either neutrally or through soft or hard selective sweeps. Thus, their claim of using SML is thoroughly and utterly misleading. In the absence of legitimate training datasets, Schrider and Kern used: (1) simulations that employ many manipulatable variables and (2) a system of data cherry-picking rivaling the worst excesses in the literature. These two factors, in addition to the lack of negative controls and the irreproducibility of their results due to incomplete methodological detail, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S/HIC) should be taken with a huge shovel of salt.

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