Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data.

The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility.

Accelerated Nano-Optical Imaging through Sparse Sampling.

The integration time and signal-to-noise ratio are inextricably linked when performing scanning probe microscopy based on raster scanning. This often yields a large lower bound on the measurement time, for example, in nano-optical imaging experiments performed using a scanning near-field optical microscope (SNOM). Here, we utilize sparse scanning augmented with Gaussian process regression to bypass the time constraint. We apply this approach to image charge-transfer polaritons in graphene residing on ruthenium trichloride (α-RuCl3) and obtain key features such as polariton damping and dispersion. Critically, nano-optical SNOM imaging data obtained via sparse sampling are in good agreement with those extracted from traditional raster scans but require 11 times fewer sampled points. As a result, Gaussian process-aided sparse spiral scans offer a major decrease in scanning time.

BrainAGE: Revisited and reframed machine learning workflow.

Since the introduction of the BrainAGE method, novel machine learning methods for brain age prediction have continued to emerge. The idea of estimating the chronological age from magnetic resonance images proved to be an interesting field of research due to the relative simplicity of its interpretation and its potential use as a biomarker of brain health. We revised our previous BrainAGE approach, originally utilising relevance vector regression (RVR), and substituted it with Gaussian process regression (GPR), which enables more stable processing of larger datasets, such as the UK Biobank (UKB). In addition, we extended the global BrainAGE approach to regional BrainAGE, providing spatially specific scores for five brain lobes per hemisphere. We tested the performance of the new algorithms under several different conditions and investigated their validity on the ADNI and schizophrenia samples, as well as on a synthetic dataset of neocortical thinning. The results show an improved performance of the reframed global model on the UKB sample with a mean absolute error (MAE) of less than 2 years and a significant difference in BrainAGE between healthy participants and patients with Alzheimer's disease and schizophrenia. Moreover, the workings of the algorithm show meaningful effects for a simulated neocortical atrophy dataset. The regional BrainAGE model performed well on two clinical samples, showing disease-specific patterns for different levels of impairment. The results demonstrate that the new improved algorithms provide reliable and valid brain age estimations.

Training machine learning potentials for reactive systems: A Colab tutorial on basic models.

In the last several years, there has been a surge in the development of machine learning potential (MLP) models for describing molecular systems. We are interested in a particular area of this field - the training of system-specific MLPs for reactive systems - with the goal of using these MLPs to accelerate free energy simulations of chemical and enzyme reactions. To help new members in our labs become familiar with the basic techniques, we have put together a self-guided Colab tutorial (https://cc-ats.github.io/mlp_tutorial/), which we expect to be also useful to other young researchers in the community. Our tutorial begins with the introduction of simple feedforward neural network (FNN) and kernel-based (using Gaussian process regression, GPR) models by fitting the two-dimensional Müller-Brown potential. Subsequently, two simple descriptors are presented for extracting features of molecular systems: symmetry functions (including the ANI variant) and embedding neural networks (such as DeepPot-SE). Lastly, these features will be fed into FNN and GPR models to reproduce the energies and forces for the molecular configurations in a Claisen rearrangement reaction.

FFLUX molecular simulations driven by atomic Gaussian process regression models.

Machine learning (ML) force fields are revolutionizing molecular dynamics (MD) simulations as they bypass the computational cost associated with ab initio methods but do not sacrifice accuracy in the process. In this work, the GPyTorch library is used to create Gaussian process regression (GPR) models that are interfaced with the next-generation ML force field FFLUX. These models predict atomic properties of different molecular configurations that appear in a progressing MD simulation. An improved kernel function is utilized to correctly capture the periodicity of the input descriptors. The first FFLUX molecular simulations of ammonia, methanol, and malondialdehyde with the updated kernel are performed. Geometry optimizations with the GPR models result in highly accurate final structures with a maximum root-mean-squared deviation of 0.064 Å and sub-kJ mol-1 total energy predictions. Additionally, the models are tested in 298 K MD simulations with FFLUX to benchmark for robustness. The resulting energy and force predictions throughout the simulation are in excellent agreement with ab initio data for ammonia and methanol but decrease in quality for malondialdehyde due to the increased system complexity. GPR model improvements are discussed, which will ensure the future scalability to larger systems.

Prediction of key quality attributes in Salvia miltiorrhiza standard decoction using a Gaussian process regression model.

INTRODUCTION: Nonstationary, nonlinear mass transfer in traditional Chinese medicine (TCM) extraction poses challenges to correlating process characteristics with quality parameters, particularly in defining clear parameter ranges for the process. OBJECTIVES: The aim of the study was to provide a solution for quality consistency analysis in TCM preparation processes. MATERIALS AND METHODS: Salvia miltiorrhiza was taken as an example for 15 batches of standard decoction. Using aqueous extract, alcoholic extract, and the content of salvianolic acid B as herb material key quality attributes, multiple nonlinear regression, Gaussian process regression, and artificial neural network models were employed to predict the key quality attributes including the paste yield, the content of salvianolic acid B, and the transfer rate. The evaluation criteria were root mean square error, mean absolute percentage error, and R2. RESULTS: The Gaussian process regression model had the best prediction effect on the paste yield, the content of salvianolic acid B, and the transfer rate, with R2 being 0.918, 0.934, and 0.919, respectively. Utilizing Gaussian process regression model confidence intervals, along with Shewhart control and intervals optimized through process capability index analysis, the quality control range of the standard decoction was determined as follows: paste yield, 25.14%-33.19%; salvianolic acid B content, 2.62%-4.78%; and transfer rate, 56.88%-64.80%. CONCLUSION: This study combined the preparation process of standard decoction with the Gaussian process regression model, accurately predicted the key quality attributes, and determined the quality parameter range by using process analysis tools, providing a new idea for the quality consistency standard of TCM processes.

Optimal Microphone Array Placement Design Using the Bayesian Optimization Method.

In addition to the filter coefficients, the location of the microphone array is a crucial factor in improving the overall performance of a beamformer. The optimal microphone array placement can considerably enhance speech quality. However, the optimization problem with microphone configuration variables is non-convex and highly non-linear. Heuristic algorithms that are frequently employed take a long time and have a chance of missing the optimal microphone array placement design. We extend the Bayesian optimization method to solve the microphone array configuration design problem. The proposed Bayesian optimization method does not depend on gradient and Hessian approximations and makes use of all the information available from prior evaluations. Furthermore, Gaussian process regression and acquisition functions make up the Bayesian optimization method. The objective function is given a prior probabilistic model through Gaussian process regression, which exploits this model while integrating out uncertainty. The acquisition function is adopted to decide the next placement point based upon the incumbent optimum with the posterior distribution. Numerical experiments have demonstrated that the Bayesian optimization method could find a similar or better microphone array placement compared with the hybrid descent method and computational time is significantly reduced. Our proposed method is at least four times faster than the hybrid descent method to find the optimal microphone array configuration from the numerical results.

Mitigating Measurement Inaccuracies in Digital Twins of Construction Machinery through Multi-Objective Optimization.

The advent of digital twins facilitates the generation of high-fidelity replicas of actual systems or assets, thereby enhancing the design's performance and feasibility. When developing digital twins, precise measurement data is essential to ensure alignment between the actual and digital models. However, inherent uncertainties in sensors and models lead to disparities between observed and predicted (simulated) behaviors. To mitigate these uncertainties, this study originally proposes a multi-objective optimization strategy utilizing a Gaussian process regression surrogate model, which integrates various uncertain parameters, such as load angle, bucket cylinder stroke, arm cylinder stroke, and boom cylinder stroke. This optimization employs a genetic algorithm to indicate the Pareto frontiers regarding the pressure exerted on the boom, arm, and bucket cylinders. Subsequently, TOPSIS is applied to ascertain the optimal candidate among the identified Pareto optima. The findings reveal a substantial congruence between the experimental and numerical outcomes of the devised virtual model, in conjunction with the TOPSIS-derived optimal parameter configuration.

Predicting Surface Roughness in Turning Complex-Structured Workpieces Using Vibration-Signal-Based Gaussian Process Regression.

Surface roughness prediction is a pivotal aspect of the manufacturing industry, as it directly influences product quality and process optimization. This study introduces a predictive model for surface roughness in the turning of complex-structured workpieces utilizing Gaussian Process Regression (GPR) informed by vibration signals. The model captures parameters from both the time and frequency domains of the turning tool, encompassing the mean, median, standard deviation (STD), and root mean square (RMS) values. The signal is from the time to frequency domain and it is executed using Welch's method complemented by time-frequency domain analysis employing three levels of Daubechies Wavelet Packet Transform (WPT). The selected features are then utilized as inputs for the GPR model to forecast surface roughness. Empirical evidence indicates that the GPR model can accurately predict the surface roughness of turned complex-structured workpieces. This predictive strategy has the potential to improve product quality, streamline manufacturing processes, and minimize waste within the industry.

Signal Processing Using a Circular Sensor Array to Measure the Torsional Angle of a Bolted Joint.

This study presents a new approach to determining the preload force of bolted joints. The concept involves measuring the torsional angle without contact. For this purpose, we present a circular magnetic sensor array integrated into the torque wrench. The torsional angle in bolted joints depends on the dimensions of the screw and the materials used and is typically less than four degrees. For this reason, one requirement is a high angular resolution so that a continuous recording of the torsion angle is feasible during the assembly process. This can be achieved using the circular sensor array and adapted signal processing methods. Two signal processing approaches are utilized. First, the direct method uses the discrete Fourier transformation to calculate the rotation angle from the signal phase. This approach is robust to signal distortion and does not depend on signal amplitude. Second, the method with a learning phase employs Gaussian process regression to minimize the angle error. In an experiment, both approaches were applied within a test bench and showed promising results. The direct method demonstrated a very good angular resolution without training and calibration. For mobile and less-complex applications where a reference system is unavailable, the direct method is preferable. However, in complex measurement systems where reference systems can be utilized initially, significant enhancements to an excellent resolution can be achieved through prior training.

Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach.

In this paper we propose PIICM, a probabilistic framework for dose-response prediction in high-throughput drug combination datasets. PIICM utilizes a permutation invariant version of the intrinsic co-regionalization model for multi-output Gaussian process regression, to predict dose-response surfaces in untested drug combination experiments. Coupled with an observation model that incorporates experimental uncertainty, PIICM is able to learn from noisily observed cell-viability measurements in settings where the underlying dose-response experiments are of varying quality, utilize different experimental designs, and the resulting training dataset is sparsely observed. We show that the model can accurately predict dose-response in held out experiments, and the resulting function captures relevant features indicating synergistic interaction between drugs.

Adaptive regularized Gaussian process regression for application in the context of hydrogen adsorption on graphene sheets.

We present a Gaussian process regression (GPR) scheme with an adaptive regularization scheme applied to the QM7 and QM9 test set, several protonated water clusters and specifically to the problem of atomic hydrogen adsorption on graphene sheets. For the last system our goal is to achieve good predictive accuracy with only a few training points. Therefore, we assess for these systems a self-correcting multilayer GPR model, in which the prediction is corrected by a chain of additional GPR models. In our adaptive regularization scheme, we impose no noise on the training data, but use an approach based on the data itself to account for its impurity. The strength of this strategy is that the data points are treated differently based on their importance and that the regularization can still be controlled by a single parameter. We assess how the accuracy of the prediction depends on this parameter. We can show that the new regularization scheme as well as the multilayer approach results in more robust predictors. Furthermore, we demonstrate that the predictor can be in good agreement with the density-functional theory results.

An adaptive soft-sensor for advanced real-time monitoring of an antibody-drug conjugation reaction.

In the production of antibody-drug conjugates (ADCs), the conjugation reaction is a central step defining the final product composition and, hence, directly affecting product safety and efficacy. To enable real-time monitoring, spectroscopic sensors in combination with multivariate regression models have gained popularity in recent years. The extended Kalman filter (EKF) can be used as so-called soft-sensor to fuse sensor predictions with long-horizon forecasts by process models. This enables the dynamic update of the current state and provides increased robustness against experimental noise or model errors. Due to the uncertainty associated with sensor and process models in biopharmaceutical applications, the deployment of such soft-sensors is challenging. In this study, we demonstrate the combination of an uncertainty-aware sensor model with a kinetic reaction model using an EKF to monitor a site-directed ADC conjugation reaction. As the sensor model, a Gaussian process regression model is presented to realize a time-variant determination of the sensor uncertainty. The EKF fuses the time-discrete predictions of the amount of conjugated drug from the sensor model with the time-continuous predictions from the kinetic model. While the ADC species are not distinguishable by on-line recorded UV/Vis spectra, the developed soft-sensor is able to dynamically update all relevant reaction species. It could be shown that the use of time-variant process and sensor noise computation approaches improved the performance of the EKF and achieved a reduction of the prediction error of up to 23% compared with the kinetic model. The developed framework proved to enhance robustness against noisy sensor measurements or wrong model initialization and was successfully transferred from batch to fed-batch mode. In future, this framework could be implemented for model-based process control and be adopted for other ADC conjugation reaction types.

Can meteorological data improve the short-term prediction of individual milk yield in dairy cows?

Many farms document daily milk yields of individual cows because these are a good indicator of cow well-being. It is established that extreme meteorological conditions influence the milk yields by causing heat and cold stress, whereas less is known about the effects of moderate changes in meteorological conditions. Thus, the aim of the present study was to evaluate whether individual daily milk yield predictions can be improved by considering such changes. We evaluated 8 years of milking and meteorological data from Eastern Switzerland with a total of 33,938 daily milkings from 145 Brown Swiss and 64 Swiss Fleckvieh cows. The cows were aged between 1.9 and 13.5 years at parturition. The data set was split into 7 periods according to the days in milk (DIM) and subsequently filtered into subsets by breed and parity. We applied Gaussian process regression to predict individual daily milk yield. We compared different models including DIM, lagged milk yield, and meteorological variables as features and found that models including the lagged milk yield performed best. Within the period of 5 to 90 DIM, we were able to predict individual next-day milk yield from the cow's last milkings with a root mean squared error (RMSE) of 2.1 kg. In contrast, without information on the previous milk yield, accuracy of milk yield prediction was lower, with an RMSE close to 8 kg. The models holding information about previous milk yields showed a substantial increase in performance. Within a more homogeneous data subset filtered by breed or parity or both, predictions were even better, with a relative RMSE of 4.3% for first-parity Fleckvieh cows. However, we found that including meteorological features, such as temperature, rainfall, wind speed, temperature humidity index, cooling degree, and barometric pressure, did not improve the predictions in any of the evaluated periods. This finding indicates that considering meteorological features in daily milk yield prediction models is not useful in moderate climates; considering lagged milk yield is sufficient. We hypothesize that this meteorological information, among other influences, is indirectly contained in the lagged milk yield.

Efficient Autonomous Exploration and Mapping in Unknown Environments.

Autonomous exploration and mapping in unknown environments is a critical capability for robots. Existing exploration techniques (e.g., heuristic-based and learning-based methods) do not consider the regional legacy issues, i.e., the great impact of smaller unexplored regions on the whole exploration process, which results in a dramatic reduction in their later exploration efficiency. To this end, this paper proposes a Local-and-Global Strategy (LAGS) algorithm that combines a local exploration strategy with a global perception strategy, which considers and solves the regional legacy issues in the autonomous exploration process to improve exploration efficiency. Additionally, we further integrate Gaussian process regression (GPR), Bayesian optimization (BO) sampling, and deep reinforcement learning (DRL) models to efficiently explore unknown environments while ensuring the robot's safety. Extensive experiments show that the proposed method could explore unknown environments with shorter paths, higher efficiencies, and stronger adaptability on different unknown maps with different layouts and sizes.

Soft Sensor Modeling Method for the Marine Lysozyme Fermentation Process Based on ISOA-GPR Weighted Ensemble Learning.

Due to the highly nonlinear, multi-stage, and time-varying characteristics of the marine lysozyme fermentation process, the global soft sensor models established using traditional single modeling methods cannot describe the dynamic characteristics of the entire fermentation process. Therefore, this study proposes a weighted ensemble learning soft sensor modeling method based on an improved seagull optimization algorithm (ISOA) and Gaussian process regression (GPR). First, an improved density peak clustering algorithm (ADPC) was used to divide the sample dataset into multiple local sample subsets. Second, an improved seagull optimization algorithm was used to optimize and transform the Gaussian process regression model, and a sub-prediction model was established. Finally, the fusion strategy was determined according to the connectivity between the test samples and local sample subsets. The proposed soft sensor model was applied to the prediction of key biochemical parameters of the marine lysozyme fermentation process. The simulation results show that the proposed soft sensor model can effectively predict the key biochemical parameters with relatively small prediction errors in the case of limited training data. According to the results, this model can be expanded to the soft sensor prediction applications in general nonlinear systems.

Lower Limb Joint Torque Prediction Using Long Short-Term Memory Network and Gaussian Process Regression.

The accurate prediction of joint torque is required in various applications. Some traditional methods, such as the inverse dynamics model and the electromyography (EMG)-driven neuromusculoskeletal (NMS) model, depend on ground reaction force (GRF) measurements and involve complex optimization solution processes, respectively. Recently, machine learning methods have been popularly used to predict joint torque with surface electromyography (sEMG) signals and kinematic information as inputs. This study aims to predict lower limb joint torque in the sagittal plane during walking, using a long short-term memory (LSTM) model and Gaussian process regression (GPR) model, respectively, with seven characteristics extracted from the sEMG signals of five muscles and three joint angles as inputs. The majority of the normalized root mean squared error (NRMSE) values in both models are below 15%, most Pearson correlation coefficient (R) values exceed 0.85, and most decisive factor (R2) values surpass 0.75. These results indicate that the joint prediction of torque is feasible using machine learning methods with sEMG signals and joint angles as inputs.

Application of Machine Learning for Calibrating Gas Sensors for Methane Emissions Monitoring.

Methane leaks are a significant component of greenhouse gas emissions and a global problem for the oil and gas industry. Emissions occur from a wide variety of sites with no discernable patterns, requiring methodologies to frequently monitor these releases throughout the entire production chain. To cost-effectively monitor widely dispersed well pads, we developed a methane point instrument to be deployed at facilities and connected to a cloud-based interpretation platform that provides real-time continuous monitoring in all weather conditions. The methane sensor is calibrated with machine learning methods of Gaussian process regression and the results are compared with artificial neural networks. A machine learning approach incorporates environmental effects into the sensor response and achieves the accuracies required for methane emissions monitoring with a small number of parameters. The sensors achieve an accuracy of 1 part per million methane (ppm) and can detect leaks at rates of less than 0.6 kg/h.

Online-Dynamic-Clustering-Based Soft Sensor for Industrial Semi-Supervised Data Streams.

In the era of big data, industrial process data are often generated rapidly in the form of streams. Thus, how to process such sequential and high-speed stream data in real time and provide critical quality variable predictions has become a critical issue for facilitating efficient process control and monitoring in the process industry. Traditionally, soft sensor models are usually built through offline batch learning, which remain unchanged during the online implementation phase. Once the process state changes, soft sensors built from historical data cannot provide accurate predictions. In practice, industrial process data streams often exhibit characteristics such as nonlinearity, time-varying behavior, and label scarcity, which pose great challenges for building high-performance soft sensor models. To address this issue, an online-dynamic-clustering-based soft sensor (ODCSS) is proposed for industrial semi-supervised data streams. The method achieves automatic generation and update of clusters and samples deletion through online dynamic clustering, thus enabling online dynamic identification of process states. Meanwhile, selective ensemble learning and just-in-time learning (JITL) are employed through an adaptive switching prediction strategy, which enables dealing with gradual and abrupt changes in process characteristics and thus alleviates model performance degradation caused by concept drift. In addition, semi-supervised learning is introduced to exploit the information of unlabeled samples and obtain high-confidence pseudo-labeled samples to expand the labeled training set. The proposed method can effectively deal with nonlinearity, time-variability, and label scarcity issues in the process data stream environment and thus enable reliable target variable predictions. The application results from two case studies show that the proposed ODCSS soft sensor approach is superior to conventional soft sensors in a semi-supervised data stream environment.

Fast and Noise-Resilient Magnetic Field Mapping on a Low-Cost UAV Using Gaussian Process Regression.

This study presents a comprehensive approach to mapping local magnetic field anomalies with robustness to magnetic noise from an unmanned aerial vehicle (UAV). The UAV collects magnetic field measurements, which are used to generate a local magnetic field map through Gaussian process regression (GPR). The research identifies two categories of magnetic noise originating from the UAV's electronics, adversely affecting map precision. First, this paper delineates a zero-mean noise arising from high-frequency motor commands issued by the UAV's flight controller. To mitigate this noise, the study proposes adjusting a specific gain in the vehicle's PID controller. Next, our research reveals that the UAV generates a time-varying magnetic bias that fluctuates throughout experimental trials. To address this issue, a novel compromise mapping technique is introduced, enabling the map to learn these time-varying biases with data collected from multiple flights. The compromise map circumvents excessive computational demands without sacrificing mapping accuracy by constraining the number of prediction points used for regression. A comparative analysis of the magnetic field maps' accuracy and the spatial density of observations employed in map construction is then conducted. This examination serves as a guideline for best practices when designing trajectories for local magnetic field mapping. Furthermore, the study presents a novel consistency metric intended to determine whether predictions from a GPR magnetic field map should be retained or discarded during state estimation. Empirical evidence from over 120 flight tests substantiates the efficacy of the proposed methodologies. The data are made publicly accessible to facilitate future research endeavors.