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1.
Heliyon ; 10(15): e34928, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39170143

ABSTRACT

Model Order Reduction (MOR) techniques have extensive applications across scientific and engineering disciplines, such as neutron field reconstruction of nuclear reactor cores, thermoelastic field reconstruction, fluid, and solid mechanics. In the process of building a Reduced Order Model (ROM), the selection of the basis functions in the offline stage is crucial and directly depends on the parameter space sampling strategy. This problem has always been a challenge in MOR. Research into adaptive sampling algorithms has become a hot topic in recent years. To better understand the application of these algorithms to MOR, this paper focuses on three prevalent adaptive sampling algorithms: pseudo-gradient sampling, adaptive sparse grid sampling, adaptive training set extension. These have been successfully applied in various applications, including nuclear reactor cores, molten salt reactor system, power system for convection problems. We systematically assess and compare their performance, finding that adaptive sampling algorithms excel in sampling divergent and oscillating areas and are generally better than the standard sampling strategy. Specifically, the pseudo-gradient sampling algorithm is effective for small-scale scenarios, while the other two algorithms are designed for large-scale sampling. Their practicality is confirmed through successful applications in nuclear reactor cores.

2.
Materials (Basel) ; 17(16)2024 Aug 17.
Article in English | MEDLINE | ID: mdl-39203269

ABSTRACT

There has always been high interest in predicting the solder joint fatigue life in advanced packaging with high accuracy and efficiency. Artificial Intelligence Plus (AI+) is becoming increasingly popular as computational facilities continue to develop. This study will introduce machine learning (a core component of AI). With machine learning, metamodels that approximate the attributes of systems or functions are created to predict the fatigue life of advanced packaging. However, the prediction ability is highly dependent on the size and distribution of the training data. Increasing the amount of training data is the most intuitive approach to improve prediction performance, but this implies a higher computational cost. In this research, the adaptive sampling methods are applied to build the machine learning model with a small dataset sampled from an existing database. The performance of the model will be visualized using predefined criteria. Moreover, ensemble learning can be used to improve the performance of AI models after they have been fully trained.

3.
Sensors (Basel) ; 24(13)2024 Jul 04.
Article in English | MEDLINE | ID: mdl-39001127

ABSTRACT

Compressive sensing (CS) is recognized for its adeptness at compressing signals, making it a pivotal technology in the context of sensor data acquisition. With the proliferation of image data in Internet of Things (IoT) systems, CS is expected to reduce the transmission cost of signals captured by various sensor devices. However, the quality of CS-reconstructed signals inevitably degrades as the sampling rate decreases, which poses a challenge in terms of the inference accuracy in downstream computer vision (CV) tasks. This limitation imposes an obstacle to the real-world application of existing CS techniques, especially for reducing transmission costs in sensor-rich environments. In response to this challenge, this paper contributes a CV-oriented adaptive CS framework based on saliency detection to the field of sensing technology that enables sensor systems to intelligently prioritize and transmit the most relevant data. Unlike existing CS techniques, the proposal prioritizes the accuracy of reconstructed images for CV purposes, not only for visual quality. The primary objective of this proposal is to enhance the preservation of information critical for CV tasks while optimizing the utilization of sensor data. This work conducts experiments on various realistic scenario datasets collected by real sensor devices. Experimental results demonstrate superior performance compared to existing CS sampling techniques across the STL10, Intel, and Imagenette datasets for classification and KITTI for object detection. Compared with the baseline uniform sampling technique, the average classification accuracy shows a maximum improvement of 26.23%, 11.69%, and 18.25%, respectively, at specific sampling rates. In addition, even at very low sampling rates, the proposal is demonstrated to be robust in terms of classification and detection as compared to state-of-the-art CS techniques. This ensures essential information for CV tasks is retained, improving the efficacy of sensor-based data acquisition systems.

4.
Pathol Int ; 2024 Jul 29.
Article in English | MEDLINE | ID: mdl-39073367

ABSTRACT

Myxoid liposarcoma (MLPS) is a rare sarcoma, typically arising in deep soft tissues during the fourth to fifth decades of life. Histologically, MLPS is composed of uniform oval cells within a background of myxoid stroma and chicken-wire capillaries. Genetically, MLPS is characterized by the FUS/EWSR1::DDIT3 fusion gene, which generally results from balanced interchromosomal translocation and is detectable via DDIT3 break-apart fluorescence in situ hybridization (FISH). Here, we report an unusual intra-articular MLPS case, negative for DDIT3 break-apart FISH but positive for EWSR1::DDIT3. An 18-year-old female was referred to our hospital complaining of an intra-articular mass in the right knee joint. Histologically, the tumor was mainly composed of mature adipocytes, brown fat-like cells, and lipoblasts. Nanopore sequencing detected DNA rearrangements between EWSR1 and DDIT3 and clustered complex rearrangements involving multiple chromosomes, suggesting chromoplexy. Methylation classification using random forest, t-distributed stochastic neighbor embedding, and unsupervised hierarchical clustering correctly classified the tumor as MLPS. The copy number was almost flat. The TERT promoter C-124T was also detected. This report highlights, for the first time, the potential value of a fast and low-cost nanopore sequencer for diagnosing sarcomas.

5.
Heliyon ; 10(11): e32355, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38961979

ABSTRACT

Estimating dispersion in populations that are extremely rare, hidden, geographically clustered, and hard to access is a well-known challenge. Conventional sampling approaches tend to overestimate the variance, even though it should be genuinely reduced. In this environment, adaptive cluster sampling is considered to be the most efficient sampling technique as it provides generally a lower variance than the other conventional probability sampling designs for the assessment of rare and geographically gathered population parameters like mean, total, variance, etc. The use of auxiliary data is very common to obtain the precise estimates of the estimators by taking advantage of the correlation between the survey variable and the auxiliary data. In this article, we introduced a generalized estimator for estimating the variance of populations that are rare, hidden, geographically clustered and hard-to-reached. The proposed estimator leverages both actual and transformed auxiliary data through adaptive cluster sampling. The expressions of approximate bias and mean square error of the proposed estimator are derived up to the first-order approximation using Taylor expansion. Some special cases are also obtained using the known parameters associated with the auxiliary variable. The proposed class of estimators is compared with available estimators using simulation and real data applications.

6.
Plants (Basel) ; 13(12)2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38931113

ABSTRACT

In this study, an advanced method for apricot tree disease detection is proposed that integrates deep learning technologies with various data augmentation strategies to significantly enhance the accuracy and efficiency of disease detection. A comprehensive framework based on the adaptive sampling latent variable network (ASLVN) and the spatial state attention mechanism was developed with the aim of enhancing the model's capability to capture characteristics of apricot tree diseases while ensuring its applicability on edge devices through model lightweighting techniques. Experimental results demonstrated significant improvements in precision, recall, accuracy, and mean average precision (mAP). Specifically, precision was 0.92, recall was 0.89, accuracy was 0.90, and mAP was 0.91, surpassing traditional models such as YOLOv5, YOLOv8, RetinaNet, EfficientDet, and DEtection TRansformer (DETR). Furthermore, through ablation studies, the critical roles of ASLVN and the spatial state attention mechanism in enhancing detection performance were validated. These experiments not only showcased the contributions of each component for improving model performance but also highlighted the method's capability to address the challenges of apricot tree disease detection in complex environments. Eight types of apricot tree diseases were detected, including Powdery Mildew and Brown Rot, representing a technological breakthrough. The findings provide robust technical support for disease management in actual agricultural production and offer broad application prospects.

7.
Entropy (Basel) ; 26(6)2024 May 26.
Article in English | MEDLINE | ID: mdl-38920460

ABSTRACT

Physics-informed neural networks (PINNs) have garnered widespread use for solving a variety of complex partial differential equations (PDEs). Nevertheless, when addressing certain specific problem types, traditional sampling algorithms still reveal deficiencies in efficiency and precision. In response, this paper builds upon the progress of adaptive sampling techniques, addressing the inadequacy of existing algorithms to fully leverage the spatial location information of sample points, and introduces an innovative adaptive sampling method. This approach incorporates the Dual Inverse Distance Weighting (DIDW) algorithm, embedding the spatial characteristics of sampling points within the probability sampling process. Furthermore, it introduces reward factors derived from reinforcement learning principles to dynamically refine the probability sampling formula. This strategy more effectively captures the essential characteristics of PDEs with each iteration. We utilize sparsely connected networks and have adjusted the sampling process, which has proven to effectively reduce the training time. In numerical experiments on fluid mechanics problems, such as the two-dimensional Burgers' equation with sharp solutions, pipe flow, flow around a circular cylinder, lid-driven cavity flow, and Kovasznay flow, our proposed adaptive sampling algorithm markedly enhances accuracy over conventional PINN methods, validating the algorithm's efficacy.

8.
Microsc Res Tech ; 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38877841

ABSTRACT

Atomic force microscopy (AFM) is a kind of high-precision instrument to measure the surface morphology of various conductive or nonconductive samples. However, obtaining a high-resolution image with standard AFM scanning requires more time. Using block compressive sensing (BCS) is an effective approach to achieve rapid AFM imaging. But, the routine BCS-AFM imaging is difficult to balance the image quality of each local area. It is easy to lead to excessive sampling in some flat areas, resulting in time-consuming. At the same time, there is a lack of sampling in some areas with significant details, resulting in poor imaging quality. Thus, an innovative adaptive BCS-AFM imaging method is proposed. The overlapped block is used to eliminate blocking artifacts. Characteristic parameters (GTV, Lu, and SD) are used to predict the local morphological characteristics of the samples. Back propagation neural network is employed to acquire the appropriate sampling rate of each sub-block. Sampling points are obtained by pre-scanning and adaptive supplementary scanning. Afterward, all sub-block images are reconstructed using the TVAL3 algorithm. Each sample is capable of achieving uniform, excellent image quality. Image visual effects and evaluation indicators (PSNR and SSIM) are employed for the purpose of evaluating and analyzing the imaging effects of samples. Compared with two nonadaptive and two other adaptive imaging schemes, our proposed scheme has the characteristics of a high degree of automation, uniformly high-quality imaging, and rapid imaging speed. HIGHLIGHTS: The proposed adaptive BCS method can address the issues of uneven image quality and slow imaging speed in AFM. The appropriate sampling rate of each sub-block of the sample can be obtained by BP neural network. The introduction of GTV, Lu, and SD can effectively reveal the morphological features of AFM images. Seven samples with different morphology are used to test the performance of the proposed adaptive algorithm. Practical experiments are carried out with two samples to verify the feasibility of the proposed adaptive algorithm.

9.
Forensic Sci Int Genet ; 71: 103048, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38640705

ABSTRACT

DNA methylation plays essential roles in regulating physiological processes, from tissue and organ development to gene expression and aging processes and has emerged as a widely used biomarker for the identification of body fluids and age prediction. Currently, methylation markers are targeted independently at specific CpG sites as part of a multiplexed assay rather than through a unified assay. Methylation detection is also dependent on divergent methodologies, ranging from enzyme digestion and affinity enrichment to bisulfite treatment, alongside various technologies for high-throughput profiling, including microarray and sequencing. In this pilot study, we test the simultaneous identification of age-associated and body fluid-specific methylation markers using a single technology, nanopore adaptive sampling. This innovative approach enables the profiling of multiple CpG marker sites across entire gene regions from a single sample without the need for specialized DNA preparation or additional biochemical treatments. Our study demonstrates that adaptive sampling achieves sufficient coverage in regions of interest to accurately determine the methylation status, shows a robust consistency with whole-genome bisulfite sequencing data, and corroborates known CpG markers of age and body fluids. Our work also resulted in the identification of new sites strongly correlated with age, suggesting new possible age methylation markers. This study lays the groundwork for the systematic development of nanopore-based methodologies in both age prediction and body fluid identification, highlighting the feasibility and potential of nanopore adaptive sampling while acknowledging the need for further validation and expansion in future research.


Subject(s)
Aging , CpG Islands , DNA Methylation , Humans , CpG Islands/genetics , Pilot Projects , Genetic Markers , Aging/genetics , Adult , Nanopores , Middle Aged , Aged , Sequence Analysis, DNA , Male , Saliva/chemistry , Female , Young Adult , Nanopore Sequencing , Semen/chemistry
10.
Front Microbiol ; 15: 1330814, 2024.
Article in English | MEDLINE | ID: mdl-38495515

ABSTRACT

Introduction: Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone. Methods: The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 105 CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed. Results: Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases. Discussion: This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.

12.
mSystems ; 9(3): e0094523, 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38376263

ABSTRACT

Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are expensive and laborious, and they might introduce a bias by enriching only for specific plasmid DNA sequences. Nanopore adaptive sampling could overcome these issues by rejecting uninteresting DNA molecules during the sequencing process. In this study, we assess the application of adaptive sampling for the enrichment of low-abundant plasmids in known bacterial isolates using two different adaptive sampling tools. We show that a significant enrichment can be achieved even on expired flow cells. By applying adaptive sampling, we also improve the quality of de novo plasmid assemblies and reduce the sequencing time. However, our experiments also highlight issues with adaptive sampling if target and non-target sequences span similar regions. IMPORTANCE: Antimicrobial resistance causes millions of deaths every year. Mobile genetic elements like bacterial plasmids are key drivers for the dissemination of antimicrobial resistance genes. This makes the characterization of plasmids via DNA sequencing an important tool for clinical microbiologists. Since plasmids are often underrepresented in bacterial samples, plasmid sequencing can be challenging and laborious. To accelerate the sequencing process, we evaluate nanopore adaptive sampling as an in silico method for the enrichment of low-abundant plasmids. Our results show the potential of this cost-efficient method for future plasmid research but also indicate issues that arise from using reference sequences.


Subject(s)
Anti-Infective Agents , Nanopores , Plasmids/genetics , Bacteria/genetics , DNA
13.
mBio ; 15(1): e0196723, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38054750

ABSTRACT

IMPORTANCE: Malaria is caused by parasites of the genus Plasmodium, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich Plasmodium DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich Plasmodium reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches Plasmodium reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.


Subject(s)
Nanopores , Parasites , Plasmodium , Animals , Humans , Parasites/genetics , Plasmodium/genetics , Whole Genome Sequencing/methods , DNA, Protozoan/genetics , Plasmodium falciparum/genetics
14.
Front Microbiol ; 14: 1307440, 2023.
Article in English | MEDLINE | ID: mdl-38075895

ABSTRACT

Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.

15.
Sensors (Basel) ; 23(23)2023 Dec 04.
Article in English | MEDLINE | ID: mdl-38067973

ABSTRACT

Adaptive information-sampling approaches enable efficient selection of mobile robots' waypoints through which the accurate sensing and mapping of a physical process, such as the radiation or field intensity, can be obtained. A key parameter in the informative sampling objective function could be optimized balance the need to explore new information where the uncertainty is very high and to exploit the data sampled so far, with which a great deal of the underlying spatial fields can be obtained, such as the source locations or modalities of the physical process. However, works in the literature have either assumed the robot's energy is unconstrained or used a homogeneous availability of energy capacity among different robots. Therefore, this paper analyzes the impact of the adaptive information-sampling algorithm's information function used in exploration and exploitation to achieve a tradeoff between balancing the mapping, localization, and energy efficiency objectives. We use Gaussian process regression (GPR) to predict and estimate confidence bounds, thereby determining each point's informativeness. Through extensive experimental data, we provide a deeper and holistic perspective on the effect of information function parameters on the prediction map's accuracy (RMSE), confidence bound (variance), energy consumption (distance), and time spent (sample count) in both single- and multi-robot scenarios. The results provide meaningful insights into choosing the appropriate energy-aware information function parameters based on sensing objectives (e.g., source localization or mapping). Based on our analysis, we can conclude that it would be detrimental to give importance only to the uncertainty of the information function (which would explode the energy needs) or to the predictive mean of the information (which would jeopardize the mapping accuracy). By assigning more importance to the information uncertainly with some non-zero importance to the information value (e.g., 75:25 ratio), it is possible to achieve an optimal tradeoff between exploration and exploitation objectives while keeping the energy requirements manageable.

16.
Sensors (Basel) ; 23(21)2023 Oct 24.
Article in English | MEDLINE | ID: mdl-37960376

ABSTRACT

An attention-aware patch-based deep-learning model for a blind 360-degree image quality assessment (360-IQA) is introduced in this paper. It employs spatial attention mechanisms to focus on spatially significant features, in addition to short skip connections to align them. A long skip connection is adopted to allow features from the earliest layers to be used at the final level. Patches are properly sampled on the sphere to correspond to the viewports displayed to the user using head-mounted displays. The sampling incorporates the relevance of patches by considering (i) the exploration behavior and (ii) a latitude-based selection. An adaptive strategy is applied to improve the pooling of local patch qualities to global image quality. This includes an outlier score rejection step relying on the standard deviation of the obtained scores to consider the agreement, as well as a saliency to weigh them based on their visual significance. Experiments on available 360-IQA databases show that our model outperforms the state of the art in terms of accuracy and generalization ability. This is valid for general deep-learning-based models, multichannel models, and natural scene statistic-based models. Furthermore, when compared to multichannel models, the computational complexity is significantly reduced. Finally, an extensive ablation study gives insights into the efficacy of each component of the proposed model.

17.
Microbiol Spectr ; : e0089523, 2023 Sep 22.
Article in English | MEDLINE | ID: mdl-37737593

ABSTRACT

Borrelia spirochetes, causative agents of Lyme disease and relapsing fever (RF), have uniquely complex genomes, consisting of a linear chromosome and both circular and linear plasmids. The plasmids harbor genes important for the vector-host life cycle of these tick-borne bacteria. The role of plasmids from Lyme disease causing spirochetes is more refined compared to RF Borrelia because of limited plasmid-resolved genome assemblies for the latter. We recently addressed this limitation and found that three linear plasmid families (F6, F27, and F28) were syntenic across all the RF Borrelia species that we examined. Given this conservation, we further investigated the three plasmid families. The F6 family, also known as the megaplasmid, contained regions of repetitive DNA. The F27 was the smallest, encoding genes with unknown function. The F28 family encoded the putative expression locus for antigenic variation in all species except Borrelia hermsii and Borrelia anserina. Taken together, this work provides a foundation for future investigations to identify essential plasmid-localized genes that drive the vector-host life cycle of RF Borrelia. IMPORTANCE Borrelia spp. spirochetes are arthropod-borne bacteria found globally that infect humans and other vertebrates. RF borreliae are understudied and misdiagnosed pathogens because of the vague clinical presentation of disease and the elusive feeding behavior of argasid ticks. Consequently, genomics resources for RF spirochetes have been limited. Analyses of Borrelia plasmids have been challenging because they are often highly fragmented and unassembled in most available genome assemblies. By utilizing Oxford Nanopore Technologies, we recently generated plasmid-resolved genome assemblies for seven Borrelia spp. found in the Western Hemisphere. This current study is an in-depth investigation into the linear plasmids that were conserved and syntenic across species. We identified differences in genome structure and, importantly, in antigenic variation systems between species. This work is an important step in identifying crucial plasmid-localized genetic elements essential for the life cycle of RF spirochetes.

18.
Front Oncol ; 13: 1205847, 2023.
Article in English | MEDLINE | ID: mdl-37601671

ABSTRACT

Genetic testing of the APC gene by sequencing analysis and MLPA is available across commercial laboratories for the definitive genetic diagnosis of familial adenomatous polyposis (FAP). However, some genetic alterations are difficult to detect using conventional analyses. Here, we report a case of a complex genomic APC-TP63 rearrangement, which was identified in a patient with FAP by a series of genomic analyses, including multigene panel testing, chromosomal analyses, and long-read sequencing. A woman in her thirties was diagnosed with FAP due to multiple polyps in her colon and underwent total colectomy. Subsequent examination revealed fundic gland polyposis. No family history suggesting FAP was noted except for a first-degree relative with desmoid fibromatosis. The conventional APC gene testing was performed by her former doctor, but no pathogenic variant was detected, except for 2 variants of unknown significance. The patient was referred to our hospital for further genetic analysis. After obtaining informed consent in genetic counseling, we conducted a multigene panel analysis. As insertion of a part of the TP63 sequence was detected within exon16 of APC, further analyses, including chromosomal analysis and long-read sequencing, were performed and a complex translocation between chromosomes 3 and 5 containing several breakpoints in TP63 and APC was identified. No phenotype associated with TP63 pathogenic variants, such as split-hand/foot malformation (SHFM) or ectrodactyly, ectodermal dysplasia, or cleft lip/palate syndrome (EEC) was identified in the patient or her relatives. Multimodal genomic analyses should be considered in cases where no pathogenic germline variants are detected by conventional genetic testing despite an evident medical or family history of hereditary cancer syndromes.

19.
HardwareX ; 15: e00451, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37497345

ABSTRACT

A low-cost Digital Signal Processor (DSP) unit for advanced Scanning Probe Microscopy measurements is presented. It is based on Red Pitaya board and custom built electronic boards with additional high bit depth AD and DA converters. By providing all the necessary information (position and time) with each data point collected it can be used for any scan path, using either existing libraries for scan path generation or creating adaptive scan paths using Lua scripting interface. The DSP is also capable of performing statistical calculations, that can be used for decision making during scan or for the scan path optimisation on the DSP level.

20.
J Comput Phys ; 4882023 Sep 01.
Article in English | MEDLINE | ID: mdl-37332834

ABSTRACT

Estimating the likelihood, timing, and nature of events is a major goal of modeling stochastic dynamical systems. When the event is rare in comparison with the timescales of simulation and/or measurement needed to resolve the elemental dynamics, accurate prediction from direct observations becomes challenging. In such cases a more effective approach is to cast statistics of interest as solutions to Feynman-Kac equations (partial differential equations). Here, we develop an approach to solve Feynman-Kac equations by training neural networks on short-trajectory data. Our approach is based on a Markov approximation but otherwise avoids assumptions about the underlying model and dynamics. This makes it applicable to treating complex computational models and observational data. We illustrate the advantages of our method using a low-dimensional model that facilitates visualization, and this analysis motivates an adaptive sampling strategy that allows on-the-fly identification of and addition of data to regions important for predicting the statistics of interest. Finally, we demonstrate that we can compute accurate statistics for a 75-dimensional model of sudden stratospheric warming. This system provides a stringent test bed for our method.

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