21 results on '"BENCHMARK DATA"'
Search Results
2. Flame structure and reaction diagnostics for ammonia diffusion flame with hydrogen flame stabilizer
- Author
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Okumura, Yukihiko, Tsubota, Tomohiro, Matsuda, Naoya, Hori, Tsukasa, and Akamatsu, Fumiteru
- Published
- 2024
- Full Text
- View/download PDF
3. Generating synthetic gait patterns based on benchmark datasets for controlling prosthetic legs
- Author
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Minjae Kim and Levi J. Hargrove
- Subjects
Generative adversarial network ,Benchmark data ,Impedance control ,Synthetic impedance parameters ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Abstract Background Prosthetic legs help individuals with an amputation regain locomotion. Recently, deep neural network (DNN)-based control methods, which take advantage of the end-to-end learning capability of the network, have been proposed. One prominent challenge for these learning-based approaches is obtaining data for the training, particularly for the training of a mid-level controller. In this study, we propose a method for generating synthetic gait patterns (vertical load and lower limb joint angles) using a generative adversarial network (GAN). This approach enables a mid-level controller to execute ambulation modes that are not included in the training datasets. Methods The conditional GAN is trained on benchmark datasets that contain the gait data of individuals without amputation; synthetic gait patterns are generated from the user input. Further, a DNN-based controller for the generation of impedance parameters is trained using the synthetic gait pattern and the corresponding synthetic stiffness and damping coefficients. Results The trained GAN generated synthetic gait patterns with a coefficient of determination of 0.97 and a structural similarity index of 0.94 relative to benchmark data that were not included in the training datasets. We trained a DNN-based controller using the GAN-generated synthetic gait patterns for level-ground walking, standing-to-sitting motion, and sitting-to-standing motion. Four individuals without amputation participated in bypass testing and demonstrated the ambulation modes. The model successfully generated control parameters for the knee and ankle based on thigh angle and vertical load. Conclusions This study demonstrates that synthetic gait patterns can be used to train DNN models for impedance control. We believe a conditional GAN trained on benchmark datasets can provide reliable gait data for ambulation modes that are not included in its training datasets. Thus, designing gait data using a conditional GAN could facilitate the efficient and effective training of controllers for prosthetic legs.
- Published
- 2023
- Full Text
- View/download PDF
4. Recent and Future Advances in Water Electrolysis for Green Hydrogen Generation: Critical Analysis and Perspectives.
- Author
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Franco, Alessandro and Giovannini, Caterina
- Abstract
This paper delves into the pivotal role of water electrolysis (WE) in green hydrogen production, a process utilizing renewable energy sources through electrolysis. The term "green hydrogen" signifies its distinction from conventional "grey" or "brown" hydrogen produced from fossil fuels, emphasizing the importance of decarbonization in the hydrogen value chain. WE becomes a linchpin, balancing surplus green energy, stabilizing the grid, and addressing challenges in hard-to-abate sectors like long-haul transport and heavy industries. This paper navigates through electrolysis variants, technological challenges, and the crucial association between electrolytic hydrogen production and renewable energy sources (RESs). Energy consumption aspects are scrutinized, highlighting the need for optimization strategies to enhance efficiency. This paper systematically addresses electrolysis fundamentals, technologies, scaling issues, and the nexus with energy sources. It emphasizes the transformative potential of electrolytic hydrogen in the broader energy landscape, underscoring its role in shaping a sustainable future. Through a systematic analysis, this study bridges the gap between detailed technological insights and the larger energy system context, offering a holistic perspective. This paper concludes by summarizing key findings, showcasing the prospects, challenges, and opportunities associated with hydrogen production via water electrolysis for the energy transition. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Generating synthetic gait patterns based on benchmark datasets for controlling prosthetic legs.
- Author
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Kim, Minjae and Hargrove, Levi J.
- Subjects
ARTIFICIAL legs ,ANKLE ,KNEE ,GENERATIVE adversarial networks ,IMPEDANCE control - Abstract
Background: Prosthetic legs help individuals with an amputation regain locomotion. Recently, deep neural network (DNN)-based control methods, which take advantage of the end-to-end learning capability of the network, have been proposed. One prominent challenge for these learning-based approaches is obtaining data for the training, particularly for the training of a mid-level controller. In this study, we propose a method for generating synthetic gait patterns (vertical load and lower limb joint angles) using a generative adversarial network (GAN). This approach enables a mid-level controller to execute ambulation modes that are not included in the training datasets. Methods: The conditional GAN is trained on benchmark datasets that contain the gait data of individuals without amputation; synthetic gait patterns are generated from the user input. Further, a DNN-based controller for the generation of impedance parameters is trained using the synthetic gait pattern and the corresponding synthetic stiffness and damping coefficients. Results: The trained GAN generated synthetic gait patterns with a coefficient of determination of 0.97 and a structural similarity index of 0.94 relative to benchmark data that were not included in the training datasets. We trained a DNN-based controller using the GAN-generated synthetic gait patterns for level-ground walking, standing-to-sitting motion, and sitting-to-standing motion. Four individuals without amputation participated in bypass testing and demonstrated the ambulation modes. The model successfully generated control parameters for the knee and ankle based on thigh angle and vertical load. Conclusions: This study demonstrates that synthetic gait patterns can be used to train DNN models for impedance control. We believe a conditional GAN trained on benchmark datasets can provide reliable gait data for ambulation modes that are not included in its training datasets. Thus, designing gait data using a conditional GAN could facilitate the efficient and effective training of controllers for prosthetic legs. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
6. A gait phase prediction model trained on benchmark datasets for evaluating a controller for prosthetic legs.
- Author
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Minjae Kim and Hargrove, Levi J.
- Subjects
ARTIFICIAL legs ,KNEE ,ANKLE ,PREDICTION models ,ASSISTIVE technology - Abstract
Powered lower-limb assistive devices, such as prostheses and exoskeletons, are a promising option for helping mobility-impaired individuals regain functional gait. Gait phase prediction plays an important role in controlling these devices and evaluating whether the device generates a gait similar to that of individuals with intact limbs. This study proposes a gait phase prediction method based on a deep neural network (DNN). The long short-term memory (LSTM)-based model predicts a continuous gait phase from the 250 ms history of the vertical load, thigh angle, knee angle, and ankle angle, commonly available on powered lower-limb assistive devices. One unified model was trained using publicly available benchmark datasets containing intact limb gaits for level-ground walking (LGW) and ascending stairs (SA). A phase prediction error of 1.28% for all benchmark datasets was obtained. The model was subsequently applied to a state machine-controlled powered prosthetic leg dataset collected fromfour individuals with unilateral transfemoral amputation. The gait phase prediction results (a phase prediction error of 5.70%) indicate that the model trained on benchmark data can be used for a system not included in the training dataset with no post-processing, such as model adaptation. Furthermore, it provided information regarding evaluation of the controller: whether the prosthetic leg generated normal gait. In conclusion, the proposed gait phase predictionmodel will facilitate efficient gait prediction and evaluation of controllers for powered lower-limb assistive devices. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
7. A gait phase prediction model trained on benchmark datasets for evaluating a controller for prosthetic legs.
- Author
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Kim, Minjae and Hargrove, Levi J.
- Subjects
ARTIFICIAL legs ,KNEE ,ANKLE ,PREDICTION models ,ASSISTIVE technology - Abstract
Powered lower-limb assistive devices, such as prostheses and exoskeletons, are a promising option for helping mobility-impaired individuals regain functional gait. Gait phase prediction plays an important role in controlling these devices and evaluating whether the device generates a gait similar to that of individuals with intact limbs. This study proposes a gait phase prediction method based on a deep neural network (DNN). The long short-term memory (LSTM)-based model predicts a continuous gait phase from the 250 ms history of the vertical load, thigh angle, knee angle, and ankle angle, commonly available on powered lower-limb assistive devices. One unified model was trained using publicly available benchmark datasets containing intact limb gaits for level-ground walking (LGW) and ascending stairs (SA). A phase prediction error of 1.28% for all benchmark datasets was obtained. The model was subsequently applied to a state machine-controlled powered prosthetic leg dataset collected fromfour individuals with unilateral transfemoral amputation. The gait phase prediction results (a phase prediction error of 5.70%) indicate that the model trained on benchmark data can be used for a system not included in the training dataset with no post-processing, such as model adaptation. Furthermore, it provided information regarding evaluation of the controller: whether the prosthetic leg generated normal gait. In conclusion, the proposed gait phase predictionmodel will facilitate effcient gait prediction and evaluation of controllers for powered lower-limb assistive devices. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
8. A framework for benchmarking clustering algorithms
- Author
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Marek Gagolewski
- Subjects
Clustering ,Machine learning ,Benchmark data ,Noise points ,External cluster validity ,Partition similarity score ,Computer software ,QA76.75-76.765 - Abstract
The evaluation of clustering algorithms can involve running them on a variety of benchmark problems, and comparing their outputs to the reference, ground-truth groupings provided by experts. Unfortunately, many research papers and graduate theses consider only a small number of datasets. Also, the fact that there can be many equally valid ways to cluster a given problem set is rarely taken into account. In order to overcome these limitations, we have developed a framework whose aim is to introduce a consistent methodology for testing clustering algorithms. Furthermore, we have aggregated, polished, and standardised many clustering benchmark dataset collections referred to across the machine learning and data mining literature, and included new datasets of different dimensionalities, sizes, and cluster types. An interactive datasets explorer, the documentation of the Python API, a description of the ways to interact with the framework from other programming languages such as R or MATLAB, and other details are all provided at https://clustering-benchmarks.gagolewski.com.
- Published
- 2022
- Full Text
- View/download PDF
9. How to Improve the Reproducibility, Replicability, and Extensibility of Remote Sensing Research.
- Author
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Kedron, Peter and Frazier, Amy E.
- Subjects
- *
REMOTE sensing , *TECHNOLOGICAL innovations , *SCIENTIFIC community , *REPRODUCIBLE research - Abstract
The field of remote sensing has undergone a remarkable shift where vast amounts of imagery are now readily available to researchers. New technologies, such as uncrewed aircraft systems, make it possible for anyone with a moderate budget to gather their own remotely sensed data, and methodological innovations have added flexibility for processing and analyzing data. These changes create both the opportunity and need to reproduce, replicate, and compare remote sensing methods and results across spatial contexts, measurement systems, and computational infrastructures. Reproducing and replicating research is key to understanding the credibility of studies and extending recent advances into new discoveries. However, reproducibility and replicability (R&R) remain issues in remote sensing because many studies cannot be independently recreated and validated. Enhancing the R&R of remote sensing research will require significant time and effort by the research community. However, making remote sensing research reproducible and replicable does not need to be a burden. In this paper, we discuss R&R in the context of remote sensing and link the recent changes in the field to key barriers hindering R&R while discussing how researchers can overcome those barriers. We argue for the development of two research streams in the field: (1) the coordinated execution of organized sequences of forward-looking replications, and (2) the introduction of benchmark datasets that can be used to test the replicability of results and methods. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
10. Benchmarking differential expression, imputation and quantification methods for proteomics data.
- Author
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Lin, Miao-Hsia, Wu, Pei-Shan, Wong, Tzu-Hsuan, Lin, I-Ying, Lin, Johnathan, Cox, Jürgen, and Yu, Sung-Huan
- Subjects
- *
PROTEOMICS , *RNA sequencing , *INTEGRATED software , *DATA analysis , *DROSOPHILA - Abstract
Data analysis is a critical part of quantitative proteomics studies in interpreting biological questions. Numerous computational tools for protein quantification, imputation and differential expression (DE) analysis were generated in the past decade and the search for optimal tools is still going on. Moreover, due to the rapid development of RNA sequencing (RNA-seq) technology, a vast number of DE analysis methods were created for that purpose. The applicability of these newly developed RNA-seq-oriented tools to proteomics data remains in doubt. In order to benchmark these analysis methods, a proteomics dataset consisting of proteins derived from humans, yeast and drosophila, in defined ratios, was generated in this study. Based on this dataset, DE analysis tools, including microarray- and RNA-seq-based ones, imputation algorithms and protein quantification methods were compared and benchmarked. Furthermore, applying these approaches to two public datasets showed that RNA-seq-based DE tools achieved higher accuracy (ACC) in identifying DEPs. This study provides useful guidelines for analyzing quantitative proteomics datasets. All the methods used in this study were integrated into the Perseus software, version 2.0.3.0, which is available at https://www.maxquant.org/perseus. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
11. Multi-Dimensional Classification via Decomposed Label Encoding
- Author
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Min-Ling Zhang and Bin-Bin Jia
- Subjects
Computer science ,business.industry ,Feature vector ,Pattern recognition ,Space (mathematics) ,Class (biology) ,Computer Science Applications ,Computational Theory and Mathematics ,Encoding (memory) ,Multi dimensional ,Decomposition (computer science) ,Artificial intelligence ,Benchmark data ,business ,Class variable ,Information Systems - Abstract
In multi-dimensional classification (MDC), a number of class variables are assumed in the output space with each of them specifying the class membership w.r.t. one heterogeneous class space. One major challenge in learning from MDC examples lies in the heterogeneity of class spaces, where the modeling outputs from different class spaces are not directly comparable. To tackle this problem, we propose a new strategy named decomposed label encoding which enables modeling alignment for MDC in an encoded label space derived from one-vs-one (OvO) decomposition. Specifically, the original MDC output space is transformed into a ternary encoded label space by conducting OvO decomposition w.r.t. each class space. Then, the manifold structure in the feature space is exploited to enrich the labeling information in the encoded label space. Finally, the predictive model is induced by fitting the metric-aligned modeling outputs with enriched labeling information. Extensive experiments over twenty benchmark data sets clearly show the superiority of the proposed MDC strategy against state-of-the-art approaches.
- Published
- 2023
- Full Text
- View/download PDF
12. Validation of codes for modeling and simulation of nuclear power plants: A review.
- Author
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Moshkbar-Bakhshayesh, Khalil and Mohtashami, Soroush
- Subjects
- *
ARTIFICIAL neural networks , *DISTRIBUTION (Probability theory) , *TESTING laboratories , *ARTIFICIAL intelligence , *NUCLEAR models , *DEEP learning - Abstract
The validation process is done to ensure the performance of nuclear codes compared to experimental results and to determine the degree of reliability of codes output. The development of nuclear power plants (NPPs) designs and the need for safer power plants has led to the increasing diversity/extension of nuclear codes and, as a result, the validation process has become more complicated. In this study, single physics validation including neutronic, core thermal-hydraulics (CTH), system thermal-hydraulics (STH), fuel performance, and multi-physics validation especially coupled neutronic and thermal-hydraulics (CNTH) are discussed. An international collective effort to provide benchmark data and test facilities including core test facility (CTF), separate effect test facility (SETF), and integral test facility (ITF) accompanied with addressing challenges related to scaling issues has been made. However, validation processes may suffer from some challenges. Non-quantifiable parameters cannot be given by experimental measurements. Moreover, for measurable parameters, faulty sensors can lead to incorrect results. Neural network, especially generative deep learning, with the ability to learn the probability distribution of training data and to generate unknown patterns may be a good candidate for the challenges mentioned above, e.g., detecting faulty sensors values and estimating non-quantifiable parameters based on quantifiable ones. Therefore, the application of artificial intelligence (AI) in the validation process may lead to a reduction of the volume of experimental measurements /construction of test facilities which alone is valuable. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
13. Liquid metal MHD research at KIT: Fundamental phenomena and flows in complex blanket geometries.
- Author
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Bühler, L., Brinkmann, H.-J., Courtessole, C., Klüber, V., Koehly, C., Lyu, B., Mistrangelo, C., and Roth, J.
- Subjects
- *
TRITIUM , *LIQUID metals , *FUSION reactor blankets , *NON-uniform flows (Fluid dynamics) , *PRESSURE drop (Fluid dynamics) - Abstract
The present paper gives an overview of liquid metal research activities performed in recent years at the Karlsruhe Institute of Technology (KIT). The work is motivated by applications in liquid metal blankets for a DEMO fusion reactor where lead lithium (PbLi), which serves as a neutron multiplier and tritium breeder, interacts with the plasma-confining magnetic field as it flows in the blanket covering the inner walls of the reactor. Liquid metal magnetohydrodynamic (MHD) research at KIT supports blanket design activities through theoretical and experimental investigations. Predictive computational tools are developed and validated by empirical data obtained for fundamental problems, such as flows in non-uniform magnetic fields or magneto-convective heat transfer from submerged obstacles. In addition, technological developments like pressure drop reduction by insulating flow channel inserts are pursued both theoretically and experimentally. Two complementary experimental facilities (MEKKA and MaPLE) provide a unique and versatile platform for MHD investigations at fusion relevant parameters. Using NaK as a model fluid in MEKKA allows experiments to be conducted at high Hartmann numbers in large complex geometries, such as scaled blanket mock-ups of ITER test blanket modules. For magneto-convection and heat transfer studies, MaPLE is well suited since it enables experiments with the prototypical fluid PbLi in test sections inclined at various orientations with respect to gravity. Some recent results have been selected to illustrate the broad spectrum of MHD activities at KIT. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
14. Methodology Based on Photogrammetry for Testing Ship-Block Resistance in Traditional Towing Tanks: Observations and Benchmark Data
- Author
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José Enrique Gutiérrez-Romero, Samuel Ruiz-Capel, Jerónimo Esteve-Pérez, Blas Zamora-Parra, and Juan Pedro Luna-Abad
- Subjects
paraffin wax blocks ,ship resistance ,photogrammetry ,uncertainties ,model-scale test ,benchmark data ,Naval architecture. Shipbuilding. Marine engineering ,VM1-989 ,Oceanography ,GC1-1581 - Abstract
The real resistance that a ship must face when it is navigating in ice floes is the key factor for knowing the necessary power and the required engine size. The aim of this work is to provide valuable data to help other research in which numerical frameworks will be developed to study ship navigation in broken ice. In this work, we used paraffin wax as an alternative to obtain affordable solutions, avoiding the high cost of ice tests. The experiments were carried out in a traditional basin facility and they consisted of towing tank tests with a ship model using different concentrations of blocks simulated by the use of paraffin wax. Photogrammetry was used as technique to determine the initial position of the ice blocks, which is important as starting data in the current development of numerical simulation code for studying the features of ship resistance in drift ice. These data are available for some ice concentrations in attached files. In addition, a procedure for testing in traditional towing facilities is presented and discussed. The results of the resistance obtained in the experiments in the presence of simulated floes are presented for three concentrations and three model speeds. Some findings may be applicable to ice sailing, under given circumstances.
- Published
- 2022
- Full Text
- View/download PDF
15. Event-based MILP models for ridepooling applications
- Author
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Michael Stiglmayr, Kathrin Klamroth, and Daniela Gaul
- Subjects
Mathematical optimization ,Information Systems and Management ,General Computer Science ,Optimization algorithm ,Computer science ,Event (computing) ,Event based ,Management Science and Operations Research ,Flow network ,Industrial and Manufacturing Engineering ,Time windows ,Modeling and Simulation ,Spatial representation ,Benchmark data - Abstract
Ridepooling services require efficient optimization algorithms to simultaneously plan routes and pool users in shared rides. We consider a static dial-a-ride problem (DARP) where a series of origin-destination requests have to be assigned to routes of a fleet of vehicles. Thereby, all requests have associated time windows for pick-up and delivery, and may be denied if they can not be serviced in reasonable time or at reasonable cost. Rather than using a spatial representation of the transportation network we suggest an event-based formulation of the problem, resulting in significantly improved computational times. While the corresponding MILP formulations require more variables than standard models, they have the advantage that capacity, pairing and precedence constraints are handled implicitly. The approach is tested and validated using a standard IP-solver on benchmark data from the literature. Moreover, the impact of, and the trade-off between, different optimization goals is evaluated on a case study in the city of Wuppertal (Germany).
- Published
- 2022
- Full Text
- View/download PDF
16. Benchmarking airborne laser scanning tree segmentation algorithms in broadleaf forests shows high accuracy only for canopy trees
- Author
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Cao, Y., Ball, J.G.C., Coomes, D.A., Steinmeier, L., Knapp, Nikolai, Wilkes, P., Disney, M., Calders, K., Burt, A., Lin, Y., Jackson, T.D., Cao, Y., Ball, J.G.C., Coomes, D.A., Steinmeier, L., Knapp, Nikolai, Wilkes, P., Disney, M., Calders, K., Burt, A., Lin, Y., and Jackson, T.D.
- Abstract
Individual tree segmentation from airborne laser scanning data is a longstanding and important challenge in forest remote sensing. Tree segmentation algorithms are widely available, but robust intercomparison studies are rare due to the difficulty of obtaining reliable reference data. Here we provide a benchmark data set for temperate and tropical broadleaf forests generated from labelled terrestrial laser scanning data. We compared the performance of four widely used tree segmentation algorithms against this benchmark data set. All algorithms performed reasonably well on the canopy trees. The point cloud-based algorithm AMS3D (Adaptive Mean Shift 3D) had the highest overall accuracy, closely followed by the 2D raster based region growing algorithm Dalponte2016 +. However, all algorithms failed to accurately segment the understory trees. This result was consistent across both forest types. This study emphasises the need to assess tree segmentation algorithms directly using benchmark data, rather than comparing with forest indices such as biomass or the number and size distribution of trees. We provide the first openly available benchmark data set for tropical forests and we hope future studies will extend this work to other regions.
- Published
- 2023
17. Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023.
- Author
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Lou R and Shui W
- Subjects
- Mass Spectrometry methods, Gene Library, Proteome analysis, Proteomics methods, Software
- Abstract
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful technology for high-throughput, accurate, and reproducible quantitative proteomics. This review provides a comprehensive overview of recent advances in both the experimental and computational methods for DIA proteomics, from data acquisition schemes to analysis strategies and software tools. DIA acquisition schemes are categorized based on the design of precursor isolation windows, highlighting wide-window, overlapping-window, narrow-window, scanning quadrupole-based, and parallel accumulation-serial fragmentation-enhanced DIA methods. For DIA data analysis, major strategies are classified into spectrum reconstruction, sequence-based search, library-based search, de novo sequencing, and sequencing-independent approaches. A wide array of software tools implementing these strategies are reviewed, with details on their overall workflows and scoring approaches at different steps. The generation and optimization of spectral libraries, which are critical resources for DIA analysis, are also discussed. Publicly available benchmark datasets covering global proteomics and phosphoproteomics are summarized to facilitate performance evaluation of various software tools and analysis workflows. Continued advances and synergistic developments of versatile components in DIA workflows are expected to further enhance the power of DIA-based proteomics., Competing Interests: Conflict of interest The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
18. Investigating deep learning model calibration for classification problems in mechanics.
- Author
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Mohammadzadeh, Saeed, Prachaseree, Peerasait, and Lejeune, Emma
- Subjects
- *
ARTIFICIAL neural networks , *DEEP learning , *MACHINE learning , *MECHANICAL behavior of materials , *CALIBRATION , *METHODS engineering - Abstract
Recently, there has been a growing interest in applying machine learning methods to problems in engineering mechanics. In particular, there has been significant interest in applying deep learning techniques to predicting the mechanical behavior of heterogeneous materials and structures. Researchers have shown that deep learning methods are able to effectively predict mechanical behavior with low error for systems ranging from engineered composites, to geometrically complex metamaterials, to heterogeneous biological tissue. However, there has been comparatively little attention paid to deep learning model calibration, i.e., the match between predicted probabilities of outcomes and the true probabilities of outcomes. In this work, we perform a comprehensive investigation into machine learning model calibration across 7 open access engineering mechanics datasets that cover three distinct types of mechanical problems. Specifically, we evaluate both model and model calibration error for multiple machine learning methods, and investigate the influence of ensemble averaging and post hoc model calibration via temperature scaling. Overall, we find that ensemble averaging of deep neural networks is both an effective and consistent tool for improving model calibration, while temperature scaling has comparatively limited benefits. Looking forward, we anticipate that this investigation will lay the foundation for future work in developing mechanics specific approaches to deep learning model calibration. • We investigate machine learning model calibration for problems in mechanics. • This investigation includes 7 open access engineering mechanics datasets. • We investigate ensemble averaging and post hoc model calibration. • Ensemble averaging of deep neural networks improves model calibration. • Temperature scaling has comparatively limited benefits. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
19. Allosteric Hotspots in the Main Protease of SARS-CoV-2
- Author
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Mauricio Barahona, Nan Wu, Léonie Strömich, Sophia N. Yaliraki, and Engineering & Physical Science Research Council (EPSRC)
- Subjects
Biochemistry & Molecular Biology ,Coronavirus disease 2019 (COVID-19) ,Protein family ,PREDICTION ,PROTEINS ,Protein Conformation ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,medicine.medical_treatment ,graph theory ,Allosteric regulation ,3C-LIKE PROTEASE ,allosteric site prediction ,Computational biology ,Biology ,0601 Biochemistry and Cell Biology ,FORCE ,atomistic graph representation ,DESIGN ,Structural Biology ,REVEALS ,medicine ,Binding site ,Molecular Biology ,Coronavirus 3C Proteases ,SARS ,SITES ,Protease ,Science & Technology ,COMPLEX ,0304 Medicinal and Biomolecular Chemistry ,SARS-CoV-2 ,Molecular Docking Simulation ,TARGET ,Targeted drug delivery ,Benchmark data ,Life Sciences & Biomedicine ,Allosteric Site ,0605 Microbiology - Abstract
Inhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.
- Published
- 2022
- Full Text
- View/download PDF
20. Learning mechanically driven emergent behavior with message passing neural networks.
- Author
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Prachaseree, Peerasait and Lejeune, Emma
- Subjects
- *
MESSAGE passing (Computer science) , *IMAGE representation , *MECHANICAL behavior of materials , *COMPUTER vision , *DATA augmentation , *SOLID mechanics , *MACHINE learning - Abstract
• Graph Neural Networks are an effective tool for metamodels of complex structures. • Point cloud-based geometry representation outperformed tested alternatives. • Ensemble learning enhanced metamodel performance. • Performance is benchmarked with open source Asymmetric Buckling Columns dataset. From designing architected materials to connecting mechanical behavior across scales, computational modeling is a critical tool for understanding and predicting the mechanical response of deformable bodies. In particular, computational modeling is an invaluable tool for predicting global emergent phenomena, such as the onset of geometric instabilities, or heterogeneity induced symmetry breaking. Recently, there has been a growing interest in both using machine learning based computational models to learn mechanical behavior directly from experimental data, and using machine learning (ML) methods to reduce the computational cost of physics-based simulations. Notably, machine learning approaches that rely on Graph Neural Networks (GNNs) have recently been shown to effectively predict mechanical behavior in multiple examples of particle-based and mesh-based simulations. However, despite this initial promise, the performance of graph based methods have yet to be investigated on a myriad of solid mechanics problems. In this work, we examine the ability of neural message passing to predict a fundamental aspect of mechanically driven emergent behavior: the connection between a column's geometric structure and the direction that it buckles. To accomplish this, we introduce the Asymmetric Buckling Columns (ABC) dataset, a dataset comprised of three types of asymmetric and heterogeneous column geometries (sub-dataset 1, sub-dataset 2, and sub-dataset 3) where the goal is to classify the direction of symmetry breaking (left or right) under compression after the onset of the buckling instability. Notably, it is difficult to parameterize these structures into a feature vector for typical ML methods. Essentially, because the geometry of these columns is discontinuous and intricate, local geometric patterns will be distorted by the low-resolution "image-like" data representations that are required to implement convolutional neural network based metamodels. Instead, we present a pipeline to learn global emergent properties while enforcing locality with message passing neural networks. Specifically, we take inspiration from point cloud based classification problems from the computer vision research field and use PointNet++ layers to perform classification on the ABC dataset. In addition to investigating GNN model architecture, we study the effect of different input data representation approaches, data augmentation, and combining multiple models as an ensemble. Overall, we were able to achieve good performance with this approach, ranging from 0.952 prediction accuracy on sub-dataset 1, to 0.913 prediction accuracy on sub-dataset 2, to 0.856 prediction accuracy on sub-dataset 3 for training dataset sizes of 20 , 000 points each. However, these results also clearly indicate that predicting solid mechanics based emergent behavior with these methods is non-trivial. Because both our model implementation and dataset are distributed under open-source licenses, we hope that future researchers can build on our work to create enhanced mechanics-specific machine learning methods. Furthermore, we also intend to provoke discussion around different methods for representing complex mechanical structures when applying machine learning to mechanics research. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
21. Methodology Based on Photogrammetry for Testing Ship-Block Resistance in Traditional Towing Tanks: Observations and Benchmark Data.
- Author
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Gutiérrez-Romero, José Enrique, Ruiz-Capel, Samuel, Esteve-Pérez, Jerónimo, Zamora-Parra, Blas, and Luna-Abad, Juan Pedro
- Subjects
SHIP resistance ,PARAFFIN wax ,ICE floes ,TANKERS ,SHIP models - Abstract
The real resistance that a ship must face when it is navigating in ice floes is the key factor for knowing the necessary power and the required engine size. The aim of this work is to provide valuable data to help other research in which numerical frameworks will be developed to study ship navigation in broken ice. In this work, we used paraffin wax as an alternative to obtain affordable solutions, avoiding the high cost of ice tests. The experiments were carried out in a traditional basin facility and they consisted of towing tank tests with a ship model using different concentrations of blocks simulated by the use of paraffin wax. Photogrammetry was used as technique to determine the initial position of the ice blocks, which is important as starting data in the current development of numerical simulation code for studying the features of ship resistance in drift ice. These data are available for some ice concentrations in attached files. In addition, a procedure for testing in traditional towing facilities is presented and discussed. The results of the resistance obtained in the experiments in the presence of simulated floes are presented for three concentrations and three model speeds. Some findings may be applicable to ice sailing, under given circumstances. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
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