Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A benchmark dataset for Hydrogen Combustion.

ABSTRACT: The generation of reference data for deep learning models is challenging for reactive systems, and more so for combustion reactions due to the extreme conditions that create radical species and alternative spin states during the combustion process. Here, we extend intrinsic reaction coordinate (IRC) calculations with ab initio MD simulations and normal mode displacement calculations to more extensively cover the potential energy surface for 19 reaction channels for hydrogen combustion. A total of ∼290,000 potential energies and ∼1,270,000 nuclear force vectors are evaluated with a high quality range-separated hybrid density functional, ωB97X-V, to construct the reference data set, including transition state ensembles, for the deep learning models to study hydrogen combustion reaction.

SUBMITTER: Guan X

PROVIDER: S-EPMC9114378 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A benchmark dataset for Hydrogen Combustion.

Guan Xingyi X Das Akshaya A Stein Christopher J CJ Heidar-Zadeh Farnaz F Bertels Luke L Liu Meili M Haghighatlari Mojtaba M Li Jie J Zhang Oufan O Hao Hongxia H Leven Itai I Head-Gordon Martin M Head-Gordon Teresa T

Scientific data 20220517 1

The generation of reference data for deep learning models is challenging for reactive systems, and more so for combustion reactions due to the extreme conditions that create radical species and alternative spin states during the combustion process. Here, we extend intrinsic reaction coordinate (IRC) calculations with ab initio MD simulations and normal mode displacement calculations to more extensively cover the potential energy surface for 19 reaction channels for hydrogen combustion. A total o ...[more]

PMID: 35581204

Similar Datasets

Dataset on flue gas composition during combustion in the fluidised bed reactor. Glycerol combustion.

Project description:The dataset presented in this article is the supplementary data for the research article by Żukowski and Berkowicz (doi:10.1016/j.combustflame.2019.05.024) [1], in which for the first time the inert and catalytic cenospheres were used as the fluidised bed material, giving the possibility to burn liquids inside the fluidised bed without the need for using specialised dosing systems. The instantaneous concentrations of the gaseous products during the combustion of glycerol samples were detected using Fourier Transform Infrared Spectroscopy (FTIR, Gasmet DX-4000). The accurate composition at the outlet of the reactor makes it possible to evaluate and verify new kinetic models of the glycerol combustion in the fluidised bed. It also will be helpful in creating new simplified models. The data presented here is essential for the evaluation of CFD combustion models which have to include accurate kinetic data.

| S-EPMC7082517 | biostudies-literature

Dataset on flue gas composition during combustion in the fluidised bed reactor. Polyethylene combustion.

Project description:The dataset presented in this article is the supplementary data for the research article titled "The combustion of polyolefins in the inert and catalytic fluidised beds", in which polyethylene combustion in the cenosphere fluidised bed were investigated. The use of cenospheres as a bed material made it possible to free sink of PE particles in the bed and rule out its combustion in freeboard. It also lead to elimination of soot formation. The quantitative and qualitative analysis of flue gases were performed by Fourier Transform Infrared Spectroscopy (FTIR, Gasmet DX-4000). This data article provides detailed information on changes in product concentration at intervals of a few seconds.

| S-EPMC7415831 | biostudies-literature

ABAG-docking benchmark: a non-redundant structure benchmark dataset for antibody-antigen computational docking.

Project description:Accurate prediction of antibody-antigen complex structures is pivotal in drug discovery, vaccine design and disease treatment and can facilitate the development of more effective therapies and diagnostics. In this work, we first review the antibody-antigen docking (ABAG-docking) datasets. Then, we present the creation and characterization of a comprehensive benchmark dataset of antibody-antigen complexes. We categorize the dataset based on docking difficulty, interface properties and structural characteristics, to provide a diverse set of cases for rigorous evaluation. Compared with Docking Benchmark 5.5, we have added 112 cases, including 14 single-domain antibody (sdAb) cases and 98 monoclonal antibody (mAb) cases, and also increased the proportion of Difficult cases. Our dataset contains diverse cases, including human/humanized antibodies, sdAbs, rodent antibodies and other types, opening the door to better algorithm development. Furthermore, we provide details on the process of building the benchmark dataset and introduce a pipeline for periodic updates to keep it up to date. We also utilize multiple complex prediction methods including ZDOCK, ClusPro, HDOCK and AlphaFold-Multimer for testing and analyzing this dataset. This benchmark serves as a valuable resource for evaluating and advancing docking computational methods in the analysis of antibody-antigen interaction, enabling researchers to develop more accurate and effective tools for predicting and designing antibody-antigen complexes. The non-redundant ABAG-docking structure benchmark dataset is available at https://github.com/Zhaonan99/Antibody-antigen-complex-structure-benchmark-dataset.

| S-EPMC10883643 | biostudies-literature

A benchmark dataset for machine learning in ecotoxicology.

Project description:The use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, which we consider a barrier of entry for this kind of research. Additionally, model performances can only be compared across studies when the same dataset, cleaning, and splittings were used. Therefore, we provide ADORE, an extensive and well-described dataset on acute aquatic toxicity in three relevant taxonomic groups (fish, crustaceans, and algae). The core dataset describes ecotoxicological experiments and is expanded with phylogenetic and species-specific data on the species as well as chemical properties and molecular representations. Apart from challenging other researchers to try and achieve the best model performances across the whole dataset, we propose specific relevant challenges on subsets of the data and include datasets and splittings corresponding to each of these challenge as well as in-depth characterization and discussion of train-test splitting approaches.

| S-EPMC10584858 | biostudies-literature

Benchmark classification dataset for laser-induced breakdown spectroscopy.

Project description:In this work, we present an extensive dataset of laser-induced breakdown spectroscopy (LIBS) spectra for the pre-training and evaluation of LIBS classification models. LIBS is a well-established spectroscopic method for in-situ and industrial applications, where LIBS is primarily applied for clustering and classification tasks. As such, our dataset is aimed at helping with the development and testing of classification and clustering methodologies. Moreover, the dataset could be used to pre-train classification models for applications where the amount of available data is limited. The dataset consists of LIBS spectra of 138 soil samples belonging to 12 distinct classes. The spectra were acquired with a state-of-the-art LIBS system. Lastly, the composition of each sample is also provided, including estimated uncertainties.

| S-EPMC7018695 | biostudies-literature

Computational fluid dynamics benchmark dataset of airflow in tracheas.

Project description:Computational Fluid Dynamics (CFD) is fast becoming a useful tool to aid clinicians in pre-surgical planning through the ability to provide information that could otherwise be extremely difficult if not impossible to obtain. However, in order to provide clinically relevant metrics, the accuracy of the computational method must be sufficiently high. There are many alternative methods employed in the process of performing CFD simulations within the airways, including different segmentation and meshing strategies, as well as alternative approaches to solving the Navier-Stokes equations. However, as in vivo validation of the simulated flow patterns within the airways is not possible, little exists in the way of validation of the various simulation techniques. The data presented here consists of very highly resolved flow data. The degree of resolution is compared to the highest necessary resolutions of the Kolmogorov length and time scales. Therefore this data is ideally suited to act as a benchmark case to which cheaper computational methods may be compared. A dataset and solution setup for one such more efficient method, large eddy simulation (LES), is also presented.

| S-EPMC5144758 | biostudies-literature

A Benchmark Dataset for RSVP-Based Brain-Computer Interfaces.

Project description:This paper reports on a benchmark dataset acquired with a brain-computer interface (BCI) system based on the rapid serial visual presentation (RSVP) paradigm. The dataset consists of 64-channel electroencephalogram (EEG) data from 64 healthy subjects (sub1,…, sub64) while they performed a target image detection task. For each subject, the data contained two groups ("A" and "B"). Each group contained two blocks, and each block included 40 trials that corresponded to 40 stimulus sequences. Each sequence contained 100 images presented at 10 Hz (10 images per second). The stimulus images were street-view images of two categories: target images with human and non-target images without human. Target images were presented randomly in the stimulus sequence with a probability of 1∼4%. During the stimulus presentation, subjects were asked to search for the target images and ignore the non-target images in a subjective manner. To keep all original information, the dataset was the raw continuous data without any processing. On one hand, the dataset can be used as a benchmark dataset to compare the algorithms for target identification in RSVP-based BCIs. On the other hand, the dataset can be used to design new system diagrams and evaluate their BCI performance without collecting any new data through offline simulation. Furthermore, the dataset also provides high-quality data for characterizing and modeling event-related potentials (ERPs) and steady-state visual evoked potentials (SSVEPs) in RSVP-based BCIs. The dataset is freely available from http://bci.med.tsinghua.edu.cn/download.html.

| S-EPMC7566171 | biostudies-literature

StrokeRehab: A Benchmark Dataset for Sub-second Action Identification.

Project description:Automatic action identification from video and kinematic data is an important machine learning problem with applications ranging from robotics to smart health. Most existing works focus on identifying coarse actions such as running, climbing, or cutting vegetables, which have relatively long durations and a complex series of motions. This is an important limitation for applications that require identification of more elemental motions at high temporal resolution. For example, in the rehabilitation of arm impairment after stroke, quantifying the training dose (number of repetitions) requires differentiating motions with sub-second durations. Our goal is to bridge this gap. To this end, we introduce a large-scale, multimodal dataset, StrokeRehab, as a new action-recognition benchmark that includes elemental short-duration actions labeled at a high temporal resolution. StrokeRehab consists of high-quality inertial measurement unit sensor and video data of 51 stroke-impaired patients and 20 healthy subjects performing activities of daily living like feeding, brushing teeth, etc. Because it contains data from both healthy and impaired individuals, StrokeRehab can be used to study the influence of distribution shift in action-recognition tasks. When evaluated on StrokeRehab, current state-of-the-art models for action segmentation produce noisy predictions, which reduces their accuracy in identifying the corresponding sequence of actions. To address this, we propose a novel approach for high-resolution action identification, inspired by speech-recognition techniques, which is based on a sequence-to-sequence model that directly predicts the sequence of actions. This approach outperforms current state-of-the-art methods on StrokeRehab, as well as on the standard benchmark datasets 50Salads, Breakfast, and Jigsaws.

| S-EPMC10530637 | biostudies-literature

A benchmark dataset of protein antigens for antigenicity measurement.

Project description:Antigenicity measurement plays a fundamental role in vaccine design, which requires antigen selection from a large number of mutants. To augment traditional cross-reactivity experiments, computational approaches for predicting the antigenic distance between multiple protein antigens are highly valuable. The performance of in silico models relies heavily on large-scale benchmark datasets, which are scattered among public databases and published articles or reports. Here, we present the first benchmark dataset of protein antigens with experimental evidence to guide in silico antigenicity calculations. This dataset includes (1) standard haemagglutination-inhibition (HI) tests for 3,867 influenza A/H3N2 strain pairs, (2) standard HI tests for 559 influenza virus B strain pairs, and (3) neutralization titres derived from 1,073 Dengue virus strain pairs. All of these datasets were collated and annotated with experimentally validated antigenicity relationships as well as sequence information for the corresponding protein antigens. We anticipate that this work will provide a benchmark dataset for in silico antigenicity prediction that could be further used to assist in epidemic surveillance and therapeutic vaccine design for viruses with variable antigenicity.

| S-EPMC7338539 | biostudies-literature

Curated benchmark dataset for ultrasound based breast lesion analysis.

Project description:A new detailed dataset of breast ultrasound scans (BrEaST) containing images of benign and malignant lesions as well as normal tissue examples, is presented. The dataset consists of 256 breast scans collected from 256 patients. Each scan was manually annotated and labeled by a radiologist experienced in breast ultrasound examination. In particular, each tumor was identified in the image using a freehand annotation and labeled according to BIRADS features and lexicon. The histopathological classification of the tumor was also provided for patients who underwent a biopsy. The BrEaST dataset is the first breast ultrasound dataset containing patient-level labels, image-level annotations, and tumor-level labels with all cases confirmed by follow-up care or core needle biopsy result. To enable research into breast disease detection, tumor segmentation and classification, the BrEaST dataset is made publicly available with the CC-BY 4.0 license.

| S-EPMC10830496 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data