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At least 217 records · Page 12

The METLIN small molecule dataset for machine learning-based retention time prediction

Machine learning has been extensively applied in small molecule analysis to predict a wide range of molecular properties and processes including mass spectrometry fragmentation or chromatographic retention time. However, current approaches for retention time prediction lack sufficient accuracy due to limited available experimental data. Here we introduce the METLIN small molecule retention time (SMRT) dataset, an experimentally acquired reverse-phase chromatography retention time dataset covering up to 80,038 small molecules. To demonstrate the utility of this dataset, we deployed a deep learning model for retention time prediction applied to small molecule annotation. Results showed that in 70% of the cases, the correct molecular identity was ranked among the top 3 candidates based on their predicted retention time. We anticipate that this dataset will enable the community to apply machine learning or first principles strategies to generate better models for retention time prediction.

59 BASIC BIOLOGICAL SCIENCES↗

Information-entropy-driven generation of material-agnostic datasets for machine-learning interatomic potentials

In contrast to their empirical counterparts, machine-learning interatomic potentials (MLIAPs) promise to deliver near-quantum accuracy over broad regions of configuration space. However, due to their generic functional forms and extreme flexibility, they can catastrophically fail to capture the properties of novel, out-of-sample configurations, making the quality of the training set a determining factor, especially when investigating materials under extreme conditions. We propose a novel automated dataset generation method based on the maximization of the information entropy of the feature distribution, aiming at an extremely broad coverage of the configuration space in a way that is agnostic to the properties of specific target materials. The ability of the dataset to capture unique material properties is demonstrated on a range of unary materials, including elements with the FCC (Al), BCC (W), HCP (Be, Re and Os), graphite (C), and trigonal (Sb, Te) ground states. MLIAPs trained to this dataset are shown to be accurate over a range of application-relevant metrics, as well as extremely robust over very broad swaths of configurations space, even without dataset fine-tuning or hyper-parameter optimization, making the approach extremely attractive to rapidly and autonomously develop general-purpose MLIAPs suitable for simulations in extreme conditions.

36 MATERIALS SCIENCE↗

A three-year dataset supporting research on building energy management and occupancy analytics

Abstract This paper presents the curation of a monitored dataset from an office building constructed in 2015 in Berkeley, California. The dataset includes whole-building and end-use energy consumption, HVAC system operating conditions, indoor and outdoor environmental parameters, as well as occupant counts. The data were collected during a period of three years from more than 300 sensors and meters on two office floors (each 2,325 m 2 ) of the building. A three-step data curation strategy is applied to transform the raw data into research-grade data: (1) cleaning the raw data to detect and adjust the outlier values and fill the data gaps; (2) creating the metadata model of the building systems and data points using the Brick schema; and (3) representing the metadata of the dataset using a semantic JSON schema. This dataset can be used in various applications—building energy benchmarking, load shape analysis, energy prediction, occupancy prediction and analytics, and HVAC controls—to improve the understanding and efficiency of building operations for reducing energy use, energy costs, and carbon emissions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Molecular structural dataset of lignin macromolecule elucidating experimental structural compositions

Abstract Lignin is one of the most abundant biopolymers in nature and has great potential to be transformed into high-value chemicals. However, the limited availability of molecular structure data hinders its potential industrial applications. Herein, we present the Lignin Structural (LGS) Dataset that includes the molecular structure of milled wood lignin focusing on two major monomeric units (coniferyl and syringyl), and the six most common interunit linkages (phenylpropane β-aryl ether, resinol, phenylcoumaran, biphenyl, dibenzodioxocin, and diaryl ether). The dataset constitutes a unique resource that covers a part of lignin’s chemical space characterized by polymer chains with lengths in the range of 3 to 25 monomer units. Structural data were generated using a sequence-controlled polymer generation approach that was calibrated to match experimental lignin properties. The LGS dataset includes 60 K newly generated lignin structures that match with high accuracy (~90%) the experimentally determined structural compositions available in the literature. The LGS dataset is a valuable resource to advance lignin chemistry research, including computational simulation approaches and predictive modelling.

Scientific data↗

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗

The Arctic Plant Aboveground Biomass Synthesis Dataset

Plant biomass is a fundamental ecosystem attribute that is sensitive to rapid climatic changes occurring in the Arctic. Nevertheless, measuring plant biomass in the Arctic is logistically challenging and resource intensive. Lack of accessible field data hinders efforts to understand the amount, composition, distribution, and changes in plant biomass in these northern ecosystems. Here, we present The Arctic plant aboveground biomass synthesis dataset, which includes field measurements of lichen, bryophyte, herb, shrub, and/or tree aboveground biomass (g m -2 ) on 2,327 sample plots from 636 field sites in seven countries. We created the synthesis dataset by assembling and harmonizing 32 individual datasets. Aboveground biomass was primarily quantified by harvesting sample plots during mid- to late-summer, though tree and often tall shrub biomass were quantified using surveys and allometric models. Each biomass measurement is associated with metadata including sample date, location, method, data source, and other information. This unique dataset can be leveraged to monitor, map, and model plant biomass across the rapidly warming Arctic.

54 ENVIRONMENTAL SCIENCES↗

A unified ensemble soil moisture dataset across the continental United States

Abstract A unified ensemble soil moisture (SM) package has been developed over the Continental United States (CONUS). The data package includes 19 products from land surface models, remote sensing, reanalysis, and machine learning models. All datasets are unified to a 0.25-degree and monthly spatiotemporal resolution, providing a comprehensive view of surface SM dynamics. The statistical analysis of the datasets leverages the Koppen-Geiger Climate Classification to explore surface SM’s spatiotemporal variabilities. The extracted SM characteristics highlight distinct patterns, with the western CONUS showing larger coefficient of variation values and the eastern CONUS exhibiting higher SM values. Remote sensing datasets tend to be drier, while reanalysis products present wetter conditions. In-situ SM observations serve as the basis for wavelet power spectrum analyses to explain discrepancies in temporal scales across datasets facilitating daily SM records. This study provides a comprehensive soil moisture data package and an analysis framework that can be used for Earth system model evaluations and uncertainty quantification, quantifying drought impacts and land–atmosphere interactions and making recommendations for drought response planning.

54 ENVIRONMENTAL SCIENCES↗

LandScan Global 30 Arcsecond Annual Global Gridded Population Datasets from 2000 to 2022

Abstract Oak Ridge National Laboratory (ORNL) annually develops the LandScan Global (LSG) dataset, a 30 arcsecond global gridded population dataset representing global ambient human population distribution. This multivariable dasymetric model disaggregates census counts within administrative boundaries using ancillary data. Each country’s distribution reflects cultural and socioeconomic patterns; manual validations yield a unique global dataset for assessing populations at risk. For over two decades, LSG has been a standard for estimating populations at risk, aiding U.S. federal government, academia and humanitarian organizations. During disasters such as the 2004 Indian Ocean tsunami and the 2010 Haiti earthquake and geopolitical crises such as the Syrian civil war and the 2022 Russian invasion of Ukraine, LSG supported scientific and operational communities in emergency response and recovery. In 2022, LSG datasets from 2000 onward were made publicly available through ORNL’s LandScan Portal. This data descriptor details our methodology and the application of geospatial science and machine learning to geographic and demographic data, highlighting uses in urban resiliency, emergency management, disaster response, and human health and security.

Science & Technology - Other Topics↗

A global dataset of terrestrial biological nitrogen fixation

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha −1 y −1 ), the percentage of nitrogen derived from the atmosphere (%N dfa ), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

Reis Ely, Carla R. [Oregon State Univ., Corvallis,↗

A dataset for understanding self-reported patterns influencing residential energy decisions

Household occupant behavior and decision-making dynamics substantially impact technology uptake and residential building energy performance. Although significant research underscores the importance of social science in energy studies, few public data with representative samples on household energy decision-making patterns are available. The dataset (UPGRADE-E: Understanding Patterns Guiding Residential Adoption and Decisions about Energy Efficiency) presents 9,919 responses from U.S. residents of single-family and small multifamily homes. Derived from a national-scale internet survey, the dataset contains 391 variables: demographics, building characteristics, home modifications, willingness to adopt new technologies, motivations for making changes, barriers, program participation, trusted information sources, and energy scenarios. Responses were validated via internal consistency checks and comparison with other U.S. national scale datasets. UPGRADE-E advances knowledge of household energy related decision-making, tying demographics, home modifications, and self-reported cognitive drivers together at a scale and breadth that has not been previously achieved. Policymakers and researchers at local, regional, and national levels may leverage this dataset to understand drivers influencing the adoption of key technologies in U.S. homes.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

CAMELSH: A Large-Sample Hourly Hydrometeorological Dataset and Attributes at Watershed-Scale for CONUS

We present CAMELSH (Catchment Attributes and Hourly HydroMeteorology for Large-Sample Studies), the first large-sample hydrometeorological dataset at the hourly scale for the contiguous United States. CAMELSH intergrates hourly meteorological time series, catchment attributes and boundaries from GAGES-II and HydroATLAS for 9,008 catchments across diverse climatic, hydrological, and anthropogenic conditions. In addition, hourly streamflow time series is provided for 3,166 catchments. The dataset spans 45 years (1980–2024) with 11 meteorological variables from the NLDAS-2 forcing dataset, from which we compute nine climate indices related to precipitation, evapotranspiration, seasonality, and snow fraction. Additionally, CAMELSH includes two sets of catchment attributes: 439 from GAGES-II and 195 derived from HydroATLAS. These attributes include factors related to climate, geology, hydrology, river/stream morphology, landscape, nutrient, soil, topography, and anthropogenic influences. Developed in accordance with FAIR (Findability, Accessibility, Interoperability, and Reusability) principles, CAMELSH is the first large-sample dataset at an hourly timescale, supporting machine learning applications for short-term streamflow (flood) prediction and advancing data-driven hydrological research across multiple timescales.

54 ENVIRONMENTAL SCIENCES↗

Material Fracturing and Failure Simulation Datasets

Fracturing is a fundamental physics phenomena with broad relevance across multiple domains, ranging from infrastructure integrity, aerospace durability, reservoir production, and seismic events. We present a diverse dataset of simulated fracture evolution and material failure generated from two numerical solvers: the phase-field method and the combined finite-discrete element method (FDEM). These solvers differ in formulation, physical fidelity, and computational efficiency. The dataset includes five materials: PBX, anisotropic shale, tungsten, aluminum, and steel. For each, phase-field simulations span 400,000 cases: 200,000 under uniaxial tension and 200,000 under biaxial tension. The computationally expensive FDEM simulations include 90,000 split evenly among PBX, shale, and tungsten under uniaxial loading. All simulations begin with randomized initial fracture patterns. Each entry includes temporal data capturing fracture propagation dynamics. This comprehensive dataset is designed to support the development of foundational or surrogate machine learning approaches for predicting material failure. While no such models are introduced here, the dataset lays a robust foundation for advancing future research and innovation in these areas.

36 MATERIALS SCIENCE↗

MArVD2: a machine learning enhanced tool to discriminate between archaeal and bacterial viruses in viral datasets

Abstract Our knowledge of viral sequence space has exploded with advancing sequencing technologies and large-scale sampling and analytical efforts. Though archaea are important and abundant prokaryotes in many systems, our knowledge of archaeal viruses outside of extreme environments is limited. This largely stems from the lack of a robust, high-throughput, and systematic way to distinguish between bacterial and archaeal viruses in datasets of curated viruses. Here we upgrade our prior text-based tool (MArVD) via training and testing a random forest machine learning algorithm against a newly curated dataset of archaeal viruses. After optimization, MArVD2 presented a significant improvement over its predecessor in terms of scalability, usability, and flexibility, and will allow user-defined custom training datasets as archaeal virus discovery progresses. Benchmarking showed that a model trained with viral sequences from the hypersaline, marine, and hot spring environments correctly classified 85% of the archaeal viruses with a false detection rate below 2% using a random forest prediction threshold of 80% in a separate benchmarking dataset from the same habitats.

Vik, Dean (ORCID:000000027546899X)↗

A cloud-free MODIS snow cover dataset for the contiguous United States from 2000 to 2017

This article presents a cloud-free snow cover dataset with a daily temporal resolution and 0.05° spatial resolution from March 2000 to February 2017 over the contiguous United States (CONUS). The dataset was developed by completely removing clouds from the original NASA’s Moderate Resolution Imaging Spectroradiometer (MODIS) Snow Cover Area product (MOD10C1) through a series of spatiotemporal filters followed by the Variational Interpolation (VI) algorithm; the filters and VI algorithm were evaluated using bootstrapping test. The dataset was validated over the period with the Landsat 7 ETM+ snow cover maps in the Seattle, Minneapolis, Rocky Mountains, and Sierra Nevada regions. The resulting cloud-free snow cover captured accurately dynamic changes of snow throughout the period in terms of Probability of Detection (POD) and False Alarm Ratio (FAR) with average values of 0.955 and 0.179 for POD and FAR, respectively. The dataset provides continuous inputs of snow cover area for hydrologic studies for almost two decades. The VI algorithm can be applied in other regions given that a proper validation can be performed.

54 ENVIRONMENTAL SCIENCES↗

Highly transferable atomistic machine-learning potentials from curated and compact datasets across the periodic table

Machine learning atomistic potentials trained using density functional theory (DFT) datasets allow for the modeling of complex material properties with near-DFT accuracy while imposing a fraction of its computational cost. The curation of the DFT datasets can be extensive in size and time-consuming to train and refine. In this study, we focus on addressing these barriers by developing minimalistic and flexible datasets for many elements in the periodic table regardless of their mass, electronic configuration, and ground state lattice. These DFT datasets have on average, ~4000 different structures and 27 atoms per structure, which we found sufficient to maintain the predictive accuracy of DFT properties and notably with high transferability. We envision these highly curated training sets as starting points for the community to expand, modify, or use with other machine learning atomistic potential models, whatever may suit individual needs, further accelerating the utilization of machine learning as a tool for material design and discovery.

42 ENGINEERING↗

Exploring the growth index γ L : Insights from different CMB dataset combinations and approaches

In this study we investigate the growth index γ L , which characterizes the growth of linear matter perturbations, while analysing different cosmological datasets. We compare the approaches implemented by two different patches of the cosmological solver : and __. In our analysis we uncover a deviation of the growth index from its expected Λ CDM value of 0.55 when utilizing the Planck dataset, both in the case and in the __ case, but in opposite directions. This deviation is accompanied by a change in the direction of correlations with derived cosmological parameters. However, the incorporation of cosmic microwave background lensing data helps reconcile γ L with its Λ -cold dark matter value in both cases. Conversely, the alternative ground-based telescopes Atacama Cosmology Telescope and South Pole Telescope consistently yield growth index values in agreement with γ L = 0.55 . We conclude that the presence of the A lens problem in the Planck dataset contributes to the observed deviations, underscoring the importance of additional datasets in resolving these discrepancies. Published by the American Physical Society 2024

Astronomy & Astrophysics↗

Collection: TD-DFT and EOM-CCSD Calculations for the GDB-9-Ex Dataset

We present two datasets that contain quantum chemical electronic structure calculations for organic molecules from the GDB-9-Ex dataset. The “GDB-9-Ex_TD-DFT-PBE0” dataset contains calculations performed using the time-dependent density functional theory (TD-DFT) first principles method, and the “GDB-9-Ex_EOMCCSD” dataset contains calculations performed using the equation-of-motion coupled cluster (EOM-CCSD) method. Both types of calculations were performed using the ORCA software and provided ultraviolet-visible spectra with a high level of accuracy.

Mehta, Kshitij [Oak Ridge National Laboratory (ORN↗

Towards Diverse and Representative Global Pretraining Datasets for Remote Sensing Foundation Models

The design of a pretraining dataset is emerging as a critical component for the generality of foundation models. In the remote sensing realm, large volumes of imagery and benchmark datasets exist that can be leveraged to pretrain foundation models, however using this imagery in absence of a well-crafted sampling strategy is inefficient and has the potential to create biased and less generalizable models. Here, we provide a discussion and vision for the curation and assessment of pretraining datasets for remote sensing geospatial foundation models. We highlight the importance of geographic, temporal, and image acquisition diversity and review possible strategies to enable such diversity at global scale. In addition to these characteristics, support for various spatial-temporal pretext tasks within the dataset is also critical. Ultimately, our primary objective is to place emphasis on and draw attention to the data curation stage of the foundation model development pipeline. By doing so, we think it is possible to reduce biases of geospatial foundation models, as well as enable broader generalization to downstream remote sensing tasks and applications.

Arndt, Jacob↗