cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10606029
title: Impact of Training Instance Selection on Automated Algorithm Selection Models for Numerical Black-box Optimization -- Reproducibility Files

description: This repository contains the files to reproduce the results from the paper "Impact of Training Instance Selection on Automated Algorithm Selection Models for Numerical Black-box Optimization".

Data Collection

In this folder, all files used to generate the raw performance data for the set of algorithms are included, as well as the code used to generate the ELA features. For the performance, the packages 'ioh', 'nevergrad', 'modde' and 'modcma' are essential, while 'pflacco' is used for ELA. For all scripts in this folder, the number of parallel threads and the folders for reading function settings (included as 3 csv files in this folder) and storing data should be set before execution. 

Note that the full performance data exceeds 50GB, so it is not included in this repository. Instead, the results of processing it (using the aocc_extraction script) are included in the 'auc_MABBOB' folder (spread across multiple csv-files, with a version using a different budget factor included as well).

The ELA data is included as 'ELA' and 'ELA_BBOB' for the affine combinations and component functions respectively.  

Data Processing, Analysis and Visualization

The remaining reproducibility files can be found in the Reproducibility folder. Within this folder are several notebooks which handle various steps in the pipeline, starting with preprocessing the data collected in the previous steps. This results in some csv-files, which are also included for convenience. Afterwards, the remaining notebooks deal with correlation analysis, instance selection methods, and all included plots from the paper. To match the environment used during our execution of these scripts. a yml-file (to be used with conda or mamba) is available as well.
DOI: 10.6084/m9.figshare.14035057
title: The bacterial volatile <i>N,N</i>-dimethyl-hexadecylamine promotes <i>Arabidopsis</i> primary root elongation through cytokinin signaling and the AHK2 receptor

description: <i>N,N</i>-dimethyl-hexadecylamine (DMHDA) is a volatile organic compound (VOC) produced by some plant growth-promoting rhizobacteria (PGPR), which inhibits the growth of pathogenic fungi and induces iron uptake by roots. In this report, through the application of a wide range of concentrations, we found that DMHDA affects <i>Arabidopsis</i> primary root growth and lateral root formation in a dose-dependent manner where 1 and 2 µM promoted root growth and higher (4–32 µM) concentrations repressed growth. Cytokinin-inducible <i>TCS::GFP</i> and <i>ARR5::uidA</i> gene constructs showed an increased expression in columella cells and root meristem, respectively, at 2 µM DMHDA, but their expression domains strongly diminished at growth repressing treatments. To test if either primary root growth promotion or repression could involve members of the cytokinin receptor family, the growth of WT and double mutant combinations <i>cre1-12 ahk2-2, cre1-12 ahk3-3</i>, and <i>ahk2-2 ahk3-3</i> was tested in control conditions or supplemented with 2 µM or 16 µM DMHDA. Noteworthy, the root growth promotion disappeared in <i>cre1-12 ahk2-2</i> and <i>ahk2-2 ahk3-3</i> combinations, whereas all double mutants had higher repression than the WT at high doses. We further show that DMHDA fails to mimic the effects of ethylene in Arabidopsis seedlings grown in darkness that include an exaggerated apical hook, stem and root shortening, and root hair elongation. Our data help unravel how <i>Arabidopsis</i> senses a growth-modulating bacterial volatile through changes in cytokinin responsiveness.
DOI: 10.5281/zenodo.4744380
title: OpenHPS: Single Floor Fingerprinting and Trajectory Dataset

description: <strong>Description</strong> This dataset contains fingerprint information of WLAN access points and BLE beacons with a known position and IMU sensor data. Data was collected on the floor of the Web and Information Systems Engineering (WISE) Lab at the VUB (Pleinlaan 9, 3rd floor) with 110 training reference points and 30 test data points. Each reference point was recorded for 20 seconds in four different orientations. More information is given in the README.pdf file included in the dataset. <strong>File Contents</strong> <code>/wlan_aps.csv</code>: Wireless access point information <code>/ble_beacons.csv</code>: BLE beacon positions <code>/misc</code>: Miscelanieous resources <code>/misc/floorplan.png</code>: PNG version of the floorplan <code>/misc/floorplan_medium.png</code>: PNG version of the floorplan (medium quality) <code>/misc/datapoints.svg</code>: Training and test data points visualisation <code>/misc/datapoints.csv</code>: Training data points CSV <code>/misc/testdatapoints.csv</code>: Test data points CSV <code>/misc/spaces.geo.json</code>: GeoJSON feature collection of symbolic spaces <code>/misc/documentation.css</code>: README documentation CSS (unrelated to the dataset) <code>/train</code>: Training data points (110 in 4 orientations) <code>/train/raw</code>: Raw unprocessed data points (not aggregated) <code>/train/raw/wlan_fingerprints.csv</code>: Raw WLAN fingerprints <code>/train/raw/imu_fingerprints.csv</code>: Raw IMU data collection <code>/train/raw/ble_fingerprints.csv</code>: Raw BLE fingerprints <code>/train/aggregated</code>: Processed aggregated data points <code>/train/aggregated/wlan_fingerprints.csv</code>: WLAN fingerprints <code>/train/aggregated/ble_fingerprints.csv</code>: BLE fingerprints <code>/train/aggregated/imu_fingerprints.csv</code>: IMU data collection <code>/train/aggregated/wlan-ble_fingerprints.csv</code>: WLAN and BLE fingerprints merged <code>/test</code>: Test data points (30 in 4 orientations) <code>/test/raw</code>: Raw unprocessed test data points (not aggregated) <code>/test/raw/wlan_fingerprints.csv</code>: Raw WLAN fingerprints <code>/test/raw/imu_fingerprints.csv</code>: Raw IMU data collection <code>/test/raw/ble_fingerprints.csv</code>: Raw BLE fingerprints <code>/test/aggregated</code>: Processed aggregated data points <code>/test/aggregated/wlan_fingerprints.csv</code>: WLAN fingerprints <code>/test/aggregated/ble_fingerprints.csv</code>: BLE fingerprints <code>/test/aggregated/imu_fingerprints.csv</code>: IMU data collection <code>/test/aggregated/wlan-ble_fingerprints.csv</code>: WLAN and BLE fingerprints merged <code>/trajectories</code>: Test trajectories (10) <code>/trajectories/???</code>: Trajectory directory, ??? is the name of the trajectory <code>/trajectories/???/???_ble.csv</code>: BLE advertisements received during the trajectory <code>/trajectories/???/???_imu.csv</code>: IMU data from the trajectory <code>/trajectories/???/???_wlan.csv</code>: WLAN signals received during the trajectory
DOI: 10.5281/zenodo.4744379
title: OpenHPS: Single Floor Fingerprinting and Trajectory Dataset

description: <strong>Description</strong> This dataset contains fingerprint information of WLAN access points and BLE beacons with a known position and IMU sensor data. Data was collected on the floor of the Web and Information Systems Engineering (WISE) Lab at the VUB (Pleinlaan 9, 3rd floor) with 110 training reference points and 30 test data points. Each reference point was recorded for 20 seconds in four different orientations. More information is given in the README.pdf file included in the dataset. <strong>File Contents</strong> <code>/wlan_aps.csv</code>: Wireless access point information <code>/ble_beacons.csv</code>: BLE beacon positions <code>/misc</code>: Miscelanieous resources <code>/misc/floorplan.png</code>: PNG version of the floorplan <code>/misc/floorplan_medium.png</code>: PNG version of the floorplan (medium quality) <code>/misc/datapoints.svg</code>: Training and test data points visualisation <code>/misc/datapoints.csv</code>: Training data points CSV <code>/misc/testdatapoints.csv</code>: Test data points CSV <code>/misc/spaces.geo.json</code>: GeoJSON feature collection of symbolic spaces <code>/misc/documentation.css</code>: README documentation CSS (unrelated to the dataset) <code>/train</code>: Training data points (110 in 4 orientations) <code>/train/raw</code>: Raw unprocessed data points (not aggregated) <code>/train/raw/wlan_fingerprints.csv</code>: Raw WLAN fingerprints <code>/train/raw/imu_fingerprints.csv</code>: Raw IMU data collection <code>/train/raw/ble_fingerprints.csv</code>: Raw BLE fingerprints <code>/train/aggregated</code>: Processed aggregated data points <code>/train/aggregated/wlan_fingerprints.csv</code>: WLAN fingerprints <code>/train/aggregated/ble_fingerprints.csv</code>: BLE fingerprints <code>/train/aggregated/imu_fingerprints.csv</code>: IMU data collection <code>/train/aggregated/wlan-ble_fingerprints.csv</code>: WLAN and BLE fingerprints merged <code>/test</code>: Test data points (30 in 4 orientations) <code>/test/raw</code>: Raw unprocessed test data points (not aggregated) <code>/test/raw/wlan_fingerprints.csv</code>: Raw WLAN fingerprints <code>/test/raw/imu_fingerprints.csv</code>: Raw IMU data collection <code>/test/raw/ble_fingerprints.csv</code>: Raw BLE fingerprints <code>/test/aggregated</code>: Processed aggregated data points <code>/test/aggregated/wlan_fingerprints.csv</code>: WLAN fingerprints <code>/test/aggregated/ble_fingerprints.csv</code>: BLE fingerprints <code>/test/aggregated/imu_fingerprints.csv</code>: IMU data collection <code>/test/aggregated/wlan-ble_fingerprints.csv</code>: WLAN and BLE fingerprints merged <code>/trajectories</code>: Test trajectories (10) <code>/trajectories/???</code>: Trajectory directory, ??? is the name of the trajectory <code>/trajectories/???/???_ble.csv</code>: BLE advertisements received during the trajectory <code>/trajectories/???/???_imu.csv</code>: IMU data from the trajectory <code>/trajectories/???/???_wlan.csv</code>: WLAN signals received during the trajectory
DOI: 10.5281/zenodo.4741503
title: TAMUoic2019 Database P32 Kernel Extension

description: The P32 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4741502
title: TAMUoic2019 Database P32 Kernel Extension

description: The P32 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4741351
title: TAMUoic2019 Database P14 Kernel Extension

description: The P14 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4741350
title: TAMUoic2019 Database P14 Kernel Extension

description: The P14 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4741257
title: TAMUoic2019 Database P13 Kernel Extension

description: The P13 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4741256
title: TAMUoic2019 Database P13 Kernel Extension

description: The P13 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4740630
title: TAMUoic2019 Database P12 Kernel Extension

description: The P12 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4740629
title: TAMUoic2019 Database P12 Kernel Extension

description: The P12 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4733071
title: TAMUoic2019 Database P31 Kernel Extension

description: The P31 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4733070
title: TAMUoic2019 Database P31 Kernel Extension

description: The P31 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4732909
title: TAMUoic2019 Database P24 Kernel Extension

description: The P24 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4732908
title: TAMUoic2019 Database P24 Kernel Extension

description: The P24 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4732648
title: TAMUoic2019 Database P23 Kernel Extension

description: The P23 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.5281/zenodo.4732647
title: TAMUoic2019 Database P23 Kernel Extension

description: The P23 kernel extension of the TAMUoic2019 database (https://doi.org/10.5281/zenodo.4718022), which is a database of the single-scattering properties of oriented ice crystals (OIC). The two major oriented particles, horizontally oriented plates (HOP) and columns (HOC), are considered in the database.
description: {"references": ["Saito, M., and P. Yang (2019), Oriented ice crystals: A single-scattering property database for applications to lidar and optical phenomenon simulations, J. Atmos. Sci., 76, 2635\u20132652."]}
DOI: 10.6084/m9.figshare.12851786
title: Mining sequences with similarity to <i>XTH</i> genes in the <i>Solanum tuberosum</i> L. transcriptome: introductory step for identifying homologous <i>XTH</i> genes

description: The <i>xyloglucan endotransglucosylase/hydrolase</i> (<i>XTH</i>) genes in <i>Arabidopsis thaliana</i> (L.) Heynh. form part of a group of mechano-stimulated genes and play an important role in abiotic stress tolerance. Mining the RNAseq transcriptomic database of 40,430 potato (<i>Solanum tuberosum</i> L.) genes based on functional annotation and homology search, our objective was to discover potentially homologous <i>XTH</i> genes. A Gene Ontology-based <i>XTH</i> homology search and functional annotation discovered, from among the 33 <i>A. thaliana</i> (<i>AtXTH</i>) and 25 tomato (<i>Solanum lycopersicum</i> L.) (<i>SlXTH</i>) <i>XTH</i> genes, 35 gene sequences corresponding to 20 <i>AtXTH</i> genes and 40 gene sequences corresponding to 21 <i>SlXTH</i> genes, respectively. Thirteen sequences corresponding to 11 putative <i>XTH</i> genes in potato, named as <i>StXTH</i> after SlXTH genes, were significantly up- or down-regulated in response to ultrasound. These putative <i>StXTH</i> genes in potato can serve for future functional genetic analyses.
DOI: 10.6084/m9.figshare.12851786.v1
title: Mining sequences with similarity to <i>XTH</i> genes in the <i>Solanum tuberosum</i> L. transcriptome: introductory step for identifying homologous <i>XTH</i> genes

description: The <i>xyloglucan endotransglucosylase/hydrolase</i> (<i>XTH</i>) genes in <i>Arabidopsis thaliana</i> (L.) Heynh. form part of a group of mechano-stimulated genes and play an important role in abiotic stress tolerance. Mining the RNAseq transcriptomic database of 40,430 potato (<i>Solanum tuberosum</i> L.) genes based on functional annotation and homology search, our objective was to discover potentially homologous <i>XTH</i> genes. A Gene Ontology-based <i>XTH</i> homology search and functional annotation discovered, from among the 33 <i>A. thaliana</i> (<i>AtXTH</i>) and 25 tomato (<i>Solanum lycopersicum</i> L.) (<i>SlXTH</i>) <i>XTH</i> genes, 35 gene sequences corresponding to 20 <i>AtXTH</i> genes and 40 gene sequences corresponding to 21 <i>SlXTH</i> genes, respectively. Thirteen sequences corresponding to 11 putative <i>XTH</i> genes in potato, named as <i>StXTH</i> after SlXTH genes, were significantly up- or down-regulated in response to ultrasound. These putative <i>StXTH</i> genes in potato can serve for future functional genetic analyses.
DOI: 10.6084/m9.figshare.13491140.v1
title: The gene expression profiles of mitochondrial respiratory components in Arabidopsis plants with differing amounts of <i>ALTERNATIVE OXIDASE1a</i> under high intensity light

description: We compared the expression of mitochondrial alternative oxidase (AOX) and other non-phosphorylating respiratory components (NPhPs) in wild type and <i>AOX1a</i> transgenic <i>Arabidopsis thaliana</i> following short-term transfer of plants to higher irradiance conditions to gain more insight into the mechanisms of AOX functioning under light. The <i>AOX1a</i> overexpressing line (XX-2) showed the highest amount of <i>AOX1a</i> transcripts and AOX1A synthesis during the entire experiment, and many NPhPs genes were down-regulated after 6–8 h under the higher light conditions. Antisense AS-12 plants displayed a compensatory effect, typically after 8 h of exposure to higher irradiance, by up-regulating their expression of the majority of genes encoding AOX and other respiratory components. In addition, AS-12 plants displayed ‘overcompensation effects’ prior to their transfer to high light conditions, i.e., they showed a higher expression level of certain genes. As a result, the ROS content in AS-12, as in XX-2, was consistently lower than in the wild type. All NPhPs genes share, in common with <i>AOX1a</i>, light- and stress-related <i>cis</i>-acting regulatory elements (CAREs) in their promoters. However, the expression of respiratory genes does not always depend on the level of <i>AOX1a</i> expression. This suggests the presence of multiple combinations of signaling pathways in gene induction. Based on our results, we outline possible directions for future research.