cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11148307
title: Data-Error Scaling Laws in Machine Learning on Combinatorial Mutation-prone Sets: Proteins and Small Molecules

description:  

Data

 This folder contains the raw data used during this work. `out_seq_total.txt` contains information on the sequences used (mutations, number of mutations, etc.). `output_energies_total.txt` contains the response variables, which include: a) unrelaxed EvoEF energies (peptides); b) relaxed EvoEF energies (peptides, `*_repaired.txt`); and c) solvation energies (molecules). 3D structures are provided in `.xyz` format in the subfolder `XYZ` (molecules).



GB1 dataset


The GB1 dataset was not generated by us (https://doi.org/10.48550/arXiv.2405.05167). If you use the GB1 dataset, please cite the original paper:


Wu, N. C., Dai, L., Olson, C. A., Lloyd-Smith, J. O., & Sun, R. (2016). Adaptation in protein fitness landscapes is facilitated by indirect paths. eLife, 5:e16965. doi:10.7554/eLife.16965


Results

This folder contains the results (outputs) of the ML models trained using the provided scripts (see github repository). Such results are incuded in the form of `.npy` files. To load the files please include the option `allow_pickle=True`.

 Each `.npy` file contains the following keys: * `initial_parameters`: script inputs. * `d_encoder`: encoder used (not always included). * `ns_train`: number of training points used for the LCs (rounded, integers). * `ns_train_float`: number of training points used for the LCs (not rounded, float). * `ns_train_norm`: number of training points used for the LCs (normalized, float). * `res`: test MAEs. * `res_tot`: (train,validation,test) MAEs. * `res_tot_mut`: (train,validation,test) MAEs sorted by mutation number. * `l_opt`: optimal kernel length used during the test. * `ls`: kernel lengths used for grid search. * `idx_seeds`: indices used to reshuffle the data. If one want to rebild the initial order use `np.argsort(idx_seeds)`. * `alpha_opt`: optimal regression parameters used to calculate the test error. To sort the data use `alpha_opt[i][ii][np.argsort(idx_seeds[ii,0:arg_train_max].astype(int)[:ns_train[i]]`. Where `i` is the replicate number (0-99) and ii is the idex in the LC. * `valid_errs`: validation error (MAE) calculated for each point in the hyperparameter (kernel scale) optimisation. * `test_errs`: test error (MAE) calculated for each point in the hyperparameter (kernel scale) optimisation.
DOI: 10.25921/gatn-v953
title: NOAA/WDS Paleoclimatology - Wiles - Deer Mountain - TSME - ITRDB AK098

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: 
# 
#  NOAA Template Raw Measurements file added 2019-02-08.
DOI: 10.25921/gg9h-gq10
title: NOAA/WDS Paleoclimatology - Zgraggen - Krauchtalfeucht - FASY - ITRDB SWIT267

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.25921/gr76-t552
title: NOAA/WDS Paleoclimatology - Esper - Pakistan high Cha2 - JUSP - ITRDB PAKI006

description: We present an analysis of 28 juniper tree-ring sites sampled over the last decades by several research teams in the Tien Shan and Karakorum mountains of western central Asia. Ring-width chronologies were developed on a site-by-site basis, using a detrending technique designed to retain low-frequency climate variations. Site chronologies were grouped according to their distance from the upper timberline in the Tien Shan (~3,400 m a.s.l.) and Karakorum (~4,000 m), and low- and high-elevation composite chronologies combining data from both mountain systems developed. Comparison of these elevational subsets revealed significant coherence (r = 0.72) over the 1438–1995 common period, which is inconsistent with the concept of differing environmental signals captured in tree-ring data along elevational gradients. It is hypothesized that the uniform growth behavior in central Asian juniper trees has been forced by solar radiation variations controlled via cloud cover changes, but verification of this assumption requires further fieldwork. The high-elevation composite chronology was further compared with existing temperature reconstructions from the Karakorum and Tien Shan, and long-term trend differences discussed. We concluded that the extent of warmth during medieval times cannot be precisely estimated based on ring-width data currently available.
description: Purpose of Collection: 
# Dendroclimatology
# 
# Cores and cross-sections are stored at: 
# WSL
# 
#  NOAA Template Raw Measurements file added 2019-04-08.
DOI: 10.25921/gzme-xs51
title: NOAA/WDS Paleoclimatology - Alla - Arguis - QUFG - ITRDB SPAI065

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.25921/g9sa-2540
title: NOAA/WDS Paleoclimatology - Bräker - Etang du Milieu, Bois-des Boulats - QUSP - ITRDB SWIT213

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Raw Measurements file added 2019-02-05.
DOI: 10.25921/g979-8c88
title: NOAA/WDS Paleoclimatology - Sauchyn - Beaver Dam Creek-Whalebacks - PSME - ITRDB CANA332

description: In western Canada growing demand for water resources has increased vulnerability to hydrological drought. The near full allocation of water supplies in the Oldman and Bow River subbasins of the South Saskatchewan River Basin has resulted in a moratorium on new surface water licenses. In this region, short instrumental records limit the detection of long-term hydrological variability. To extend the historical record, we collected 14 new moisture-sensitive tree ring chronologies and reconstructed the average October through September flow of the Oldman (1618-2004) and South Saskatchewan (SSR) (1400-2004) rivers. Our SSR proxy record updates a previously published reconstruction. While the 20th century is representative of drought frequency over the long term, droughts are of greater severity and duration in the preinstrumental proxy record. A spectral analysis of the reconstructed flows revealed quasiperiodic cycles at interannual to multidecadal scales.
description: NOAA Template Raw Measurements file added 2019-02-04.
DOI: 10.25921/g5sg-m725
title: NOAA/WDS Paleoclimatology - Esper - Kyrgyzstan High Bon - JUSP - ITRDB KYRG002

description: We present an analysis of 28 juniper tree-ring sites sampled over the last decades by several research teams in the Tien Shan and Karakorum mountains of western central Asia. Ring-width chronologies were developed on a site-by-site basis, using a detrending technique designed to retain low-frequency climate variations. Site chronologies were grouped according to their distance from the upper timberline in the Tien Shan (~3,400 m a.s.l.) and Karakorum (~4,000 m), and low- and high-elevation composite chronologies combining data from both mountain systems developed. Comparison of these elevational subsets revealed significant coherence (r = 0.72) over the 1438–1995 common period, which is inconsistent with the concept of differing environmental signals captured in tree-ring data along elevational gradients. It is hypothesized that the uniform growth behavior in central Asian juniper trees has been forced by solar radiation variations controlled via cloud cover changes, but verification of this assumption requires further fieldwork. The high-elevation composite chronology was further compared with existing temperature reconstructions from the Karakorum and Tien Shan, and long-term trend differences discussed. We concluded that the extent of warmth during medieval times cannot be precisely estimated based on ring-width data currently available.
description: Purpose of Collection: 
# Dendroclimatology
# 
# Cores and cross-sections are stored at: 
# WSL
#  NOAA Template Raw Measurements file added 2019-04-08.
DOI: 10.25921/gnss-jy51
title: NOAA/WDS Paleoclimatology - Wiles - Excursion Ridge - CHNO - ITRDB AK118

description: Yellow-cedar (Callitropsis nootkatensis (D. Don) Orsted ex D.P. Little) is in a century-long decline coinciding with the end of the Little Ice Age (LIA). The leading hypothesis explaining this decline is a decrease in insulating snowpack due to warming and increased susceptibility to damaging frosts in the root zone. A ring-width series from yellow-cedar on Excursion Ridge (260 m a.s.l.) in Glacier Bay National Park and Preserve, Alaska, and another from trees on Pleasant Island (150 m a.s.l.) in the Tongass National Forest in Icy Strait were compared with regional monthly temperature and precipitation data from Sitka, Alaska, to investigate the changing growth response to temperature at these sites. Comparisons with monthly temperatures from 1832 to 1876 during the end of the Little Ice Age show that the high-elevation Excursion Ridge and the low-elevation Pleasant Island sites strongly favored warmer January through July temperatures. Both tree populations have markedly changed their response from a positive to a strong negative correlation with January through July temperatures since 1950. This strong negative response to warming by the yellow-cedar together with a positive relationship with total March and April precipitation suggests that these yellow-cedar sites may be susceptible to decline. Furthermore, these analyses are consistent with the hypothesis that the yellow-cedar decline is linked to decreased snowpack.
description: NOAA Template Chronology file added 2018-12-20. NOAA Template Raw Measurements file added 2019-02-08.
DOI: 10.25921/gppj-y331
title: NOAA/WDS Paleoclimatology - Viau and Gajewski 2009 Boreal Canada Holocene Climate Recons

description: Regional paleoclimate reconstructions for northern Canada quantify Holocene climate variability on orbital and millennial time scales and provide a context to better understand the current global warming. The reconstructions are based on available pollen diagrams from the boreal and low Arctic zones of Canada and use the modern analog technique (MAT). Four regional reconstructions document the space–time evolution of the climate during the Holocene. Highest summer and winter temperatures anomalies are found in central Canada during the early Holocene. Eastern Canada was relatively cool in the early Holocene, whereas central Canada was warmest at that time. Labrador was relatively dry in the early to mid-Holocene during which time western Canada was relatively moist. Millennial-scale temperature variations, especially the Medieval Warm Period and Little Ice Age are seen across the continent, with some suggestion of time-transgressive changes from west to east. At the millennial scale, precipitation anomalies are of opposite signs in eastern and western Canada. The results herein indicate that modern increases in temperatures in northern Canada far exceed natural millennial-scale climate variability.
DOI: 10.25921/gh33-hz70
title: NOAA/WDS Paleoclimatology - Cléroux et al. 2009 W. Atlantic 12KYr G. trunc. Calcification Depth Data

description: Measurements of the δ18O in tests of planktonic and benthic foraminifera in the Florida Straits are used to reconstruct the properties of the water column through time over the last 12 ka (Lynch-Stieglitz et al., in press). The isotopic composition of the foraminifera largely reflects the vertical density gradient. We use this reconstruction and δ18O measurements on Globorotalia truncatulinoides in a nearby core to track the depth habitat of this species from the last deglaciation to 1.6 ka B.P. Around 9 ka, G. truncatulinoides was calcifying in much shallower water than during the late Holocene. The downward migration toward its modern habitat is a regional phenomenon over the western tropical Atlantic continental slope. The cause is still unclear but we hypothesize that the shallower calcification depth may be a response to the presence of glacial melt water or to circulation changes. This study points to the value of further study of the ecology, life cycle and calcification depth for G. truncatulinoides and other planktonic foraminifera that are used to reconstruct the history of the thermocline and upper water column structure.
DOI: 10.25921/gy3d-0n72
title: NOAA/WDS Paleoclimatology - Came et al. 2008 Florida Current 27KYr Seawater Cadmium Data

description: Benthic foraminiferal Cd/Ca from a Florida Current sediment core documents the history of the northward penetration of southern source waters within the surface return flow of the Atlantic meridional overturning circulation (AMOC). Cd seawater estimates (CdW) indicate that intermediate‐depth southern source waters crossed the equator and contributed to the Florida Current during the Bølling-Allerød warm period of the last deglaciation, consistent with evidence of only a modest AMOC reduction compared to today. The CdW  estimates also provide the first paleoceanographic evidence of a reduction in the influence of intermediate-depth southern source waters within the Florida Current during the Younger Dryas, a deglacial cold event characterized by a weak North Atlantic AMOC. Our results reveal a close correspondence between the northward penetration of intermediate-depth southern source waters and the influence of North Atlantic Deep Water, suggesting a possible link between intermediate-depth southern source waters and the strength of the Atlantic AMOC.
description: Cd/Ca ratios were measured in the tests of the benthic foraminifer Hoeglundina elegans, which records bottom water Cd concentrations with a partition coefficient DP = [(Cd/Ca)foram/(Cd/Ca)water] ≈ 1.0 [Boyle et al., 1995]. The partition coefficient for the aragonitic species H. elegans is constant with depth, unlike the partition coefficients of calcitic foraminifera, which are depth dependent [Boyle, 1992]. A constant seawater Ca concentration of 0.01 mol kg−1 was assumed to estimate Cd water concentrations.
DOI: 10.25921/gqkr-h330
title: NOAA/WDS Paleoclimatology - Hegerl et al. 2007 1500 Year N. Hemisphere Temperature Recons

description: Climate records over the last millennium place the twentieth-century warming in a longer historical context. Reconstructions of millennial temperatures show a wide range of variability, raising questions about the reliability of currently available reconstruction techniques and the uniqueness of late-twentieth-century warming. A calibration method is suggested that avoids the loss of low-frequency variance. A new reconstruction using this method shows substantial variability over the last 1500 yr. This record is consistent with independent temperature change estimates from borehole geothermal records, compared over the same spatial and temporal domain. The record is also broadly consistent with other recent reconstructions that attempt to fully recover low-frequency climate variability in their central estimate.

High variability in reconstructions does not hamper the detection of greenhouse gas–induced climate change, since a substantial fraction of the variance in these reconstructions from the beginning of the analysis in the late thirteenth century to the end of the records can be attributed to external forcing. Results from a detection and attribution analysis show that greenhouse warming is detectable in all analyzed high-variance reconstructions (with the possible exception of one ending in 1925), and that about a third of the warming in the first half of the twentieth century can be attributed to anthropogenic greenhouse gas emissions. The estimated magnitude of the anthropogenic signal is consistent with most of the warming in the second half of the twentieth century being anthropogenic.
DOI: 10.25921/gqph-x765
title: NOAA/WDS Paleoclimatology - Stahle - Upper Withlacoochee River - TADI - ITRDB FL009

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Chronology file added 2018-12-12. NOAA Template Raw Measurements file added 2019-01-23.
DOI: 10.25921/gx1a-ka35
title: NOAA/WDS Paleoclimatology - St-Onge - Prelude Lake - PIBN - ITRDB CANA291

description: Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives.  Most data sets include raw treering measurements (most are annual ring width, with some collections of earlywood or latewood width or wood density), plus chronologies (standardized growth indices for a site compiled from multiple treering samples). Reconstructions of climate variables are included with some of these data sets.  Each data type is stored in a separate data file; the data type is coded into the file name. For details please see: http://www.ncdc.noaa.gov/paleo/treeinfo.htmll
description: NOAA Template Raw Measurements file added 2019-02-04.
DOI: 10.25921/g53d-cq43
title: NOAA/WDS Paleoclimatology - Kavieng - Sr/Ca and Ba/Ca Ratios

description: A Porites coral from New Ireland (2.5°S, 150.5°E), at the heart of the Pacific warm pool, records variations of Ba/Ca back to the early 1820s. The New Ireland Coastal Undercurrent, which flows along the north coast and transports high-nutrient thermocline waters, is thought to be the main source of the Ba enrichment observed in the coral during El Niño. Between the 1850s and the 1960s, frequent large Ba peaks indicate that nutrients were available during both phases of El Niño–Southern Oscillation (ENSO). During La Niña, Ba could be advected along the South Equatorial Current. Also during this period, clusters of Ba/Ca peaks at nearly decadal timescale generally coincide with the return time of a strong El Niño, in accord with the high decadal variance of NINO3 sea surface temperatures. Ba enrichment in this coral primarily reflects the stratification in the thermocline that controls vertical mixing. The coral records long-term changes in those properties affecting nutrients in surface waters, with reduced Ba after the 1960s, and even less between 1823 and 1850. These reductions are tentatively attributed to the high rate of warming at the end of the Dalton Minimum and since the mid-20th century. An ensuing weakening of the trade winds may have produced a more stratified equatorial thermocline, hindering the transport of Ba and nutrients from the undercurrent to the shallow coastal waters north of New Ireland.
description: This data set contains a timeseries of Sr/Ca and Ba/Ca ratios reported at monthly resolution for a 2.1 m long Porites coral core designated as "NEP", collected in April 1997 near Kavieng (2.5°S, 150.5°E), Papua New Guinea. Sr/Ca and Ba/Ca ratios were determined by laser ablation ICPMS, using procedures described in Part 1 of the paper.
DOI: 10.25921/g24z-sk73
title: NOAA/WDS Paleoclimatology - Wiles - Juneau Mountain - TSME - ITRDB AK130

description: Recent observations of divergence between tree growth at high-latitude sites and temperature, as well as the decline of yellow cedar [Callitropsis nootkatensis (D. Don) Oerst. ex D.P. Little] in southeast Alaska due to warming, emphasize a need to investigate nonstationary climate response of Alaskan coastal forests to warming in other tree species.Comparison of annual tree growth in mountain hemlock [Tsuga mertensiana (Bong.)Carriere] to mean monthly temperature and precipitation data from Sitka, Alaska, from A.D. 1830s to 1990s along an elevational transect reveals nonstationarity in tree growth response to climate that suggests an ongoing biome shift.  We observe a marked weakening in the positive relationship between annual growth and warmer growth season temperatures at low-elevation hemlock sites, and a concurrent increase in growth and sensitivity at higher elevations coupled with increased correlation between growth and April precipitation at all sites along our transects. As previously observed with yellow cedar, the mechanism of the hemlock biome shift may be due to an increased susceptibility of roots to damage from late frosts resulting from earlier seasonal loss of protective snowpack.
description:  NOAA Template Chronology file added 2018-12-20. NOAA Template Raw Measurements file added 2019-02-08.