cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1345332
title: Embeddings Augmented By Random Permutations (Earp)

description: This data set includes the word embeddings used for our CoNLL 2018 paper, "<em>Bringing Order to Neural Word Embeddings with Embeddings Augmented By Random Permutations"</em>.

As described in the paper, encoding word order with random permutations leads to substantive improvements in performance across multiple analogical retrieval tasks, most notably for "syntactic" analogies that involve mapping between morphological derivatives. Smaller improvements are also evident in downstream sequence labeling tasks. 

Both baseline Skipgram-with-negative-sampling and permutation-based vectors are provided in two: formats - the Semantic Vectors (https://github.com/semanticvectors/semanticvectors) binary format (.bin) and the word2vec binary format (<em>.w2v.bin</em>).

All models were created with two different sliding window configurations - radius 2 (<em>r2</em>) and radius (<em>r5</em>); as well as with and without subword embeddings (<em>sw</em>). The models are as follows:

<em>basic, fastText</em>: standard Skipgram-with-negative-sampling, implemented in Semantic Vectors and fastText respectively

<em>earp_directional</em>: these models use random permutations (EARP) to distinguish between positions before and after the focus term in a sliding window

<em>earp_positional</em>: these models use random permutations (EARP) to distinguish between each position in a sliding window

<em>earp_proximity</em>: these models use random permutations (EARP) to generate encodings that are different, but not orthogonal, for neighboring positions in a sliding window. 

<em>earpx variants</em>: these models use exact sliding window position without replacing subsampled terms, as occurs in other models. 

The word2vec binary editions include random vectors for some characters and terms that were eliminated by Semantic Vectors' Lucene-based tokenization procedure - in particular punctuation marks - as these are useful for certain downstream machine learning tasks.
description: This work was supported in part by US National Library of Medicine  Grant RO1-LM011563
DOI: 10.5281/zenodo.1345333
title: Embeddings Augmented By Random Permutations (Earp)

description: This data set includes the word embeddings used for our CoNLL 2018 paper, "<em>Bringing Order to Neural Word Embeddings with Embeddings Augmented By Random Permutations"</em>.

As described in the paper, encoding word order with random permutations leads to substantive improvements in performance across multiple analogical retrieval tasks, most notably for "syntactic" analogies that involve mapping between morphological derivatives. Smaller improvements are also evident in downstream sequence labeling tasks. 

Both baseline Skipgram-with-negative-sampling and permutation-based vectors are provided in two: formats - the Semantic Vectors (https://github.com/semanticvectors/semanticvectors) binary format (.bin) and the word2vec binary format (<em>.w2v.bin</em>).

All models were created with two different sliding window configurations - radius 2 (<em>r2</em>) and radius (<em>r5</em>); as well as with and without subword embeddings (<em>sw</em>). The models are as follows:

<em>basic, fastText</em>: standard Skipgram-with-negative-sampling, implemented in Semantic Vectors and fastText respectively

<em>earp_directional</em>: these models use random permutations (EARP) to distinguish between positions before and after the focus term in a sliding window

<em>earp_positional</em>: these models use random permutations (EARP) to distinguish between each position in a sliding window

<em>earp_proximity</em>: these models use random permutations (EARP) to generate encodings that are different, but not orthogonal, for neighboring positions in a sliding window. 

<em>earpx variants</em>: these models use exact sliding window position without replacing subsampled terms, as occurs in other models. 

The word2vec binary editions include random vectors for some characters and terms that were eliminated by Semantic Vectors' Lucene-based tokenization procedure - in particular punctuation marks - as these are useful for certain downstream machine learning tasks.
description: This work was supported in part by US National Library of Medicine  Grant RO1-LM011563
DOI: 10.5281/zenodo.1403776
title: Atherosclerosis and Bone Loss in Humans – Results from Deceased Donors and Patients Submitted to Carotid Endarterectomy

description: The files contain the raw data supporting the findings of this work.
DOI: 10.5281/zenodo.1403777
title: Atherosclerosis and Bone Loss in Humans – Results from Deceased Donors and Patients Submitted to Carotid Endarterectomy

description: The files contain the raw data supporting the findings of this work.
DOI: 10.5517/ccdc.csd.cc1z0224
title: CCDC 1817315: Experimental Crystal Structure Determination

description: Related Article: Johanne Ling, Maxime Laugeois, Virginie Ratovelomanana-Vidal, Maxime R. Vitale|2018|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.1346306
title: Simulation dataset for "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters"

description: Simulated Illumina reads for SNP distance method evaluation and comparison used in the article "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters".

Details for simulation can be found at https://gitlab.com/rki_bioinformatics/panpasco/tree/master/simulation_dataset.
DOI: 10.5281/zenodo.1346307
title: Simulation dataset for "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters"

description: Simulated Illumina reads for SNP distance method evaluation and comparison used in the article "Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters".

Details for simulation can be found at https://gitlab.com/rki_bioinformatics/panpasco/tree/master/simulation_dataset.
DOI: 10.17632/7ct5nbmy43.1
title: Data for: Perioperative factors associated with favorable outcomes of posterior decompression and instrumented fusion for cervical ossification of the posterior longitudinal ligament: a retrospective multicenter study

description: This data comprised of 27 patients with K-line (-)-type OPLL treated with posterior decompression and fusion.
DOI: 10.5517/ccdc.csd.cc1yywf6
title: CCDC 1816179: Experimental Crystal Structure Determination

description: Related Article: Jinxiang Ye, Yuqi Lin, Qing Liu, Dekang Xu, Fan Wu, Bin Liu, Yu Gao, Haijun Chen|2018|Org.Lett.|20|5457|doi:10.1021/acs.orglett.8b02377
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zstyj
title: CCDC 1841119: Experimental Crystal Structure Determination

description: Related Article: Jinxiang Ye, Yuqi Lin, Qing Liu, Dekang Xu, Fan Wu, Bin Liu, Yu Gao, Haijun Chen|2018|Org.Lett.|20|5457|doi:10.1021/acs.orglett.8b02377
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zw7rv
title: CCDC 1843438: Experimental Crystal Structure Determination

description: Related Article: Rory P. Kelly, Davide Toniolo, Farzaneh Fadaei Tirani, Laurent Maron, Marinella Mazzanti|2018|Chem.Commun.|54|10268|doi:10.1039/C8CC04169E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zw7sw
title: CCDC 1843439: Experimental Crystal Structure Determination

description: Related Article: Rory P. Kelly, Davide Toniolo, Farzaneh Fadaei Tirani, Laurent Maron, Marinella Mazzanti|2018|Chem.Commun.|54|10268|doi:10.1039/C8CC04169E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zw7tx
title: CCDC 1843440: Experimental Crystal Structure Determination

description: Related Article: Rory P. Kelly, Davide Toniolo, Farzaneh Fadaei Tirani, Laurent Maron, Marinella Mazzanti|2018|Chem.Commun.|54|10268|doi:10.1039/C8CC04169E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zw7vy
title: CCDC 1843441: Experimental Crystal Structure Determination

description: Related Article: Rory P. Kelly, Davide Toniolo, Farzaneh Fadaei Tirani, Laurent Maron, Marinella Mazzanti|2018|Chem.Commun.|54|10268|doi:10.1039/C8CC04169E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc202hwh
title: CCDC 1849456: Experimental Crystal Structure Determination

description: Related Article: Ke-Xin Huang, Ming-Sheng Xie, Qi-Ying Zhang, Hong-Ying Niu, Gui-Rong Qu, Hai-Ming Guo|2018|Org.Lett.|20|5398|doi:10.1021/acs.orglett.8b02309
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203t0z
title: CCDC 1850700: Experimental Crystal Structure Determination

description: Related Article: Zhuang Mao Png, Jaime R. Cabrera-Pardo, Jorge Peiró Cadahía, Matthew J. Gaunt|2018|Chemical Science|9|7628|doi:10.1039/C8SC02855A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6073/pasta/09128d1df7d7ae09cba3e26aaebc9bef
title: McMurdo Dry Valleys Ice Thickness for Taylor Valley Lakes, Antarctica

description: Ice thickness was measured from the bottom of the ice cover to the piezometric water level and to the top of the ice cover. Because most limnological sampling holes are drilled in low-lying areas, it was thought that ice thickness measurements were biased. Therefore, random ice thickness measurements were performed in a 1000 m^2 sampling grid on each lake in past years. Statistical analyses by Dr. Priscu have shown that measurements from three ice holes are representative of the ice thickness measured by this grid system.
DOI: 10.5281/zenodo.1403510
title: Cardelino: Integrating Whole Exomes And Single-Cell Transcriptomes To Reveal Phenotypic Impact Of Somatic Variants

description: This dataset consists of the reference data files, metadata and processed results files for the paper "Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants," which investigates clonality in normal human dermal fibroblast cell populations in 32 cell lines from distinct donors, using bulk whole-exome sequencing and single-cell RNA-sequencing data.

This dataset contains everything required to reproduce the results presented in the paper from processed data and results of our data processing workflows. Our analyses can be reproduced using the source code and instructions available at our project website.

The <em>entire</em> analysis workflow from raw data to final results is also reproducible but is substantially more complicated and computationally intensive. It also requires large datasets to be obtained from other repositories. Specifically, single-cell RNA-seq data have been deposited in the ArrayExpress database at EMBL-EBI under accession number E-MTAB-7167. Whole-exome sequencing data is available through the HipSci portal (www.hipsci.org). Combined with the dataset in this repository and following the instructions on the project website, it is possible to run our entire analysis pipeline.
DOI: 10.5517/ccdc.csd.cc1lpqll
title: CCDC 1480640: Experimental Crystal Structure Determination

description: Related Article: Irene Ling, Harshita Kumari, Marzieh Mirzamani, Alexandre N. Sobolev, Christopher J. Garvey, Jerry L. Atwood, Colin L. Raston|2018|Chem.Commun.|54|10824|doi:10.1039/C8CC05650A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zlqny
title: CCDC 1835251: Experimental Crystal Structure Determination

description: Related Article: Pavel Golubev, Mikhail Krasavin|2018|Tetrahedron Lett.|59|3532|doi:10.1016/j.tetlet.2018.08.025
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpmcn
title: CCDC 1838032: Experimental Crystal Structure Determination

description: Related Article: Lucia Garcia, Mathew D. Anker, Mary F. Mahon, Laurent Maron, Michael S. Hill|2018|Dalton Trans.|47|12684|doi:10.1039/C8DT03124J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zpmgr
title: CCDC 1838035: Experimental Crystal Structure Determination

description: Related Article: Lucia Garcia, Mathew D. Anker, Mary F. Mahon, Laurent Maron, Michael S. Hill|2018|Dalton Trans.|47|12684|doi:10.1039/C8DT03124J
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zqr1h
title: CCDC 1839107: Experimental Crystal Structure Determination

description: Related Article: Xinyao Liu, Bing Liu, Guanghua Li, Yunling Liu|2018|J.Mater.Chem.A|6|17177|doi:10.1039/C8TA03807D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zqtyg
title: CCDC 1839197: Experimental Crystal Structure Determination

description: Related Article: Xinyao Liu, Bing Liu, Guanghua Li, Yunling Liu|2018|J.Mater.Chem.A|6|17177|doi:10.1039/C8TA03807D
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zrc25
title: CCDC 1839697: Experimental Crystal Structure Determination

description: Related Article: Lifei Zou, Xiaodong Sun, Jiaqi Yuan, Guanghua Li, Yunling Liu|2018|Inorg.Chem.|57|10679|doi:10.1021/acs.inorgchem.8b01330
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zwbdl
title: CCDC 1843520: Experimental Crystal Structure Determination

description: Related Article: Nikolay V. Tkachenko, Roman V. Ottenbacher, Oleg Y. Lyakin, Alexandra M. Zima, Denis G. Samsonenko, Evgenii P. Talsi, Konstantin P. Bryliakov|2018|ChemCatChem|10|4052|doi:10.1002/cctc.201800832
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zwr0m
title: CCDC 1843911: Experimental Crystal Structure Determination

description: Related Article: Petr A. Buikin, Andrey B. Ilyukhin, Nikolai P. Simonenko, Veronika K. Laurinavichyute, Vitalii Yu. Kotov|2018|Polyhedron|154|430|doi:10.1016/j.poly.2018.08.017
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc203t10
title: CCDC 1850701: Experimental Crystal Structure Determination

description: Related Article: Zhuang Mao Png, Jaime R. Cabrera-Pardo, Jorge Peiró Cadahía, Matthew J. Gaunt|2018|Chemical Science|9|7628|doi:10.1039/C8SC02855A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2080kw
title: CCDC 1854747: Experimental Crystal Structure Determination

description: Related Article: Chenxing Guo, Shantao Sun, Qing He, Vincent M. Lynch, Jonathan L. Sessler|2018|Org.Lett.|20|5414|doi:10.1021/acs.orglett.8b02322
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2089p9
title: CCDC 1855030: Experimental Crystal Structure Determination

description: Related Article: Shuhai Qiu, Chaoqiang Wang, Sheng Xie, Xiaobo Huang, Lanlan Chen, Yunhui Zhao, Zebing Zeng|2018|Chem.Commun.|54|11383|doi:10.1039/C8CC05929B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2089rc
title: CCDC 1855032: Experimental Crystal Structure Determination

description: Related Article: Shuhai Qiu, Chaoqiang Wang, Sheng Xie, Xiaobo Huang, Lanlan Chen, Yunhui Zhao, Zebing Zeng|2018|Chem.Commun.|54|11383|doi:10.1039/C8CC05929B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2089sd
title: CCDC 1855033: Experimental Crystal Structure Determination

description: Related Article: Shuhai Qiu, Chaoqiang Wang, Sheng Xie, Xiaobo Huang, Lanlan Chen, Yunhui Zhao, Zebing Zeng|2018|Chem.Commun.|54|11383|doi:10.1039/C8CC05929B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20954n
title: CCDC 1855850: Experimental Crystal Structure Determination

description: Related Article: Lalita Negi, Ashutosh Shrivastava, Dinabandhu Das|2018|Chem.Commun.|54|10675|doi:10.1039/C8CC05859H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc20955p
title: CCDC 1855851: Experimental Crystal Structure Determination

description: Related Article: Lalita Negi, Ashutosh Shrivastava, Dinabandhu Das|2018|Chem.Commun.|54|10675|doi:10.1039/C8CC05859H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.