cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.56b4qy
title: Occurrence Download

description: A dataset containing 882 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium klotzschianum Andersson"
 ]
}

 The dataset includes 882 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032673-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.25949767
title: Class-Distributed Learning for Multinomial Logistic Regression with High Dimensional Features and a Large Number of Classes

description: Estimating a high-dimensional multinomial logistic regression model with a larger number of categories is of fundamental importance but it presents two challenges. Computationally, it leads to heavy computation cost. Statistically, it suffers unsatisfactory statistical efficiency. Therefore, how to solve this problem in a computationally and statistically efficient way is of great interest. To tackle these challenges, we have developed a new class-distributed learning algorithm with a rank-reducible coefficient structure. The key innovation here is piecing together two important techniques for distributed computing and improved statistical efficiency. The two techniques are, respectively, dimension reduction and a circular-structured working model. Dimension reduction effectively alleviates the curse of dimensionality due to high dimensional features. A circular-structured working model allows the use of a class-distributed algorithm for distributed computing. To support our new methodology, we develop rigorous asymptotic theory and present extensive numerical experiments. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.25949767.v1
title: Class-Distributed Learning for Multinomial Logistic Regression with High Dimensional Features and a Large Number of Classes

description: Estimating a high-dimensional multinomial logistic regression model with a larger number of categories is of fundamental importance but it presents two challenges. Computationally, it leads to heavy computation cost. Statistically, it suffers unsatisfactory statistical efficiency. Therefore, how to solve this problem in a computationally and statistically efficient way is of great interest. To tackle these challenges, we have developed a new class-distributed learning algorithm with a rank-reducible coefficient structure. The key innovation here is piecing together two important techniques for distributed computing and improved statistical efficiency. The two techniques are, respectively, dimension reduction and a circular-structured working model. Dimension reduction effectively alleviates the curse of dimensionality due to high dimensional features. A circular-structured working model allows the use of a class-distributed algorithm for distributed computing. To support our new methodology, we develop rigorous asymptotic theory and present extensive numerical experiments. Supplementary materials for this article are available online.
DOI: 10.5281/zenodo.10844253
title: Artifact for "Program Repair and LLMs for Intelligent Tutoring of Programming"

description: This is the supplementary material for our work on "Program Repair and LLMs for Intelligent Tutoring of Programming". The corresponding paper has been submitted to the Technical Symposium on Computer Science Education (SIGCSE TS) 2025.

Our material includes (1) the artifacts for our user evaluations and (beyond what we describe in our paper) (2) additional information on the student projects used in our software engineering course. In this course, third-year CS students focus on developing the intelligent tutoring system.

1. Artifacts for the User Evaluations

The user_evaluation/students folder includes the main artifacts for the conducted experiments with the first-year CS students:



students_questionnaire_part1.pdf -- It shows the PDF version of the web form of our survey for students before they solve the programming assignment.

students_questionnaire_part2_groupA.pdf -- It shows the PDF version of the web form of our survey for group A students after they solve programming assignments with ITS.

students_questionnaire_part2_groupB.pdf -- It shows the PDF version of the web form of our survey for group B students after they solve the programming assignments without ITS.

students_responses.xlsx -- It shows all students' responses.


The user_evaluation/tutors folder includes the main artifacts for the conducted surveys with the CS tutors:



tutors_questionnaire_part1.pdf -- It shows the PDF version of the web form of our survey for tutors before they grade students' programming assignments.

tutors_questionnaire_part3.pdf -- It shows the PDF version of the web form of our in-person interview for tutors after they grade students' programming assignments.

tutors_responses.xlsx -- It shows all tutors' responses.


2. Course Project Descriptions

The projects folder includes the main artifacts for the conducted experiments with the first-year CS students:



2022_project.pdf -- It includes the project descriptions, which have been provided to the third-year students in the first instance of our Software Engineering course.

2023_project.pdf -- It includes the project descriptions, which have been provided to the third-year students in the second instance of our Software Engineering course.

project_schedule.pdf -- It includes the overview of the assignments in our course illustrating the project's overall schedule.
DOI: 10.5281/zenodo.12794818
title: Organoid tiny dataset for stitching (tiled, tif input)

description: Dataset acquired on Yokogawa CV8000 on 2023.11.29 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research

Dataset contains 3 x 4 (12) tiled fields of view (each 1000 x 1000 pix) acquired with 50 pix overlap. Partial tile (gridded) acquisition.

60x water objective, 2x2 binning, zyx spacing (10, 0.21667, 0.21667) um per pixel. Each field of view has 5 z-slices.

Mouse small intestinal organoids immunostained with the following dyes (2 fluorescence channels):

Channel 1 (C01, 405nm) = DAPI nuclear stainChannel 3 (C03, 568nm) = B-catenin membrane stain
DOI: 10.5281/zenodo.12794819
title: Organoid tiny dataset for stitching (tiled, tif input)

description: Dataset acquired on Yokogawa CV8000 on 2023.11.29 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research

Dataset contains 3 x 4 (12) tiled fields of view (each 1000 x 1000 pix) acquired with 50 pix overlap. Partial tile (gridded) acquisition.

60x water objective, 2x2 binning, zyx spacing (10, 0.21667, 0.21667) um per pixel. Each field of view has 5 z-slices.

Mouse small intestinal organoids immunostained with the following dyes (2 fluorescence channels):

Channel 1 (C01, 405nm) = DAPI nuclear stainChannel 3 (C03, 568nm) = B-catenin membrane stain
DOI: 10.5281/zenodo.7870622
title: Artifact for "Program Repair and LLMs for Intelligent Tutoring of Programming"

description: This is the supplementary material for our work on "Program Repair and LLMs for Intelligent Tutoring of Programming". The corresponding paper has been submitted to the Technical Symposium on Computer Science Education (SIGCSE TS) 2025.

Our material includes (1) the artifacts for our user evaluations and (beyond what we describe in our paper) (2) additional information on the student projects used in our software engineering course. In this course, third-year CS students focus on developing the intelligent tutoring system.

1. Artifacts for the User Evaluations

The user_evaluation/students folder includes the main artifacts for the conducted experiments with the first-year CS students:



students_questionnaire_part1.pdf -- It shows the PDF version of the web form of our survey for students before they solve the programming assignment.

students_questionnaire_part2_groupA.pdf -- It shows the PDF version of the web form of our survey for group A students after they solve programming assignments with ITS.

students_questionnaire_part2_groupB.pdf -- It shows the PDF version of the web form of our survey for group B students after they solve the programming assignments without ITS.

students_responses.xlsx -- It shows all students' responses.


The user_evaluation/tutors folder includes the main artifacts for the conducted surveys with the CS tutors:



tutors_questionnaire_part1.pdf -- It shows the PDF version of the web form of our survey for tutors before they grade students' programming assignments.

tutors_questionnaire_part3.pdf -- It shows the PDF version of the web form of our in-person interview for tutors after they grade students' programming assignments.

tutors_responses.xlsx -- It shows all tutors' responses.


2. Course Project Descriptions

The projects folder includes the main artifacts for the conducted experiments with the first-year CS students:



2022_project.pdf -- It includes the project descriptions, which have been provided to the third-year students in the first instance of our Software Engineering course.

2023_project.pdf -- It includes the project descriptions, which have been provided to the third-year students in the second instance of our Software Engineering course.

project_schedule.pdf -- It includes the overview of the assignments in our course illustrating the project's overall schedule.
DOI: 10.15468/dl.3gaen9
title: Occurrence Download

description: A dataset containing 98 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium laxum L.Ll.Phillips"
 ]
}

 The dataset includes 98 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032675-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12786323
title: Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching

description: In order to obtain a high-quality LC-MS/MS reference database for spectral library matching, we selected 22 high-quality GNPS tandem mass spectrometry databases generated under the positive ion mode. Further preprocessing similar to Huber et al involving mass-to-charge (m/z) and intensity filtering yields the database found in the file LCMS_GNPS_reference_library.csv which contains 14,705 electrospray ionization (ESI) mass spectra, each of which corresponds to a unique compound. The NIST WebBook database was used to construct GC-MS database contained in the file GCMS_NIST_WebBook.csv. This database contains 23,721 electron ionization (EI) mass spectra, each of which corresponds to a unique non-hyphenated Chemical Abstract Service (CAS) Registry Number.

 

Both LC-MS/MS and GC-MS databases are organized into three columns: one for the identifier, one for the m/z values, and one for the intensity values. For example, if spectrum A has 20 ion fragments, then there will be 20 rows corresponding to spectrum A in the corresponding database with the identifier A repeated 20 times with the corresponding m/z and intensity values.
DOI: 10.5281/zenodo.12786324
title: Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) and Gas Chromatography - Mass Spectrometry (GC-MS) Reference Libraries from Global Natural Products Social Molecular Networking (GNPS) and National Institute of Standards and Technology (NIST) WebBook Processed for Spectral Library Matching

description: In order to obtain a high-quality LC-MS/MS reference database for spectral library matching, we selected 22 high-quality GNPS tandem mass spectrometry databases generated under the positive ion mode. Further preprocessing similar to Huber et al involving mass-to-charge (m/z) and intensity filtering yields the database found in the file LCMS_GNPS_reference_library.csv which contains 14,705 electrospray ionization (ESI) mass spectra, each of which corresponds to a unique compound. The NIST WebBook database was used to construct GC-MS database contained in the file GCMS_NIST_WebBook.csv. This database contains 23,721 electron ionization (EI) mass spectra, each of which corresponds to a unique non-hyphenated Chemical Abstract Service (CAS) Registry Number.

 

Both LC-MS/MS and GC-MS databases are organized into three columns: one for the identifier, one for the m/z values, and one for the intensity values. For example, if spectrum A has 20 ion fragments, then there will be 20 rows corresponding to spectrum A in the corresponding database with the identifier A repeated 20 times with the corresponding m/z and intensity values.
DOI: 10.15468/dl.7qre8y
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Magnistipula multinervia Burgt"
 ]
}

 The dataset includes 38 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032676-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sf9hh6
title: Occurrence Download

description: A dataset containing 66912 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Culex quinquefasciatus Say, 1823"
 ]
}

 The dataset includes 66912 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032674-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7spsp5
title: Occurrence Download

description: A dataset containing 121 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium lobatum Gentry"
 ]
}

 The dataset includes 121 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032677-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.12770/ee5fd99f-d88f-4c6c-9b77-bfe1c88ca86f
title: Crassostrea gigas hemocytes scRNA-seq sequences

description: scRNA-seq reads from a Pacific oyster (Crassostrea gigas) hemocyte preparation. Hemocytes were isolated from a unique immunologically naive animal (Ifremer Standardized Animal, 18 months) and single-cell drop-seq technology was applied to 3,000 individual hemocytes.
DOI: 10.6084/m9.figshare.26349109
title: FWWC23 DATABASE

description: Notational database - Ball possessions FWWC23
DOI: 10.6084/m9.figshare.26349109.v1
title: FWWC23 DATABASE

description: Notational database - Ball possessions FWWC23
DOI: 10.15468/dl.3um9z7
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium longicalyx J.B.Hutch. & B.J.S.Lee"
 ]
}

 The dataset includes 54 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032679-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4wrebf
title: Occurrence Download

description: A dataset containing 39143 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Comunidad Ficoperifítica en el área de influencia del Proyecto Hidroeléctrico Ituango"
 ]
}

 The dataset includes 39143 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032678-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4d98jp
title: Occurrence Download

description: A dataset containing 142 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "GadmGid is one of (BRA.4_1, COL.1_2, PER.1_1, VEN.1_1, ECU.15.1.1_1)",
 "OccurrenceStatus is Present",
 "TaxonKey is Brosimum guianense (Aubl.) Huber ex Ducke"
 ]
}

 The dataset includes 142 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032680-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.576kmg
title: Occurrence Download

description: A dataset containing 293 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium raimondii Ulbr."
 ]
}

 The dataset includes 293 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032681-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebc3mj
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Maranthes sanagensis F.White"
 ]
}

 The dataset includes 78 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032682-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25574/01126
title: Chandra X-ray Observatory ObsId 01126
DOI: 10.15468/dl.37aeq8
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium schwendimanii Fryxell & S.D.Koch"
 ]
}

 The dataset includes 51 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032683-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vdpzpb
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium stocksii Mast."
 ]
}

 The dataset includes 125 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032684-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12795604
title: Organoid tiny dataset for stitching (tiled, ome-zarr)

description: Ome-zarr dataset that is the output of raw tifs (doi 10.5281/zenodo.12794818) processed by Fractal task (see .json file). 

Dataset acquired on Yokogawa CV8000 on 2023.11.29 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research

Dataset contains 3 x 4 (12) tiled fields of view (each 1000 x 1000 pix) acquired with 50 pix overlap. Partial tile (gridded) acquisition.

60x water objective, 2x2 binning, zyx spacing (10, 0.21667, 0.21667) um per pixel. Each field of view has 5 z-slices.

Mouse small intestinal organoids immunostained with the following dyes (2 fluorescence channels):

Channel 1 (C01, 405nm) = DAPI nuclear stainChannel 3 (C03, 568nm) = B-catenin membrane stain
DOI: 10.5281/zenodo.12795605
title: Organoid tiny dataset for stitching (tiled, ome-zarr)

description: Ome-zarr dataset that is the output of raw tifs (doi 10.5281/zenodo.12794818) processed by Fractal task (see .json file). 

Dataset acquired on Yokogawa CV8000 on 2023.11.29 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research

Dataset contains 3 x 4 (12) tiled fields of view (each 1000 x 1000 pix) acquired with 50 pix overlap. Partial tile (gridded) acquisition.

60x water objective, 2x2 binning, zyx spacing (10, 0.21667, 0.21667) um per pixel. Each field of view has 5 z-slices.

Mouse small intestinal organoids immunostained with the following dyes (2 fluorescence channels):

Channel 1 (C01, 405nm) = DAPI nuclear stainChannel 3 (C03, 568nm) = B-catenin membrane stain
DOI: 10.15468/dl.qh2w98
title: Occurrence Download

description: A dataset containing 1148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium thurberi Tod."
 ]
}

 The dataset includes 1148 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032686-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2p75x8
title: Occurrence Download

description: A dataset containing 124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (ARG, CHL, PRY, URY, FLK, BRA.21_1, BRA.16_1, BRA.24_1)",
 "TaxonKey is one of (Helanthium bolivianum (Rusby) Lehtonen & Myllys, Helanthium tenellum (Mart. ex Schult.f.) J.G.Sm.)"
 ]
}

 The dataset includes 124 records from 42 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032687-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z7tn6w
title: Occurrence Download

description: A dataset containing 330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Observation)",
 "Country is Colombia",
 "Geometry POLYGON((-77.25716 -4.27014,-64.64602 -4.27014,-64.64602 3.44493,-77.25716 3.44493,-77.25716 -4.27014))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Crax alector Linnaeus, 1766",
 "Year 2004-2024"
 ]
}

 The dataset includes 330 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032688-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.46xgt6
title: Occurrence Download

description: A dataset containing 127 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium trilobum (DC.) Skovst."
 ]
}

 The dataset includes 127 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032689-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gd3uva
title: Occurrence Download

description: A dataset containing 63 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Harvard University Herbaria: All Records",
 "OccurrenceStatus is Present",
 "TaxonKey is Aquilegia brevistyla Hook."
 ]
}

 The dataset includes 63 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032690-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.was9m9
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gossypium turneri Fryxell"
 ]
}

 The dataset includes 61 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032691-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzm82j
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Combretum exellii Jongkind"
 ]
}

 The dataset includes 39 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032692-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.