cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14931678
title: Replication Package for NeuralState

description: Overview

This repository serves as a replication package for the research paper titled "Typestate-based Fault Localization of API Usage Violations in a Deep Learning Program"

Benchmarks

Two benchmarks were utilized in the research:





Benchmark1 from NeuraLint:



Location: NLBench/SOSamples





Benchmark2 from Humbatova et al.:



Location: ExternalBench/SOSamples




Reproducing Results

To replicate the results presented in the paper, follow these steps:



Download the NeuralStateAnalysis Zip file.

Extract the file and navigate to the NeuralStateAnlaysis directory.

(Optional) Install the necessary requirements by executing pip install requirements.txt. Note: The requirements.txt file is already available in this repository.


Running NeuralState on NLBench:



Navigate to the NLBench/SOSamples directory.

Open any of the programs you wish to execute.

Set the path to the NeuralStateAnalysis directory: Path-to-folder/NeuralStateAnalysis/

Run the program using the command python program_id. Since the 'NeuralStateAnalysis(model).debug()' call is already present in all programs, you will be able to reproduce the results.


Running NeuralState on ExternalBench:



Navigate to the ExternalBench/SOSamples directory.

Open any of the programs you wish to execute.

Set the path to the NeuralStateAnalysis directory: Path-to-folder/NeuralStateAnalysis/

Run the program using the command python program_id. Since the 'NeuralStateAnalysis(model).debug()' call is already present in all programs, you will be able to reproduce the results.
DOI: 10.5281/zenodo.14931679
title: Replication Package for NeuralState

description: Overview

This repository serves as a replication package for the research paper titled "Typestate-based Fault Localization of API Usage Violations in a Deep Learning Program"

Benchmarks

Two benchmarks were utilized in the research:





Benchmark1 from NeuraLint:



Location: NLBench/SOSamples





Benchmark2 from Humbatova et al.:



Location: ExternalBench/SOSamples




Reproducing Results

To replicate the results presented in the paper, follow these steps:



Download the NeuralStateAnalysis Zip file.

Extract the file and navigate to the NeuralStateAnlaysis directory.

(Optional) Install the necessary requirements by executing pip install requirements.txt. Note: The requirements.txt file is already available in this repository.


Running NeuralState on NLBench:



Navigate to the NLBench/SOSamples directory.

Open any of the programs you wish to execute.

Set the path to the NeuralStateAnalysis directory: Path-to-folder/NeuralStateAnalysis/

Run the program using the command python program_id. Since the 'NeuralStateAnalysis(model).debug()' call is already present in all programs, you will be able to reproduce the results.


Running NeuralState on ExternalBench:



Navigate to the ExternalBench/SOSamples directory.

Open any of the programs you wish to execute.

Set the path to the NeuralStateAnalysis directory: Path-to-folder/NeuralStateAnalysis/

Run the program using the command python program_id. Since the 'NeuralStateAnalysis(model).debug()' call is already present in all programs, you will be able to reproduce the results.
DOI: 10.15468/dl.7vjx7b
title: Occurrence Download

description: A dataset containing 11133 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coriandrum sativum L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 11133 records from 463 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000208-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26007/4nkq-cm03
title: New Horizons Solar Wind Around Pluto Kuiper Belt Extended Mission (KEM1) Encounter Raw Data, Version 1.0

description: This collection contains a set of raw real-time, science summary, and science histogram 
 data in FITS format for the New Horizons (NH) Solar Wind Around Pluto (SWAP) instrument 
 during the Kuiper Belt Extended Mission (KEM1) ENCOUNTER mission phase. This collection 
 includes data acquired by the spacecraft between 08/14/2018 and 04/30/2022. It only 
 includes data downlinked before 05/01/2022. Future datasets may include more data acquired 
 by the spacecraft after 08/13/2018 but downlinked after 04/30/2022. The data includes SWAP 
 observations and plasma rolls in the approach and departure of Arrokoth. A gain test was 
 also performed.
DOI: 10.26007/5kcd-y977
title: New Horizons Solar Wind Around Pluto Kuiper Belt Extended Mission (KEM1) Encounter Calibrated Data, Version 1.0

description: This collection contains a set of calibrated real-time and science histogram data in FITS 
 format for the New Horizons Solar Wind Around Pluto (SWAP) instrument during the Kuiper 
 Belt Extended Mission (KEM1) ENCOUNTER mission phase. This collection includes data 
 acquired by the spacecraft between 08/14/2018 and 04/24/2022. It only includes data 
 downlinked before 05/01/2022. Future datasets may include more data acquired by the 
 spacecraft after 08/13/2018 but downlinked after 04/30/2022. The data includes SWAP 
 observations and plasma rolls in the approach and departure of Arrokoth. A gain test 
 was also performed.
DOI: 10.26007/mzpe-2c98
title: New Horizons (NH) Documents for Solar Wind Around Pluto (SWAP) instrument, Version 1.0

description: This collection contains documents applicable to the Solar Wind Around Pluto (SWAP) instrument 
 onboard the New Horizons spacecraft, such as documents describing the SWAP instrument, and mission 
 phase sequences. These documents were migrated from the Planetary Data System (PDS) PDS3 format 
 datasets, NH-A-SWAP-2-KEM1-V6.0 and NH-A-SWAP-3-KEM1-V6.0. Labels were redesigned during migration.
DOI: 10.6084/m9.figshare.26021831
title: Experiences of racism and racial disparities in health care among children and youth with autism and their caregivers: a systematic review

description: Although the health benefits of early diagnosis and therapeutic approaches for children and youth with autism spectrum disorder (ASD), racial disparities persist. This systematic review explored the experiences of racism and racial disparities in health care among children and youth with ASD and their caregivers. We conducted a systematic review, drawing on six international databases. Two reviewers screened titles, abstracts, and full texts. Thirty-seven studies met our inclusion criteria and we applied a narrative synthesis to develop themes. Four themes were identified: (1) experiences and aspects of racism and racial disparities (i.e., language and cultural barriers, poor quality health care interactions, stereotypes and discrimination, family and community stigma, and indirect barriers); (2) racial disparities in health care (i.e., screening and referral, diagnosis, health care services, and care coordination and medication); (3) facilitators to accessing health care services; and (4) recommendations from caregivers. This review highlights the extensive racial disparities experienced by children with autism. More research is needed to explore youth’s perspectives on racism in addition to exploring potential interventions to address racial disparities and improve health equity for youth with ASD. Racial minoritized youth with autism experience many barriers in accessing health care and there is an urgent need to address the systemic racism within our health care systems.Health care leaders and decision-makers should advocate for policy and systems change to enhance equitable access to health services for all youth with disabilities, especially those who belong to minoritized groups.Health care providers should consider engaging in relevant training to provide culturally safe and appropriate services for racially diverse clients with autism.Health care providers and decision-makers should work together to remove barriers to accessing health care for racial minoritized youth with autism. Racial minoritized youth with autism experience many barriers in accessing health care and there is an urgent need to address the systemic racism within our health care systems. Health care leaders and decision-makers should advocate for policy and systems change to enhance equitable access to health services for all youth with disabilities, especially those who belong to minoritized groups. Health care providers should consider engaging in relevant training to provide culturally safe and appropriate services for racially diverse clients with autism. Health care providers and decision-makers should work together to remove barriers to accessing health care for racial minoritized youth with autism.
DOI: 10.6084/m9.figshare.26021831.v1
title: Experiences of racism and racial disparities in health care among children and youth with autism and their caregivers: a systematic review

description: Although the health benefits of early diagnosis and therapeutic approaches for children and youth with autism spectrum disorder (ASD), racial disparities persist. This systematic review explored the experiences of racism and racial disparities in health care among children and youth with ASD and their caregivers. We conducted a systematic review, drawing on six international databases. Two reviewers screened titles, abstracts, and full texts. Thirty-seven studies met our inclusion criteria and we applied a narrative synthesis to develop themes. Four themes were identified: (1) experiences and aspects of racism and racial disparities (i.e., language and cultural barriers, poor quality health care interactions, stereotypes and discrimination, family and community stigma, and indirect barriers); (2) racial disparities in health care (i.e., screening and referral, diagnosis, health care services, and care coordination and medication); (3) facilitators to accessing health care services; and (4) recommendations from caregivers. This review highlights the extensive racial disparities experienced by children with autism. More research is needed to explore youth’s perspectives on racism in addition to exploring potential interventions to address racial disparities and improve health equity for youth with ASD. Racial minoritized youth with autism experience many barriers in accessing health care and there is an urgent need to address the systemic racism within our health care systems.Health care leaders and decision-makers should advocate for policy and systems change to enhance equitable access to health services for all youth with disabilities, especially those who belong to minoritized groups.Health care providers should consider engaging in relevant training to provide culturally safe and appropriate services for racially diverse clients with autism.Health care providers and decision-makers should work together to remove barriers to accessing health care for racial minoritized youth with autism. Racial minoritized youth with autism experience many barriers in accessing health care and there is an urgent need to address the systemic racism within our health care systems. Health care leaders and decision-makers should advocate for policy and systems change to enhance equitable access to health services for all youth with disabilities, especially those who belong to minoritized groups. Health care providers should consider engaging in relevant training to provide culturally safe and appropriate services for racially diverse clients with autism. Health care providers and decision-makers should work together to remove barriers to accessing health care for racial minoritized youth with autism.
DOI: 10.5281/zenodo.7902539
title: Serializing Java Objects in Plain Code

description: This is the anonymized replication package for "<em>Serializing Java Objects in Plain Code</em>". The zip file contains the following directory structure: <pre><code>. ├── BroadleafCommerce ├── BroadleafDemoSite ├── generated-tests ├── gephi ├── graphhopper ├── pdfbox └── prodj</code></pre> The tool exists under "prodj", the generated tests can be found in "generated-tests" and the other projects are in their respective directories and are configured to run with prodj. You can run prodj from the "prodj/rockstofetch" directory by executing `java -jar target/rocks-to-fetch.jar --help`. Our configurations can be found in "prodj/rockstofetch/src/test/resources".
DOI: 10.5281/zenodo.14888887
title: Serializing Java Objects in Plain Code

description: This is the anonymized replication package for "Serializing Java Objects in Plain Code".


The zip file contains the following directory structure:


.
├── BroadleafCommerce
├── BroadleafDemoSite
├── generated-tests
├── gephi
├── graphhopper
├── pdfbox
└── prodj


The tool exists under "prodj", the generated tests can be found in "generated-tests" and the other projects are in their respective directories and are configured to run with prodj. You can run prodj from the "prodj/rockstofetch" directory by executing `java -jar target/rocks-to-fetch.jar --help`. Our configurations can be found in "prodj/rockstofetch/src/test/resources".
DOI: 10.5281/zenodo.7902538
title: Serializing Java Objects in Plain Code

description: This is the anonymized replication package for "Serializing Java Objects in Plain Code".


The zip file contains the following directory structure:


.
├── BroadleafCommerce
├── BroadleafDemoSite
├── generated-tests
├── gephi
├── graphhopper
├── pdfbox
└── prodj


The tool exists under "prodj", the generated tests can be found in "generated-tests" and the other projects are in their respective directories and are configured to run with prodj. You can run prodj from the "prodj/rockstofetch" directory by executing `java -jar target/rocks-to-fetch.jar --help`. Our configurations can be found in "prodj/rockstofetch/src/test/resources".
DOI: 10.5281/zenodo.14827515
title: Molecular simulations of SCAP protein

description: These files contain all tpr and gro file for the mdrun in the manuscript. It also contains all the output from Chai-1 prediction
DOI: 10.5281/zenodo.14827514
title: Molecular simulations of SCAP protein

description: These files contain mdp, itp tpr and gro file for the mdrun in the manuscript. It also contains all the output from Chai-1 prediction
DOI: 10.5281/zenodo.14931703
title: Molecular simulations of SCAP protein

description: These files contain mdp, itp tpr and gro file for the mdrun in the manuscript. It also contains all the output from Chai-1 prediction
DOI: 10.15468/dl.cgn7mg
title: Occurrence Download

description: A dataset containing 15483 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-75.08282 6.42614,-75.00508 6.32011,-74.8764 6.41122,-74.95841 6.50707,-75.08282 6.42614))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 15483 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000212-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.1336892
title: Global Co2 Emissions From Cement Production

description: These data are associated with the research publication with the same title, published in Earth System Science Data.

The dataset includes process emissions from cement production in most countries of the world, beginning in the earliest year of available source data. The dataset also includes almost all source data used to produce the emissions dataset. See the associated article for details.
DOI: 10.5281/zenodo.1491562
title: Global Co2 Emissions From Cement Production

description: These data are associated with the research publication with the same title, published in Earth System Science Data.

The dataset includes process emissions from cement production in most countries of the world, beginning in the earliest year of available source data. The dataset also includes almost all source data used to produce the emissions dataset. See the associated article for details.
DOI: 10.5281/zenodo.831455
title: Global Co2 Emissions From Cement Production

description: These data are associated with the research publication with the same title, in press.

The dataset includes process emissions from cement production in most countries of the world, beginning in the earliest year of available source data. The dataset also includes almost all source data used to produce the emissions dataset. See the associated article for details.
DOI: 10.15468/dl.cpgzb2
title: Occurrence Download

description: A dataset containing 362 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lactuca undulata Ledeb."
 ]
}

 The dataset includes 362 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000213-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14919401
title: AD Leonis: Stellar Flare Observations

description: Polarimetric observations of AD Leonis taken with PRISM on the Perkins Telescope
DOI: 10.5281/zenodo.14919402
title: AD Leonis: Stellar Flare Observations

description: Polarimetric observations of AD Leonis taken with PRISM on the Perkins Telescope
DOI: 10.15468/dl.6eb66v
title: Occurrence Download

description: A dataset containing 424291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "Geometry POLYGON((-74.733 41.33269,-74.87821 41.22356,-74.98713 41.10512,-75.07183 40.97734,-75.08394 40.84931,-75.21705 40.75771,-75.19285 40.63844,-75.08394 40.56494,-75.04763 40.44532,-74.90242 40.39004,-74.26105 40.54655,-74.17634 40.65681,-74.01902 40.72104,-73.92221 41.05039,-73.98272 41.20535,-74.733 41.33269))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 2005-2025"
 ]
}

 The dataset includes 424291 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000210-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ae594k
title: Occurrence Download

description: A dataset containing 9173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Reseda alba L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9173 records from 279 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000216-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bgshxu
title: Occurrence Download

description: A dataset containing 6742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Symphoricarpos occidentalis (R.Br.) Hook.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6742 records from 118 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000217-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2txc5r
title: Occurrence Download

description: A dataset containing 741 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Malaysia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhizophoraceae"
 ]
}

 The dataset includes 741 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000218-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qkcb6y
title: Occurrence Download

description: A dataset containing 362 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lactuca undulata Ledeb."
 ]
}

 The dataset includes 362 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000219-250226125047203/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10522951
title: Bakta database

description: This data repository contains the mandatory DB for Bakta.

It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz).

Bakta is a tool for the rapid & standardized local annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readble JSON & bioinformatics standard file formats for automatic downstream analysis: https://github.com/oschwengers/bakta

This db provides protein sequence hash digests and lengths of UniProt's UniRef100 clusters, UniParc and NCBI RefSeq sequences for ultra-fast identification & lookups. It has been pre-annotated with several specialized db and enriched with Dbxrefs. Furthermore, seed sequences of UniProt's UniRef90 clusters are stored for fallback homology searches via Diamond sequence alignments. All conducted pre-annotations are logged and provided in the db.log.gz file.

External DB versions:



NCBI AMRFinderPlus: 2023-11-15.1

COG: 2020

DoriC: 12

ISFinder: 2019-09-25

Mob-suite: 3

Pfam: 36

RefSeq: r220

Rfam: 14.10

UniProtKB/Swiss-Prot: 2023_05

VFDB: 2024-01-15
DOI: 10.5281/zenodo.14916843
title: Bakta database

description: This data repository contains the mandatory DB for Bakta.

It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz).

Bakta is a tool for the rapid & standardized local annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readble JSON & bioinformatics standard file formats for automatic downstream analysis: https://github.com/oschwengers/bakta

This db provides protein sequence hash digests and lengths of UniProt's UniRef100 clusters, UniParc and NCBI RefSeq sequences for ultra-fast identification & lookups. It has been pre-annotated with several specialized db and enriched with Dbxrefs. Furthermore, seed sequences of UniProt's UniRef90 clusters are stored for fallback homology searches via Diamond sequence alignments. All conducted pre-annotations are logged and provided in the db.log.gz file.

External DB versions:



NCBI AMRFinderPlus: 2024-12-18.1

COG: 2024

DoriC: 12

ISFinder: 2019-09-25

Mob-suite: 3

Pfam: 37.2

RefSeq: r228

Rfam: 15

UniProtKB/Swiss-Prot: 2025_01

VFDB: 2025-02-14
DOI: 10.5281/zenodo.4247252
title: Bakta database

description: This data repository contains the mandatory DB for Bakta.

It is available in two versions: the default (db.tar.gz or) and a lightweight alternative (db-light.tar.gz).

Bakta is a tool for the rapid & standardized local annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readble JSON & bioinformatics standard file formats for automatic downstream analysis: https://github.com/oschwengers/bakta

This db provides protein sequence hash digests and lengths of UniProt's UniRef100 clusters, UniParc and NCBI RefSeq sequences for ultra-fast identification & lookups. It has been pre-annotated with several specialized db and enriched with Dbxrefs. Furthermore, seed sequences of UniProt's UniRef90 clusters are stored for fallback homology searches via Diamond sequence alignments. All conducted pre-annotations are logged and provided in the db.log.gz file.

External DB versions:



NCBI AMRFinderPlus: 2024-12-18.1

COG: 2024

DoriC: 12

ISFinder: 2019-09-25

Mob-suite: 3

Pfam: 37.2

RefSeq: r228

Rfam: 15

UniProtKB/Swiss-Prot: 2025_01

VFDB: 2025-02-14