cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.7gj2ta
title: Occurrence Download

description: A dataset containing 961 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triticum turgidum subsp. dicoccum (Schrank ex Schübl.) Thell.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 961 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041741-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jd945s
title: Occurrence Download

description: A dataset containing 31184 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triticum turgidum subsp. durum (Desf.) Husn.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 31184 records from 101 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041742-240626123714530/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.26400445
title: ROME Demo Colab Notebook

description: Demo for the ROME tool which automates the hardware design process via LLMs
DOI: 10.5281/zenodo.13127211
title: LocalizeAgent Reproducibility Package

description: Replication Package: An LLM-Based Agent-Oriented Approach for Automated Code Design Issue Localization

This replication package contains the necessary code and instructions to run the experiments described in the paper, "An LLM-Based Agent-Oriented Approach for Automated Code Design Issue Localization".

Prerequisites



Python 3.12.2

Required Python packages:



pip install anthropic

pip install openai

pip install google-generativeai

pip install tqdm

pip install joblib

pip install javalang

pip install numpy




Installation

1. Clone the repository or extract the replication package.2. Install the required Python packages

Running the Experiments

Generating LLM Responses

To generate responses from language models (LLMs) like Claude, OpenAI, or Gemini, use the run.py script with the appropriate arguments.

 python3 run.py --MODEL_NAME --output ./openai/ --path PATH_TO_EVALUATION_DATASET

For example,

 python3 run.py --openai --output ./openai/move_m --path EvaluationDataset/move_m/single



--openai: Use the OpenAI API (alternatively, use --claude or --gemini for other LLMs).

--output: Specify the directory to save the LLM responses.

--path: Provide the path to the directory containing the Java files.


You can also use additional arguments like --limit to limit the number of files to process, --context to add context to the prompt, and --log_file to specify a log file path.

Evaluating LLM Responses

To evaluate the LLM responses by comparing function names extracted from file IDs and response texts, use the eval_llms.py script.

python3 run.py --eval --path /openai/move_m/llm_responses.json



--eval: Enable evaluation mode.

--path: Provide the path to the JSON file containing the LLM responses.


Running the Evaluation Script

The run_eval.sh script is provided to automate the evaluation process for multiple LLM responses. It loops through a predefined set of paths and executes the evaluation command for each path.

bash ./run_eval.sh

Customization

You can modify the source code files (eval_llms.py, llm_interfaces.py, prompt_generation.py, and utils.py) to customize the behavior or add new features as needed.

Additional Notes



The "EvaluationDataset" directory is already included in the replication package.

The output directory specified with the --output argument will be created if it doesn't already exist.
DOI: 10.5281/zenodo.13127212
title: LocalizeAgent Reproducibility Package

description: Replication Package: An LLM-Based Agent-Oriented Approach for Automated Code Design Issue Localization

This replication package contains the necessary code and instructions to run the experiments described in the paper, "An LLM-Based Agent-Oriented Approach for Automated Code Design Issue Localization".

Prerequisites



Python 3.12.2

Required Python packages:



pip install anthropic

pip install openai

pip install google-generativeai

pip install tqdm

pip install joblib

pip install javalang

pip install numpy




Installation

1. Clone the repository or extract the replication package.2. Install the required Python packages

Running the Experiments

Generating LLM Responses

To generate responses from language models (LLMs) like Claude, OpenAI, or Gemini, use the run.py script with the appropriate arguments.

 python3 run.py --MODEL_NAME --output ./openai/ --path PATH_TO_EVALUATION_DATASET

For example,

 python3 run.py --openai --output ./openai/move_m --path EvaluationDataset/move_m/single



--openai: Use the OpenAI API (alternatively, use --claude or --gemini for other LLMs).

--output: Specify the directory to save the LLM responses.

--path: Provide the path to the directory containing the Java files.


You can also use additional arguments like --limit to limit the number of files to process, --context to add context to the prompt, and --log_file to specify a log file path.

Evaluating LLM Responses

To evaluate the LLM responses by comparing function names extracted from file IDs and response texts, use the eval_llms.py script.

python3 run.py --eval --path /openai/move_m/llm_responses.json



--eval: Enable evaluation mode.

--path: Provide the path to the JSON file containing the LLM responses.


Running the Evaluation Script

The run_eval.sh script is provided to automate the evaluation process for multiple LLM responses. It loops through a predefined set of paths and executes the evaluation command for each path.

bash ./run_eval.sh

Customization

You can modify the source code files (eval_llms.py, llm_interfaces.py, prompt_generation.py, and utils.py) to customize the behavior or add new features as needed.

Additional Notes



The "EvaluationDataset" directory is already included in the replication package.

The output directory specified with the --output argument will be created if it doesn't already exist.
DOI: 10.15468/dl.jew2gb
title: Occurrence Download

description: A dataset containing 556 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Catálogo de autoridad taxonómica del género Quercus, Fagaceae en México"
 ]
}

 The dataset includes 556 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041743-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3ymy3c
title: Occurrence Download

description: A dataset containing 1045124 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2024-06-03",
 "EventDate is less than or equal to 2024-07-03",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 }
 ]
}

 The dataset includes 1045124 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041713-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xwg6cy
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triticum turgidum subsp. polonicum (L.) Thell.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 156 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041744-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tyqja
title: Occurrence Download

description: A dataset containing 186 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 (Cynanchum caudiculatum Rapini, Cynanchum montevidense Spreng., Cynanchum rioparanense Sundell, Cynanchum roulinioides (E.Fourn.) Rapini)"
 ]
}

 The dataset includes 186 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041745-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13127184
title: The high latitude ionospheric response to the major May 2024 geomagnetic storm: A synoptic view (Datasets)

description: Manually scaled ionosonde, ionosonde drift, and ISR datasets for the paper.
DOI: 10.15468/dl.4sykyx
title: Occurrence Download

description: A dataset containing 691 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triticum turgidum subsp. turgidum)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 691 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041747-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5067/j7gvfm11ogix
title: Sounder SIPS: AQUA AIRS IR + MW Level 2 CLIMCAPS: Retrieved atmospheric state V2.1
DOI: 10.5067/wzvj68exnlk7
title: Sounder SIPS: AQUA AIRS IR-only Level 2 CLIMCAPS: retrieved atmospheric state V2.1
DOI: 10.5067/5ghjwkuxqsp6
title: Sounder SIPS: JPSS-1 CrIMSS Level 2 CLIMCAPS: retrieved atmospheric state V2.1
DOI: 10.5067/ku5l6axrnqx8
title: Sounder SIPS: Suomi NPP CrIMSS Level 2 CLIMCAPS Normal Spectral Resolution: retrieved atmospheric state V2.1
DOI: 10.5067/sd6worv4gx8p
title: Sounder SIPS: Suomi NPP CrIMSS Level 2 CLIMCAPS Full Spectral Resolution: retrieved atmospheric state V2.1
DOI: 10.18738/t8/lhphc3/onmwri
title: README_Goudge_et_al_2024_Mars_VN_Data_Repository.txt

description: :unav
DOI: 10.15468/dl.wc9u38
title: Occurrence Download

description: A dataset containing 15548 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trochulus striolatus (C.Pfeiffer, 1828))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 15548 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041748-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6drvjx
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Trochus erithreus Brocchi, 1821)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 6 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041749-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.aasjde
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (BOLD:ADY0245)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 }
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041750-240626123714530/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.25213355
title: <b><i>Eye size does not change with artificial selection on relative telencephalon size in guppies (Poecilia reticulata)</i></b>

description: <b><i>Introduction:</i></b> Variation in eye size is sometimes closely associated with brain morphology. Visual information, detected by the retina, is transferred to the optic tectum to coordinate eye and body movements towards stimuli, and thereafter distributed into other brain regions for further processing. The telencephalon is an important visual processing region in many vertebrate species and a highly developed region in visually dependent species. Yet, the existence of a coevolutionary relationship between telencephalon size and eye size remains relatively unknown. <b><i>Methods:</i></b> Here, we use male and female guppies artificially selected for small- and large-relative-telencephalon-size to test if artificial selection on telencephalon size results in changes in eye size. In addition, we performed an optomotor test as a proxy for visual acuity. <b><i>Results:</i></b> We found no evidence that eye size changes with artificial selection on telencephalon size. Eye size was similar in both absolute and relative terms between the two selection regimes, but was larger in females. This is most likely because of the larger body size in females, but it could also reflect their greater need for visual capacity due to sex-specific differences in foraging and mating behaviour. Although the optomotor response was stronger in guppies with a larger telencephalon, we found no evidence for differences in visual acuity between the selection regimes. <b><i>Conclusion:</i></b> Our study suggests that eye size and visual perception in guppies does not change rapidly with strong artificial selection on telencephalon size.
DOI: 10.6084/m9.figshare.25213355.v1
title: <b><i>Eye size does not change with artificial selection on relative telencephalon size in guppies (Poecilia reticulata)</i></b>

description: <b><i>Introduction:</i></b> Variation in eye size is sometimes closely associated with brain morphology. Visual information, detected by the retina, is transferred to the optic tectum to coordinate eye and body movements towards stimuli, and thereafter distributed into other brain regions for further processing. The telencephalon is an important visual processing region in many vertebrate species and a highly developed region in visually dependent species. Yet, the existence of a coevolutionary relationship between telencephalon size and eye size remains relatively unknown. <b><i>Methods:</i></b> Here, we use male and female guppies artificially selected for small- and large-relative-telencephalon-size to test if artificial selection on telencephalon size results in changes in eye size. In addition, we performed an optomotor test as a proxy for visual acuity. <b><i>Results:</i></b> We found no evidence that eye size changes with artificial selection on telencephalon size. Eye size was similar in both absolute and relative terms between the two selection regimes, but was larger in females. This is most likely because of the larger body size in females, but it could also reflect their greater need for visual capacity due to sex-specific differences in foraging and mating behaviour. Although the optomotor response was stronger in guppies with a larger telencephalon, we found no evidence for differences in visual acuity between the selection regimes. <b><i>Conclusion:</i></b> Our study suggests that eye size and visual perception in guppies does not change rapidly with strong artificial selection on telencephalon size.
DOI: 10.15468/dl.87yq4e
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-61.15768 14.85863,-61.13385 14.85863,-61.13385 14.87736,-61.15768 14.87736,-61.15768 14.85863))",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 54 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041751-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zcb46a
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-105.07999 24.69763,-105.00018 24.69763,-105.00018 24.74656,-105.07999 24.74656,-105.07999 24.69763))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia"
 ]
}

 The dataset includes 20 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041753-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9rwwy8
title: Occurrence Download

description: A dataset containing 138 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Butia eriospatha (Mart. ex Drude) Becc."
 ]
}

 The dataset includes 138 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041754-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bj7ven
title: Occurrence Download

description: A dataset containing 24445616 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "Geometry POLYGON((-127.81506 -45.11270,27.81506 -45.11270,27.81506 17.11270,-127.81506 17.11270,-127.81506 -45.11270))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "IucnRedListCategory is one of (EX, EW, CR, EN, VU, NT, LC, DD, NE)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 24445616 records from 3307 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0041709-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/icpsr35276.v2
title: Survey of Consumer Attitudes and Behavior, October 2000
title: Version 2

description: The Survey of Consumer Attitudes and Behavior series was undertaken to measure changes in consumer attitudes and expectations, to understand why such changes occur, and to evaluate how they relate to consumer decisions to save, borrow, or make discretionary purchases. Since the 1940s, these surveys have been produced quarterly through 1977 and monthly thereafter. The surveys conducted in 2000 focused on topics such as evaluations and expectations about personal finances, employment, price changes, and the national business situation. Opinions were collected regarding respondents' appraisals of present market conditions for purchasing houses, automobiles, computers, and other durables. Also explored in this survey, were respondents' types of savings and financial investments, loan use, family income, retirement planning, and health and well-being. Other topics in this series typically include ownership, lease, and use of automobiles, respondents' use of personal computers at home and in the office, and respondents' familiarity with and use of the Internet. Demographic information includes ethnic origin, sex, age, marital status, and education.
description: The purpose of this survey series is to forecast changes in aggregate consumer behavior.
description: The data are not weighted, however, this collection contains four weight variables that can be used in any analysis: WT_AD (ADULT WEIGHT), WT_HH (HOUSEHOLD WEIGHT), WT_ADHD (ADULT HEAD WEIGHT), and WT (HOUSEHOLD HEAD WEIGHT). For more information on weights and sampling please visit the

Surveys of Consumers Web site and refer to the documentation on Sample Design, and the section on Sample Weights.
description: National sample of dwelling units selected by area probability sampling.
description: Datasets: 
DS0: Study-Level Files
DS1: Public-Use Data
DS2: Restricted-Use Data
description: Persons aged 18 years or older living in households with telephones within the United States. Smallest Geographic Unit: FIPS code
description: computer-assisted telephone interview (CATI)Information on the Index of Consumer Sentiment, the Index of Current Economic Conditions, and the Index of Consumer Expectations and how they were created can be found in the P.I. Codebook.Additional information on the Surveys of Consumers can be found by visiting the

Surveys of Consumers Web site.
DOI: 10.15468/dl.s7cpc2
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sedum confertiflorum Boiss."
 ]
}

 The dataset includes 89 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060704-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qyeart
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Sweden",
 "Geometry POLYGON((17.87705 59.28256,18.19994 59.28256,18.19994 59.45001,17.87705 59.45001,17.87705 59.28256))",
 "HasCoordinate is true",
 "TaxonKey is Schizophyllum commune Fr."
 ]
}

 The dataset includes 78 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060703-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.495pef
title: Occurrence Download

description: A dataset containing 49654 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Abudefduf saxatilis (Linnaeus, 1758)"
 ]
}

 The dataset includes 49654 records from 213 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060706-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.559tvy
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Microcystis Lemmermann, 1907",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0060708-250525065834625/datasets/export for details.