cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.nv7vu7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Spirogyra maxima f. woronichinia Poljansk.;Spirogyra maxima f. woronichinia)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091641-230530130749713/datasets/export for details.
DOI: 10.15468/dl.s5p6jv
title: Occurrence Download

description: A dataset containing 830901 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is Acrocephalus scirpaceus",
 "BasisOfRecord is one of (Machine Observation, Human Observation)",
 "Year 2011-2021",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen, Specimen, Material citation, Material sample)"
 ]
 }
 }
 ]
}

 The dataset includes 830901 records from 84 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057959-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8ckfa9
title: Occurrence Download

description: A dataset containing 2114 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fuscospora solandri (Hook.f.) Heenan & Smissen"
 ]
}

 The dataset includes 2114 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0067700-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r5cf44
title: Occurrence Download

description: A dataset containing 2176330 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-118.88803 30.06134,-115.71422 26.27746,-108.30074 19.85245,-106.67683 31.92582,-105.54716 37.43298,-105.90018 41.95167,-109.2186 44.98767,-115.57301 46.47036,-122.84527 45.62311,-128.21122 41.59865,-118.88803 30.06134))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Buteo jamaicensis (Gmelin, 1788)"
 ]
}

 The dataset includes 2176330 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050607-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m9j6n3
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scutellaria asperiflora Nakai"
 ]
}

 The dataset includes 13 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0121304-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qzn2pk
title: Occurrence Download

description: A dataset containing 200 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucaster caniflorus (Mart.) Choisy"
 ]
}

 The dataset includes 200 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008558-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgx9pd
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aristolochia oranensis Ahumada"
 ]
}

 The dataset includes 4 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050709-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yu2tmy
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygala rivularis Gürke"
 ]
}

 The dataset includes 21 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091642-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.223d5y
title: Occurrence Download

description: A dataset containing 1852 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Bidens pilosa L."
 ]
}

 The dataset includes 1852 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007199-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.n4a584
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucas tettensis Vatke"
 ]
}

 The dataset includes 136 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008550-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trmcu8
title: Occurrence Download

description: A dataset containing 128 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Scutellaria balearica Barceló"
 ]
}

 The dataset includes 128 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0121319-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thxfz6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Characidae, Loricariidae, Cichlidae)",
 "Continent is South America",
 "EstablishmentMeans is NATIVE"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0068302-240506114902167/datasets/export for details.
DOI: 10.15468/dl.z8rsxt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Scenedesmus polessicus P.Tsarenko;Scenedesmus polessicus)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091645-230530130749713/datasets/export for details.
DOI: 10.15468/dl.2jv3uw
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Monnina equatoriensis Chodat"
 ]
}

 The dataset includes 83 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042967-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fzmkap
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acanthocercus minutus (Klausewitz, 1957))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 40 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050700-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7vamww
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Japan",
 "OccurrenceStatus is Present",
 "TaxonKey is Clerodendrum bungei Steud."
 ]
}

 The dataset includes 61 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0121340-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.95nc7w
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aristolochia olivieri Colleg. ex Boiss."
 ]
}

 The dataset includes 21 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050702-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yn7w59
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucas usagarensis Gürke"
 ]
}

 The dataset includes 20 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008553-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f6r4hq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Uronema confervicolum var. uncinatum Popova;Uronema confervicolum var. uncinatum)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091646-230530130749713/datasets/export for details.
DOI: 10.15468/dl.tcadwx
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepanthes schizix Luer"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007200-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uugjb2
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucas welwitschii Gürke"
 ]
}

 The dataset includes 19 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008555-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.huj5z5
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.6_1",
 "TaxonKey is Nyctinomops macrotis (Gray, 1840)"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091656-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yhfbcz
title: Occurrence Download

description: A dataset containing 295 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melanoplus calidus Scudder, 1899"
 ]
}

 The dataset includes 295 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050705-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g59xe5
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hebecarpa robinsonii (S.F.Blake) J.R.Abbott & J.F.B.Pastore"
 ]
}

 The dataset includes 28 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091647-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzhg64
title: Occurrence Download

description: A dataset containing 13143 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carpinus caroliniana Walter",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 13143 records from 190 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046003-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pvyngt
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aristolochia ophioides L.Marión"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050706-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5mqxyc
title: Occurrence Download

description: A dataset containing 95 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leucheria candidissima Gillies & D.Don"
 ]
}

 The dataset includes 95 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008565-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.brsb75
title: Occurrence Download

description: A dataset containing 311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is USA.6_1",
 "TaxonKey is Myotis evotis (H.Allen, 1864)"
 ]
}

 The dataset includes 311 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091672-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11506892
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.11506893
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.78fqrp
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-128299.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Aniba perutilis Hemsl.",
 "Year 2000-2023"
 ]
}

 The dataset includes 40 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007226-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e9shv2
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "VerbatimScientificName is one of (Chlamydomonas ucrainica Demchenko, A. Massalski, Kostikov & L. Hoffm.;Chlamydomonas ucrainica)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Country is Ukraine"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091650-230530130749713/datasets/export for details.
DOI: 10.15468/dl.xc5vm5
title: Occurrence Download

description: A dataset containing 45 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lycaste dowiana Endrés ex Rchb.f."
 ]
}

 The dataset includes 45 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016171-230530130749713/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.26011705
title: 的数据和代码适宜环境中与生物营养病原体感染相关的较高叶片位置”

description: 了解真菌病原体之间病害位置（即受感染叶子的平均高度）的差异对于预测和管理植物病害至关重要。然而，我们对不同疾病和寄主植物类型的病害位置如何变化，以及当地气候（即温度和降水）是否影响病害位置知之甚少。本文研究了青藏高原、内蒙古高原和华北平原等中国主要生态系统中草本植物的病害分布。我们测试了真菌病原体特征（例如，疾病类型和生活史）、寄主植物特征（例如，生物量、自然高度和植物生长类型）和气候条件（例如，年平均温度和降水量）如何影响疾病位置。与坏死性病原体相比，生物营养病原体的病害位置往往更高，这种模式在杂草和豆科植物中最为明显。疾病位置也与环境有关;较高的温度和降水显著增加了疾病的位置，但这些影响因疾病类型而异。对于生物营养和坏死营养病原体，较大和较高的寄主植物的平均病害位置较低。 在这项研究中，我们提供了疾病类型和气候条件如何影响疾病位置的证据;我们的研究结果强调了疾病位置对于了解感染模式和管理疾病爆发的重要性。
DOI: 10.15468/dl.5vapmz
title: Occurrence Download

description: A dataset containing 628 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nemacladus ramosissimus Nutt."
 ]
}

 The dataset includes 628 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046022-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tx5sff
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Lygosoma schneideri Werner, 1900)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050711-230224095556074/datasets/export for details.
DOI: 10.15468/dl.85k2kd
title: Occurrence Download

description: A dataset containing 46 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygala robusta Gürke"
 ]
}

 The dataset includes 46 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0091654-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/cc8sn2r
title: CCDC 262014: Experimental Crystal Structure Determination

description: Related Article: P.J.Shapiro, S.-J.Lee, P.Perrotin, T.Cantrell, A.Blumenfeld, B.Twamley|2005|Polyhedron|24|1366|doi:10.1016/j.poly.2005.04.014
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.