cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17197892
title: Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input

description: This dataset supports SMARTBind (Small Molecule Approaches to RNA Targeting Binder Discovery), a structure-agnostic ligand discovery framework that combines an RNA large language model with contrastive learning and a ligand-specific decoy enhancement strategy. Please cite the following publication when using the dataset:



Jiang, Shiyu, Amirhossein Taghavi, Tenghui Wang, Samantha M. Meyer, Jessica L. Childs-Disney, Chenglong Li, Mattew D. Disney, and Yanjun Li. "Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input." bioRxiv (2025): 2025-09.


Overview

The dataset contains model checkpoint and training data for SMARTBind including RNAmigos1 10-fold random-split, Hariboss 10-fold random-split, and Hariboss 5-fold sequence-based-split. All data is organized under the archive file SMARTBind_dataset.zip.

Contents

SMARTBind_weights.zip: Saved checkpoint of 10-fold SMARTBind model.

hariboss_merged_5fd.pkl: SMARTBind training data from the HARIBOSS database under 5-fold sequence-based-split cross-validation.

hariboss_merged_10fd.pkl: SMARTBind training data from the HARIBOSS database under 10-fold random-split cross-validation.

rnamigos_10fd.pkl: SMARTBind training data from the RNAmigos1 under 10-fold random-split cross-validation.

Decoy library.smi: a chemical diverse decoy library with 92,626 entries that is curated for the ligand-specific decoy enhancement strategy.
DOI: 10.5281/zenodo.17254230
title: Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input

description: This dataset supports SMARTBind (Small Molecule Approaches to RNA Targeting Binder Discovery), a structure-agnostic ligand discovery framework that combines an RNA large language model with contrastive learning and a ligand-specific decoy enhancement strategy. Please cite the following publication when using the dataset:



Jiang, Shiyu, Amirhossein Taghavi, Tenghui Wang, Samantha M. Meyer, Jessica L. Childs-Disney, Chenglong Li, Mattew D. Disney, and Yanjun Li. "Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input." bioRxiv (2025): 2025-09.


Overview

The dataset contains model checkpoint and training data for SMARTBind including RNAmigos1 10-fold random-split, Hariboss 10-fold random-split, and Hariboss 5-fold sequence-based-split. All data is organized under the archive file SMARTBind_dataset.zip.

Contents

SMARTBind_weights.zip: Saved checkpoint of 10-fold SMARTBind model.

hariboss_merged_5fd.pkl: SMARTBind training data from the HARIBOSS database under 5-fold sequence-based-split cross-validation.

hariboss_merged_10fd.pkl: SMARTBind training data from the HARIBOSS database under 10-fold random-split cross-validation.

rnamigos_10fd.pkl: SMARTBind training data from the RNAmigos1 under 10-fold random-split cross-validation.

Decoy library.smi: a chemical diverse decoy library with 92,626 entries that is curated for the ligand-specific decoy enhancement strategy.
DOI: 10.26023/wzx2-tjgc-e70y
title: Volcanic Ash Advisory Center - Darwin Ash Graphic. Version 1.0

description: This dataset contains Darwin Ash Graphical products produced by the Volcanic Ash Advisory Center (VAAC) during the HIPPO-4 project. The imagery are in GIF and PNG format. The imagery cover the time span from 2011-06-01 00:31:00 to 2011-07-13 12:16:00.
DOI: 10.15468/dl.sx4f55
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bostrichus capucinus",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042138-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26023/gmay-n3kx-es0c
title: Volcanic Ash Advisory Center - Tokyo Ash Advisory. Version 1.0

description: This dataset contains Tokyo Ash Advisory text products produced by the Volcanic Ash Advisory Center (VAAC) during the HIPPO-4 project. The files are in TXT format and cover the time span from 2011-06-19 21:02:00 to 2011-08-03 12:10:00.
DOI: 10.15468/dl.87tk83
title: Occurrence Download

description: A dataset containing 94 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "TaxonKey is Neonauclea reticulata"
 ]
}

 The dataset includes 94 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042139-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cvexch
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Minthea rugicollis",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042140-250920141307145/datasets/export for details.
DOI: 10.15468/dl.rxhfmb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Minthea rugicollis",
 "Country is France",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042141-250920141307145/datasets/export for details.
DOI: 10.26023/540c-zn7q-hm04
title: Volcanic Ash Advisory Center - Wellington Ash Advisory. Version 1.0

description: This dataset contains Wellington Ash Advisory text products produced bythe Volcanic Ash Advisory Center (VAAC) during the HIPPO-4 project. The files are in TXT format and cover the time span from 2011-06-22 17:41:00 to 2011-06-24 11:51:00.
DOI: 10.15468/dl.3yfg73
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Minthea rugicollis",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042142-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57783/nssh-g520
title: LibreChat-TEST
DOI: 10.6084/m9.figshare.27367194
title: LAURA: Enhancing Code Review Generation with Context-Enriched Retrieval-Augmented LLM

description: <b>LAURA: Enhancing Code Review Generation with Context-Enriched Retrieval-Augmented LLM</b><b>Introduction</b>LAURA is an LLM-based retrieval-augmented, context-aware framework for code review generation, which integrates context augmentation, review exemplar retrieval, and prompt tuning to enhance the performance of LLMs (in our study, ChatGPT-4o and DeepSeek v3) in generating code review comments.The experiments show that LAURA outperforms the direct application of ChatGPT-4o and DeepSeek v3 for code review generation and significantly surpasses the performance of the pre-trained model CodeReviewer.Since our experiments are based on ChatGPT-4o and DeepSeek v3, we have released the data processing code and dataset used in our research. The code section includes the Python scripts we used for data collection, cleaning, merging, and retrieval. The dataset section contains 301k entries from 1,807 high-quality projects sourced from GitHub, covering four programming languages: C, C++, Java, and Python. We also provide the time-split dataset used as the retrieval database (which is also used for fine-tuning CodeReviewer) and the human-annotated evaluation dataset.<b>File Structure</b><b>codes</b>: Data collection, filtering and post-processing codes used in our study<br><b>data_collection_and_filtering.py</b>: Code for collecting data via the GitHub GraphQL API and filtering with rule-based and LLM-based methods<br><b>data_embedding.py</b>: Code for data embedding<br><b>data_merging.py</b>: Code for data merging, used to merge the review comments with the same target diff<br><b>data_retrieval.py</b>: Code for data retrieval<br><b>diff_extension.py</b>: Code for extending the code diffs by integrating the full code contexts into the diffs<b>datasets</b>: Datasets built and used in our study<br><b>database_for_retrieve.csv</b>: The dataset we built for retrieval-augmented generation, containing 298,494 entries prior to December 26, 2024<br><b>evaluation_data.csv</b>: The evaluation dataset we manually annotated, containing 384 entries later than December 26, 2024<br><b>full_dataset.csv</b>: The full dataset we collected, containing 301,256 entries<b>prompts:</b> The prompts used in data filtering, generation and evaluation<br><b>direct_generation.txt</b>: The prompt we used for direct generation as baselines<br><b>LAURA_generation.txt</b>: The prompt we used for LAURA generation<br><b>LLM_evaluation.txt</b>: The prompt we used for LLM evaluation<br><b>LLM_filtering.txt</b>: The prompt we used for LLM filtering in data filtering process<b>README.md</b>: Description of our submission<br>
DOI: 10.6084/m9.figshare.27367194.v1
title: LAURA: Enhancing Code Review Generation with Context-Enriched Retrieval-Augmented LLM

description: <b>LAURA: Enhancing Code Review Generation with Context-Enriched Retrieval-Augmented LLM</b><b>Introduction</b>LAURA is an LLM-based retrieval-augmented, context-aware framework for code review generation, which integrates context augmentation, review exemplar retrieval, and prompt tuning to enhance the performance of LLMs (in our study, ChatGPT-4o and DeepSeek v3) in generating code review comments.The experiments show that LAURA outperforms the direct application of ChatGPT-4o and DeepSeek v3 for code review generation and significantly surpasses the performance of the pre-trained model CodeReviewer.Since our experiments are based on ChatGPT-4o and DeepSeek v3, we have released the data processing code and dataset used in our research. The code section includes the Python scripts we used for data collection, cleaning, merging, and retrieval. The dataset section contains 301k entries from 1,807 high-quality projects sourced from GitHub, covering four programming languages: C, C++, Java, and Python. We also provide the time-split dataset used as the retrieval database (which is also used for fine-tuning CodeReviewer) and the human-annotated evaluation dataset.<b>File Structure</b><b>codes</b>: Data collection, filtering and post-processing codes used in our study<br><b>data_collection_and_filtering.py</b>: Code for collecting data via the GitHub GraphQL API and filtering with rule-based and LLM-based methods<br><b>data_embedding.py</b>: Code for data embedding<br><b>data_merging.py</b>: Code for data merging, used to merge the review comments with the same target diff<br><b>data_retrieval.py</b>: Code for data retrieval<br><b>diff_extension.py</b>: Code for extending the code diffs by integrating the full code contexts into the diffs<b>datasets</b>: Datasets built and used in our study<br><b>database_for_retrieve.csv</b>: The dataset we built for retrieval-augmented generation, containing 298,494 entries prior to December 26, 2024<br><b>evaluation_data.csv</b>: The evaluation dataset we manually annotated, containing 384 entries later than December 26, 2024<br><b>full_dataset.csv</b>: The full dataset we collected, containing 301,256 entries<b>prompts:</b> The prompts used in data filtering, generation and evaluation<br><b>direct_generation.txt</b>: The prompt we used for direct generation as baselines<br><b>LAURA_generation.txt</b>: The prompt we used for LAURA generation<br><b>LLM_evaluation.txt</b>: The prompt we used for LLM evaluation<br><b>LLM_filtering.txt</b>: The prompt we used for LLM filtering in data filtering process<b>README.md</b>: Description of our submission<br>
DOI: 10.26023/3h6t-ryd7-m20n
title: Volcanic Ash Advisory Center - Wellington Ash Graphic. Version 1.0

description: This dataset contains Wellington Ash Graphical products produced by the Volcanic Ash Advisory Center (VAAC) during the HIPPO-4 project. The imagery are in PNG format. The imagery cover the time span from 2011-06-22 17:41:00 to 2011-06-22 17:41:00.
DOI: 10.26023/app8-gze7-n10j
title: OMI Southern Hemisphere Columnar Sulfur Dioxide Imagery. Version 1.0

description: This dataset contains South Polar Sulfur Dioxide imagery from the OMI satellite taken during the HIPPO-4 project. The imagery are in GIF format. The imagery cover the time span from 2011-06-18 12:00:00 to 2011-07-13 12:00:00.
DOI: 10.15468/dl.mfwwtg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Minthea rugicollis",
 "Country is Sweden",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042144-250920141307145/datasets/export for details.
DOI: 10.26188/30218614
title: ChloroScan test data

description: This article provides two lightweight test data for users to run ChloroScan.Both data contain:An assembly in fasta.A table matching every contig in assembly to their abundance, with each column a different sample.To download, run:wget --referer=https://figshare.unimelb.edu.au --user-agent="Mozilla/5.0" -O "test_large.tar.gz" https://figshare.unimelb.edu.au/ndownloader/files/58315609. wget --referer=https://figshare.unimelb.edu.au --user-agent="Mozilla/5.0" -O "test_small.tar.gz" https://figshare.unimelb.edu.au/ndownloader/files/58315606 <br><br>
DOI: 10.26188/30218614.v3
title: ChloroScan test data

description: This article provides two lightweight test data for users to run ChloroScan.Both data contain:An assembly in fasta.A table matching every contig in assembly to their abundance, with each column a different sample.To download, run:wget --referer=https://figshare.unimelb.edu.au --user-agent="Mozilla/5.0" -O "test_large.tar.gz" https://figshare.unimelb.edu.au/ndownloader/files/58315609. wget --referer=https://figshare.unimelb.edu.au --user-agent="Mozilla/5.0" -O "test_small.tar.gz" https://figshare.unimelb.edu.au/ndownloader/files/58315606 <br><br>
DOI: 10.26188/30218614.v2
title: ChloroScan test data

description: description
DOI: 10.26023/h4mh-h8fg-910n
title: OMI Mid-Latitude Columnar Sulfur Dioxide Imagery. Version 1.0

description: This dataset contains mid-latitude Sulfur Dioxide imagery from the OMI satellite taken during the HIPPO-4 project. The imagery are in GIF format. The imagery cover the time span from 2011-06-18 12:00:00 to 2011-07-13 12:00:00.
DOI: 10.5281/zenodo.16525291
title: Multi-phase intra-plate rifting and deformable plate modelling of the Northeast Atlantic back to the Permian

description: Supplementary data bundle for “Multi-phase intra-plate rifting and deformable plate modelling of the Northeast Atlantic back to the Permian” Grace. E. Shephard, Mansour M. Abdelmalak, Jan Inge Faleide, Edward Clennett, Sabin Zahirovic, Sebastien Gac, Peter Haas, Carmen Gaina, Trond H. Torsvik. (2025) with Gondwana Research. https://doi.org/10.1016/j.gr.2025.09.002
DOI: 10.5281/zenodo.16525292
title: Multi-phase intra-plate rifting and deformable plate modelling of the Northeast Atlantic back to the Permian

description: Supplementary data bundle for “Multi-phase intra-plate rifting and deformable plate modelling of the Northeast Atlantic back to the Permian” Grace. E. Shephard, Mansour M. Abdelmalak, Jan Inge Faleide, Edward Clennett, Sabin Zahirovic, Sebastien Gac, Peter Haas, Carmen Gaina, Trond H. Torsvik. (2025) with Gondwana Research. https://doi.org/10.1016/j.gr.2025.09.002
DOI: 10.15468/dl.98zxdn
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neonauclea viridiflora"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042145-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26023/ewhv-61jn-x007
title: PAN and other Trace Hydrohalocarbon ExpeRiment Data (PANTHER) Electron Capture Detectors (ECD) Data. Version 1.0

description: PANTHER (PAN and other Trace Hydrohalocarbon ExpeRiment) is an in situ 6-channel gas chromatograph (GC) containing four Electron Capture Dectors (ECD) that was flown aboard the NSF/NCAR GV during HIPPO-4. The dataset contains mixing ratios in NASA Ames format.
DOI: 10.15468/dl.7keu6r
title: Occurrence Download

description: A dataset containing 10743294 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Month is July",
 "Year 2014-2014"
 ]
}

 The dataset includes 10743294 records from 5100 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0042086-250920141307145/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.26710499.v1
title: Additional file 14 of Identification and validation of genes associated with prognosis of cisplatin-resistant ovarian cancer

description: Supplementary Material 14.
DOI: 10.6084/m9.figshare.26710502
title: Additional file 15 of Identification and validation of genes associated with prognosis of cisplatin-resistant ovarian cancer

description: Supplementary Material 15.
DOI: 10.6084/m9.figshare.26710502.v1
title: Additional file 15 of Identification and validation of genes associated with prognosis of cisplatin-resistant ovarian cancer

description: Supplementary Material 15.
DOI: 10.6084/m9.figshare.26710532
title: Additional file 10 of Whole-brain connections of glutamatergic neurons in the mouse lateral habenula in both sexes

description: Supplementary Material 10
DOI: 10.6084/m9.figshare.26710532.v1
title: Additional file 10 of Whole-brain connections of glutamatergic neurons in the mouse lateral habenula in both sexes

description: Supplementary Material 10
DOI: 10.6084/m9.figshare.26710562
title: Additional file 5 of Development and internal validation of an algorithm for estimating mortality in patients encountered by physician-staffed helicopter emergency medical services

description: Additional file 5. Performance measures for each individual model.
DOI: 10.6084/m9.figshare.26710562.v1
title: Additional file 5 of Development and internal validation of an algorithm for estimating mortality in patients encountered by physician-staffed helicopter emergency medical services

description: Additional file 5. Performance measures for each individual model.
DOI: 10.6084/m9.figshare.25678448
title: Additional file 1 of Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

description: Supplementary Table S1: Locations of populations of Akebia trifoliata sampled, sample sizes(n), the cpDNA haplotype and ITS haplotype frequency, haplotype distribution type, haplotype (gene) diversity (Hd) and nucleotide diversity (π × 10 − 3) of each population
DOI: 10.6084/m9.figshare.25678448.v1
title: Additional file 1 of Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

description: Supplementary Table S1: Locations of populations of Akebia trifoliata sampled, sample sizes(n), the cpDNA haplotype and ITS haplotype frequency, haplotype distribution type, haplotype (gene) diversity (Hd) and nucleotide diversity (π × 10 − 3) of each population
DOI: 10.6084/m9.figshare.25678710
title: Additional file 2 of Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

description: Supplementary Table S2: The taxa of Ranunculales used for estimating the crown group age of Akebia trifoliata
DOI: 10.6084/m9.figshare.25678710.v1
title: Additional file 2 of Conserved DNA sequence analysis reveals the phylogeography and evolutionary events of Akebia trifoliata in the region across the eastern edge of the Tibetan Plateau and subtropical China

description: Supplementary Table S2: The taxa of Ranunculales used for estimating the crown group age of Akebia trifoliata
DOI: 10.6084/m9.figshare.26710604
title: Additional file 4 of Blood cell parameters and risk of nonalcoholic fatty liver disease: a comprehensive Mendelian randomization study

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26710604.v1
title: Additional file 4 of Blood cell parameters and risk of nonalcoholic fatty liver disease: a comprehensive Mendelian randomization study

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.25678577
title: Additional file 1 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.25678577.v1
title: Additional file 1 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.25678721
title: Additional file 2 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25678721.v1
title: Additional file 2 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26710619
title: Additional file 3 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26710619.v1
title: Additional file 3 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26710622
title: Additional file 4 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26710622.v1
title: Additional file 4 of Shared genetic factors and causal association between chronic hepatitis C infection and diffuse large B cell lymphoma

description: Supplementary Material 4
DOI: 10.5281/zenodo.13338569
title: psammophis_sibilans_spades_01.fasta.gz

description: .
DOI: 10.5281/zenodo.13338570
title: psammophis_sibilans_spades_01.fasta.gz

description: .
DOI: 10.6084/m9.figshare.25678567
title: Additional file 1 of Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.25678567.v1
title: Additional file 1 of Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.25678730
title: Additional file 2 of Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.25678730.v1
title: Additional file 2 of Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26710655
title: Additional file 3 of Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

description: Supplementary Material 3