Find research datasets worth reusing

opencc-by-4.0Nov 2009View details →

Figure 18. A–J, Hydroides simplidentatus n in Descriptions of New Serpulid Polychaetes from the Kimberleys of Australia and Discussion of Australian and Indo-West Pacific Species of Spirobranchus and Superficially Similar Taxa

Figure 18. A–J, Hydroides simplidentatus n.sp., from holotype AM W21415. (A) anterior end of

opencc-by-4.0Apr 2020View details →

DUPS: Diachronic Usage Pair Similarity

The DUPS (Diachronic Usage Pair Similarity) dataset contains similarity judgements of English word usage pairs from different time periods, as described in the paper below.  The WUG version of the DUPS dataset (version 2.0.0) contains diachronic Word Usage Graphs constructed from the similarity judgements of English word usage pairs contained in DUPS. In a word usage graph, the usages of a word are represented as nodes connected by edges weighted according to (human-annotated) semantic proximity. A description of the data format as well as the code used to generate the graphs from DUPS can be found at <a href="https://www.ims.uni-stuttgart.de/data/wugs">https://www.ims.uni-stuttgart.de/data/wugs</a>. Both versions of the DUPS dataset can be downloaded from the Files section of this web page. Please cite this paper if you use any version of the dataset in your work: <blockquote> Mario Giulianelli, Marco Del Tredici, and Raquel Fernández. 2020. <a href="https://aclanthology.org/2020.acl-main.365/">Analysing Lexical Semantic Change with Contextualised Word Representations</a>. In Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics (ACL-2020). Association for Computational Linguistics. </blockquote>

opencc-by-4.0Sep 2021View details →

Datasets from the RecSys 2021 article "Cold Start Similar Artists Ranking with Gravity-Inspired Graph Autoencoders"

We publicly release : <ol> <li>the anonymized deezer_graph.csv and deezer_features.csv datasets</li> <li>the pre-trained node embedding vectors from all pre-trained models</li> </ol> described in the <a href="https://github.com/deezer/similar_artists_ranking/">deezer/similar_artists_ranking/</a> GitHub repository.

opencc-by-4.0Sep 2021View details →

Abundance decline in the avifauna of the European Union reveals global similarities in biodiversity change: Input datasets & species results

This archive contain the two input datasets of bird population estimates and trend estimates underpinning the journal article: Abundance decline in the avifauna of the European Union reveals global similarities in biodiversity change.  It also contains the species level results obtained from the Bayesian hierarchical model described in section 2.2.1 of the paper.

opencc-by-nc-4.0Dec 2016View details →

Sets of mutually similar public GitHub repositories (October 2016)

The format is JSON, the list of lists. Each list is the group of very similar repositories (Weighted Jaccard Similarity threshold 0.8~0.9).

opencc-zeroNov 2022View details →

Climatic similarity and genomic background shape the extent of parallel adaptation in Timema stick insects

Evolution can repeat itself, resulting in parallel adaptations in independent lineages occupying similar environments. Moreover, parallel evolution sometimes, but not always, uses the same genes. Two main hypotheses have been put forth to explain the probability and extent of parallel evolution. First, parallel evolution is more likely when shared ecologies result in similar patterns of natural selection in different taxa. Second, parallelism is more likely when genomes are similar, because of shared standing variation and similar mutational effects in closely related genomes. Here we combine ecological, genomic, experimental, and phenotypic data with Bayesian modeling and randomization tests to quantify the degree of parallelism and its relationship with ecology and genetics. Our results show that the extent to which genomic regions associated with climate are parallel among species of Timema stick insects is shaped collectively by shared ecology and genomic background. Specifically, the extent of genomic parallelism decays with divergence in climatic conditions (i.e., habitat or ecological similarity) and genomic similarity. Moreover, we find that climate-associated loci are likely subject to selection in a field experiment, overlap with genetic regions associated with cuticular hydrocarbon traits, and are not strongly shaped by introgression between species. Our findings shed light on when evolution is most expected to repeat itself.

opencc-zeroDec 2022View details →

Data and code for: Two dominant forms of multisite similarity decline – their origins and interpretation

Contains data and code for peer review of the draft manuscript 'Two dominant forms of multisite similarity decline – their origins and interpretation' in review at Ecology and Evolution (Manuscript ID: ECE-2022-10-01523). The data are a subset of the metaCommunity Ecology: Species, Traits, Environment and Space; "CESTES" database reported in A global database for metacommunity ecology, integrating species, traits, environment and space by A. Jeliazkov, D. Mijatovic, S. Chantepie, N. Andrew, R. Arlettaz, L. Barbaro, et al. Scientific Data 2020 Vol. 7 Issue 1 Pages e6. Data were downloaded from the Figshare repository: <a href="https://doi.org/10.6084/m9.figshare.c.4459637">https://doi.org/10.6084/m9.figshare.c.4459637</a> on 9 Nov 2021.

opencc-by-4.0Dec 2022View details →

Data from an eye-tracking based study of solution strategies in similar mathematical and physical tasks

Eye-tracking data: The .nas file "ET_data" contains the eyetracking project in software tobii studio with gaze data of all 131 participants. To open this project, the software tobii studio is required. ---------------------------------------- Interview data: All .txt files contain transcribed interview data in German language.    The files are labeled by subject number (e.g., P01 for the first participant) and the item for which the interview was recorded (e.g., M8). The files contain interview data of participants explaining their solution strategy for the given item. ---------------------------------------- Descriptive data: The file descriptive_data.csv contains the descriptive data of all participants (N=131). The column labels are as follows: code: code of participant, p01-p131     survey_period: survey period, summer_2021 / autumn_2020 / spring_2020 age: age of participant in years     grade: grade of participant     gen: gender, male (m) / female (f) / diverse (d)     ger_nat_speak: German native speaker, yes / no     repeater: Repeater of the last grade?, yes / no math_course: basic course (basic) or advanced course (advanced) in mathematics physics_course: basic course (basic) or advanced course (advanced) in physics grade_math: last grade in mathematics, 1-6         grade_phy: last grade mark in physics, 1-6         grade_ger: last report mark in german, 1-6         glasses: wearer of glasses?, yes / no motivation: four-point lickert scale, very motivated (1) to not motivated at all (0)     test: physics tasks before math tasks (pm) or vice versa (mp)     For each test item 2 columns are created. Example Item k1:     ac_k1: answer correctness of item k1, not correct and/or guessed (0), correct (1).         cf_k1: confidence of item k1, four-point lickert scale, very confident (1) to guessed (0)

opencc-by-4.0Aug 2022View details →

Long document similarity dataset, Wikipedia excerptions for movies collections

Movies-related articles extracted from Wikipedia. For all articles, the figures and tables have been filtered out, as well as the categories and "see also" sections. The article structure, and particularly the sub-titles and paragraphs are kept in these datasets   Movies The Wikipedia Movies dataset consists of 100,371 articles describing various movies. Each article may consist of text passages describing the plot, cast, production, reception, soundtrack, and more.

opencc-zeroDec 2022View details →

Similar vegetation-geomorphic disturbance feedbacks shape unstable glacier forelands across mountain regions

Glacier forelands are among the most rapidly changing landscapes on Earth. Stable ground is rare as geomorphic processes move sediments across large areas of glacier forelands for decades to centuries following glacier retreat. Yet, most ecological studies sample exclusively on stable terrain to fulfil chronosequence criteria, thus missing potential feedbacks between geomorphic disturbances and vegetation colonization. By influencing vegetation and soil development, such vegetation-geomorphic disturbance feedbacks could be crucial to understand glacier foreland ecosystem development in a changing climate. We surveyed vegetation and environmental properties, including geomorphic disturbance intensities, in 105 plots located on both stable and unstable moraine terrain in two geomorphologically active glacier forelands in New Zealand and Switzerland. Our plot data showed that geomorphic disturbance intensities changed permanently from high/moderate to low/stable when vegetation reached cover values around 40%. Around this cover value, species with response and effect traits adapted to geomorphic disturbances dominated. This suggests that such species can act as 'biogeomorphic' ecosystem engineers that stabilize ground through positive feedback loops. Across floristic regions, biogeomorphic ecosystem engineer traits creating ground stabilization, such as mat growth and association with mycorrhiza, are remarkably similar. Non-metric multidimensional scaling revealed a linked sequence of decreasing geomorphic disturbance intensities and changing species composition from pioneer to late successional species. We interpret this linked geomorphic disturbance-vegetation succession sequence as 'biogeomorphic succession', a common successional pathway in unstable river and coastal ecosystems across the world. Soil and vegetation development were related to this sequence, and only advanced once biogeomorphic ecosystem engineer species covered 40–45% of a plot, indicating a crucial role of biogeomorphic ecosystem engineer stabilization. Different topoclimatic conditions could explain variance in biogeomorphic succession timescales and ecosystem engineer root traits between the glacier forelands. As glacier foreland ground is widely unstable, we propose to consider glacier forelands as 'biogeomorphic ecosystems' in which ecosystem structure and function are shaped by geomorphic disturbances and their feedbacks with adapted plant species, similar to rivers and coasts.

opencc-by-4.0Dec 2022View details →

ATM: Black-box Test Case Minimization based on Test Code Similarity and Evolutionary Search – Replication Package

This is the replication package associated with the paper "ATM: Black-box Test Case Minimization based on Test Code Similarity and Evolutionary Search" accepted at the 45th IEEE/ACM International Conference on Software Engineering (ICSE 2023) – Technical Track. Cite this paper using the following: @inproceedings{pan2023atm,   title={ATM: Black-box Test Case Minimization based on Test Code Similarity and Evolutionary Search},   author={Pan, Rongqi and Ghaleb, Taher A. and Briand, Lionel},   booktitle={Proceedings of the 45th IEEE/ACM International Conference on Software Engineering},   year={2023},   pages={1--12} } Replication Package Contents: The replication package contains all the necessary data and code required to reproduce the results reported in the paper. We also provide the results for other minimization budgets, and detailed FDR, execution time, and statistical test results. In addition, we provide the data and code required to reproduce the results of baselines techniques: FAST-R and random minimization. Data: We provide in the Data directory the data used in our experiments, which is based on 16 projects from <a href="https://github.com/rjust/defects4j">Defects4J</a>, whose characteristics can be found in Data/subject_projects.csv. Code: We provide in the Code directory the code and scripts (Java, Python, and Bash) required to run the experiments and reproduce the results. Results: We provide in the Results directory the results for each technique independently, and also a summary of all results together for comparison purposes. The source code for this step is in the Code/ATM/CodeToAST directory. The source code for this step is in the Code/ATM/Similarity directory. _________________________________ ATM - Code to AST transformation: Requirements: * Eclipse IDE (we used 2021-12) * The libraries (the .jar files in the Code/ATM/CodeToAST/lib directory) Input: All zipped data files should be unzipped before running each step. * Data/test_suites/all_test_cases.zip → Data/test_suites/all_test_cases * Data/test_suites/changed_test_cases.zip → Data/test_suites/changed_test_cases * Data/test_suites/relevant_test_cases.zip → Data/test_suites/relevant_test_cases Output: * Data/ATM/ASTs/all_test_cases * Data/ATM/ASTs/changed_test_cases Running the experiment: To generate ASTS for all test cases in the project test suites, the Code/ATM/CodeToAST/src/CodeToAST.java file should be compiled and run using the Eclipse IDE by including all the required .jar files in the Code/ATM/CodeToAST/lib directory as part of the classpath. A bash script is provided along with a pre-generated .jar file in the Code/ATM/CodeToAST/bin directory to run this step, as follows: <pre><code class="language-bash">cd Code/ATM/CodeToAST bash transform_code_to_ast.sh</code></pre> Each test file in the Data/test_suites/all_test_cases and Data/test_suites/changed_test_cases directories is parsed to generate a corresponding AST for each test case method (saved in an XML format in Data/ATM/ASTs/all_test_cases and Data/ATM/ASTs/changed_test_cases for each project version) _________________________________ ATM - Similarity Measurement: Requirements: * Eclipse IDE (we used 2021-12) * The libraries (the .jar files in the Code/ATM/Similarity/lib directory) Input: * Data/test_suites/all_test_cases * Data/test_suites/changed_test_cases Output: * Data/ATM/similarity_measurements Running the experiment: To measure the similarity between each pair of test cases, the Code/ATM/Similarity/src/SimilarityMeasurement.java file should be compiled and run using the Eclipse IDE by including all the required .jar files in the Code/ATM/Similarity/lib directory as part of the classpath. A bash script is provided along with a pre-generated .jar file in the Code/ATM/Similarity/bin directory to run this step, as follows: <pre><code class="language-bash">cd Code/ATM/Similarity bash measure_similarity.sh</code></pre> ASTs of each project in the Data/ATM/ASTs/all_test_cases and Data/ATM/ASTs/changed_test_cases directories are parsed to create pairs of ASTs containing one test case from the Data/ATM/ASTs/all_test_cases directory with another test case from the Data/ATM/ASTs/changed_test_cases directory (redundant pairs are discarded). Then, all similarity measurements are saved in the Data/ATM/similarity_measurements.zip file. __________________________________________ Search-based Minimization Algorithms: The source code for this step is in the Code/ATM/Search directory. Requirements: To run this step, Python 3 is required (we used Python 3.10). Also, the libraries in the Code/AMT/Search/requirements.txt file should be installed, as follows: <pre><code class="language-bash">cd Code/ATM/Search pip install -r requirements.txt</code></pre> Input: * Data/ATM/similarity_measurements Output: * Results/ATM/minimization_results Running the experiment: To minimize the test suites in our dataset, the following bash script should be executed: <pre><code class="language-bash">bash minimize.sh</code></pre> All similarity measurements are parsed for each version of the projects, independently. Each version is run 10 times using three minimization budgets (25%, 50%, and 75%). Genetic Algorithm (GA) is run using four similarity measures, namely top-down, bottom-up, combined, and tree edit distance. NSGA-II is run using two combinations of similarity measures: top-down & bottom-up and combined & tree edit distance. The minimization results are generated in the Results/ATM/minimization_results directory. __________________ Evaluate results: To evaluate and summarize the minimization results, run the following: <pre><code class="language-bash">cd Code/ATM/Evaluation bash evaluate.sh</code></pre> This will generate summarized FDR and execution time results (per-project and per-version) for each minimization budget, which can all be found in Results/ATM. In this replication package, we provide the final, merged FDR with execution time results. _________________________________ Running FAST-R experiments ATM was compared to <a href="https://github.com/ICSE19-FAST-R/FAST-R">FAST-R</a>, a state-of-the-art baseline, which is a set of test case minimization techniques called: FAST++, FAST-CS, FAST-pw, and FAST-all, which we adapted to our data and experimental setup. Requirements: To run this step, Python 3.7 is required. Also, the libraries in the Code/FAST-R/requirements.txt file should be installed, as follows: <pre><code class="language-bash">cd Code/FAST-R pip install -r requirements.txt</code></pre> Input: * Data/FAST-R/test_methods * Data/FAST-R/test_classes Output: * Results/FAST-R/test_methods/FDR_and_Exec_Time_Results_[budget]%_budget.csv * Results/FAST-R/test_classes/FDR_and_Exec_Time_Results_[budget]%_budget.csv To run FAST-R experiments, the following bash script should be executed: <pre><code class="language-bash">bash fast_r.sh test_methods #method level bash fast_r.sh test_classes #class level</code></pre> Results are generated in .csv files for each budget. For example, for the 50% budget, results are saved in FDR_and_Exec_Time_Results_50%_budget.csv in the Results/FAST-R/test_methods and Results/FAST-R/test_classes directories. _________________________________ Running the random minimization experiments ATM was also compared to random minimization as a standard baseline. Requirements: To run this step, Python 3 is required (we used Python 3.10). Also, the libraries in the Code/RandomMinimization/requirements.txt file should be installed, as follows: <pre><code class="language-bash">cd Code/RandomMinimization pip install -r requirements.txt</code></pre> Input: N/A Output: * Results/RandomMinimization/FDR_and_Exec_Time_Results_[budget]%_budget.csv To run the random selection experiments, the following bash script should be executed: <pre><code class="language-bash">bash random_minimization.sh</code></pre> Results are generated in .csv files for each budget. For example, for the 50% budget, results are saved in FDR_and_Exec_Time_Results_50%_budget.csv in the Results/RandomMinimization directory.

opencc-by-4.0Dec 2022View details →

Supplementary Materials for "An Automated Detection of Confusing Variable Pairs with Highly Similar Compound Names in Java and Python Programs"

This is a dataset contains the data collected through the empirical study in our paper "An Automated Detection of Confusing Variable Pairs with Highly Similar Compound Names in Java and Python Programs."

opencc-zeroJan 2023View details →

Data for: Male-specific nocturnal song functions similar to day song in a diurnal bird species

Historically, birdsong research has been biased towards song of male birds at dawn and during the day, even though some diurnal birds sing at night. To address this gap, we studied how song in the willie wagtail, Rhipidura leucophrys—a diurnal species with prolific male-specific nocturnal song during the breeding season—varies with time of day, breeding status, and simulated intrusions. We recorded male nocturnal and dawn song over three breeding seasons and examined how this related to fertile and non-fertile breeding stages of females. To test whether song functions for territory defence, we simulated territorial intrusion experimentally in both sexes with daytime and nighttime playback of male and female song. To test whether nocturnal song could function for mate guarding or post-pairing mate attraction, we describe the mating system of willie wagtails using molecular genetic methods. We showed that both nocturnal and daytime song of male willie wagtails has roles in mate attraction and territory defence, while daytime song by females functioned primarily for territorial defence. Males increased song behaviour during fertile periods of resident females, suggesting possible roles in mate stimulation and mate guarding. Males and females responded similarly to simulated daytime intrusions and no differences were seen in male responses dependent on the time of day. We found 10%-14% of offspring were fathered by extra-pair males, suggesting song may also function for mate guarding and post-pairing mate attraction. In a species with small repertoires and simple songs like the willie wagtail, differences between males in overall song output achieved through nocturnal singing may be important in mate attraction and territory defence.

opencc-zeroJan 2023View details →

Simulated trapping and trawling exert similar selection on fish morphology

Commercial fishery harvest can influence the evolution of wild fish populations. Our knowledge of selection on morphology is however limited, with most previous studies focusing on body size, age and maturation. Within species, variation in morphology can influence locomotor ability, possibly making some individuals more vulnerable to capture by fishing gears. Additionally, selection on morphology has the potential to influence other foraging, behavioural, and life-history related traits. Here we carried out simulated fishing using two types of gears: a trawl (active gear) and trap (a passive gear), to assess morphological trait-based selection in relation to capture vulnerability. Using geometric morphometrics, we assessed differences in shape between high and low vulnerability fish, showing that high vulnerability individuals display shallower body shapes regardless of gear type. For trawling, low vulnerability fish displayed morphological characteristics that may be associated with higher burst-swimming, including a larger caudal region and narrower head, similar to evolutionary responses seen in fish populations responding to natural predation. Taken together, these results suggest that divergent selection can lead to phenotypic differences in harvested fish populations.

Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase

We have provided all the necessary files, outputs, as well as the ReadMe file for this work to be redone.

Raw data and scripts for "Non-uniform sampling of similar NMR spectra and its application to studies of the interaction between alpha-synuclein and liposomes" by Shchukina et al.

A series of 15N HSQC spectra of aSyn at temperatures 15,17..43C acquired with and without the addition of POPG-based liposomes. The spectra can be processed with sparse undersampling at various levels (scripts are provided).

Data set of simulated rimed aggregates for "A riming-dependent parameterization of scattering by snowflakes using the self-similar Rayleigh-Gans approximation"

Simulated rimed aggregates generated with https://github.com/jleinonen/aggregation in setting "aggregation followed by riming". Aggregates were built from between 10 to 700 monomer crystals of columns, dendrites, needles, plates or rosettes with mean sizes of 100 or 200 micrometer. Then they were exposed to ELWP = 2.0 kg m⁻². Monomer crystals are composed of cubical elements with resolution 20 micrometer. Frozen rime droplets are also represented by 20 micrometer cubes. The data set contains folders with evolution (evol) and shape files for each monomer crystal type. For each particle one evolution and one corresponding shape file exists. The evolution (evol) file contains particle mass, rime mass, area, size, fall speed (Heymsfield&Westbrook, 2010), fall speed (Khvorostyanov&Curry, 2005) for each step during the aggregation and riming process. The corresponding shape file contains the x,y,z positions of the cubical elements that compose the particle for each step. For further documentation see readme.

opencc-zeroMar 2023View details →

Behavioral responses to a series of similar but distinct novel objects in house sparrows

Generalization refers to the process by which animals assign different stimuli into cognitive categories based on their similarity/dissimilarity to previously experienced stimuli. Stimuli which strongly deviate from previous experience may be avoided due to their novelty (i.e., neophobia), while stimuli which are sufficiently similar to a known/recognized cue may elicit the same response as that cue (i.e., generalization). While generalization has been widely researched, few studies have examined among-individual variance in its expression. Our study quantified among-individual variation in neophobia and generalization in house sparrows (Passer domesticus) by placing a series of different objects next to each subject's food source on successive days and measuring the subject's latency to approach the food source in the presence vs. absence of each object. Similarly to previous work, we found that house sparrows are neophobic on average and exhibit significant among-individual variance in neophobia. More interestingly, we found that the neophobic response declined across presentations of different novel objects. This implies that the sparrows generalized some aspect(s) of the objects. We also found significant among-individual variance in the rate at which approach latency changed across this series, possibly reflecting individual differences in propensity to generalize. These results raise new questions about how neophobia, habituation, and generalization are linked and about the potential for selection to act on these traits under different ecological conditions.

Automatically Answering Developer Questions on Discord with Similar Conversations from the Past

Replication Package for "Automatically Answering Developer Questions on Discord with  Similar Conversations from the Past"