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159 results for “code prediction”
Predicting Code Comprehension: A Novel Approach to Align Human Gaze with Code Using Deep Neural Networks
<p><strong>Checkout our Github-Repo for more information, issues, and pull requests: </strong></p> <p><a href="https://github.com/Taremeh/predicting-code-comprehension-eye-tracking/">https://github.com/Taremeh/predicting-code-comprehension-eye-tracking/</a></p> <p> </p> <p>Dataset and Replication Package for our paper "Predicting Code Comprehension: A Novel Approach to Align Human Gaze with Code Using Deep Neural Networks"</p>
Data and code for testing leaf temperture predictions with NicheMapR
Open the record for dataset details and reuse information.
Predicting and containing epidemic risk using on-line friendship networks - data and code
<p>Contains code and data I used for the paper</p>
Model codes and data for ``A control volume finite element model for predicting the morphology of cohesive-frictional debris flow deposits"
<p>The code and the dataset can be read/run by using Matlab. The description is as follows:</p> <p>1. Dataset (field_data) includes transect data of three field debris flow deposits from Coussot et al. (1996). The data can be read and calibrated with the analytical solution by the code field_calibration.m.</p> <p>2. Dataset (data_T01-T04, T11-T15_DT) includes experimental fan topography data, calibrated parameters, and simulation outputs. </p> <p>3. Two calibration codes are used for the model parameter calibrations of the two sets of experiments.</p> <p>4. Function aggradation_DT.m is the CVFEM model for simulating fan morphology. Use CVFEM_exp_simulation.m code to run simulations for the experiments.</p>
Efficient Probabilistic Prediction and Uncertainty Quantification of Tropical Cyclone-driven Storm Tides and Inundation: Model Data and Analysis Code
<p>This repository contains model data and analysis codes related to the manuscript entitled "Efficient Probabilistic Prediction and Uncertainty Quantification of Tropical Cyclone-driven Storm Tides and Inundation", as follows:</p> <ol> <li>Model data are maximum water surface elevations of ensemble 48-hr forecast ADCIRC model simulations for three historical US landfalling hurricanes: 2017 Irma, 2018 Florence, and 2020 Laura. These are located in the "NameYYYY_Results.tar" archive files as "maxele.63.nc" files. Also included in the tar files are the hurricane forecast track files in Automated Tropical Cyclone Forecasting (ATCF) system format (*.22) and the error variable parameters (*.json) for each forecast. </li> <li>Model data of best-track runs for the 2017 Irma, 2018 Florence, and 2020 Laura hurricanes, and astronomical tide-only runs for the corresponding time periods are located in the "NameYYYY_besttrack+tides.tar" archive files. Both the maximum water surface elevations "maxele.63.nc" and the time series of water surface elevations "fort.63.nc" are included. </li> <li>ADCIRC input mesh (*.14) and mesh property files (*.13) are included in "ADCIRC_mesh_files.zip".</li> <li>Joint Karhunen-Loeve Polynomial Chaos (KL-PC) analysis python scripts with and without considering inundation are located in "klpc_analysis_scripts.zip". Requires <a href="https://github.com/noaa-ocs-modeling/EnsemblePerturbation">EnsemblePerturbation</a> python toolbox. </li> <li>Python scripts for analyzing and plotting the KL-PC results (Figures 6-14 and Table 1 in the manuscript) are located in "results_plotting_scripts.zip". Requires <a href="https://github.com/noaa-ocs-modeling/EnsemblePerturbation">EnsemblePerturbation</a> python toolbox. </li> </ol>
Supplemental Material for Predictive Reranking using Code Smells for Information Retrieval Fault Localization
<pre># Predictive Reranking using Code Smells for Information Retrieval Fault Localization This repository constitutes the supplementary material, data, and source code for the paper "Predictive Reranking using Code Smells for Information Retrieval Fault Localization", by Thomas Hirsch and Birgit Hofer, 2023. Source code and results are also made available on GitHub: https://github.com/AmadeusBugProject/PredictiveRerankingUsingCodeSmellsForIRFL </pre> <pre>## Preliminaries ### Python environment - python=3.8 - pandas - numpy - joblib - scikit-learn==1.0.2 - keras - tensorflow - nltk - sentence-transformers - matplotlib - seaborn Conda files are located in the root directory of the repository, [conda_from_history.yml](<em>conda_from_history.yml</em>). ### Datasets The [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) dataset was used in our evaluation. All data necessary for our machine learning and localization experiments is included in this repository. However, if the data is to be re-imported and recalculated directly from Bench4BL: Bench4BL has to be downloaded and paths to the benchmark root set accordingly in [paths.py](<em>paths.py</em>). BugLocator, BRTracer, and BLIA have to be run on the Bench4BL dataset using the scripting provided by the benchmark. PMD has to be installed in version 6.45.0 and path to PMD set accordingly in [paths.py](<em>paths.py</em>). # Structure of this repository ## General utility functions - [constants.py](<em>constants.py</em>) Contains parameters for the NN model, and other parameters. - [paths.py](<em>paths.py</em>) Contains paths to external datasources and tools, e.g. Bench4BL and PMD. - [utils/bench4bl_utils.py](<em>utils/bench4bl_utils.py</em>) Helper functions for resolving paths to Bench4BL benchmark. - [utils/dataset_utils.py](<em>utils/dataset_utils.py</em>) Helper functions for loading datasets and performing dataset splits. - [utils/Logger.py](<em>utils/Logger.py</em>) Logging. - [utils/nn_classifier.py](<em>utils/nn_classifier.py</em>) NN classifier model. - [utils/scoring_utils.py](<em>utils/scoring_utils.py</em>) Metrics. - [utils/stats_utils.py](<em>utils/stats_utils.py</em>) Wrapper methods for statistical tests. ## Experiment ### Dataset setup and preparation The following scripts are responsible to create, import, and set up data that is used in our experiments. The produced data is already part of this repository, the execution of these scripts is therefore only necessary when data is to be re-imported from the Bench4BL repository. - [a00_pmd_bench4bl.py](<em>a00_pmd_bench4bl.py</em>) Runs PMD on all projects and versions contained in the Bench4BL dataset. The utilized ruleset is defined in [all_java_ruleset.xml](<em>all_java_ruleset.xml</em>). Results are stored in [pmd_results](<em>pmd_results</em>). - [a01_vectorize_pmd.py](<em>a01_vectorize_pmd.py</em>) Creates csv vectors from PMD outputs. - [a02_cloc_bench4bl.py](<em>a02_cloc_bench4bl.py</em>) Runs cloc on all projects and versions contained in the Bench4BL dataset. Only Java files are considered. Results are stored in [cloc_results](<em>cloc_results</em>). - [a02_pmd_usage_in_bench4bl_projects.py](<em>a02_pmd_usage_in_bench4bl_projects.py</em>) Searches for occurrence of PMD in the build files of all projects and versions contained in the Bench4BL dataset. Results are stored in [pmd_usage_in_bench4bl_projects](<em>pmd_usage_in_bench4bl_projects</em>). - [a03_import_bugs_from_bench4bl.py](<em>a03_import_bugs_from_bench4bl.py</em>) Imports textual bug reports and corresponding fixed files ground truth from Bench4BL. Results are stored in [bench4bl_summary](<em>bench4bl_summary</em>). - [a04_normalize_smells_by_loc.py](<em>a04_normalize_smells_by_loc.py</em>) Normalizes the smell vectors for each file with its LOC count. Results are stored in [pmd_results](<em>pmd_results</em>). - [a05_bench4bl_file_features.py](<em>a05_bench4bl_file_features.py</em>) Creates feature vectors for each bug report from PMD smells. Results are stored in [bug_smell_vectors](<em>bug_smell_vectors</em>). - [a05_bench4bl_ranking_results.py](<em>a05_bench4bl_ranking_results.py</em>) Imports the results of BugLocator, BRTracer, and BLIA from the Bench4BL benchmark. Results are stored in [bench4bl_localization_results](<em>bench4bl_localization_results</em>). - [a09_bench4bl_stackoverflow_mpnet.py](<em>a09_bench4bl_stackoverflow_mpnet.py</em>) Creates document embeddings for all textual bug reports using the [stackoverflow_mpnet-base](<em>https://huggingface.co/flax-sentence-embeddings/stackoverflow_mpnet-base</em>) model. Results are stored in [stackoverflow_mpnet_embeddings](<em>stackoverflow_mpnet_embeddings</em>). ### Preliminary experiments and dataset splitting The following scripts perform data set splitting, and the preliminary experiments used for feature selection as discussed in Section VI of the paper. - [b00_analyze_most_promising_smells.py](<em>b00_analyze_most_promising_smells.py</em>) Assumes a perfect smell oracle (by using the known smells of the ground truth files) and applies it to rerank the IRFL tools outputs on the Classification Training Set (the older half of versions in the dataset). Then evaluates the achievable localization performance increase for each smell group. Results are stored in [h_analyze_most_promising_smells](<em>h_analyze_most_promising_smells</em>). - [c00_make_dataset_splits_bootstrap.py](<em>c00_make_dataset_splits_bootstrap.py</em>) Performs dataset splitting. Splits are performed on a temporal ordering of versions of each contained software project. Data is greedily split into 50/25/25, resulting in a Classification training set (used for NN model training), a ranking training set (used to estimate weights for linear combination of smell distance and IRFL suspicousness scores), and a test set (used for evaluating the localization performance achievable by our pipeline). Bootstrapping is applied by resampling fractions of 0.8, 20 times, resulting in 20 sets of the three splits to be used in the following eperiments. Datasets are stored in [p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap](<em>p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap</em>) for the full Bench4BL dataset, for the single project experiments please refer to p_FINAL_CAMEL, p_FINAL_HBASE, and p_FINAL_ROO accordingly. - [c01_full_dataset_stats.py](<em>c01_full_dataset_stats.py</em>) Calculates various statistics on the created datasets. Results are stored in [px_summary_dataset](<em>px_summary_dataset</em>). - [d00_model_for_smell_classification_performance_all_groups_bootstrap.py](<em>d00_model_for_smell_classification_performance_all_groups_bootstrap.py</em>) Trains a NN model on the Classification data set and evaluates its classification performance on the Ranking training set. This is performed for all 20 bootstrap iterations, the resulting data is stored in [p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap](<em>p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap</em>) for the full Bench4BL dataset, for the single project experiments please refer to p_FINAL_CAMEL, p_FINAL_HBASE, and p_FINAL_ROO accordingly. - [d01_classification_performance_evaluation_for_feature_selection_preliminariy_all_smell_groups.py](<em>d01_classification_performance_evaluation_for_feature_selection_preliminariy_all_smell_groups.py</em>) Creates summary and bootstrap statistics from the previous step. Results are stored in [p_FINAL_Bench4BL/p_summary_classification](<em>p_FINAL_Bench4BL/p_summary_classification</em>) for the full Bench4BL dataset. ### Localization experiments The following scripts perform our actual localization experiments. These scripts are applied to bootstrapped dataset splits. Results are stored in [p_FINAL_Bench4BL](<em>p_FINAL_Bench4BL</em>) for the full Bench4BL dataset, for the single project experiments please refer to p_FINAL_CAMEL, p_FINAL_HBASE, and p_FINAL_ROO accordingly. For a detailed experiment setup we refer to our paper. - [e01_model_for_localization_bootstrap.py](<em>e01_model_for_localization_bootstrap.py</em>) Trains NN models for smell classification and performs predictions on the corresponding test sets. Results are stored in [p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap](<em>p_FINAL_Bench4BL/p_model_for_smell_classification_bootstrap</em>). - [e02_ranking_training_bootstrap.py](<em>e02_ranking_training_bootstrap.py</em>) Performs reranking of the Ranking training set based on predicted smells by the model created in the previous step. Score combination is performed by linear combination of IRFL tools suspicousness scores and smell distances calculated based on our predictions. Results are stored in [p_FINAL_Bench4BL/p_ranking_training_bootstrap](<em>p_FINAL_Bench4BL/p_ranking_training_bootstrap</em>). - [e03_get_best_weigths_per_project_bootstrap.py](<em>e03_get_best_weigths_per_project_bootstrap.py</em>) Evaluates the outputs of the previous steps in order to pick the best weights for each project and IRFL tool. Results are stored in [p_FINAL_Bench4BL/p_ranking_training_bootstrap](<em>p_FINAL_Bench4BL/p_ranking_training_bootstrap</em>). - [e04_ranking_test_project_wise_bootstrap.py](<em>e04_ranking_test_project_wise_bootstrap.py</em>) Uses predictions of the final NN model and the weights obtained from the previous step to perform rerankings on the Test set. Results are stored in [p_FINAL_Bench4BL/p_ranking_test_proejct_wise_bootstrap](<em>p_FINAL_Bench4BL/p_ranking_test_proejct_wise_bootstrap</em>). ### Result collection and evaluation The following scripts calculate final scores and statistics from the 20 bootstrap iterations of the previous block of scripts. - [f00_bootstrap_summary_compare_map_and_ttest.py](<em>f00_bootstrap_summary_compare_map_and_ttest.py</em>) Calculates localization performance using the MAP metric and performs statistical tests. Results are stored in [p_FINAL_Bench4BL/p_summary_bootstrap](<em>p_FINAL_Bench4BL/p_summary_bootstrap</em>). - [f01_boostrap_summary_compare_classification_performance.py](<em>f01_boostrap_summary_compare_classification_performance.py</em>) Calculates classifier performance of our final model. Results are stored in [p_FINAL_Bench4BL/p_summary_bootstrap](<em>p_FINAL_Bench4BL/p_summary_bootstrap</em>). - [f02_bootstrap_summary_model_classification_performance_eval_test_set_for_all_projects.py](<em>f02_bootstrap_summary_model_classification_performance_eval_test_set_for_all_projects.py</em>) Calculates classifier performance and project wise classifier performance of our final model. Results are stored in [p_FINAL_Bench4BL/p_summary_classification_test_set](<em>p_FINAL_Bench4BL/p_summary_classification_test_set</em>). ### Further analysis The following scripts collect statistics and results to create latex tables and additional analysis used in our paper. - [g00_project_wise_perf_stats.py](<em>g00_project_wise_perf_stats.py</em>) Creates overview latex table comparing the Bench4BL and single project trained pipelines. Results are stored in [px_summary_performance](<em>px_summary_performance</em>). - [g01_project_multiple_file_smell_distances.py](<em>g01_project_multiple_file_smell_distances.py</em>) Analyses smell distances within each bug's ground truth files. Results are stored in [px_summary_dataset](<em>px_summary_dataset</em>). - [g02_performance_correlation_analysis.py](<em>g02_performance_correlation_analysis.py</em>) Performs correlation analysis of our pipeline's MAP localization performance, classification performance, and smell distance measures from previous step. Results are stored in [p_FINAL_Bench4BL/p_summary_correlations](<em>p_FINAL_Bench4BL/p_summary_correlations</em>) for the full Bench4BL dataset. ## Results - [pmd_catalogue/all_smells.json](<em>pmd_catalogue/all_smells.json</em>) lists all PMD smells and associated groups that occur in the dataset. - [px_summary_dataset](<em>px_summary_dataset</em>) contains statistics and information about the utilized dataset. Results for preliminary experiments for feature selection: - [h_analyze_most_promising_smells](<em>h_analyze_most_promising_smells</em>) contains the results of our preliminary experiment into each smell group's information content towards localization. - [p_FINAL_Bench4BL/p_summary_classification](<em>p_FINAL_Bench4BL/p_summary_classification</em>) contains the results of our preliminary experiments into the classifiability of smell groups from textual bug reports. Results of our localization eperiments: - [p_FINAL_Bench4BL/p_summary_bootstrap](<em>p_FINAL_Bench4BL/p_summary_bootstrap</em>) contains the results of our localization experiments, project wise MAP performance summary can be found in [p_FINAL_Bench4BL/p_summary_bootstrap/project_scores_tool_wise_others.tex](<em>p_FINAL_Bench4BL/p_summary_bootstrap/project_scores_tool_wise_others.tex</em>). - [p_FINAL_Bench4BL/p_summary_classification_test_set](<em>p_FINAL_Bench4BL/p_summary_classification_test_set</em>) contains the results of our classification performance analysis of the predictions used in localization. A project wise classification performance summary can be found in [p_FINAL_Bench4BL/p_summary_classification_test_set/macro_average_classification_performances_per_projectother.tex](<em>p_FINAL_Bench4BL/p_summary_classification_test_set/macro_average_classification_performances_per_projectother.tex</em>) ## Licence All code and results are licensed under [AGPL v3](<em>https://www.gnu.org/licenses/agpl-3.0.html.en</em>), according to LICENSE file. Other licences may apply for some tools and datasets contained in this repo: [cloc-1.92.pl](<em>https://github.com/AlDanial/cloc</em>) under [GPL v2](<em>https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html</em>), and data originating from [Bench4BL](<em>https://github.com/exatoa/Bench4BL</em>) under [CCA 4.0](<em>https://creativecommons.org/licenses/by/4.0/</em>). </pre>
A Feasibility Study to Improve Colorectal Cancer Screening Among Racially Diverse Zip Codes in a Persistent Poverty County Using Navigation and Machine Learning Predictive Algorithms
ClinicalTrials.gov study NCT05383976. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Code from: Realistic genetic architecture enables organismal adaptation as predicted under the folk definition of inclusive fitness
Open the record for dataset details and reuse information.
Data and code from: Accounting for species interactions is necessary for predicting how arctic arthropod communities respond to climate change
Open the record for dataset details and reuse information.
The Stat3/GR interaction code: predictive value of direct/indirect DNA recruitment for transcription outcome
GEO Series GSE37235. Mus musculus. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Prediction of novel non-coding RNAs relevant for the growth of Pseudomonas putida in a bioreactor
GEO Series GSE129947. Pseudomonas putida. 36 samples. Type: Expression profiling by high throughput sequencing.
tRNA-derived small non-coding RNAs (tDRs) as novel predictive biomarkers for trastuzumab-resistant breast cancer.
GEO Series GSE107473. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
Data & Code for Using Artificial Intelligence to Predict the Financial Impact of Climate Transition Risks Within Organisations
<p>This repository contains the code used for the article</p> <p>"Pérez-Pérez, Juan F., Bonet, Isis, Sánchez-Pinzón, María Solange, Caraffini, Fabio, Lochmuller, Christian, Using Artificial Intelligence to Predict the Financial Impact of Climate Transition Risks Within Organisations, <em>International Journal of Intelligent Systems</em>, 2024, 3334263, 21 pages, 2024. <a href="https://doi.org/10.1155/int/3334263">https://doi.org/10.1155/int/3334263</a>"</p> <p> including the code for generating data sets. Shall you use this code and data, please acknowledge the published article and this repository.</p>
Code and data for GRL paper: The role of soil moisture in predicting photosynthesis and evapotranspiration
<p>The scripts used for collecting and processing raw data for the study are included as well as the datasets after processing which are used to train the models in the study. The results are also included. </p>
Investigating the Plasticity of Human Predictive Coding Through Neuromodulation
ClinicalTrials.gov study NCT06374433. IPD Sharing: NO. Countries: 1. Publications: 0.
Second Follow-up Study of COPD Patients and Healthy Controls for Evaluation of Predictive Non-coding RNA Biomarkers
ClinicalTrials.gov study NCT04895124. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Follow-up-study of COPD Patients and Healthy Controls for Evaluation of Predictive Non-coding RNA Biomarkers
ClinicalTrials.gov study NCT02522026. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Voice Analysis Using the LPC (Linear Predictive Coding)Method for the Prediction of Aspiration
ClinicalTrials.gov study NCT01981239. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Predominant TRUB1-dependent pseudouridylation of mammalian mRNA via a predictable and conserved code
GEO Series GSE90851. Homo sapiens. 27 samples. Type: Other.
Down-regulation of long non-coding RNA TINCR induces cell dedifferentiation and predicts progression in oral squamous cell carcinoma
GEO Series GSE160042. Homo sapiens. 20 samples. Type: Expression profiling by array; Non-coding RNA profiling by array.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.