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3,739 results for “RePAIR”
PRISM Proof Repair Dataset
<p>This is the first release of a sample of the PRISM Coq proof repair dataset. We will update with later versions when repair mining is complete and goes through DARPA's approval process. The initial release (data and limitations) is documented here: https://docs.google.com/document/d/19A6YMm1glkcd7ze8wi87pxmUgogA3Mitny7mDl-192c/edit?usp=sharing. It includes about 200 unique changes. Later versions will include more data and better line number information, and will be deduplicated.</p>
2 patch AVSD repair, 96th AATS
<p>2 Patch AVSD Repair Talk Delivered at 96th AATS Baltimore, Dr. K S IYER, FORTIS HEART INSTITUTE</p>
Early Clinical Outcomes of High-Purity Type I Collagen as a Biologic Reinforcement in Selected Hernia Repair Scenarios
ClinicalTrials.gov study NCT07360691. IPD Sharing: YES. Countries: 1. Publications: 7.
Evaluation of High-Purity Type I Collagen Biologic Wrap to Improve Function After Extensor Tendon Repair of the Hand
ClinicalTrials.gov study NCT07335653. IPD Sharing: YES. Countries: 1. Publications: 7.
Data from: Double-strand break repair pathways differentially affect processing and transduction by dual AAV vectors
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Data from: Seasonal brain regeneration and chromosome instability are linked to selection on DNA repair in Sorex araneus
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[Dataset] ERRATUM: Repairing Broken Locators in Web Test Scripts using Tree Matching
<p>Dataset and evaluation for the paper "ERRATUM: Repairing Broken Locators in Web Test Scripts using Tree Matching".</p> <p>Two datasets were used:</p> <p>- The wayback dataset (wayback_dataset.json)</p> <p>- The mutation dataset (mutation_dataset.json)</p> <p>Each one was used to evaluate both state-of-the-art locator repair solution WATER and our novel tree matching-based approach.<br> The results of this evaluation presented in our paper are in the following files:</p> <p>- eval_mutation.json</p> <p>- eval_wayback.json</p>
How to repair a solar module
<p>First video-tutorial shooting at Universidade Evora of an educational series on how to proceed with reparation of solar Photovoltaic modules.</p>
The dataset of the APSEC'20 paper titled "Understanding the Non-Repairability Factors of Automated Program Repair Techniques"
<p>The file <strong>ExecutionLogs.zip</strong> includes all execution logs that we take into consideration in the study. </p> <p>The file <strong>Exception_Statistics.xlsx</strong> includes the distribution of each type of exception in our study. </p> <p> </p> <p>All logs are located in directories that are named by fault localization strategy and the corresponding automated program repair tool. Specifically, in the directories of <strong>ExecutionLogs</strong> there are four sub-directories: <em>GZ-0.1</em>, <em>GZ-1.7</em>, <em>No_FL_Required</em>, and <em>Perfect_FL</em>.</p> <ul> <li><em>GZ-0.1</em> means fault localization strategy with GZoltar-v0.1 (from the <a href="https://dl.acm.org/doi/10.1145/3338906.3338911">FSE19</a> paper).</li> <li><em>GZ-1.7</em> means fault localization strategy with GZoltar-v1.7 (from the <a href="https://zenodo.org/record/3678960#.XwcRNIgzaUk">ICSE20</a> paper).</li> <li><em>Perfect_FL</em> means directly feeding ground-truth bug positions to APR tools (from the <a href="https://zenodo.org/record/3678960#.XwcRNIgzaUk">ICSE20</a> paper).</li> <li><em>No_FL_Required</em> means that the tool does not require fault localization process (from <a href="https://dl.acm.org/doi/10.1145/3338906.3338911">FSE19</a> paper).</li> </ul> <p>For example, the log of bug <em>Chart-1</em> generated by <em>Cardumen</em> with <em>Gzoltar-0.1</em> are stored in the directory <strong>GZ-0.1/Chart/1/Cardumen/</strong>. </p> <p> </p> <p>In the file <strong>Exception_Statistics.xlsx</strong>, we demonstrate the detailed distribution of each type of exception.</p> <p><strong>Format of the content</strong></p> <p>We use format like <em>Fault_localization_strategy-project_id-version_id-tool_name</em> to represent each log.</p> <p>Take <em>GZ0.1-Chart-1-Cardumen</em> as an example, this log is generated by <em>Cardumen</em> on bug <em>Chart-1</em> with fault localization strategy <em>GZoltar-v0.1</em>.</p> <p><strong>About compliance level</strong></p> <p>Take the log of <em>GZ0.1-Mockito-1-Cardumen</em> as an example. We can get the compliance level from the parameter <em>javacompliancelevel</em>. For example, 4 corresponds to java 1.4, 5 corresponds to java 1.5 and so on. Hence, we can know what compliance level authors used during the original experiment.</p> <pre><code class="language-java">time java -Xmx4048m -cp /home/tdurieux/RepairThemAll/script/../libs/jtestex7.jar:/home/tdurieux/RepairThemAll/script/../repair_tools/astor.jar fr.inria.main.evolution.AstorMain \ -mode cardumen \ -location . \ -id Chart-1 \ -failing org.jfree.chart.renderer.category.junit.AbstractCategoryItemRendererTests \ -jvm4testexecution /home/tdurieux/openjdk-1.7.0/bin/ \ -jvm4evosuitetestexecution /home/tdurieux/openjdk-1.7.0/bin/ \ -maxgen 1000000 \ -maxtime 120 \ -stopfirst true \ -seed 0 \ -scope local \ -population 1 \ -javacompliancelevel 4 \ ......</code></pre> <p><strong>About the server</strong></p> <p>In the end of each log, it illustrates the brief information about the cloud node. Hence, we can know which logs are from the same node.</p> <pre><code class="language-java">...... Node: suno-2.sophia.grid5000.fr Date: Fri Dec 28 21:21:00 EST 2018</code></pre> <p>We next give introduction to the omitted three types of exceptions in the paper.</p> <ul> <li><strong>NumberFormat exception</strong></li> </ul> <p>Below is an example of this type of exception. As we have mentioned in the paper, due to the impossibility of integrating GZoltar-v1.7 into APR tools, researchers choose to read the FL results from independent files. From the content of the log, Astor needs to get suspicious line numbers during initialization (executing <em>createEngine</em>) but triggers an exception. This exception only occurs for Closure-76 and we have confirmed with the authors of reference[9] that it is due to the wrong content of the input file. We thus categorized it into <strong>Improper operation of replication study</strong>.</p> <pre><code class="language-java">Exception in thread "main" java.lang.NumberFormatException: For input string: "" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:592) at java.lang.Integer.parseInt(Integer.java:615) at fr.inria.main.evolution.AstorMain.createEngine(AstorMain.java:172) at ......</code></pre> <ul> <li><strong>IO exception</strong></li> </ul> <p>During the experiment, the generated output files (i.e., the execution logs and the generated patches) can sometimes be more than 10 trillions of bites. Meanwhile, the system may generate and store abundant template files such as the variants of the buggy program. If there is not enough space left on the machine, the execution logs will not be outputted successfully and an IO exception will occur as shown below. This indicates that these exceptions may not occur if the template files can be cleaned in time. We thus classified this type into <strong>Improper operation of replication study</strong> in that researchers ignore the storage state of the machine.</p> <pre><code class="language-java">Exception in thread "main" java.lang.RuntimeException: java.io.IOException: No space left on device at fr.inria.astor.core.setup.ProjectRepairFacade.setupWorkingDirectories(ProjectRepairFacade.java:46) at fr.inria.main.evolution.AstorMain.initProject(AstorMain.java:61) at fr.inria.main.evolution.AstorMain.run(AstorMain.java:239)</code></pre> <ul> <li><strong>NoClassDefFound exception</strong></li> </ul> <p>An example of this type of exception is illustrated below. We failed to reproduce this exception in our own machine. We further tried the docker file provided in the project page of reference[8] but still did not succeed. We noted that the experiment in reference[8] was performed on cloud instances whose experimental environment may be unstable. Bugs that throw this exception are consecutive (i.e., the IDs of these bugs are consecutive which are from Math 39 to Math 52 in the Defects4J benchmark), which further confirms our hypothesis that the environment might be problematic during these executions. We thus categorized this type into <strong>Unstable environment</strong>.</p> <pre><code class="language-java">Exception in thread "main" java.lang.NoClassDefFoundError: com/gzoltar/core/spectra/Spectra at com.gzoltar.core.GZoltar.run(GZoltar.java:50) at us.msu.cse.repair.core.faultlocalizer.GZoltarFaultLocalizer.<init>(GZoltarFaultLocalizer.java:42) at us.msu.cse.repair.core.AbstractRepairProblem.invokeFaultLocalizer(AbstractRepairProblem.java:298) at us.msu.cse.repair.core.AbstractRepairProblem.invokeModules(AbstractRepairProblem.java:269) at us.msu.cse.repair.core.AbstractRepairProblem.<init>(AbstractRepairProblem.java:244) at us.msu.cse.repair.algorithms.kali.Kali.<init>(Kali.java:37) at ......</code></pre> <p> </p>
Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
<p class="BodyAA">The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.</p>
Dataset of 'Using Sequence-to-Sequence Learning for Repairing C Vulnerabilities'
<p>This is the dataset we collected for the 'Using Sequence-to-Sequence Learning for Repairing C Vulnerabilities' paper. See the description in the paper for how the dataset was collected. Please cite 'Using Sequence-to-Sequence Learning for Repairing C Vulnerabilities' if you use the dataset.</p> <p> </p> <p>src-all.txt and tgt-all.txt contain the tokenized function pairs and are ready to used as training data. Each line in both txt file corresponds to a function before and after a commit that was classified as a bug fix commit.</p> <p> </p> <p>The two tar files contain the raw data that was used to generate both txt files. Both containing the commits that were collected during the respective year.</p>
Data from: Bony lesions in early tetrapods and the evolution of mineralized tissue repair
Bone healing is an important survival mechanism, allowing vertebrates to recover from injury and disease. Here we describe newly recognized paleopathologies in the hindlimbs of the early tetrapods Crassigyrinus scoticus and Eoherpeton watsoni from the Early Carboniferous of Cowdenbeath, Scotland. These pathologies are among the oldest known instances of bone healing in tetrapod limb bones in the fossil record (about 325 Myr old). X-ray microtomographic imaging of the internal bone structure of these lesions shows that they are characterized by a mass of trabecular bone separated from the shaft's trabeculae by a layer of cortical bone. We frame these paleopathologies in an evolutionary context, including additional data on bone healing and its pathways across extinct and extant sarcopterygians. These data allowed us to synthesize information on cell-mediated repair of bone and other mineralized tissues in all vertebrates, to reconstruct the evolutionary history of skeletal tissue repair mechanisms. We conclude that bone healing is ancestral for sarcopterygians. Furthermore, other mineralized tissues (aspidin and dentine) were also capable of healing and remodeling early in vertebrate evolution, suggesting that these repair mechanisms are synapomorphies of vertebrate mineralized tissues. The evidence for remodeling and healing in all of these tissues appears concurrently, so in addition to healing these early vertebrates had the capacity to restore structure and strength by remodeling their skeleton. Healing appears to be an inherent property of these mineralized tissues, and its linkage to their remodeling capacity has previously been under-appreciated.
Human DNA Cross-Link Repair 1A (DCLRE1A. SNM1A); A Target Enabling Package
<p>Cancer cells experience genomic instability, probably through a combination of excessive replicative activity and the loss of function of checkpoint and DNA repair pathways that may have contributed to the oncogenic transformation. Chemotherapy by DNA-damaging agents such as cisplatin and nitrogen mustards create DNA interstrand crosslinks (ICL), which can lead to double-strand breaks and cell death when the cells replicate their DNA. Genotoxic drugs are counteracted by the cell’s DNA damage response. Hence, it is expected that inhibiting DNA repair proteins would sensitise cells to chemotherapy.<br> Here we address an enzyme that participates in the repair of ICLs, DCLRE1A. The TEP includes expression clones and methods for producing the catalytic domain and high-throughput activity assays. Furthermore, we provide a crystallization system that generates thousands of reproducible crystals that allow soaking of small-molecule ligands. We provide crystal structures of several small molecule fragments and inhibitors, opening the way to development of more potent and selective inhibitors.</p>
Review4Repair: Code Review Aided Automatic Program Repairing
<p>The natural language instructions scripted on the review comments are enormous sources of information about code bug’s nature and expected solutions. In this study, we investigate the performance improvement of repair techniques using code review comments. We train a sequence-to-sequence model on 55,060 code reviews and associated code changes. We also introduce new tokenization and preprocessing approaches that help to achieve significant improvement over state-of-the-art learning-based repair techniques. We boost the top-1 accuracy by 20.33% and top-10 accuracy by 34.82%. We could provide a suggestion for stylistics and non-code errors unaddressed by prior techniques.</p>
Re-assembling the past: The RePAIR dataset and benchmark for real world 2D and 3D puzzle solving
<p><em>Accepted by NeurIPS 2024 Datasets and Benchmarks Track</em></p> <p>We introduce the RePair puzzle-solving dataset, a large-scale real world dataset of fractured frescoes from the archaelogical campus of Pompeii. Our dataset consists of over 1000 fractured frescoes. The RePAIR stands as a realistic computational challenge for methods for 2D and 3D puzzle solving, and serves as a benchmark that enables the study of fractured object reassembly and presents new challenges for geometric shape understanding. Please visit <a href="https://repairproject.github.io/RePAIR_dataset/">our website</a> for more dataset information, access to source code scripts and for an interactive gallery viewing of the dataset samples.</p> <div> <h3>Access the entire dataset</h3> <p>We provide a compressed version of our dataset in two seperate files. One for the 2D version and one for the 3D version.</p> <p>Our full dataset contains over one thousand individual fractured fragments divided into groups with its corresponding folder and all compressed into their individual sub-set format regarding whether they are 2D or 3D. Regarding the 2D dataset, each fragment is saved as a .PNG image and each group has the corresponding ground truth transformation to solve the puzzle as a <strong><em>.TXT</em></strong> file. Considering the 3D dataset, each fragment is saved as a mesh using the widely <strong><em>.OBJ</em></strong> format with the corresponding material (<strong><em>.MTL</em></strong>) and texture (<strong><em>.PNG</em></strong>) file. The meshes are already in the assembled position and orientation, so that no additional information is needed. All additional metadata information are given as <strong><em>.JSON</em></strong> files.</p> <p> </p> <h1>Important Note</h1> <p><strong>Please be advised that downloading and reusing this dataset is permitted only upon acceptance of the following license terms.</strong></p> <p><em><strong>The Istituto Italiano di Tecnologia (IIT) declares, and the user (“User”) acknowledges, that the "RePAIR puzzle-solving dataset" contains 3D scans, texture maps, rendered images and meta-data of fresco fragments acquired at the Archaeological Site of Pompeii. IIT is authorised to publish the RePAIR puzzle-solving dataset herein only for scientific and cultural purposes and in connection with an academic publication referenced as Tsemelis et al., "Re-assembling the past: The RePAIR dataset and benchmark for real world 2D and 3D puzzle solving", NeurIPS 2024. Use of the RePAIR puzzle-solving dataset by User is limited to downloading, viewing such images; comparing these with data or content in other datasets. User is not authorised to use, in particular explicitly excluding any commercial use nor in conjunction with the promotion of a commercial enterprise and/or its product(s) or service(s), reproduce, copy, distribute the RePAIR puzzle-solving dataset. User will not use the RePAIR puzzle-solving dataset in any way prohibited by applicable laws. RePAIR puzzle-solving dataset therein is being provided to User without warranty of any kind, either expressed or implied. User will be solely responsible for their use of such RePAIR puzzle-solving dataset. In no event shall IIT be liable for any damages arising from such use.</strong></em></p> </div>
Next-generation Sequencing Data Associated with "Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches"
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Uncoupling of programmed DNA cleavage and repair jeopardizes the assembly of the Paramecium somatic genome
<p>In the ciliate <i>Paramecium</i>, the precise excision of numerous Internal Eliminated Sequences (IESs) from the somatic genome is essential at each sexual cycle. DNA double strands breaks (DSBs) are introduced by the PiggyMac endonuclease, and repaired in a highly concerted manner by the Non-Homologous End Joining pathway (NHEJ), as illustrated by the complete inhibition of DNA cleavage when Ku70/80 proteins are missing. We show here that expression of a DNA binding-deficient Ku70 mutant (Ku70-6E) permits DNA cleavage but not DSB repair, leading to accumulation of unrepaired DSBs. When wildtype and mutant Ku are co-expressed, the DSBs induced by Ku70-6E can be repaired by wildtype Ku, which uncouples DNA repair from the cleavage step. High-throughput sequencing of the developing MAC genome in these conditions reveals the presence of extremities healed by <i>de novo</i> telomere addition and numerous translocations between IES-flanking sequences. We conclude that coupling the two steps of IES excision ensures that both extremities are maintained together throughout the process, and propose that Ku assists PiggyMac during assembly of the synaptic pre-cleavage complex.</p>
Data from: "A framework for performing comparative LCA between repairing flooded houses and construction of dikes in non-stationary climate with changing risk of flooding"
<p>In the paper "A framework for performing comparative LCA between repairing flooded houses and construction of dikes in a non-stationary climate with changing risk of flooding", life cycle assessment is used to compare two ways to maintain the state of a coastal urban area in a changing climate with increasing flood risk. On one side, the construction of a dike, a hard and proactive scenario, is modeled using a bottom-up approach. On the other, the systematic repair of houses flooded by sea surges, a post-disaster measure, is assessed using a Monte Carlo simulation allowing for aleatory uncertainties in predicting future sea level rise and occurrences of extreme events. Two metrics are identified, normalized mean impacts and probability of dike being most efficient. The methodology is applied to three case studies in Denmark representing three contrasting areas, Copenhagen, Frederiksværk, and Esbjerg. For all case studies the distribution of the calculated impact of repairing houses is highly right skewed, which in some cases has implications for the comparative LCA. </p><p>This dataset contains the underlying data to support the findings of the paper. In particular, two sets of characterized environmental impacts are reported: (1) the impacts of flood-related repairs summed over a century, for each Monte Carlo simulation and (2) the impacts of building a dam. Both sets of results are reported for each of the three cities studied.</p>
Artifact for the paper "Mutation-based Lifted Repair of Software Product Lines"
<p>This work presents a novel lifted repair algorithm for program families (Software Product Lines - SPLs) based on code mutations.<br>The inputs of our tool are an erroneous SPL and a specification given in the form of assertions. We use variability encoding to transform the given SPL into a single program, called family simulator, which is translated into a set of SMT formulas whose conjunction is satisfiable iff the simulator (i.e. the input SPL) violates an assertion. We use a predefined set of mutations applied to feature and program expressions of the given SPL. The tool repeatedly mutates the erroneous family simulator and checks if it becomes (bounded) correct. The outputs of our tool are all minimal repairs in the form of minimal number of (feature and program) expression replacements such that the repaired SPL is (bounded) correct with respect to a given set of assertions.</p> <p>We present a prototype tool for repairing #ifdef-based C programs (i.e., annotative SPLs). The experimental results show that our approach is able to successfully repair various interesting SPLs.</p>
Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability
<p>This repository contains the data used to generate the figures in paper: Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability.</p>
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