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1,063 results for “Search”
Experimental Data for "What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way" at SIGIR2020
<p>This deposit contains data used for the experiments reported in the paper "<a href="https://doi.org/10.1145/3397271.3401048">What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way</a>", most notably the ElasticSearch 5.4 indices used for the reported experiments.</p> <p>To load the indices into an ElasticSearch cluster of your own, use the restore function described in the <a href="https://www.elastic.co/guide/en/elasticsearch/reference/5.4/modules-snapshots.html">ElasticSearch documentation</a>.</p> <p>The names of the index snapshots contained here are</p> <ul> <li>ct1718 for the indexed ClinicalTrials data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ct19 for the indexed ClinicalTrials data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> <li>ba1718 for the indexed PubMed data used in the TREC-PM challenges in <a href="http://www.trec-cds.org/2017.html">2017</a> and <a href="http://www.trec-cds.org/2018.html">2018</a>.</li> <li>ba19 for the indexed PubMed data used in the TREC-PM challenge in <a href="http://www.trec-cds.org/2019.html">2019</a>.</li> </ul> <p>The other file contains the original output that <a href="https://www.automl.org/automated-algorithm-design/algorithm-configuration/smac/">SMAC</a> wrote to disc during the parameter optimization process. There are directories for the biomedical abstracts (BA) and clinical trials (ct) and for each respective 10 fold cross validation split. Those file contain the exact parameter configurations and their evalation score (the infNDCG metric was used) in live-runXX.json files.</p> <p>The code to these files is located in <a href="https://zenodo.org/record/3856403">this Zenodo deposit</a>.</p>
SoSEN-KG: Knowledge Graph Dump v0 for SoSEn: Software Search Engine.
<p>SoSEn is a semantic search engine for scientific software. We index scientific software in a knowledge graph, which is used for search and understanding of the software. The graph `graph.ttl` contains information about the software, and `keywords.ttl` contains keyword information about the software. `graph.ttl` can be used alone, or it can be combined with `keywords.ttl` to facilitate tf-idf based keyword search.</p>
Python Annotated Code Search (PACS) Datasets & Pretrained Models
<p>This upload contains datasets and pre-trained models used for the paper <em>Neural Code Search Revisited: Enhancing Code Snippet Retrieval through Natural Language Intent. </em>The code for easily loading these datasets and models will be made available here: <a href="http://github.com/nokia/codesearch">http://github.com/nokia/codesearch</a> </p> <p><strong>Datasets</strong><br> There are three types of datasets:</p> <ul> <li>snippet collections (code snippets + natural language descriptions): so-ds-feb20, staqc-py-cleaned, conala-curated</li> <li>code search evaluation data (queries linked to relevant snippets of one of the snippet collections): so-ds-feb20-{valid|test}, staqc-py-raw-{valid|test}, conala-curated-0.5-test</li> <li>training data (datasets used to train code retrieval models): so-duplicates-pacs-train, so-python-question-titles-feb20</li> </ul> <p>The staqc-py-cleaned snippet collection, and the conala-curated datasets were derived from existing corpora:</p> <ul> <li>staqc-py-cleaned was derived from the Python StaQC snippet collection. See <a href="https://github.com/LittleYUYU/StackOverflow-Question-Code-Dataset">https://github.com/LittleYUYU/StackOverflow-Question-Code-Dataset</a>, <a href="https://github.com/LittleYUYU/StackOverflow-Question-Code-Dataset/blob/master/LICENSE.txt">LICENSE</a>. </li> <li>conala-curated was derived from the conala corpus. See <a href="https://conala-corpus.github.io/">https://conala-corpus.github.io/</a> , <a href="https://creativecommons.org/licenses/by-sa/4.0/">LICENSE</a></li> </ul> <p>The other datasets were mined directly from a recent Stack Overflow dump (https://archive.org/details/stackexchange, <a href="https://creativecommons.org/licenses/by-sa/4.0/">LICENSE</a>). <br> <br> <strong>Pre-trained models</strong><br> Each model can embed queries and (annotated) code snippets in the same space. The models are released under a BSD 3-Clause License.</p> <ul> <li>ncs-embedder-so-ds-feb20</li> <li>ncs-embedder-staqc-py</li> <li>tnbow-embedder-so-ds-feb20</li> <li>use-embedder-pacs</li> <li>ensemble-embedder-pacs</li> </ul>
Expanding Search-Based Software Modularization to Enterprise-Level Projects: A Case Study at Adyen (Master's Thesis)
<p>The zip file uploaded contains the interactive 3d graphs shown in chapter 6 in the thesis. The thesis can be found on the TU Delft repository.</p>
Mate searching context of prey influences predator-prey space race
<p>Predation risk is a strong driver of prey distribution and movement. However, fitness-influencing behaviours, such as mating, can alter risk and influence predator-prey space-use dynamics. In tree crickets, <i>Oecanthus henryi</i>, mate searching involves acoustic signalling by immobile males and phonotactic movement by females. Space-use patterns in tree crickets relative to their primary predators, green lynx spiders (<i>Peucetia viridans</i>), should therefore depend on their current mate-searching state; whether males are calling or non-calling and whether females are phonotactic or non-phonotactic. We first measured the degree of spatial anchoring of crickets to specific bushes in the field, and whether that influenced the probability of broad-scale spatial overlap with spiders. In the absence of spiders, all crickets, independent of sex or male calling status, were found to be spatially anchored to specific types of bushes and not uniformly distributed on the landscape. At the broad spatial scale, spiders were more likely to be found on bushes with female crickets, and to a lesser degree, calling male crickets. At a finer spatial scale within a bush, movement strategies of crickets not only varied depending on the presence or absence of a spider, but also on their current mate searching state. Phonotactic females showed clear predator avoidance, whereas calling and non-calling males moved towards the spider instead of away, similar to predator-inspection behaviour seen in many taxa. As the strongly-selected sex, males are more likely to undertake risky mate searching activities, which includes inspection of predator positions. Overall, we found that all crickets were predictably anchored at the landscape scale, but their sex and mate seeking behaviour influenced the degree of overlap with predators, and their antipredator movement strategies. Reproductive strategies within a prey species, therefore, can alter predator-prey space race at multiple spatial scales.</p>
Experimental Repository for "Cutting to the Core of Pseudo-Boolean Optimization: Combining Core-Guided Search with Cutting Planes Reasoning"
<p>Code and Data supplement to "Cutting to the Core of Pseudo-Boolean Optimization: Combining Core-Guided Search with Cutting Planes Reasoning"</p>
The clinical impact of high-profile animal-based research reported in the UK national press: a detailed discussion of articles from 1995, and full search results from the Nexis database
<p><span><span><span><span><span><span><span><span><span><span><span><b>Objectives</b>: We evaluated animal-based biomedical 'breakthroughs' reported in the UK national press in 1995 (25 years prior to the conclusion of this study). Based on evidence of over-speculative reporting of biomedical research in other areas (e.g. press releases and scientific papers), we specifically examined animal research in the media, asking, "In a given year, what proportion of animal research 'breakthroughs' published in the UK national press had translated, more than 20 years later, to approved interventions?"</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods</b>: We searched the Nexis media database (LexisNexis.com) for animal-based biomedical reports in the UK national press. The only restrictions were that the intervention should be specific, such as a named drug, gene, biomedical pathway, to facilitate follow-up, and that there should be claims of some clinical promise. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Main Outcome Measures</b>: Were any interventions approved for human use? If so, when and by which agency? If not, why, and how far did development proceed? Were any other, directly related interventions approved? Did any of the reports over-state human relevance?</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results</b>: Over-speculation and exaggeration of human relevance was evident in all the articles examined. Of 27 unique published 'breakthroughs', only one had clearly resulted in human benefit. Twenty were classified as failures, three were inconclusive, and three were partially successful.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions</b>: The results of animal-based pre-clinical research studies are commonly over-stated in media reports, to prematurely imply often-imminent 'breakthroughs' relevant to human medicine.</span></span></span></span></span></span></span></span></span></span></span></p>
Supporting user preferences in Search-Based Product Line Architecture Design using Machine Learning
<p>Presentation of the paper Supporting user preferences in Search-Based Product Line Architecture Design using Machine Learning to the SBCARS 2020.</p>
The search for sexually antagonistic genes: practical insights from studies of local adaptation and statistical genomics
<p>Sexually antagonistic (SA) genetic variation—in which alleles favored in one sex are disfavored in the other—is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterization of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research—including <em>F</em><sub>ST</sub> and <em>F</em><sub>IS</sub> statistics, genome‐wide association studies, pedigree analyses, reciprocal transplant studies, and evolve‐and‐resequence experiments—to evaluate methods for identifying SA genes and genome‐wide signals of SA genetic variation. We begin by developing theoretical models for between‐sex <em>F</em><sub>ST</sub> and <em>F</em><sub>IS</sub>, including explicit null distributions for each statistic, and using them to critically evaluate putative multilocus signals of sex‐specific selection in previously published datasets. We then highlight new statistics that address some of the limitations of <em>F</em><sub>ST</sub>and <em>F</em><sub>IS</sub>, along with applications of more direct approaches for characterizing SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.</p>
Extensive literature search for grayanotoxins and 5-hydroxymethylfurfural - summary tables and EndNote libraries
<p>An extensive literature search to identify and collect studies related to the toxicity of grayanotoxins and 5-hydroxymethylfurfural (5-HMF) was performed in the three databases PubMed, Web of Science and SciFinder® for six and four Areas, respectively. After combination of the searches from the three databases and removal of the duplicates, the total number of references for the grayanotoxins was 652 and for 5-HMF Area 1b was 3,862, for Area 2b was 37, for Area 3b was 221 and for Area 4b was 500. The evaluation of all retrieved references for relevance by screening the title and abstract (if available) and applying eligibility criteria (inclusion/exclusion) resulted in a total number of relevant references for the grayanotoxins for Area 1a of 71, for Area 2a of 3, for Area 3a of 5, for Area 4a of 75, for Area 5a of 141, and for Area 6a of 78 and for 5-HMF for Area 1b of 55, for Area 2b of 14, for Area 3b of 15 and for Area 4b of 8.</p>
Search-based Test Data Generation for Mutation Testing: a tool for Python programs
<p>Test data generation for mutation testing consists of identifying a set of inputs that maximizes the number of mutants killed. Mutation Testing is an excellent test criterion for detecting faults and measuring the effectiveness of test data sets. However, it is not widely used in practice due to the cost and complexity to perform some activities as generating test data. Although test suites can be produced and selected manually by a tester this practice is susceptible to errors and tools are needed to facilitate it. Several tools have been developed to automate mutation testing, but, only a few address the test data generation. The present paper proposes an automated test data generation tool based on weak mutation for Python programming language using the Hill Climbing algorithm. For evaluation, we performed an experiment concerning the effectiveness and cost computational of the tool in a database composed of 348 mutants and we compare it with random generation. Overall, the experiment achieved an average mutation score of 86% for our proposed tool and random testing 64% on average.</p>
The names don't matter but the numbers do: searching for stability in Carboniferous brachiopod paleocommunities from the North American Midcontinent
A key question in paleoecology and macroevolution is whether assemblages of species (paleocommunities) are persistent entities that endure over millions of years. Whilst community turnover in the face of abiotic change is the presumed norm, paleocommunities have been shown to persist for long time periods and regardless of environmental disruption. It remains an open question however, as to what processes allow for this. We investigate these questions by analyzing the Carboniferous brachiopod paleocommunities from the Midcontinent of North America. These diverse communities were subjected to repeated and geologically rapid changes in sea level. Using a suite of statistical techniques, we characterize the nature and scope of changes in these paleocommunities over time. We find that, at the paleocommunity scale, there is no evidence for obdurate ecological stasis, with fluctuations in both taxonomic composition and the associated abundance of taxa. However, at a higher ecological scale, stability is manifest, as diversity patterns remain stable across time, with a consistent number of species that can exist in any given paleocommunity. This suggests ecological rules such as taxon packing are in effect, resulting in a form of ecological stability even in the face of constant disequilibrium, and parallels ecological patterns of disruption and recovery previously observed for invertebrate communities from modern marine systems. Based on these results, we advocate for consideration of different hierarchical entities and scales when interpreting the ecological dynamics of fossil assemblages, as focusing exclusively on changes in taxon identity/abundance or diversity levels can lead to very different results.
Data from: In search of an optimal DNA diagnosis for taxonomic descriptions with MOLD, a novel tool to identify diagnostic nucleotide characters
<p>While DNA characters are increasingly used for phylogenetic inference, taxa delimitation and identification, their use for formal description of taxa remains scarce and inconsistent. The major impediments until recently was a lack of a suitable algorithm to identify signature DNA characters. The 2019-2020 however were marked by an almost simultaneous release of three softwares, simple to run and designed specifically for taxonomists. There is, nevertheless, a major concern, whether taxonomy will benefit from wide application of these, or any of the previously available tools. The reluctance of using DNA data in taxonomy is partly due to concerns of insufficient reliability of DNA characters, as robustness of DNA based diagnoses, depending on the sampled fraction of the species diversity has not thus far been assessed.</p> <p>We propose a novel program, named MOLD that recovers diagnostic nucleotide combinations (DNCs) for selected taxa with DNA sequences available. We carried our random iterated haplotype subsampling on species in six published DNA data sets of varying complexity, providing a diagnosis to each subsample to evaluate how the robustness of DNA based diagnosis changes depending on the sampled fraction of the taxon's diversity. We demonstrate that the currently used diagnostic DNA characters, or combinations thereof (DNCs) often do not exist for a particular species in a particular data set, or are not sufficiently reliable. We propose a new type of DNA diagnosis, termed herein rDNCs, which is compiled to suit pre-defined criteria of reliability, and is implemented in MOLD. We demonstrate that rDNCs can be successfully identified even in data sets comprising hundreds of species, and allow for notably more reliable diagnoses, than the currently used diagnostic DNA characters. MOLD recovers reliable and reproducible diagnoses in traditionally problematic cases, such as cryptic species or species with pronounced genetic structure, and shows unparalleled efficiency in large DNA data sets, making a valuable complement to the currently existing toolkit.</p>
Complementary materials for: Looking For Novelty in Search-based Software Product Line Testing (TSE)
<p>In this repository, we provide complementary materials for the following paper: </p> <pre>Y. Xiang, H. Huang, M. Li, S. Li and X. Yang, "Looking For Novelty in Search-based Software Product Line Testing" in <em>IEEE Transactions on Software Engineering</em>, vol. , no. 01, pp. 1-1, 5555. doi: 10.1109/TSE.2021.3057853 url: https://doi.ieeecomputersociety.org/10.1109/TSE.2021.3057853</pre> <p>1. Correlation analysis results (Pearson'r and p-value) are tabulated in <a href="https://www.zenodo.org/api/files/f6451296-91dc-4c9c-89fc-28ebf315be10/CorrelationAnalysisResults.xlsx?versionId=2f4ec2ab-3e48-420d-9819-b5e60ea43c06">CorrelationAnalysisResults.xlsx</a>; </p> <p>2. MATLAB scripts and raw data, which were used to perform correlation analyses, are given in <a href="https://zenodo.org/api/files/f6451296-91dc-4c9c-89fc-28ebf315be10/RawDataForCorrelationAnalysis.rar?versionId=5a168e2e-df32-4773-b8f3-4bf49de8d01d">RawDataForCorrelationAnalysis.rar</a>. </p> <p>---------------------------------------------------------------------------------------------------------------------------------------</p> <p>We suggest reproducing the correlation analysis, and other experiments described in the paper, using the codes provided at Github: <a href="https://github.com/gzhuxiangyi/TSE_NS">https://github.com/gzhuxiangyi/TSE_NS </a></p> <p> </p>
Investigating Transformers as Context-aware Word Search Engines - Data and Code
<p>This is the review version, please use the published record: </p> <p> https://zenodo.org/record/6425595</p> <p> </p> <p>Data and code for the paper 'Investigating Transformers as Context-aware Word Search Engines' as submitted for review at ACL21. </p> <p> </p>
The updated SLR Search Result
<p>The uploaded bib files are the search results used for our systematic literature review chapter: Enactment of Adaptation in Data Stream Processing: A Survey.</p> <p>The search results retrieved from ACM: ACM_Search_Result.bib</p> <p>The search results retrieved from ScienceDirect: ScienceDirect_Search_Result.bib</p>
Data from: Murky waters: searching for structure in genetically depauperate blue threadfin populations of Western Australia
The blue threadfin (Eleutheronema tetradactylum) is an exploited fishery species in southeast Asia and Australia. Demographic studies have revealed fine-scale stock structure throughout the Australian coastline, with demographically isolated populations separated by only tens of km. Similarly, population genetic analysis revealed fine-scale structure across most of its Australian range with important implications for fisheries management. However, in northern Western Australia, genetic stock structure analysis showed a contradictory lack of structure. In the present study, one mtDNA marker and a suite of five microsatellite loci were used to further investigate the stock structure of Western Australian blue threadfin populations. By increasing sample sizes from previously investigated areas: Roebuck Bay (n = 93 adults) and Eighty-mile Beach (n = 92 adults and 163 recruits from two settlement cohorts), we were able to detect subtle genetic differentiation that was previously obscured by low levels of genetic polymorphism. Therefore, the same fine-scale stock structure that has been observed elsewhere in this species also appears to exist in Western Australia. This has clear ramifications for a revised management strategy that incorporates the fine scale structuring of northwest Western Australian stocks of the blue threadfin.
Data from: Empirical evidence that large marine predator foraging behavior is consistent with area-restricted search theory
When prey is patchily distributed, predators are expected to spend more time searching for food in proximity of recent prey captures before searching in other areas. This behavior, known as area-restricted search, results in predators remaining localized in areas where prey had been detected previously because of the higher probability of encountering additional prey. However, few studies have tested these predictions on marine species because of the difficulties of observing feeding behavior. In this study, we utilized passive acoustic detections of echolocating dolphins to identify foraging behavior. C-PODs (click train detectors) were deployed for two years with an acoustic recorder attached to the same mooring during the second year. The time series of feeding buzzes, indicative of foraging behavior, revealed that both bottlenose (Tursiops truncatus) and common dolphins (Delphinus delphis) were more likely to stay in the area longer when foraging activity was high at the beginning of the encounter. The probability of foraging was also higher following previous foraging activity. This suggests that dolphins were feeding on spatially patchy prey and previous foraging experience influenced their movement behavior. This is consistent with the predictions of area-restricted search behavior, a nonrandom foraging strategy.
Data from: The evolution of colour polymorphism in British winter‐active Lepidoptera in response to search image use by avian predators
Phenotypic polymorphism in cryptic species is widespread. This may evolve in response to search image use by predators exerting negative frequency‐dependent selection on intraspecific colour morphs, "apostatic selection". Evidence exists to indicate search image formation by predators and apostatic selection operating on wild prey populations, though not to demonstrate search image use directly resulting in apostatic selection. The present study attempted to address this deficiency, using British Lepidoptera active in winter as a model system. It has been proposed that the typically polymorphic wing colouration of these species represents an anti‐search image adaptation against birds. To test (a) for search image driven apostatic selection, dimorphic populations of artificial moth‐like models were established in woodland at varying relative morph frequencies and exposed to predation by natural populations of birds. In addition, to test (b) whether abundance and degree of polymorphism are correlated across British winter‐active moths, as predicted where search image use drives apostatic selection, a series of phylogenetic comparative analyses were conducted. There was a positive relationship between artificial morph frequency and probability of predation, consistent with birds utilising search images and exerting apostatic selection. Abundance and degree of polymorphism were found to be positively correlated across British Lepidoptera active in winter, though not across all taxonomic groups analysed. This evidence is consistent with polymorphism in this group having evolved in response to search image driven apostatic selection and supports the viability of this mechanism as a means by which phenotypic and genetic variation may be maintained in natural populations.
Data from: Association between stock market gains and losses and Google searches
Experimental studies in the area of Psychology and Behavioral Economics have suggested that people change their search pattern in response to positive and negative events. Using Internet search data provided by Google, we investigated the relationship between stock-specific events and related Google searches. We studied daily data from 13 stocks from the Dow-Jones and NASDAQ100 indices, over a period of 4 trading years. Focusing on periods in which stocks were extensively searched (Intensive Search Periods), we found a correlation between the magnitude of stock returns at the beginning of the period and the volume, peak, and duration of search generated during the period. This relation between magnitudes of stock returns and subsequent searches was considerably magnified in periods following negative stock returns. Yet, we did not find that intensive search periods following losses were associated with more Google searches than periods following gains. Thus, rather than increasing search, losses improved the fit between people's search behavior and the extent of real-world events triggering the search. The findings demonstrate the robustness of the attentional effect of losses.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.