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Parameter Curation for Benchmark Queries [chapter]

Andrey Gubichev, Peter Boncz
2015 Lecture Notes in Computer Science  
We show that uniform random sampling of the substitution parameters is not well suited for such benchmarks, since it results in unpredictable runtime behavior of queries.  ...  We present our approach of Parameter Curation with the goal of selecting parameter bindings that have consistently low-variance intermediate query result sizes throughout the query plan.  ...  Parameter Curation time Finally, we report the runtime of the parameter curation procedure for the LDBC Benchmark.  ... 
doi:10.1007/978-3-319-15350-6_8 fatcat:sbryv2q6ybgmhhiqei6a2fjvai

Parameter Curation and Data Generation for Benchmarking Multi-model Queries

Chao Zhang
2018 Very Large Data Bases Conference  
In this paper, we discuss the motivations and challenges for benchmarking multi-model databases, and then present our current research on the data generation and parameter curation for benchmarking multi-model  ...  queries.  ...  The second benchmarking challenge is the problem of Parameter Curation [9] , with the goal of selecting the substitution parameters for the multi-model query template to yield stable runtime behaviors  ... 
dblp:conf/vldb/Zhang18 fatcat:gqwk5axaibawfohtlw66ovcklm

Holistic evaluation in multi-model databases benchmarking

Chao Zhang, Jiaheng Lu
2019 Distributed and parallel databases  
Furthermore, in order to generate a comprehensive and unbiased query set, we develop an efficient algorithm to solve a new problem called multi-model parameter curation to judiciously control the query  ...  In this paper, we propose UniBench, a generic multi-model benchmark for a holistic evaluation of state-of-the-art MMDBs.  ...  The third key component is the parameter curation component. This component is responsible for curating parameters for the query to introduce the query diversity into the benchmarking process.  ... 
doi:10.1007/s10619-019-07279-6 fatcat:abvnwc6m2ne27ppdjqcwociwim

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas, Kristoffer Forslund, Luis Pedro Coelho, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
2017 Molecular biology and evolution  
Orthology assignment is ideally suited for functional inference.  ...  EggNOG-mapper predictions scored within the top-5 methods in the three GO categories using the CAFA2 NK-partial benchmark.  ...  This parameter is automatically adjusted for every sequence, without the need of predefining any taxonomic filter and allowing each query to be annotated using the most suitable taxonomic source.  ... 
doi:10.1093/molbev/msx148 pmid:28460117 pmcid:PMC5850834 fatcat:dvdoactxljd6ldc73vantqinf4

DBPal: Weak Supervision for Learning a Natural Language Interface to Databases [article]

Nathaniel Weir, Andrew Crotty, Alex Galakatos, Amir Ilkhechi, Shekar Ramaswamy, Rohin Bhushan, Ugur Cetintemel, Prasetya Utama, Nadja Geisler, Benjamin Hättasch, Steffen Eger, Carsten Binnig
2019 arXiv   pre-print
training data for every new database schema.  ...  data, which results in substantial overhead for supporting each new database schema.  ...  For testing different linguistic variants, we curated a new benchmark, called the Patients 1 benchmark, that covers different linguistic variations for the user NL input and maps it to an expected SQL  ... 
arXiv:1909.06182v1 fatcat:gvoe4rtymfesdpeqlbmj7xlgii

The LDBC Social Network Benchmark

Orri Erling, Alex Averbuch, Josep Larriba-Pey, Hassan Chafi, Andrey Gubichev, Arnau Prat, Minh-Duc Pham, Peter Boncz
2015 Proceedings of the 2015 ACM SIGMOD International Conference on Management of Data - SIGMOD '15  
The Linked Data Benchmark Council (LDBC) is now two years underway and has gathered strong industrial participation for its mission to establish benchmarks, and benchmarking practices for evaluating graph  ...  This paper describes the LDBC Social Network Benchmark (SNB), and presents database benchmarking innovation in terms of graph query functionality tested, correlated graph generation techniques, as well  ...  Now, the problem of selecting (curating) parameters from the corresponding domain P with properties P1-P3 can be formalized as follows: Parameter Curation: for the Intended Query Plan QI and the parameter  ... 
doi:10.1145/2723372.2742786 dblp:conf/sigmod/ErlingALCGPPB15 fatcat:r7xm6c62vnbh5bikj4d77w4ozm

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper [article]

Jaime Huerta-Cepas, Kristoffer Forslund, Damian Szklarczyk, Lars Juhl Jensen, Christian von Mering, Peer Bork
2016 bioRxiv   pre-print
Orthology assignment is ideally suited for functional inference.  ...  To validate our method, we benchmarked Gene Ontology predictions against two widely used homology-based approaches: BLAST and InterProScan.  ...  This parameter is automatically adjusted for every sequence, without the need of prefixing any taxonomic filter and allowing each query to be annotated using the most suitable taxonomic source.  ... 
doi:10.1101/076331 fatcat:gb7ez66vgjhrnnfbxj24i4auoi

Benchmarking Data Curation Systems

Patricia C. Arocena, Boris Glavic, Giansalvatore Mecca, Renée J. Miller, Paolo Papotti, Donatello Santoro
2016 IEEE Data Engineering Bulletin  
Finally, we consider benchmarks.  ...  First, we consider the outputs generated by a data curation system (for example, an integrated or cleaned database or a set of constraints produced by a schema discovery system).  ...  We should use data and metadata generators to create new, community-accepted benchmarks for different curation tasks.  ... 
dblp:journals/debu/ArocenaGMMPS16 fatcat:ulieruy7vneghl5pnosrp3dgsq

neXtA5: accelerating annotation of articles via automated approaches in neXtProt

Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, Patrick Ruch
2016 Database: The Journal of Biological Databases and Curation  
The second component is an existing search engine, which retrieves the most relevant MEDLINE records for any given query.  ...  The current search methods significantly improve the search effectiveness of curators for three important curation axes.  ...  To construct our reference benchmark, also called QREL (Query Relevance document), we used annotations supplied by neXtProt for 100 kinases.  ... 
doi:10.1093/database/baw098 pmid:27374119 pmcid:PMC4930835 fatcat:pbcdaf65ujffdp2diglunz6lva

Overlook: Differentially Private Exploratory Visualization for Big Data [article]

Pratiksha Thaker and Mihai Budiu and Parikshit Gopalan and Udi Wieder and Matei Zaharia
2020 arXiv   pre-print
Because Overlook's synopses do not require costly precomputation or storage, data curators can also use Overlook to explore the impact of privacy parameters interactively.  ...  We introduce Overlook, a system that enables private data exploration at interactive latencies for both data analysts and data curators.  ...  Recall that the quantization parameters for a column are established by the data curator.  ... 
arXiv:2006.12018v1 fatcat:w6ebbdjuancvjcrwoikyrkvb7y

Evaluating Pretrained Transformer Models for Entity Linking in Task-Oriented Dialog [article]

Sai Muralidhar Jayanthi, Varsha Embar, Karthik Raghunathan
2021 arXiv   pre-print
, as well as some improvements for short-forms, numeric and phonetic variations in entity mentions.  ...  The wide applicability of pretrained transformer models (PTMs) for natural language tasks is well demonstrated, but their ability to comprehend short phrases of text is less explored.  ...  Type-II Parameters-reduced models which are also trained for language modeling tasks through different parameter reduction techniques.  ... 
arXiv:2112.08327v1 fatcat:3zvmiodhtfhmte6zdfk6gigvg4

Bongard-HOI: Benchmarking Few-Shot Visual Reasoning for Human-Object Interactions [article]

Huaizu Jiang, Xiaojian Ma, Weili Nie, Zhiding Yu, Yuke Zhu, Anima Anandkumar
2022 arXiv   pre-print
our benchmarks.  ...  We carefully curate the few-shot instances with hard negatives, where positive and negative images only disagree on action labels, making mere recognition of object categories insufficient to complete  ...  Bongard-HOI Benchmark For a few-shot binary prediction instance in Bonagrd-HOI, it has a set of positive examples P, a set of negative samples N , and a query image I q .  ... 
arXiv:2205.13803v1 fatcat:i5xjizil6rb4fbrsmllnhjnoje

SASBDB and DARA as biological solution-scattering teaching tools

Alexey Kikhney, Alejandro Panjkovich, Dmitri I. Svergun
2017 Acta Crystallographica Section A: Foundations and Advances  
There are also "benchmark" experimental data available from a set of well-characterised commercially available proteins.  ...  The Small Angle Scattering Biological Data Bank (SASBDB, is a curated repository of freely accessible and fully searchable small angle scattering experimental data, which are deposited  ...  There are also "benchmark" experimental data available from a set of well-characterised commercially available proteins.  ... 
doi:10.1107/s2053273317089951 fatcat:q7mrkvsjojcynmuzh442ko5jbm

The Manchester OWL Repository: System Description

Nicolas Matentzoglu, Daniel Tang, Bijan Parsia, Uli Sattler
2014 International Semantic Web Conference  
well curated ontologies.  ...  Findings of surveys and results of benchmarking activities may be biased, even heavily, towards manually assembled sets of "somehow suitable" ontologies.  ...  of engineering environments [4] and benchmarking activities for reasoning services such as Description Logic (DL) classification [2] .  ... 
dblp:conf/semweb/MatentzogluTPS14 fatcat:2ywjwyddsfdexh63i3jwolgeo4

Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy [article]

Shaoqi Chen, Bin Duan, Chenyu Zhu, Chen Tang, Shuguang Wang, Yicheng Gao, Shaliu Fu, Lixin Fan, Qiang Yang, Qi Liu
2022 bioRxiv   pre-print
We evaluated scPrivacy on a comprehensive set of publicly available benchmark datasets for singlecell type identification to stimulate the scenario that the reference datasets are rapidly generated and  ...  AbstractThe rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses.  ...  For Seurat v3, all parameters were the defaults. For mtSC, all parameters were the defaults.  ... 
doi:10.1101/2022.05.23.493074 fatcat:icyrbtoam5hude5rzvrskyzf5q
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