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Dissociation and Propagation for Approximate Lifted Inference with Standard Relational Database Management Systems [article]

Wolfgang Gatterbauer, Dan Suciu
2016 arXiv   pre-print
We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers  ...  This paper proposes an alternative approach for approximate evaluation of conjunctive queries with standard relational databases: In our approach, every query is evaluated entirely in the database engine  ...  We like to thank Abhay Jha for help with the experiments in the workshop version of this paper, Alexandra Meliou for suggesting the name "dissociation", and Vibhav Gogate for guidance in using his tool  ... 
arXiv:1310.6257v4 fatcat:ematfjcsdbavzd7siv3q2bikza

Approximate lifted inference with probabilistic databases

Wolfgang Gatterbauer, Dan Suciu
2015 Proceedings of the VLDB Endowment  
This paper proposes a new approach for approximate evaluation of #P-hard queries with probabilistic databases.  ...  We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers  ...  This work was supported in part by NSF grants IIS-0513877, IIS-0713576, IIS-0915054, and IIS-1115188. We thank the reviewers for their careful reading of this manuscript and their detailed feedback.  ... 
doi:10.14778/2735479.2735494 fatcat:safh6aiiwfdlxpitp3bipdxg7y

Approximate Lifted Inference with Probabilistic Databases [article]

Wolfgang Gatterbauer, Dan Suciu
2014 arXiv   pre-print
This paper proposes a new approach for approximate evaluation of #P-hard queries with probabilistic databases.  ...  We give a detailed experimental evaluation of our approach and, in the process, provide a new way of thinking about the value of probabilistic methods over non-probabilistic methods for ranking query answers  ...  This work was supported in part by NSF grants IIS-0513877, IIS-0713576, IIS-0915054, and IIS-1115188. We thank the reviewers for their careful reading of this manuscript and their detailed feedback.  ... 
arXiv:1412.1069v1 fatcat:pqzm45dp5rh6njv5wrybpdj3xq

A General Framework for Anytime Approximation in Probabilistic Databases [article]

Maarten Van den Heuvel, Floris Geerts, Wolfgang Gatterbauer, Martin Theobald
2018 arXiv   pre-print
Anytime approximation algorithms that compute the probabilities of queries over probabilistic databases can be of great use to statistical learning tasks.  ...  We present here a more general branch-and-bound framework that extends the possible bounds by using 'dissociation', which yields tighter bounds.  ...  This work has been supported in part by NSF IIS-1762268 and FWO G042815N.  ... 
arXiv:1806.10078v2 fatcat:xybhqidwi5cudbt5xfgnr2hhgq

Query Processing on Probabilistic Data: A Survey

Guy Van den Broeck, Dan Suciu
2017 Foundations and Trends in Databases  
Acknowledgements Acknowledgments Guy Van den Broeck was partially supported by NSF grants IIS-1657613, IIS-1633857 and DARPA XAI grant N66001-17-2-4032.  ...  When evaluated over a probabilistic database D, the plan returns a probability for each query answer: this is called extensional query evaluation.  ...  Discuss theoretical properties of query evaluation under this data model, identifying and delineating both tractable queries and hard queries that are unlikely to support efficient evaluation on probabilistic  ... 
doi:10.1561/1900000052 fatcat:jzifdhyvsnh7thqrnuptxbpejy

Probabilistic Databases

Dan Suciu, Dan Olteanu, Christopher Ré, Christoph Koch
2011 Synthesis Lectures on Data Management  
Acknowledgments The authors would like to acknowledge many collaborators and friends who, through their discussions and comments have helped shape our thinking and, thus, have directly or indirectly  ...  Sen and Deshpande [2007] discuss query evaluation over probabilistic databases represented by a graphical model.  ...  the possible worlds (answers), and the work by Gatterbauer et al. [2010] who propose a semantics called propagation that can always be evaluated efficiently.  ... 
doi:10.2200/s00362ed1v01y201105dtm016 fatcat:2bpr73ml4ffkhmnj37mjbmwgsu

Beta Probabilistic Databases

Niccolo' Meneghetti, Oliver Kennedy, Wolfgang Gatterbauer
2017 Proceedings of the 2017 ACM International Conference on Management of Data - SIGMOD '17  
We introduce Beta Probabilistic Databases (B-PDBs), a generalization of TI-PDBs designed to support both (i) belief updating and (ii) parameter learning in a principled and scalable way.  ...  Tuple-independent probabilistic databases (TI-PDBs) handle uncertainty by annotating each tuple with a probability parameter; when the user submits a query, the database derives the marginal probabilities  ...  Acknowledgements: We like to thank our reviewers for their helpful feedback.  ... 
doi:10.1145/3035918.3064026 dblp:conf/sigmod/MeneghettiKG17 fatcat:yc6mvudslzdqdi7ijy5e5vb62u

UDA-GIST

Kun Li, Daisy Zhe Wang, Alin Dobra, Christopher Dudley
2015 Proceedings of the VLDB Endowment  
We show that the in-database framework allows us to tackle a 27 times larger problem than solved by the state-of-the-art for the first application and achieves 43 times speedup over the state-of-the-art  ...  This paper presents General Iterative State Transition (GIST), a new database operator for parallel iterative state transitions over large states.  ...  and loopy belief propagation [19] for image denoising.  ... 
doi:10.14778/2735479.2735488 fatcat:bw7rdfn6izcjrjwyj4sllufewy

Modeling and simulating networks of interdependent protein interactions [article]

Bianca K Stoecker, Johannes Koester, Eli Zamir, Sven Rahmann
2017 bioRxiv   pre-print
The construction of these networks is based on public interaction databases and known as well as text-mined interaction dependencies.  ...  The efficiency of the model allows a fast simulation and enables the analysis of many proteins in large networks.  ...  In the dissociation phase, existing interactions probabilistically dissociate, potentially breaking large complexes into smaller ones.  ... 
doi:10.1101/229435 fatcat:h3q7xz3e6be2xn7o52ngopdpwq

Machine learning in chemoinformatics and drug discovery

Yu-Chen Lo, Stefano E. Rensi, Wen Torng, Russ B. Altman
2018 Drug Discovery Today  
databases to design drugs with important biological properties.  ...  With the rapid explosion of chemical 'big' data from HTS and combinatorial synthesis, machine learning has become an indispensable tool for drug designers to mine chemical information from large compound  ...  Acknowledgments We thank all members of the Helix group at Stanford University for their helpful feedback and suggestions.  ... 
doi:10.1016/j.drudis.2018.05.010 pmid:29750902 pmcid:PMC6078794 fatcat:ckxznjxuujajle6iqycgi74d7i

Analyzing and Evaluating Data Freshness in Data Integration Systems

Verónika Peralta, Raúl Ruggia, Mokrane Bouzeghoub
2004 Ingénierie des Systèmes d'Information  
The materialization of some views over source databases allows speeding up OLAP queries and reduces the overload of the sources.  ...  Useful metadata will depend on the cost models used for modeling query evaluation cost and update propagation cost.  ... 
doi:10.3166/isi.9.5-6.145-162 fatcat:mby7k2jdvbe2tfwh3adeeu2qky

Incorporating functional inter-relationships into protein function prediction algorithms

Gaurav Pandey, Chad L Myers, Vipin Kumar
2009 BMC Bioinformatics  
We present experiments on several large genomic data sets, each of which is used for the modeling and prediction of over hundred classes from the GO Biological Process ontology.  ...  Using a standard measure for evaluating the semantic similarity between nodes in an ontology, we quantify and incorporate these inter-relationships into the knearest neighbor classifier.  ...  Acknowledgements We are thankful to Zafer Barutcuoglu, Yves Lussier and Jianrong Li for several fruitful discussions, and for providing us with useful information and data for the project.  ... 
doi:10.1186/1471-2105-10-142 pmid:19435516 pmcid:PMC2693438 fatcat:7aa5mhcmnjdwzdm34oysf7bweu

Answering table queries on the web using column keywords

Rakesh Pimplikar, Sunita Sarawagi
2012 Proceedings of the VLDB Endowment  
Given a set of Web tables T1, . . ., Tn, and a query Q with q sets of keywords Q1, . . ., Qq, decide for each Ti if it is relevant to Q and if so, identify the mapping between the columns of Ti and query  ...  Experiments on a workload of 59 queries over a 25 million web table corpus shows significant boost in accuracy over baseline IR methods.  ...  seven query groups separately and over all queries combined.  ... 
doi:10.14778/2336664.2336665 fatcat:bfamub4ip5fqblfgcdxpapi5n4

Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

Jose C. Jimenez-Lopez, Emma W. Gachomo, Sweta Sharma, Simeon O. Kotchoni
2013 American Journal of Molecular Biology  
We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks.  ...  However, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management.  ...  knowledge and efficiency.  ... 
doi:10.4236/ajmb.2013.32016 fatcat:qqfycymt2fh6pl6ifudliybm2q

Navigating the amino acid sequence space between functional proteins using a deep learning framework

Tristan Bitard-Feildel
2021 PeerJ Computer Science  
AAEs are tested on three protein families known for their multiple functions the sulfatase, the HUP and the TPP families.  ...  The study also reports and analyzes for the first time two sampling strategies based on latent space interpolation and latent space arithmetic to generate intermediate protein sequences sharing sequential  ...  ACKNOWLEDGEMENTS TBF thanks the NVIDIA society for providing a TitanXp GPU to perform computations.  ... 
doi:10.7717/peerj-cs.684 pmid:34616884 pmcid:PMC8459775 fatcat:duzshsxuz5g6thznyazm5d2aay
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