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FIVES: Feature Interaction Via Edge Search for Large-Scale Tabular Data [article]

Yuexiang Xie, Zhen Wang, Yaliang Li, Bolin Ding, Nezihe Merve Gürel, Ce Zhang, Minlie Huang, Wei Lin, Jingren Zhou
2021 arXiv   pre-print
To possess both of their merits, we propose a novel method named Feature Interaction Via Edge Search (FIVES), which formulates the task of interactive feature generation as searching for edges on the defined  ...  High-order interactive features capture the correlation between different columns and thus are promising to enhance various learning tasks on ubiquitous tabular data.  ...  As Figure 7 shows, although we formulate the edge search task as a bilevel optimization problem, FIVES achieves comparable validation AUC at each different number of training steps, which indicates a  ... 
arXiv:2007.14573v2 fatcat:dgrovnieezhdhfnyuxr64lsn6m

Combining Business Intelligence with Semantic Technologies: The CUBIST Project [chapter]

Frithjof Dau, Simon Andrews
2014 Lecture Notes in Computer Science  
CUBIST's purpose was to provide end-users with "conceptually relevant and user friendly visual analytics" to allow them to explore their data in new ways, discovering hidden meaning and solving hitherto  ...  Via different user interactions, nodes and edges can be added to or removed from the view.  ...  A main feature of CUBIST was the integration factual search, explorative search and visual analytics data (9) .  ... 
doi:10.1007/978-3-319-08389-6_23 fatcat:atqg5vflavbixjteg6udr3ebby

PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

Sapan Mandloi, Saikat Chakrabarti
2015 Scientific Reports  
PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network.  ...  various interactions of biological entities for better understanding  ...  Acknowledgements SM acknowledges DST for INSPIRE fellowship. SC acknowledges CSIR GENESIS (Code: BSC021) project for funding.  ... 
doi:10.1038/srep10021 pmid:25989388 pmcid:PMC4437304 fatcat:rxqm5ds54nfklfjtcf5ekwzc24

A Multi-scale Visual Analytics Approach for Exploring Biomedical Knowledge [article]

Fahd Husain, Rosa Romero-Gomez, Emily Kuang, Dario Segura, Adamo Carolli, Lai Chung Liu, Manfred Cheung, Yohann Paris
2021 arXiv   pre-print
Early interactions with domain experts support our approach for use cases with graphs with over 40,000 nodes and 350,000 edges.  ...  This paper describes an ongoing multi-scale visual analytics approach for exploring and analyzing biomedical knowledge at scale.We utilize global and local views, hierarchical and flow-based graph layouts  ...  We use the following scale to encode edge polarity: blue for "positive", red for "negative", and gray for "unknown."  ... 
arXiv:2109.06828v2 fatcat:b6ej4vtx3fgzhpujpks56j5mwe

Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive

Mike Wong, Paul Previde, Jack Cole, Brook Thomas, Nayana Laxmeshwar, Emily Mallory, Jake Lever, Dragutin Petkovic, Russ B. Altman, Anagha Kulkarni
2021 Journal of Biomedical Informatics  
The former generates small amounts of high-quality data, and the later offers large volumes of mixed quality data.  ...  GeneDive offers multiple search modalities, visualizations, and other features that guide the user efficiently to the information of their interest.  ...  We are grateful to the PharmGKB team and Dan Sosa for their valuable suggestions and insights.  ... 
doi:10.1016/j.jbi.2021.103732 pmid:33737208 fatcat:cks2iys2nvefni3kusw7avn56a

GraphCrunch: A tool for large network analyses

Tijana Milenković, Jason Lai, Nataša Pržulj
2008 BMC Bioinformatics  
The recent explosion in biological and other real-world network data has created the need for improved tools for large network analyses.  ...  on which to perform compute intensive searches for local network properties.  ...  Acknowledgements We thank the Institute for Genomics and Bioinformatics (IGB) at UC Irvine for providing computing resources. This project was supported by the NSF CAREER IIS-0644424 grant.  ... 
doi:10.1186/1471-2105-9-70 pmid:18230190 pmcid:PMC2275247 fatcat:kinw4egt6fcn5juiead2dma5i4

HTSvis: A web app for exploratory data analysis and visualization of arrayed high-throughput screens [article]

Christian Scheeder, Florian Heigwer, Michael Boutros
2017 bioRxiv   pre-print
Here we present HTSvis, an R/Shiny open-source web application for interactive visualization and exploratory analysis of arrayed high-throughput data.  ...  Using a light-weight infrastructure suitable for desktop computers, HTSvis can be used to visualize raw data, perform quality control and interactively visualize screening results from single- to multi-channel  ...  Acknowledgements We thank Luisa Henkel for helpful suggestions and comments on the manuscript and the Boutros lab for discussions. Funding Work in the lab of M.  ... 
doi:10.1101/107821 fatcat:fjn7tm5zmbfzxmxtmpsu7snnqi

SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets

Jing Guo, Hui Liu, Jie Zheng
2015 Nucleic Acids Research  
We also developed a statistical analysis module to estimate the druggability and sensitivity of cancer cells upon drug treatments targeting human SL partners, based on large-scale genomic data, gene expression  ...  To help users access and mine the wealth of the data, we developed other practical functionalities, such as search and filtering, orthology search, gene set enrichment analysis.  ...  We would like to thank Oliver Pelz for kindly answering our questions about the usage of GenomeRNAi.  ... 
doi:10.1093/nar/gkv1108 pmid:26516187 pmcid:PMC4702809 fatcat:h47izyloufej7ati5cxczai3wi

GreeningDB: A Database of Host–Pathogen Protein–Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease

Cristian D. Loaiza, Naveen Duhan, Rakesh Kaundal
2021 International Journal of Molecular Sciences  
Within the last decade, citrus greening disease (also known as huanglongbing or HLB) has emerged as the biggest threat for the citrus industry.  ...  scale.  ...  Advanced Search Module GreeningDB's advanced search module provides an interface via which users may search for information filtered by various keywords and other parameters, such as protein length, genomic  ... 
doi:10.3390/ijms221910897 pmid:34639237 pmcid:PMC8509195 fatcat:s5wuphibgba5plsvcf7u7zt2me

RSATree: Distribution-Aware Data Representation of Large-Scale Tabular Datasets for Flexible Visual Query

Honghui Mei, Wei Chen, Yating Wei, Yuanzhe Hu, Shuyue Zhou, Bingru Lin, Ying Zhao, Jiazhi Xia
2019 IEEE Transactions on Visualization and Computer Graphics  
large-scale dataset.  ...  This study presents and implements a web-based visual query system that supports visual specification, query, and exploration of large-scale tabular data with user-adjustable granularities.  ...  ACKNOWLEDGMENTS We wish to thank all the anonymous reviewers for their valuable comments, and all the participants for their active participation.  ... 
doi:10.1109/tvcg.2019.2934800 pmid:31443022 fatcat:snxchwdn3ffpvffxx2vxtmmeqm

Visual Exploration System for Analyzing Trends in Annual Recruitment Using Time-varying Graphs [article]

Toshiyuki T. Yokoyama, Masashi Okada, Tadahiro Taniguchi
2020 arXiv   pre-print
The proposed system integrates a time-varying graph model and dynamic graph visualization for heterogeneous tabular data.  ...  Using this system, human resource specialists can interactively inspect the relationships between two attributes of prospective employees across multiple years.  ...  Acknowledgements The authors thank Hideki Sugiyama, Kentaro Kuroda, and Kimio Minami from Panasonic Corporation for their support on requirement collection.  ... 
arXiv:2008.10039v1 fatcat:xu7rwc6p2zduvouvuwlvtrhhia

2014 Index IEEE Transactions on Visualization and Computer Graphics Vol. 20

2015 IEEE Transactions on Visualization and Computer Graphics  
Saket, B., +, TVCG Dec. 2014 2231-2240 OnSet: A Visualization Technique for Large-scale Binary Set Data.  ...  Saket, B., +, TVCG Dec. 2014 2231-2240 OnSet: A Visualization Technique for Large-scale Binary Set Data.  ... 
doi:10.1109/tvcg.2014.2368193 fatcat:nm3sijdvbza5nmxyina4rqinnu

Panacea: Visual exploration system for analyzing trends in annual recruitment using time-varying graphs

Toshiyuki T Yokoyama, Masashi Okada, Tadahiro Taniguchi
2021 PLoS ONE  
The proposed system integrates a time-varying graph model and dynamic graph visualization for heterogeneous tabular data.  ...  Such unnormalized data hinder effective comparison of the relationship between applicants in the early stage of data analysis.  ...  Acknowledgments The authors thank Hideki Sugiyama, Kentaro Kuroda, and Kimio Minami from Panasonic Corporation for their support on requirement collection.  ... 
doi:10.1371/journal.pone.0247587 pmid:33647012 pmcid:PMC7920367 fatcat:gsrbylnvxba4djp4tn5kmm7nhe

Visual Exploration System in an Industrial Context

Andrew Fish, Claudio Gargiulo, Delfina Malandrino, Donato Pirozzi, Vittorio Scarano
2016 IEEE Transactions on Industrial Informatics  
together with interactions methods to explore, select and compare sets of simulation data.  ...  This paper describes ExploraTool a new interactive tool to visually explore data from multiple repositories.  ...  Furthermore, the algorithm to process any tabular dataset and build a hierarchy can be executed by using the map/reduce paradigm on large data sets in a distributed environment using for instance Apache  ... 
doi:10.1109/tii.2016.2521613 fatcat:tgym5mziobb4hppnvygzdjcuiy

Using biological networks to integrate, visualize and analyze genomics data

Theodosia Charitou, Kenneth Bryan, David J. Lynn
2016 Genetics Selection Evolution  
The falling cost of next-generation sequencing is now enabling researchers to routinely catalogue the molecular components of these networks at a genome-wide scale and over a large number of different  ...  In this review, we describe how to use publicly available bioinformatics tools to integrate genome-wide 'omics' data into a network of experimentally-supported molecular interactions.  ...  Additional information associated with the nodes (e.g. gene expression data) or edges (e.g. a confidence score) can also be easily integrated via the use of node and edge attributes.  ... 
doi:10.1186/s12711-016-0205-1 pmid:27036106 pmcid:PMC4818439 fatcat:css7ozur7fdgdmrj363yekz7oq
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