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Fair Evaluation of Global Network Aligners [article]

Joseph Crawford, Yihan Sun, Tijana Milenković
2014 arXiv   pre-print
Together, our results give several general recommendations for a fair evaluation of network alignment methods.  ...  Biological network alignment identifies topologically and functionally conserved regions between networks of different species.  ...  Our results represent a set of general recommendations for a fair evaluation of any global network alignment method, not just MI-GRAAL and GHOST.  ... 
arXiv:1407.4824v1 fatcat:xqfaqrqvsrdr7es23i6bhuzzt4

Fair evaluation of global network aligners

Joseph Crawford, Yihan Sun, Tijana Milenković
2015 Algorithms for Molecular Biology  
Conclusion: Taken together, our results represent general recommendations for a fair evaluation of network alignment methods and in particular of two-stage NCF-AS approaches.  ...  Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species.  ...  Thus, methods for global network alignment (GNA) have been proposed, which aim to optimize global similarity between different networks and can thus find large conserved subgraphs [2, 3, 5-7, 9, 20-31  ... 
doi:10.1186/s13015-015-0050-8 pmid:26060505 pmcid:PMC4460690 fatcat:4cemszxlxzctte4m2ibjcxeomu

Fair evaluation of global network aligners

Joseph Crawford, Yihan Sun, Tijana Milenkovic
2015 Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15  
Conclusion: Taken together, our results represent general recommendations for a fair evaluation of network alignment methods and in particular of two-stage NCF-AS approaches.  ...  Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species.  ...  Thus, methods for global network alignment (GNA) have been proposed, which aim to optimize global similarity between different networks and can thus find large conserved subgraphs [2, 3, 5-7, 9, 20-31  ... 
doi:10.1145/2808719.2811423 dblp:conf/bcb/CrawfordSM15 fatcat:qsifwf25wrg77cd3g4v56b5yxq

The post-genomic era of biological network alignment

Fazle E Faisal, Lei Meng, Joseph Crawford, Tijana Milenković
2015 EURASIP Journal on Bioinformatics and Systems Biology  
Here, we review computational challenges behind the network alignment problem, existing approaches for solving the problem, ways of evaluating their alignment quality, and the approaches' biomedical applications  ...  We discuss recent innovative efforts of improving the existing view of network alignment.  ...  are similar (see above), it was established that Fig. 4 Fair evaluation of two-step global network aligners.  ... 
doi:10.1186/s13637-015-0022-9 pmid:28194172 pmcid:PMC5270500 fatcat:3mee3vqx3zew7fslxmuqernft4

Pairwise versus multiple global network alignment

Vipin Vijayan, Shawn Gu, Eric Krebs, Lei Meng, Tijana Milenkovic
2020 IEEE Access  
Biological network alignment (NA) aims to identify similar regions between molecular networks of different species. NA can be local or global.  ...  Just as the recent trend in the NA field, we also focus on global NA, which can be pairwise (PNA) and multiple (MNA). PNA produces aligned node pairs between two networks.  ...  OUR CONTRIBUTIONS Thus, we propose an evaluation framework for a fair comparison of PNA and MNA (Fig. 2) .  ... 
doi:10.1109/access.2020.2976487 pmid:33747670 pmcid:PMC7971151 fatcat:mz4ljah3krcbhkuhetkhly3auq

LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules

Sawal Maskey, Young-Rae Cho
2019 BMC Genomics  
The proposed algorithm exploits the results of a pairwise global alignment algorithm with many-to-many node mapping.  ...  Although a wide variety of network alignment algorithms have been introduced, developing a scalable local network alignment algorithm with high accuracy is still challenging.  ...  The full contents of the supplement are available at https://bmcgenomics. biomedcentral.com/articles/supplements/volume-20-supplement-9  ... 
doi:10.1186/s12864-019-6271-3 pmid:31874635 pmcid:PMC6929407 fatcat:trejbzfq3ne23db2edi45o3pza

Local versus Global Biological Network Alignment [article]

Lei Meng, Aaron Striegel, Tijana Milenkovic
2015 arXiv   pre-print
Network alignment (NA) aims to find regions of similarities between molecular networks of different species. There exist two NA categories: local (LNA) or global (GNA).  ...  We introduce new measures of alignment quality that allow for fair comparison of the different LNA and GNA outputs, as such measures do not exist.  ...  If so, this would confirm that additional biological knowledge is encoded in network topology compared to sequence data.  ... 
arXiv:1509.08524v1 fatcat:swl5nonamrgkfar3fwnhuq6l2q

Quantifying FAIR: automated metadata improvement and guidance in the DataONE repository network

Matthew B. Jones, Peter Slaughter, Ted Habermann
2019 Zenodo  
The current statistics are based on version 0.2.0 of the DataONE FAIR suite.  ...  The services produce guidance for FAIRness at both the level of an individual data set and trends through time for repository, user, and funder data collections.  ...  Modeling the FAIR Rubrics Landscape What The FAIR Data Principles 1 are the gold standard for evaluating the management and sharing of data and research resources.  ... 
doi:10.5281/zenodo.3408466 fatcat:qbpz75bdovfknevfkxvz2qydey

Open Science and reproducibility

Julián Garrido, Lourdes Verdes-Montenegro, Susana Sánchez-Exposito, Sebastián Luna, Mike G. Jones
2019 Zenodo  
A worldwide distributed network of SKA Regional Centres (SRCs) will provide access to the SKA data, to the analysis tools and processing power.  ...  IAA-CSIC has started prototyping a SRC that will be fully aligned with the Open Science Principles.  ...  Alignment of Open Access policies • No publication should be locked behind a paywall • OA must be immediate, i.e. no embargo periods • @OpenScienceMOOC info@opensciencemooc.eu https://github.com  ... 
doi:10.5281/zenodo.3470826 fatcat:6lponij7bnf53m72yjkewjacrm

An Extensive Assessment of Network Embedding in PPI Network Alignment

Marianna Milano, Chiara Zucco, Marzia Settino, Mario Cannataro
2022 Entropy  
network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms  ...  network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.  ...  In fact, for both global and local and for both pairwise and multiple classical network alignment algorithms, new unifying alignment quality measures are developed to enable the fair comparison of different  ... 
doi:10.3390/e24050730 fatcat:zpiu4mmmvza5rggc2xksajdscm

Range Adaptation for 3D Object Detection in LiDAR [article]

Ze Wang, Sihao Ding, Ying Li, Minming Zhao, Sohini Roychowdhury, Andreas Wallin, Guillermo Sapiro, Qiang Qiu
2019 arXiv   pre-print
Our model adaptation consists of an adversarial global adaptation, and a fine-grained local adaptation.  ...  The proposed cross range adaptation framework is validated on three state-of-the-art LiDAR based object detection networks, and we consistently observe performance improvement on the far-range objects,  ...  We adopt combinations of local and global adaptation. For the global adaptation, we adopt adversarial learning to align the feature in the network feature space.  ... 
arXiv:1909.12249v1 fatcat:gbw6hklyyrhl3ih2zxlv5u4wqa

Evaluation of Procedures and Processes of Certification Mechanisms Provided

Ilona Von Stein, Frans Huigen, Hervé L'Hours, Olivier Rouchon, Jerry De Vries, Patricia Herterich
2020 Zenodo  
Our recommendation is to consider the FAIR implications for CoreTrustSeal requirements by FAIR-aligning the Extended Requirements for the core certification of repositories.  ...  To formalize the interpretation and evaluation of FAIR principles and on the question how repositories can demonstrate their FAIRness, an assessment process has to be designed.  ...  Different evaluation processes can exist e.g. one process for global FAIR and another to cover data in the life science context. Evaluation processes can use different assessment methods.  ... 
doi:10.5281/zenodo.3738965 fatcat:clj2beadwjhhndf7xpvjyrvph4

RAGA: Relation-aware Graph Attention Networks for Global Entity Alignment [article]

Renbo Zhu, Meng Ma, Ping Wang
2021 arXiv   pre-print
Furthermore, we propose a global alignment algorithm to make one-to-one entity alignments with a fine-grained similarity matrix.  ...  The majority of the existing embeddings-based entity alignment methods embed entities and relations into a vector space based on relation triples of KGs for local alignment.  ...  To our best knowledge, DGMC and CEA are the state-of-the-art methods for local and global entity alignment respectively without additional information. Evaluation Metrics.  ... 
arXiv:2103.00791v1 fatcat:wsl2vp74bnfuzhzuv6xeki4ohu

Reproducible Big Data Science: A Case Study In Continuous Fairness

Kyle Chard, Ravi Madduri, Michael D'Arcy, Segun Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, Cory Funk, Ben Heavner, Matthew Richards, Paul Shannon, Gustavo Glusman (+3 others)
2018 Zenodo  
We illustrate the use of these tools via a case study involving a multi- step analysis that creates an atlas of putative transcription factor binding sites from terabytes of ENCODE DNase I hypersensitive  ...  We will describe the tools, services developed to create an end-to-end reproducible analysis pipelines while adhering to FAIR principles.  ...  Reproducibility requires continuous FAIRness • Make all data findable, accessible, interoperable, reusable at every stage, via pervasive use of simple identifier and exchange format conventions • Build  ... 
doi:10.5281/zenodo.1484403 fatcat:mqztdeowdff6tb4vpy7km54rn4

Multiple network alignment via multiMAGNA++ [article]

Vipin Vijayan, Tijana Milenkovic
2016 arXiv   pre-print
Then, they evaluate alignment quality by measuring the amount of conserved edges, but only after the alignment is constructed.  ...  Network alignment (NA) aims to find a node mapping between molecular networks of different species that identifies topologically or functionally similar network regions.  ...  In the process of method evaluation, we introduce new alignment quality measures for MNA to allow for more complete alignment characterization as well as more fair MNA method evaluation compared to using  ... 
arXiv:1604.01740v1 fatcat:5n6vw4t5xrgtzihwtkitnkaoda
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