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Fair Evaluation of Global Network Aligners
[article]
2014
arXiv
pre-print
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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
2015
Algorithms for Molecular Biology
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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
2015
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15
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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
2015
EURASIP Journal on Bioinformatics and Systems Biology
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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
2020
IEEE Access
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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
Cross-Silo Federated Learning Across Divergent Domains with Iterative Parameter Alignment
[article]
2024
arXiv
pre-print
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2023 pre-print arXiv:2311.04818v1 fatcat:uexcnjt54vbmrfuz52vislh4yiOther Versions
Learning from the collective knowledge of data dispersed across private sources can provide neural networks with enhanced generalization capabilities. ...
The resulting framework, Iterative Parameter Alignment, applies naturally to the cross-silo setting, and has the following properties: (i) a unique solution for each participant, with the option to globally ...
Key to the global convergence of a peer model is the alignment of parameters during training. ...
arXiv:2311.04818v5
fatcat:f36mtct7kbhfzfdbn7wrfu7qmu
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules
2019
BMC Genomics
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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
Global Open Science Cloud (GOSC) Flyer 2023
2023
Zenodo
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The idea to bring together partners to co-design and co-build the Global Open Science Cloud (GOSC) originated at the CODATA 2019 Beijing conference. ...
CODATA and the Computer Network Information Center (CNIC), CAS work together to coordinate and support the international collaborations around GOSC. ...
and alignment in the area of data interoperability. ...
doi:10.5281/zenodo.10429768
fatcat:25l2etlgb5hjbp7dxbtkoqsure
Local versus Global Biological Network Alignment
[article]
2015
arXiv
pre-print
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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
2019
Zenodo
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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
2019
Zenodo
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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
Range Adaptation for 3D Object Detection in LiDAR
[article]
2019
arXiv
pre-print
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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
An Extensive Assessment of Network Embedding in PPI Network Alignment
2022
Entropy
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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
pmid:35626613
pmcid:PMC9141406
fatcat:zpiu4mmmvza5rggc2xksajdscm
Evaluation of Procedures and Processes of Certification Mechanisms Provided
2020
Zenodo
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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
Towards Fair Graph Federated Learning via Incentive Mechanisms
[article]
2023
arXiv
pre-print
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To achieve this, we first introduce an agent valuation function aimed at quantifying agent contributions through the introduction of two criteria: gradient alignment and graph diversity. ...
Extensive experiments show that our model achieves the best trade-off between accuracy and the fairness of model gradient, as well as superior payoff fairness. ...
To evaluate the fairness of our allocation, we consider two perspectives: model gradient and payoff. ...
arXiv:2312.13306v1
fatcat:3yqugtrj2zbdtmv6hbwhjeuoh4
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