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Tools for analysis of biochemical network topology

Tatjana Rubina
2012 Biosystems and Information technology  
The network structure measures and properties are categorized in five groups: topological parameters, topological features, network metrics, network motifs and quantitative parameters of whole network  ...  Research resulted in overview on biochemical network structure analysis, on used topological features with the following goals: 1) to accumulate the existing knowledge about the network structure analysis  ...  All the mentioned software tools can calculate shortest path between all nodes, shortest path between two given nodes and perform finding of feed-forward loops.  ... 
doi:10.11592/bit.121101 fatcat:zfmljfiv55eetgy2j35ln3336u

Single Inventory Cycled Data Population in LEACH-Cluster

Chandan Maity, Ashutosh Gupta, Chaitanya Garg
2011 Proceedings of the Asia-Pacific Advanced Network  
close-loop energy path" algorithm.  ...  Inside a cluster in LEACH based sensor network architecture, data from individual nodes are being populated by individual query or command governed by Cluster-head following TDMA slots.  ...  George Varkey, Executive Director C-DAC Noida to give enough space and freedom to cultivate and nurture the research areas in wireless sensor network domain, Dr. P.C.  ... 
doi:10.7125/apan.32.14 fatcat:x4d4kqvubjga7kzaqg5atfnrzq

A hop-by-hop energy efficient distributed routing scheme

Chenying Hou, Fa Zhang, Antonio Fernández Anta, Lin Wang, Zhiyong Liu
2014 Performance Evaluation Review  
We can also achieve near global optimal in a distributed manner, while mostly used shortest path routing protocols such as OSPF cannot make it.  ...  Also, our method outperforms the widely applied shortest path routing strategy with 30% energy saving.  ...  This research was supported in part by the National Natural Science Foundation of China grant 61020106002, 61161160566 and 61202059, and the Comunidad de Madrid grant S2009TIC-1692, Spanish MICINN grant  ... 
doi:10.1145/2567529.2567559 fatcat:vqsaxt4u3vap7p2r5w77qkytuu

Congestion-triggered Multipath Routing based on Shortest Path Information

Soonyong Sohn, Brian Mark, John Brassil
2006 Computer Communications and Networks  
We present a multipath routing scheme that is designed to increase throughput and alleviate congestion in networks employing shortest path routing.  ...  The algorithm for finding multipath routes is based on shortest path routing and does not require pre-establishment of paths or support for source routing.  ...  ACKNOWLEDGEMENT This work was supported in part by DARPA Contract N66001-05-9-8904 and by the National Science Foundation under Grant CCF-0133390.  ... 
doi:10.1109/icccn.2006.286271 dblp:conf/icccn/SohnMB06 fatcat:ksja3v2evfecdps72o6sv7gqy4

A path finding implementation for multi-layer networks

Freek Dijkstra, Jeroen van der Ham, Paola Grosso, Cees de Laat
2009 Future generations computer systems  
A shortest path in a multi-layer network can contain loops, and a segment of a shortest path may not be a shortest path in itself.  ...  We will show that there are situations where algorithms as used in single layer networks, such as BGP, SS7 and OSPF-TE, cannot find the shortest path.  ...  Bert Andree and Karst Koymans have been very helpful in establishing the abstract multi-layer model. Niels Roosen aided in programming parts of the path walk algorithm.  ... 
doi:10.1016/j.future.2008.07.002 fatcat:hx7v6z2f4fdajm3cwnanaapqo4

Computational Methods for Calculating Multimodal Multiclass Traffic Network Equilibrium: Simulation Benchmark on a Large-Scale Test Case

Mostafa Ameli, Jean-Patrick Lebacque, Ludovic Leclercq, Victor L. Knoop
2021 Journal of Advanced Transportation  
Mode and path choices are carried out at the same level; therefore, travel times depend on the travel path and the mode attributes of travelers.  ...  This study reviews existing computational methods to calculate simulation-based dynamic network equilibrium. We consider a trip-based multimodal approach for the dynamic network loading.  ...  P i * e set of shortest paths in iteration k for class i. z j e path flow distribution of the outer-loop iteration j. z k e path flow distribution of the inner-loop iteration k.  ... 
doi:10.1155/2021/8815653 fatcat:7qfgeuvqmzdoth7jvxweie6p24

Adapted and constrained Dijkstra for elastic optical networks

Ireneusz Szczesniak, Bozena Wozna-Szczesniak
2016 2016 International Conference on Optical Network Design and Modeling (ONDM)  
We present an optimal and efficient algorithm for finding a shortest path in an elastic optical network.  ...  probability of establishing a connection using the edge-disjoint shortest paths, and the Yen K shortest paths.  ...  CONCLUSION We proposed the adaptation and the constriction of the Dijkstra shortest path algorithm for finding shortest paths in elastic optical networks.  ... 
doi:10.1109/ondm.2016.7494087 dblp:conf/ondm/SzczesniakW16 fatcat:j5biky2kkbhq5mv4alesysjkj4

Multipath Routing Mathematical Model to Solve the Traffic Engineering in Multi-Protocol Label Switching Network

Hani Attar
2017 Journal of Computer and Communications  
paper tackles, where the TE is identified as the optimal distribution of flows in the existing network.  ...  In [10], the author proposed rateless layered for multiple description video delivery through a relay, and it showed as well how the proposed scenario exploited the path delivery over a mobile network  ...  For example, the idea of a distributed algorithm for multipath routing M-path [15] is to find the routing graph that does not contain loops and presented the set of arcs are given in Equation (5) where  ... 
doi:10.4236/jcc.2017.514009 fatcat:iofp4h6cine3xmzb67phiq5xtu

An Efficient Calculation for TI-LFA Rerouting Path

2021 IEICE transactions on communications  
It does so by using segment routing to forward sections that may cause loops in the rerouting path.  ...  When a failure occurs in a network, TI-LFA quickly restores packet forwarding without waiting for other nodes to update their routing tables.  ...  Similarly, the shortest-path tree T ′ r based on the network after the failure can be used to find m ′ r→d .  ... 
doi:10.1587/transcom.2021cep0003 fatcat:oywycasj6fghbkgtpboriiuvpu

Optimal topology of gene-regulatory networks: role of the average shortest path

Ahmed Abdelzaher, Thang Dinh, Michael Mayo, Preetam Ghosh
2016 Proceedings of the 9th EAI International Conference on Bio-inspired Information and Communications Technologies (formerly BIONETICS)  
of the role in which the average shortest path affects system function, such as with noise or other signaling disruptions.  ...  This paper utilizes an integer linear program formulation to gauge the exact structural optimality of scale-free networks measured using the average shortest path between transcription factors and the  ...  In this paper, we investigate how another topological metricthe average shortest path between any two networked nodesis affected by different scale-free architectures with identical degree distribution  ... 
doi:10.4108/eai.3-12-2015.2262473 dblp:journals/sas/AbdelzaherDMG16 fatcat:ufupexhbanejpah4kqrpffj6d4

Engineering shortest-path algorithms for dynamic networks

Mattia D'Emidio, Daniele Frigioni
2014 Italian Conference on Theoretical Computer Science  
The problem of updating shortest paths in networks whose topology dynamically changes over time is a core functionality of many nowadays networked systems.  ...  In fact, the problem finds application in many real-world scenarios such as Internet routing and route planning in road networks.  ...  the corresponding link, the problem can be solved by the distributed computation of all-pairs shortest paths.  ... 
dblp:conf/ictcs/DEmidioF14 fatcat:icoz7ylnsneabmxj5ikauskdla

A distributed approach for multi-constrained path selection and routing optimization

Zhenjiang Li, J. J. Garcia-Luna-Aceves
2006 Proceedings of the 3rd international conference on Quality of service in heterogeneous wired/wireless networks - QShine '06  
routing of data packets, and implements constrained path optimization by distributively constructing an ¥ -optimal path set (i.e., the shortest, the second shortest and up to the ¥ th shortest path in  ...  For constrained path optimization, MPOR has high probabilities of finding feasible paths that are also optimal or near-optimal for the given optimization metric.  ...  Unlike WSP, shortest-widest path (SWP) routing attempts to find the path having the maximal bandwidth, and the one with shortest distance is selected if multiple such paths are found with the same bandwidth  ... 
doi:10.1145/1185373.1185420 dblp:conf/qshine/LiG06 fatcat:wemj7mot2feszlzl77og3jvefa

Simulation‐based dynamic traffic assignment: Meta‐heuristic solution methods with parallel computing

Mostafa Ameli, Jean‐Patrick Lebacque, Ludovic Leclercq
2020 Computer-Aided Civil and Infrastructure Engineering  
With parallel simulation, the algorithm runs more simulations in comparison with existing methods, but the algorithm explores the solution space better and therefore obtains better solutions in terms of  ...  This is because the existing algorithms need to know the results of the last iteration to determine the next best path flow for the next iteration.  ...  Therefore, we choose a framework from the literature which expresses the solution algorithm in two loops: the outer loop to find the shortest path and the inner loop to find the optimal path flow distribution  ... 
doi:10.1111/mice.12577 fatcat:bct3greylnbo3c4pdfdyqwncdm

Analysis of Dijkstra's Algorithm and A* Algorithm in Shortest Path Problem

Dian Rachmawati, Lysander Gustin
2020 Journal of Physics, Conference Series  
Finding the shortest path in direction effective is essential. To solve this shortest path problem, we usually using Dijkstra or A* algorithm.  ...  These two algorithms are often used in routing or road networks. This paper's objective is to compare those two algorithms in solving this shortest path problem.  ...  This can be proven by the loop count of Dijkstra and A*, the more points (nodes) the higher the difference between the loop count nor the time.  ... 
doi:10.1088/1742-6596/1566/1/012061 fatcat:yre6shdakzdwnkkggmk7oscixi

Quality-of-service routing for supporting multimedia applications

Zheng Wang, J. Crowcroft
1996 IEEE Journal on Selected Areas in Communications  
Theorem 5: Shortest-widest paths are loop-free in a distributed computation. Proof: By contradiction. Suppose that node A and node B are involved in a loop for destination C (Fig. 5) .  ...  With a centralized algorithm, an ordered scanning of the nodes should avoid such loops. In a distributed algorithm, however, loops can occur.  ...  and 1993 He is a Professor of networked systems in the Department of Computer Science, University College London, U.K., where he is responsible for a number of European and US funded research projects  ... 
doi:10.1109/49.536364 fatcat:xphdhg6oxbdxfhqqmd7j2tbpoy
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