1,651 Hits in 6.8 sec

Designing ecologically-optimised vaccines using population genomics [article]

Caroline Colijn, Jukka Corander, Nicholas Croucher
2019 bioRxiv   pre-print
Here, we demonstrate that vaccines optimised using this framework can minimise IPD and antibiotic-resistant disease more effectively than existing formulations in the model, through mitigating the consequences  ...  Recent advances in genomics and modeling have enabled forecasting of which non-vaccine serotypes will be successful post-vaccination.  ...  S3. 4 The three measures of IPD burden used to optimise vaccine formulations as a function of time for a 5 random selection of strategies simulated as being implemented in the Massachusetts population.  ... 
doi:10.1101/672733 fatcat:o7au7mx7fbcitevbojs6lcagku

Overview on Binary Optimisation using Swarm-inspired Algorithms

Mariana Macedo, Hugo Siqueira, Elliackin Figueiredo, Clodomir Santana, Rodrigo C. Lira, Anuradha Gokhale, Carmelo Bastos-Filho
2021 IEEE Access  
This scenario gets even more challenging when considering binary optimisation because of the absence of overview papers that assembles the trends, benefits and limitations of swarmbased techniques.  ...  is more efficient for binary optimisation in accuracy and computational cost.  ...  By introducing nonlinear dynamic adjustment learning factors and inertia weight, the convergence and optimisation of the proposed algorithm are improved compared to BPSO.  ... 
doi:10.1109/access.2021.3124710 fatcat:v7heosioojg3pcwpswm3yvmrmy

Intelligent host engineering for metabolic flux optimisation in biotechnology

Lachlan J. Munro, Douglas B. Kell
2021 Biochemical Journal  
Optimising the function of a protein of length N amino acids by directed evolution involves navigating a 'search space' of possible sequences of some 20N.  ...  In this combinatorial sense, then, the problems of directed protein evolution and of host engineering are broadly equivalent.  ...  which optimisation can be performed.  ... 
doi:10.1042/bcj20210535 pmid:34673920 pmcid:PMC8589332 fatcat:difpodhky5c3vcmmchymd6csl4

Metaheuristics for Rich Portfolio Optimisation and Risk Management: Current State and Future Trends

Jana Doering, Renatas Kizys, Angel A. Juan, Àngels Fitó, Onur Polat
2019 Operations Research Perspectives  
Secondly, it identifies the linkages between portfolio optimisation and risk management and presents a unified view and classification of both problems.  ...  This paper reviews the scientific literature on the use of metaheuristics for solving NP-hard versions of these optimisation problems and illustrates their capacity to provide high-quality solutions under  ...  Acknowledgement This work has been partially supported with a doctoral grant from the Universitat Oberta de Catalunya and the Erasmus+ program (2018-1-ES01-KA103-049767).  ... 
doi:10.1016/j.orp.2019.100121 fatcat:ncxpgmkqczdgfl34albgx7z32m

An overview of population-based algorithms for multi-objective optimisation

Ioannis Giagkiozis, Robin C. Purshouse, Peter J. Fleming
2013 International Journal of Systems Science  
In this work we present an overview of the most prominent population-based algorithms and the methodologies used to extend them to multiple objective problems.  ...  Another advantage is that since a population of decision vectors is considered in each generation these algorithms are implicitly parallelizable and can generate an approximation of the entire Pareto front  ...  Genetic Algorithms ("genetic" AND ("algorithm" OR "algorithms") AND ("optimization" OR "optimisation")) Evolution Strategies ("evolution" AND ("strategy" OR "strategies") AND ("optimization" OR "optimisation  ... 
doi:10.1080/00207721.2013.823526 fatcat:3sli2fd3tzhwtkapcy25nj5vrq

Analysis of Randomised Search Heuristics for Dynamic Optimisation

Thomas Jansen, Christine Zarges
2015 Evolutionary Computation  
Dynamic optimisation is an area of application where randomised search heuristics like evolutionary algorithms and artificial immune systems are often successful.  ...  After setting the stage this way the framework is made concrete by presenting the results of thorough theoretical and statistical analysis for mutation-based evolutionary algorithms and artificial immune  ...  To the best of our knowledge Branke and Wang (2003) are the only ones to consider the scenario of change during a generation and provide a detailed analysis of a simple (1, 2) evolution strategy, an  ... 
doi:10.1162/evco_a_00164 pmid:26241197 fatcat:y2ossbibsrbx7j5ha4slgb2rsi

Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

Francisco J. Sánchez-Luque, Michael Stich, Susanna Manrubia, Carlos Briones, Alfredo Berzal-Herranz
2014 Scientific Reports  
López and M.C. Thomas for instrumental support. The support of Aptus Biotech is also acknowledged.  ...  Esté and C. Romero-López for critical reading of the manuscript, J.A. Reyes-Darias for his help with inhibition assays and HIV-1 detection by EIA, and V.  ...  The yield of complex formation increased along the selection process, as shown by the evolution of B max 32 (Fig. 2) .  ... 
doi:10.1038/srep06242 pmid:25175101 pmcid:PMC4150108 fatcat:qzraqjna4vfilioctzoeztdj7e

Fixed and flexible shape facility layout problems using biogeography-based optimisation algorithm

Supriya Ingole, Dinesh Singh
2021 International Journal of Industrial and Systems Engineering  
For any manufacturing and production industry to be efficient in terms of revenue, the layout of the industry must be arranged to minimise the total material handling and transporting cost of that industry  ...  The results obtained using BBO algorithm are compared and found better than previous known results.  ...  An encoding of layout representation for unequal area FLPs with FBS was introduced by Ulutas and Kulturel- Konak (2012) and optimised the large size problems using clonal selection algorithm (CSA).  ... 
doi:10.1504/ijise.2021.112469 fatcat:kcpiyrnmrjglten7qrnxtca5ou

Fast Immune System Inspired Hypermutation Operators for Combinatorial Optimisation [article]

D. Corus, P. S. Oliveto, D. Yazdani
2020 arXiv   pre-print
We rigorously prove the effectiveness of the proposed operators for all the benchmark functions where the performance of HMP is rigorously understood in the literature and validating the gained insights  ...  Through a comparative performance study of other 'fast mutation' operators from the literature, we conclude that a power-law distribution for the parabolic evaluation scheme is the best compromise in black  ...  runtimes for the BALANCE function from dynamic optimisation [12] .  ... 
arXiv:2009.00990v1 fatcat:tshmnsunfnh3nongacrpb4lvgi

Optimised chronic infection models demonstrate that siderophore 'cheating' in Pseudomonas aeruginosa is context specific

Freya Harrison, Alan McNally, Ana C da Silva, Stephan Heeb, Stephen P Diggle
2017 The ISME Journal  
The potential for siderophore mutants of Pseudomonas aeruginosa to attenuate virulence during infection, and the possibility of exploiting this for clinical ends, have attracted much discussion.  ...  This has largely been based on the results of in vitro experiments conducted in iron-limited growth medium, in which siderophore mutants act as social 'cheats:' increasing in frequency at the expense of  ...  Author contributions FH and SPD conceived the study and designed experiments. FH, AM and ACS carried out experimental work. FH and AM analysed the data. SH reconstructed the genealogy of PAO6609.  ... 
doi:10.1038/ismej.2017.103 pmid:28696423 pmcid:PMC5649161 fatcat:zjngrbyi4jddtjp3dulo6jkveq

On clonal selection

Chris McEwan, Emma Hart
2011 Theoretical Computer Science  
We examine existing clonal selection algorithms for learning from a theoretical and empirical perspective and assert that the widely accepted computational interpretation of clonal selection is compromised  ...  We suggest a more capable abstraction of the clonal selection principle grounded in probabilistic estimation and approximation and demonstrate how it addresses some of the shortcomings in existing algorithms  ...  The anonymous reviewers also provided feedback that measurably improved the manuscript.  ... 
doi:10.1016/j.tcs.2010.11.017 fatcat:a67vxb6ktveytel7an5shgiyrm

On the design of generalist strategies for swarms of simulated robots engaged in a task-allocation scenario

Elio Tuci, Alexandre Rabérin
2015 Swarm Intelligence  
selection criteria used to create new populations (i.e., single and multi-objective evolutionary optimisation algorithms).  ...  We compare the results of three different evolutionary design approaches, which differ in terms of the agents' genetic relatedness (i.e., groups of clones and groups of unrelated individuals), and/or the  ...  We acknowledge that it is relatively difficult to analyse, compare, and interpret the evolutionary dynamics of an ESR experiment.  ... 
doi:10.1007/s11721-015-0113-y fatcat:qxwcd76hafbsxcja3o3wkozn6y

On AIRS and Clonal Selection for Machine Learning [chapter]

Chris McEwan, Emma Hart
2009 Lecture Notes in Computer Science  
Previous analysis of the algorithm consists almost exclusively of empirical benchmarks and the reason for its success remains somewhat speculative.  ...  In this paper, we decouple the statistical and immunological aspects of AIRS and consider their merits individually.  ...  Typically, clonal selection is applied in a (black-box) optimisation setting: each cell represents a solution; their "stimulation" reflecting an objective function value.  ... 
doi:10.1007/978-3-642-03246-2_11 fatcat:kq3oix24hja73iwoxdjvjzu7ue

Application Areas of AIS: The Past, The Present and The Future [chapter]

Emma Hart, Jonathan Timmis
2005 Lecture Notes in Computer Science  
After a decade of research into the area of Artificial Immune Systems, it is worthwhile to take a step back and reflect on the contributions that the paradigm has brought to the application areas to which  ...  This paper attempts to take stock of the application areas that have been tackled in the past, and ask the difficult question "was it worth it ?".  ...  Acknowledgments Many of the ideas in this paper have evolved from useful and stimulating discussions at the ICARIS conferences with many people in the field, and in particular at meetings of the UK based  ... 
doi:10.1007/11536444_37 fatcat:v5chpo5tevhlpkxhleim3vxjzi

Application areas of AIS: The past, the present and the future

Emma Hart, Jon Timmis
2008 Applied Soft Computing  
After a decade of research into the area of Artificial Immune Systems, it is worthwhile to take a step back and reflect on the contributions that the paradigm has brought to the application areas to which  ...  This paper attempts to take stock of the application areas that have been tackled in the past, and ask the difficult question "was it worth it ?".  ...  Acknowledgments Many of the ideas in this paper have evolved from useful and stimulating discussions at the ICARIS conferences with many people in the field, and in particular at meetings of the UK based  ... 
doi:10.1016/j.asoc.2006.12.004 fatcat:osqn67c7ubfglgiso6qa2ktjjy
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