Being able to infer the clonal evolution and progression of cancer makes it possible to devise targeted therapies to treat the disease. As discussed in several studies, understanding the history of accumulation and the evolution of mutations during cancer progression is of key importance when devising treatment strategies. Given the importance of the task, many methods for phylogeny reconstructions have been developed over the years, mostly employing probabilistic frameworks. Our goal was to explore different methods to take on this phylogeny inference problem; therefore, we devised and implemented three different metaheuristic approaches—Particle Swarm Optimization (PSO), Genetic Programming (GP) and Variable Neighbourhood Search (VNS)—under the Perfect Phylogeny and the Dollo-k evolutionary models. We adapted the algorithms to be applied to this specific context, specifically to a tree-based search space, and proposed six different experimental settings, in increasing order of difficulty, to test the novel methods amongst themselves and against a state-of-the-art method. Of the three, the PSO shows particularly promising results and is comparable to published tools, even at this exploratory stage. Thus, we foresee great improvements if alternative definitions of distance and velocity in a tree space, capable of better handling such non-Euclidean search spaces, are devised in future works.

Ciccolella, S., Della Vedova, G., Filipović, V., Soto Gomez, M. (2023). Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. ALGORITHMS, 16(7) [10.3390/a16070333].

Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison

Ciccolella, S;Della Vedova, G
;
2023

Abstract

Being able to infer the clonal evolution and progression of cancer makes it possible to devise targeted therapies to treat the disease. As discussed in several studies, understanding the history of accumulation and the evolution of mutations during cancer progression is of key importance when devising treatment strategies. Given the importance of the task, many methods for phylogeny reconstructions have been developed over the years, mostly employing probabilistic frameworks. Our goal was to explore different methods to take on this phylogeny inference problem; therefore, we devised and implemented three different metaheuristic approaches—Particle Swarm Optimization (PSO), Genetic Programming (GP) and Variable Neighbourhood Search (VNS)—under the Perfect Phylogeny and the Dollo-k evolutionary models. We adapted the algorithms to be applied to this specific context, specifically to a tree-based search space, and proposed six different experimental settings, in increasing order of difficulty, to test the novel methods amongst themselves and against a state-of-the-art method. Of the three, the PSO shows particularly promising results and is comparable to published tools, even at this exploratory stage. Thus, we foresee great improvements if alternative definitions of distance and velocity in a tree space, capable of better handling such non-Euclidean search spaces, are devised in future works.
Articolo in rivista - Articolo scientifico
cancer phylogeny; genetic programming; metaheuristic; particle swarm optimization; variable neighbourhood search;
English
12-lug-2023
2023
16
7
333
open
Ciccolella, S., Della Vedova, G., Filipović, V., Soto Gomez, M. (2023). Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. ALGORITHMS, 16(7) [10.3390/a16070333].
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/444598
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