Some biological experiments show that the tubular structures of Physarum polycephalum are often analogous to those of Steiner trees. Therefore, the emerging Physarum-inspired Algorithms (PAs) have the potential of computing Steiner trees. In this paper, we propose two PAs to solve the Steiner Tree Problem in Graphs (STPG). We apply some widely-used artificial and real-world VLSI design instances to evaluate the performance of our PAs. The experimental results show that: 1) for instances with hundreds of vertices, our first PA can find feasible solutions with an average error of 0.19 , while the Genetic Algorithm (GA), the Discrete Particle Swarm Optimization (DPSO) algorithm and a widely-used Steiner tree approximation algorithm: the Shortest Path Heuristic (SPH) algorithm can only find feasible solutions with an average error above 4.96 ; and 2) for larger instances with up to tens of thousands of vertices, where our first PA, GA and DPSO are too slow to be used, our second PA can find feasible solutions with an average error of 3.69 , while SPH can only find feasible solutions with an average error of 6.42 . These experimental results indicate that PAs can compute Steiner trees, and it may be preferable to apply our PAs to solve STPG in some cases.
Recently it has been shown that Physarum-inspired algorithms can solve some network optimization problems. However, it is not yet shown that Physarum-inspired algorithm can solve Node Weighted Steiner Tree Problem (NWSTP). Two new Physarum-inspired algorithms are proposed in this paper to solve NWSTP for the first time. Since all the existing NWSTP benchmark instances have an empty terminal set, new benchmark instances with non-empty terminal sets are generated to cover the shortage of existing benchmark instances. Both proposed algorithms are compared with Genetic Algorithm (GA) and Discrete Particle Swarm Optimization (DPSO) in these benchmark instances. Furthermore, an adapted Dijkstra's algorithm is proposed to provide the optimal solutions for part of these benchmark instances where there are two terminals and the node weights are negative. Simulation results show that our first proposed algorithm can find the optimal solutions for NWSTP with two terminals in graphs with negative node weights, and our second proposed algorithm can find close approximate solutions for NWSTP with multiple terminals in any node weighted graph. Both proposed algorithms provide faster and better NWSTP solutions than GA and DPSO. Physarum polycephalum is a unicellular, multinucleate slime mold in the Mycetozoa group that exhibits remarkable capabilities, including the ability to construct efficient networks when foraging food [1]. The Physarum cell grows, as long as nutrition is abundant. When nutrition is limited, Physarum forms a network of interconnected veins; the veins are gel-like tubes in which the cytoplasm flows. It has been experimentally observed that, with two food sources, Physarum's tubular network often retracts to the shortest path between the food sources. Tero, Kobayashi and Nakagaki [2] proposed a model for the dynamics of the Physarum, which in the computer simulations converged to the shortest path on any initial network. We analytically prove that, under this model, the mass of the mold has to eventually converge to the shortest path in the initial network between the two food sources, independently of the structure of the initial network or of the initial mass distribution. This presentation is based on the work in [3,4] and is supported by the Italian Flagship Initiative "InterOmics" (PB.P05). References [1] Toshiyuki Nakagaki, Hiroyasu Yamada, Agota Toth: Maze-solving by an amoeboid organism. Nature 407:470 (2000) [2] Atsushi Tero, Ryo Kobayashi, Toshiyuki Nakagaki: A mathematical model for adaptive transport network in path finding by true slime mold. Journal of Theoretical Biology 244: 553-564 (2007) [3] Vincenzo Bonifaci, Kurt Mehlhorn, Girish Varma: Physarum can compute shortest paths. Journal of Theoretical Biology 309: 121-133 (2012) [4] Vincenzo Bonifaci: Physarum can compute shortest paths: A short proof. Information Processing Letters 113(1-2): 4-7 (2013)  We have proposed a mathematical model for the adaptive dynamics of the transport network in an amoeba-like organism, the true slime mold Physarum polycephalum. The model is based on physiological observations of this species, but can also be used for path-finding in the complicated networks of mazes and road maps. In this paper, we describe the physiological basis and the formulation of the model, as well as the results of simulations of some complicated networks. The path-finding method used by Physarum is a good example of cellular computation. Using insights from biological processes could help to design new optimization techniques for long-standing computational problems. This paper exploits a cellular computing model in the slime mold physarum polycephalum to solve the Steiner tree problem which is an important NP-hard problem in various applications, especially in network design. Inspired by the path-finding and network formation capability of physarum, we develop a new optimization algorithm, named as the physarum optimization, with low complexity and high parallelism. To validate and evaluate our proposed models and algorithm, we further apply the physarum optimization to the minimal exposure problem which is a fundamental problem corresponding to the worst-case coverage in wireless sensor networks. Complexity analysis and simulation results show that our proposed algorithm could achieve good performance with low complexity. Moreover, the core mechanism of our physarum optimization also may provide a useful starting point to develop some practical distributed algorithms for network design.