The directed Physarum dynamics is known to solve positive linear programs: minimize @math subject to @math and @math for a positive cost vector @math . The directed Physarum dynamics evolves a positive vector @math according to the dynamics @math . Here @math is the solution to @math that minimizes the "energy" @math . In this paper, we study the non-uniform directed dynamics @math , where @math is a positive diagonal matrix. The non-uniform dynamics is more complex than the uniform dynamics (with @math being the identity matrix), as it allows each component of @math to react with different speed to the differences between @math and @math . Our contribution is to show that the non-uniform directed dynamics solves positive linear programs.
is a slime mold that apparently is able to solve shortest path problems. Nakagaki, Yamada, and T ' o th @cite_0 report about the following experiment; see Figure . They built a maze, covered it by pieces of Physarum (the slime can be cut into pieces which will reunite if brought into vicinity), and then fed the slime with oatmeal at two locations. After a few hours the slime retracted to a path following the shortest path in the maze connecting the food sources. The authors report that they repeated the experiment with different mazes; in all experiments, Physarum retracted to the shortest path.
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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) Physarum Polycephalum is a slime mold that apparently is able to solve shortest path problems. A mathematical model has been proposed by biologists to describe the feedback mechanism used by the slime mold to adapt its tubular channels while foraging two food sources s0 and s1. We prove that, under this model, the mass of the mold will eventually converge to the shortest s0-s1 path of the network that the mold lies on, independently of the structure of the network or of the initial mass distribution. This matches the experimental observations by the biologists and can be seen as an example of a "natural algorithm", that is, an algorithm developed by evolution over millions of years. When two food sources are presented to the slime mold Physarum in the dark, a thick tube for absorbing nutrients is formed that connects the food sources through the shortest route. When the light-avoiding organism is partially illuminated, however, the tube connecting the food sources follows a different route. Defining risk as the experimentally measurable rate of light-avoiding movement, the minimum-risk path is exhibited by the organism, determined by integrating along the path. A model for an adaptive-tube network is presented that is in good agreement with the experimental observations. We describe here a mathematical model of the adaptive dynamics of a transport network of the true slime mold Physarum polycephalum, an amoeboid organism that exhibits path-finding behavior in a maze. This organism possesses a network of tubular elements, by means of which nutrients and signals circulate through the plasmodium. When the organism is put in a maze, the network changes its shape to connect two exits by the shortest path. This process of path-finding is attributed to an underlying physiological mechanism: a tube thickens as the flux through it increases. The experimental evidence for this is, however, only qualitative. We constructed a mathematical model of the general form of the tube dynamics. Our model contains a key parameter corresponding to the extent of the feedback regulation between the thickness of a tube and the flux through it. We demonstrate the dependence of the behavior of the model on this parameter. 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. In this paper we study dynamics inspired by Physarum polycephalum (a slime mold) for solving linear programs [NTY00, IJNT11, JZ12]. These dynamics are arrived at by a local and mechanistic interpretation of the inner workings of the slime mold and a global optimization perspective has been lacking even in the simplest of instances. Our first result is an interpretation of the dynamics as an optimization process. We show that Physarum dynamics can be seen as a steepest-descent type algorithm on a certain Riemannian manifold. Moreover, we prove that the trajectories of Physarum are in fact paths of optimizers to a parametrized family of convex programs, in which the objective is a linear cost function regularized by an entropy barrier. Subsequently, we rigorously establish several important properties of solution curves of Physarum. We prove global existence of such solutions and show that they have limits, being optimal solutions of the underlying LP. Finally, we show that the discretization of the Physarum dynamics is efficient for a class of linear programs, which include unimodular constraint matrices. Thus, together, our results shed some light on how nature might be solving instances of perhaps the most complex problem in P: linear programming. Physarum polycephalum (true slime mold) has recently emerged as a fascinating example of biological computation through morphogenesis. Despite being a single cell organism, experiments have observed that through its growth process, the Physarum is able to solve various minimum cost flow problems. This paper analyzes a mathematical model of the Physarum growth dynamics. We show how to encode general linear programming (LP) problems as instances of the Physarum. We prove that under the growth dynamics, the Physarum is guaranteed to converge to the optimal solution of the LP. We further derive an efficient discrete algorithm based on the Physarum model, and experimentally verify its performance on assignment problems. 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. The plasmodium of the slime mould Physarum polycephalum is a large amoeba-like cell consisting of a dendritic network of tube-like structures (pseudopodia). It changes its shape as it crawls over a plain agar gel and, if food is placed at two different points, it will put out pseudopodia that connect the two food sources. Here we show that this simple organism has the ability to find the minimum-length solution between two points in a labyrinth. Many biological systems are composed of unreliable components which self-organize efficiently into systems that can tackle complex problems. One such example is the true slimemold Physarum polycephalum which is an amoeba-like organism that seeks food sources and efficiently distributes nutrients throughout its cell body. The distribution of nutrients is accomplished by a self-assembled resource distribution network of small tubes with varying diameter which can evolve with changing environmental conditions without any global control. In this paper, we use a phenomenological model for the tube evolution in slime mold and map it to a path formation protocol for wireless sensor networks. By selecting certain evolution parameters in the protocol, the network may evolve toward single paths connecting data sources to a data sink. In other parameter regimes, the protocol may evolve toward multiple redundant paths. We present detailed analysis of a small model network. A thorough understanding of the simple network leads to design insights into appropriate parameter selection. We also validate the design via simulation of large-scale realistic wireless sensor networks using the QualNet network simulator. We show how to preprocess a polygonal domain with a fixed starting point s in order to answer efficiently the following queries: Given a point q, how should one move from s in order to see q as soon as possible? This query resembles the well-known shortest-path-to-a-point query, except that the latter asks for the fastest way to reach q, instead of seeing it. Our solution methods include a data structure for a different generalization of shortest-path-to-a-point queries, which may be of independent interest: to report efficiently a shortest path from s to a query segment in the domain. We study the problems of processing single-source and two-point shortest path queries among weighted polygonal obstacles in the rectilinear plane. For the single-source case, we construct a data structure in O(nlog3 2n) time and O(nlog n) space, where n is the number of obstacle vertices; this data structure enables us to report the length of a shortest path between the source and any query point in O(log n) time, and an actual shortest path in O(log n+ k) time, where k is the number of edges on the output path. For the two-point case, we construct a data structure in O(n2 log2n) time and space; this data structure enables us to report the length of a shortest path between two arbitrary query points in O(log2 n) time, and an actual shortest path in O(log2 n + k) time. Our work improves and generalizes the previously best-known results on computing rectilinear shortest paths among weighted polygonal obstacles. We also apply our techniques to processing two-point L1 shortest obstacle-avoiding path queries among arbitrary (i.e., not necessarily rectilinear) polygonal obstacles in the plane. No algorithm for processing two-point shortest path queries among weighted obstacles was previously known. The problem of processing shortest pa th queries in graphs arises in application areas such as intelligent t ranspor ta t ion system (ITS), geographic information system (GIS), and robotics. In this paper, we present an efficient algorithmic solution for processing shortest pa th queries in undirected planar graphs with non-negative edge weights. Previous algorithms for this problem on planar graphs all have a tradeoff between the query t ime and the da ta structure space used by the solutions. The previously best known trade-off on an n-vertex planar graph G in the worst case is O(v -r) t ime for a pa th length query and O(v -r + L) t ime for report ing an actual shortest path, with a da ta structure of O(n2 x ) space, where r is an integer parameter with 1 < r _< n and L is the number of edges on the output shortest path. We present a new scheme, called frame search, that exploits the graph planari ty in a novel fashion. Wi th this scheme, we build an improved da ta structure of O(n + pv -r + p2 r) space (in O(n + p2 v + pr 3 4) time), where p is the minimum cardinality of a face-covering of the planar embedding of G with 1 < p < O(n), and r is an integer parameter with 1 < r < p. This da ta structure enables us to process each length query in O(v -rlog r + a(n)) t ime and report an actual shortest path in an addit ional O(L) time, where a(n) is the inverse of Ackermann's function. In the worst case, our approach reduces the previously best query t ime by a factor of up to O(n 1 4) if the same amount of space is used. Our technique can also be applied to improve the previous query algorithms for some geometric shortest pa th problems on the plane. Let @math be any undirected graph on @math vertices and @math edges. A path @math between any two vertices @math is said to be @math -approximate shortest path if its length is at most @math times the length of the shortest path between @math and @math . We consider the problem of building a compact data structure for a given graph @math which is capable of answering the following query for any @math and @math . report @math -approximate shortest path between @math and @math when vertex @math fails We present data structures for the single source as well all-pairs versions of this problem. Our data structures guarantee optimal query time. Most impressive feature of our data structures is that their size nearly match the size of their best static counterparts. We consider the two-point query version of the fundamental geometric shortest path problem: Given a set h of polygonal obstacles iu the plane, having a total of n vertices, build a data structure such that for any two query points s and t we can efficiently determine the length, d(s,t), of an Euclidean shortest obstacle-avoiding path, *(s,t), from s to t. Additionally, our data structure should allow one to report the path x(s, t), in time proportional to its (combinatorial) size. We present various methods for solving this two-point query problem, including algorithms with o(n), O(log n+h), 0( h log n), O(log’ n) or optimal O(log n) query times, using polynomial-space data structures, with various tradeoffs between space and query time. While severa results have been known for approtimate twepoint Euclidean shortest path queries, it has been a well-publicized open problem to obtain sublinear query time for the exact version of the problem. Our methods also yield data structures for twc+point shortest path queries on nonconvex polyhedral We obtain the following results related to dynamic versions of the shortest-paths problem: (i) Reductions that show that the incremental and decremental single-source shortest-paths problems, for weighted directed or undirected graphs, are, in a strong sense, at least as hard as the static all-pairs shortest-paths problem. We also obtain slightly weaker results for the corresponding unweighted problems. (ii) A randomized fully-dynamic algorithm for the all-pairs shortest-paths problem in directed unweighted graphs with an amortized update time of O(mn) and a worst case query time is O(n 3 4 ). (iii) A deterministic O(n 2 log n) time algorithm for constructing a (log n)-spanner with O(n) edges for any weighted undirected graph on n vertices. The algorithm uses a simple algorithm for incrementally maintaining single-source shortest-paths tree up to a given distance. Demand-robust versions of common optimization problems were recently introduced by [4] motivated by the worst-case considerations of two-stage stochastic optimization models. We study the demand robust min-cut and shortest path problems, and exploit the nature of the robust objective to give improved approximation factors. Specifically, we give a @math approximation for robust min-cut and a 7.1 approximation for robust shortest path. Previously, the best approximation factors were O(log n) for robust min-cut and 16 for robust shortest paths, both due to [4]. Our main technique can be summarized as follows: We investigate each of the second stage scenarios individually, checking if it can be independently serviced in the second stage within an acceptable cost (namely, a guess of the optimal second stage costs). For the costly scenarios that cannot be serviced in this way (“rainy days”), we show that they can be fully taken care of in a near-optimal first stage solution (i.e., by ”paying today”). We also consider “hitting-set” extensions of the robust min-cut and shortest path problems and show that our techniques can be combined with algorithms for Steiner multicut and group Steiner tree problems to give similar approximation guarantees for the hitting-set versions of robust min-cut and shortest path problems respectively. This paper introduces a new, practical routing algorithm, Maze-routing, to tolerate faults in network-on-chips. The algorithm is the first to provide all of the following properties at the same time: 1) fully-distributed with no centralized component, 2) guaranteed delivery (it guarantees to deliver packets when a path exists between nodes, or otherwise indicate that destination is unreachable, while being deadlock and livelock free), 3) low area cost, 4) low reconfiguration overhead upon a fault. To achieve all these properties, we propose Maze-routing, a new variant of face routing in on-chip networks and make use of deflections in routing. Our evaluations show that Maze-routing has 16X less area overhead than other algorithms that provide guaranteed delivery. Our Maze-routing algorithm is also high performance: for example, when up to 5 links are broken, it provides 50 higher saturation throughput compared to the state-of-the-art. We obtain the following results related to dynamic versions of the shortest-paths problem: Reductions that show that the incremental and decremental single-source shortest-paths problems, for weighted directed or undirected graphs, are, in a strong sense, at least as hard as the static all-pairs shortest-paths problem. We also obtain slightly weaker results for the corresponding unweighted problems. A randomized fully-dynamic algorithm for the all-pairs shortest-paths problem in directed unweighted graphs with an amortized update time of @math (we use @math to hide small poly-logarithmic factors) and a worst case query time is O(n3 4). A deterministic O(n2log n) time algorithm for constructing an O(log n)-spanner with O(n) edges for any weighted undirected graph on n vertices. The algorithm uses a simple algorithm for incrementally maintaining single-source shortest-paths tree up to a given distance. We give a randomized parallel algorithm for computing single-source shortest paths in weighted digraphs. We show that the exact shortest-path problem can be efficiently reduced to solving a series of approximate shortest-path subproblems. Our algorithm for the approximate shortest-path problem is based on the technique used by Ullman and Yannakakis in a parallel algorithm for breadth-first search.