The Moran process is a randomised algorithm that models the spread of genetic mutations through graphs. If the graph is connected, the process eventually reaches "fixation", where every vertex is a mutant, or "extinction", where no vertex is a mutant. Our main result is an almost-tight bound on the expected running time of the algorithm. For all epsilon > 0, we show that the expected running time on an n-vertex graph is o(n^(3+epsilon)). In fact, we show that it is at most n^3 * exp(O((log log n)^3)) and that there is a family of graphs where it is Omega(n^3). In the course of proving our main result, we also establish a phase transition in the probability of fixation, depending on the fitness parameter r of the mutation. We show that no similar phase transition occurs for digraphs, where it is already known that the expected running time can also be exponential. Finally, we give an improved FPRAS for approximating the probability of fixation. Its running time is independent of the size of the graph when the maximum degree is bounded.
We have already discussed the previously best-known family of suppressors from @cite_9 ; note that using [Lemma 6] Gia2016 , one can show that they have fixation probability @math and so are improved on by Theorem . Theorem provides the first known family of digraphs with fixation probability @math when @math .
@cite_9
1965299092 2884699236 2552612746 2170546552
Selective families, a weaker variant of superimposed codes [KS64, F92, 197, CR96], have been recently used to design Deterministic Distributed Broadcast (DDB) protocols for unknown radio networks (a radio network is said to be unknown when the nodes know nothing about the network but their own label) [CGGPR00, CGOR00]. We first provide a general almost tight lower bound on the size of selective families. Then, by reverting the selective families - DDB protocols connection, we exploit our lower bound to construct a family of “hard” radio networks (i.e. directed graphs). These networks yield an O(n log D) lower bound on the completion time of DDB protocols that is superlinear (in the size n of the network) even for very small maximum eccentricity D of the network, while all the previous lower bounds (e.g. O(D log n) [CGGPR00]) are superlinear only when D is almost linear. On the other hand, the previous upper bounds are all superlinear in n independently of the eccentricity D and the maximum in-degree d of the network. We introduce a broadcast technique that exploits selective families in a new way. Then, by combining selective families of almost optimal size with our new broadcast technique, we obtain an O(Dd log3 n) upper bound that we prove to be almost optimal when d = O(n D). This exponentially improves over the best known upper bound [CGR00) when D, d = O(polylogn). Furthermore, by comparing our deterministic upper bound with the best known randomized one [BGI87] we obtain a new, rather surprising insight into the real gap between deterministic and randomized protocols. It turns out that this gap is exponential (as discovered in [BGI87]), but only when the network has large maximum in-degree (i.e. d = O(na), for some constant a > O). We then look at the multibroadcast problem on unknown radio networks. A similar connection to that between selective families and (single) broadcast also holds between superimposed codes and multibroadcast. We in fact combine a variant of our (single) broadcast technique with superimposed codes of almost optimal size available in literature [EFF85, HS87, I97, CHI99]. This yields a multibroadcast protocol having completion time O(Dd2 log3 n). Finally, in order to determine the limits of our multibroadcast technique, we generalize (and improve) the best known lower bound [CR96] on the size of superimposed codes. Motivated by the error behavior in the DNA storage channel, in this paper, we extend the previously studied sequence reconstruction problem by Levenshtein. The reconstruction problem studies the model in which the information is read through multiple noisy channels, and the decoder, which receives all channel estimations, is required to decode the information. For the combinatorial setup, the assumption is that all the channels cause at most some @math errors. Levenshtein considered the case in which all the channels have the same behavior, and we generalize this model and assume that the channels are not identical. Thus, different channels may cause different maximum numbers of errors. For example, we assume that there are @math channels, which cause at most @math or @math errors, where @math t_ 1 @math pN @math 0 . If the information codeword belongs to a code with minimum distance @math , the problem is then to find the minimum number of channels that guarantees successful decoding in the worst case. A different problem we study in this paper is where the number of channels is fixed, and the question is finding the minimum distance @math that provides exact reconstruction. We study these problems and show how to apply them for the cases of substitutions and transpositions. We consider the classic Moran process modeling the spread of genetic mutations, as extended to structured populations by (Nature, 2005). In this process, individuals are the vertices of a connected graph G. Initially, there is a single mutant vertex, chosen uniformly at random. In each step, a random vertex is selected for reproduction with a probability proportional to its fitness: mutants have fitness r > 1, while non-mutants have fitness 1. The vertex chosen to reproduce places a copy of itself to a uniformly random neighbor in G, replacing the individual that was there. The process ends when the mutation either reaches fixation (i.e., all vertices are mutants), or gets extinct. The principal quantity of interest is the probability with which each of the two outcomes occurs. A problem that has received significant attention recently concerns the existence of families of graphs, called strong amplifiers of selection, for which the fixation probability tends to 1 as the order n of the graph increases, and the existence of strong suppressors of selection, for which this probability tends to 0. For the case of directed graphs, it is known that both strong amplifiers and suppressors exist. For the case of undirected graphs, however, the problem has remained open, and the general belief has been that neither strong amplifiers nor suppressors exist. In this paper we disprove this belief, by providing the first examples of such graphs. The strong amplifier we present has fixation probability 1 − ˜ O(n^ −1 3), and the strong suppressor has fixation probability ˜O(n^−1 4). Both graph constructions are surprisingly simple. We also prove a general upper bound of 1 − ˜Ω(n^−1 3) on the fixation probability of any undirected graph. Hence, our strong amplifier is existentially optimal. Mulmuley [Mul12a] recently gave an explicit version of Noether’s Normalization lemma for ring of invariants of matrices under simultaneous conjugation, under the conjecture that there are deterministic black-box algorithms for polynomial identity testing (PIT). He argued that this gives evidence that constructing such algorithms for PIT is beyond current techniques. In this work, we show this is not the case. That is, we improve Mulmuley’s reduction and correspondingly weaken the conjecture regarding PIT needed to give explicit Noether Normalization. We then observe that the weaker conjecture has recently been nearly settled by the authors ([FS12]), who gave quasipolynomial size hitting sets for the class of read-once oblivious algebraic branching programs (ROABPs). This gives the desired explicit Noether Normalization unconditionally, up to quasipolynomial factors. As a consequence of our proof we give a deterministic parallel polynomial-time algorithm for deciding if two matrix tuples have intersecting orbit closures, under simultaneous conjugation. We also study the strength of conjectures that Mulmuley requires to obtain similar results as ours. We prove that his conjectures are stronger, in the sense that the computational model he needs PIT algorithms for is equivalent to the well-known algebraic branching program (ABP) model, which is provably stronger than the ROABP model. Finally, we consider the depth-3 diagonal circuit model as defined by Saxena [Sax08], as PIT algorithms for this model also have implications in Mulmuley’s work. Previous work (such as [ASS12] and [FS12]) have given quasipolynomial size hitting sets for this model. In this work, we give a much simpler construction of such hitting sets, using techniques of Shpilka and Volkovich [SV09].