Leaderless deterministic chemical reaction networks

This paper answers an open question of Chen, Doty, and Soloveichik [1], who showed that a function f:N^k --> N^l is deterministically computable by a stochastic chemical reaction network (CRN) if and only if the graph of f is a semilinear subset of N^{k+l}. That construction crucially used "leaders": the ability to start in an initial configuration with constant but non-zero counts of species other than the k species X_1,...,X_k representing the input to the function f. The authors asked whether deterministic CRNs without a leader retain the same power. We answer this question affirmatively, showing that every semilinear function is deterministically computable by a CRN whose initial configuration contains only the input species X_1,...,X_k, and zero counts of every other species. We show that this CRN completes in expected time O(n), where n is the total number of input molecules. This time bound is slower than the O(log^5 n) achieved in [1], but faster than the O(n log n) achieved by the direct construction of [1] (Theorem 4.1 in the latest online version of [1]), since the fast construction of that paper (Theorem 4.4) relied heavily on the use of a fast, error-prone CRN that computes arbitrary computable functions, and which crucially uses a leader.Comment: arXiv admin note: substantial text overlap with arXiv:1204.417

Efficient size estimation and impossibility of termination in uniform dense population protocols

We study uniform population protocols: networks of anonymous agents whose pairwise interactions are chosen at random, where each agent uses an identical transition algorithm that does not depend on the population size $n$. Many existing polylog$(n)$ time protocols for leader election and majority computation are nonuniform: to operate correctly, they require all agents to be initialized with an approximate estimate of $n$ (specifically, the exact value $\lfloor \log n \rfloor$). Our first main result is a uniform protocol for calculating $\log(n) \pm O(1)$ with high probability in $O(\log^2 n)$ time and $O(\log^4 n)$ states ($O(\log \log n)$ bits of memory). The protocol is converging but not terminating: it does not signal when the estimate is close to the true value of $\log n$. If it could be made terminating, this would allow composition with protocols, such as those for leader election or majority, that require a size estimate initially, to make them uniform (though with a small probability of failure). We do show how our main protocol can be indirectly composed with others in a simple and elegant way, based on the leaderless phase clock, demonstrating that those protocols can in fact be made uniform. However, our second main result implies that the protocol cannot be made terminating, a consequence of a much stronger result: a uniform protocol for any task requiring more than constant time cannot be terminating even with probability bounded above 0, if infinitely many initial configurations are dense: any state present initially occupies $\Omega(n)$ agents. (In particular, no leader is allowed.) Crucially, the result holds no matter the memory or time permitted. Finally, we show that with an initial leader, our size-estimation protocol can be made terminating with high probability, with the same asymptotic time and space bounds.Comment: Using leaderless phase cloc

Composable computation in discrete chemical reaction networks

We study the composability of discrete chemical reaction networks (CRNs) that stably compute (i.e., with probability 0 of error) integer-valued functions $f:\mathbb{N}^d\to\mathbb{N}$. We consider output-oblivious CRNs in which the output species is never a reactant (input) to any reaction. The class of output-oblivious CRNs is fundamental, appearing in earlier studies of CRN computation, because it is precisely the class of CRNs that can be composed by simply renaming the output of the upstream CRN to match the input of the downstream CRN. Our main theorem precisely characterizes the functions $f$ stably computable by output-oblivious CRNs with an initial leader. The key necessary condition is that for sufficiently large inputs, $f$ is the minimum of a finite number of nondecreasing quilt-affine functions. (An affine function is linear with a constant offset; a quilt-affine function is linear with a periodic offset)

Composable Computation in Leaderless, Discrete Chemical Reaction Networks

We classify the functions f:?^d ? ? that are stably computable by leaderless, output-oblivious discrete (stochastic) Chemical Reaction Networks (CRNs). CRNs that compute such functions are systems of reactions over species that include d designated input species, whose initial counts represent an input x ? ?^d, and one output species whose eventual count represents f(x). Chen et al. showed that the class of functions computable by CRNs is precisely the semilinear functions. In output-oblivious CRNs, the output species is never a reactant. Output-oblivious CRNs are easily composable since a downstream CRN can consume the output of an upstream CRN without affecting its correctness. Severson et al. showed that output-oblivious CRNs compute exactly the subclass of semilinear functions that are eventually the minimum of quilt-affine functions, i.e., affine functions with different intercepts in each of finitely many congruence classes. They call such functions the output-oblivious functions. A leaderless CRN can compute only superadditive functions, and so a leaderless output-oblivious CRN can compute only superadditive, output-oblivious functions. In this work we show that a function f:?^d ? ? is stably computable by a leaderless, output-oblivious CRN if and only if it is superadditive and output-oblivious

Hardness of Computing and Approximating Predicates and Functions with Leaderless Population Protocols

Population protocols are a distributed computing model appropriate for describing massive numbers of agents with very limited computational power (finite automata in this paper), such as sensor networks or programmable chemical reaction networks in synthetic biology. A population protocol is said to require a leader if every valid initial configuration contains a single agent in a special "leader" state that helps to coordinate the computation. Although the class of predicates and functions computable with probability 1 (stable computation) is the same whether a leader is required or not (semilinear functions and predicates), it is not known whether a leader is necessary for fast computation. Due to the large number of agents n (synthetic molecular systems routinely have trillions of molecules), efficient population protocols are generally defined as those computing in polylogarithmic in n (parallel) time. We consider population protocols that start in leaderless initial configurations, and the computation is regarded finished when the population protocol reaches a configuration from which a different output is no longer reachable. In this setting we show that a wide class of functions and predicates computable by population protocols are not efficiently computable (they require at least linear time), nor are some linear functions even efficiently approximable. It requires at least linear time for a population protocol even to approximate division by a constant or subtraction (or any linear function with a coefficient outside of N), in the sense that for sufficiently small gamma > 0, the output of a sublinear time protocol can stabilize outside the interval f(m) (1 +/- gamma) on infinitely many inputs m. In a complementary positive result, we show that with a sufficiently large value of gamma, a population protocol can approximate any linear f with nonnegative rational coefficients, within approximation factor gamma, in O(log n) time. We also show that it requires linear time to exactly compute a wide range of semilinear functions (e.g., f(m)=m if m is even and 2m if m is odd) and predicates (e.g., parity, equality)

Message Complexity of Population Protocols

The standard population protocol model assumes that when two agents interact, each observes the entire state of the other agent. We initiate the study of $\textit{message complexity}$ for population protocols, where the state of an agent is divided into an externally-visible $\textit{message}$ and an internal component, where only the message can be observed by the other agent in an interaction. We consider the case of $O(1)$ message complexity. When time is unrestricted, we obtain an exact characterization of the stably computable predicates based on the number of internal states $s(n)$: If $s(n) = o(n)$ then the protocol computes semilinear predicates (unlike the original model, which can compute non-semilinear predicates with $s(n) = O(\log n)$), and otherwise it computes a predicate decidable by a nondeterministic $O(n \log s(n))$-space-bounded Turing machine. We then introduce novel $O(\mathrm{polylog}(n))$ expected time protocols for junta/leader election and general purpose broadcast correct with high probability, and approximate and exact population size counting correct with probability 1. Finally, we show that the main constraint on the power of bounded-message-size protocols is the size of the internal states: with unbounded internal states, any computable function can be computed with probability 1 in the limit by a protocol that uses only $\textit{1-bit}$ messages

On the Runtime of Chemical Reaction Networks Beyond Idealized Conditions

This paper studies the (discrete) chemical reaction network (CRN) computational model that emerged in the last two decades as an abstraction for molecular programming. The correctness of CRN protocols is typically established under one of two possible schedulers that determine how the execution advances: (1) a stochastic scheduler that obeys the (continuous time) Markov process dictated by the standard model of stochastic chemical kinetics; or (2) an adversarial scheduler whose only commitment is to maintain a certain fairness condition. The latter scheduler is justified by the fact that the former one crucially assumes "idealized conditions" that more often than not, do not hold in real wet-lab experiments. However, when it comes to analyzing the runtime of CRN protocols, the existing literature focuses strictly on the stochastic scheduler, thus raising the research question that drives this work: Is there a meaningful way to quantify the runtime of CRNs without the idealized conditions assumption? The main conceptual contribution of the current paper is to answer this question in the affirmative, formulating a new runtime measure for CRN protocols that does not rely on idealized conditions. This runtime measure is based on an adapted (weaker) fairness condition as well as a novel scheme that enables partitioning the execution into short rounds and charging the runtime for each round individually (inspired by definitions for the runtime of asynchronous distributed algorithms). Following that, we turn to investigate various fundamental computational tasks and establish (often tight) bounds on the runtime of the corresponding CRN protocols operating under the adversarial scheduler. This includes an almost complete chart of the runtime complexity landscape of predicate decidability tasks

Optimal Information Encoding in Chemical Reaction Networks

Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has been widely studied in the molecular programming and distributed computing communities. While for Turing-universal systems there is a universal measure of optimal information encoding based on Kolmogorov complexity, chemical reaction networks are not Turing universal unless error and unbounded molecular counts are permitted. Nonetheless, here we show that the optimal number of reactions to generate a specific count x ? ? with probability 1 is asymptotically equal to a "space-aware" version of the Kolmogorov complexity of x, defined as K?s(x) = min_p {|p|/log|p| + log(space(?(p))) : ?(p) = x}, where p is a program for universal Turing machine ?. This version of Kolmogorov complexity incorporates not just the length of the shortest program for generating x, but also the space usage of that program. Probability 1 computation is captured by the standard notion of stable computation from distributed computing, but we limit our consideration to chemical reaction networks obeying a stronger constraint: they "know when they are done" in the sense that they produce a special species to indicate completion. As part of our results, we develop a module for encoding and unpacking any b bits of information via O(b/log{b}) reactions, which is information-theoretically optimal for incompressible information. Our work provides one answer to the question of how succinctly chemical self-organization can be encoded - in the sense of generating precise molecular counts of species as the desired state

Space-Optimal Majority in Population Protocols

Population protocols are a model of distributed computing, in which $n$ agents with limited local state interact randomly, and cooperate to collectively compute global predicates. An extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task, in which agents need to collectively reach a decision as to which one of two states $A$ or $B$ had a higher initial count. Two complexity metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires. It is known that majority requires $\Omega(\log \log n)$ states per agent to allow for poly-logarithmic time stabilization, and that $O(\log^2 n)$ states are sufficient. Thus, there is an exponential gap between the upper and lower bounds. We address this question. We provide a new lower bound of $\Omega(\log n)$ states for any protocol which stabilizes in $O( n^{1-c} )$ time, for any $c > 0$ constant. This result is conditional on basic monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a significant departure from previous lower bounds. Instead of relying on dense configurations, we introduce a new surgery technique to construct executions which contradict the correctness of algorithms that stabilize too fast. Subsequently, our lower bound applies to general initial configurations. We give an algorithm for majority which uses $O(\log n)$ states, and stabilizes in $O(\log^2 n)$ time. Central to the algorithm is a new leaderless phase clock, which allows nodes to synchronize in phases of $\Theta(n \log{n})$ consecutive interactions using $O(\log n)$ states per node. We also employ our phase clock to build a leader election algorithm with $O(\log n )$ states, which stabilizes in $O(\log^2 n)$ time