Synchronous Counting and Computational Algorithm Design

Consider a complete communication network on $n$ nodes, each of which is a state machine. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are "odd" and which are "even". We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates $f$ Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states. This work consists of two parts. In the first part, we use computational techniques (often known as synthesis) to construct very compact deterministic algorithms for the first non-trivial case of $f = 1$. While no algorithm exists for $n < 4$, we show that as few as 3 states per node are sufficient for all values $n \ge 4$. Moreover, the problem cannot be solved with only 2 states per node for $n = 4$, but there is a 2-state solution for all values $n \ge 6$. In the second part, we develop and compare two different approaches for synthesising synchronous counting algorithms. Both approaches are based on casting the synthesis problem as a propositional satisfiability (SAT) problem and employing modern SAT-solvers. The difference lies in how to solve the SAT problem: either in a direct fashion, or incrementally within a counter-example guided abstraction refinement loop. Empirical results suggest that the former technique is more efficient if we want to synthesise time-optimal algorithms, while the latter technique discovers non-optimal algorithms more quickly.Comment: 35 pages, extended and revised versio

Synchronous counting and computational algorithm design

Consider a complete communication network on n nodes, each of which is a state machine with s states. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are “odd” and which are “even”. We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates f Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states s. We use computational techniques to construct very compact deterministic algorithms for the first non-trivial case of f = 1. While no algorithm exists for n < 4, we show that as few as 3 states are sufficient for all values n ≥ 4. We prove that the problem cannot be solved with only 2 states for n = 4, but there is a 2-state solution for all values n ≥ 6.Peer reviewe

Synchronous Counting and Computational Algorithm Design

Consider a complete communication network on $n$ nodes, each of which is a state machine. In synchronous 2-counting, the nodes receive a common clock pulse and they have to agree on which pulses are "odd" and which are "even". We require that the solution is self-stabilising (reaching the correct operation from any initial state) and it tolerates $f$ Byzantine failures (nodes that send arbitrary misinformation). Prior algorithms are expensive to implement in hardware: they require a source of random bits or a large number of states. This work consists of two parts. In the first part, we use computational techniques (often known as synthesis) to construct very compact deterministic algorithms for the first non-trivial case of $f = 1$. While no algorithm exists for $n < 4$, we show that as few as 3 states per node are sufficient for all values $n \ge 4$. Moreover, the problem cannot be solved with only 2 states per node for $n = 4$, but there is a 2-state solution for all values $n \ge 6$. In the second part, we develop and compare two different approaches for synthesising synchronous counting algorithms. Both approaches are based on casting the synthesis problem as a propositional satisfiability (SAT) problem and employing modern SAT-solvers. The difference lies in how to solve the SAT problem: either in a direct fashion, or incrementally within a counter-example guided abstraction refinement loop. Empirical results suggest that the former technique is more efficient if we want to synthesise time-optimal algorithms, while the latter technique discovers non-optimal algorithms more quickly

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing

Towards Optimal Synchronous Counting

Consider a complete communication network of $n$ nodes, where the nodes receive a common clock pulse. We study the synchronous $c$-counting problem: given any starting state and up to $f$ faulty nodes with arbitrary behaviour, the task is to eventually have all correct nodes counting modulo $c$ in agreement. Thus, we are considering algorithms that are self-stabilizing despite Byzantine failures. In this work, we give new algorithms for the synchronous counting problem that (1) are deterministic, (2) have linear stabilisation time in $f$, (3) use a small number of states, and (4) achieve almost-optimal resilience. Prior algorithms either resort to randomisation, use a large number of states, or have poor resilience. In particular, we achieve an exponential improvement in the space complexity of deterministic algorithms, while still achieving linear stabilisation time and almost-linear resilience.Comment: 17 pages, 2 figure

Counting to Ten with Two Fingers: Compressed Counting with Spiking Neurons

We consider the task of measuring time with probabilistic threshold gates implemented by bio-inspired spiking neurons. In the model of spiking neural networks, network evolves in discrete rounds, where in each round, neurons fire in pulses in response to a sufficiently high membrane potential. This potential is induced by spikes from neighboring neurons that fired in the previous round, which can have either an excitatory or inhibitory effect. Discovering the underlying mechanisms by which the brain perceives the duration of time is one of the largest open enigma in computational neuro-science. To gain a better algorithmic understanding onto these processes, we introduce the neural timer problem. In this problem, one is given a time parameter t, an input neuron x, and an output neuron y. It is then required to design a minimum sized neural network (measured by the number of auxiliary neurons) in which every spike from x in a given round i, makes the output y fire for the subsequent t consecutive rounds. We first consider a deterministic implementation of a neural timer and show that Theta(log t) (deterministic) threshold gates are both sufficient and necessary. This raised the question of whether randomness can be leveraged to reduce the number of neurons. We answer this question in the affirmative by considering neural timers with spiking neurons where the neuron y is required to fire for t consecutive rounds with probability at least 1-delta, and should stop firing after at most 2t rounds with probability 1-delta for some input parameter delta in (0,1). Our key result is a construction of a neural timer with O(log log 1/delta) spiking neurons. Interestingly, this construction uses only one spiking neuron, while the remaining neurons can be deterministic threshold gates. We complement this construction with a matching lower bound of Omega(min{log log 1/delta, log t}) neurons. This provides the first separation between deterministic and randomized constructions in the setting of spiking neural networks. Finally, we demonstrate the usefulness of compressed counting networks for synchronizing neural networks. In the spirit of distributed synchronizers [Awerbuch-Peleg, FOCS\u2790], we provide a general transformation (or simulation) that can take any synchronized network solution and simulate it in an asynchronous setting (where edges have arbitrary response latencies) while incurring a small overhead w.r.t the number of neurons and computation time

Shift-Symmetric Configurations in Two-Dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration

The search for symmetry as an unusual yet profoundly appealing phenomenon, and the origin of regular, repeating configuration patterns have long been a central focus of complexity science and physics. To better grasp and understand symmetry of configurations in decentralized toroidal architectures, we employ group-theoretic methods, which allow us to identify and enumerate these inputs, and argue about irreversible system behaviors with undesired effects on many computational problems. The concept of so-called configuration shift-symmetry is applied to two-dimensional cellular automata as an ideal model of computation. Regardless of the transition function, the results show the universal insolvability of crucial distributed tasks, such as leader election, pattern recognition, hashing, and encryption. By using compact enumeration formulas and bounding the number of shift-symmetric configurations for a given lattice size, we efficiently calculate the probability of a configuration being shift-symmetric for a uniform or density-uniform distribution. Further, we devise an algorithm detecting the presence of shift-symmetry in a configuration. Given the resource constraints, the enumeration and probability formulas can directly help to lower the minimal expected error and provide recommendations for system's size and initialization. Besides cellular automata, the shift-symmetry analysis can be used to study the non-linear behavior in various synchronous rule-based systems that include inference engines, Boolean networks, neural networks, and systolic arrays.Comment: 22 pages, 9 figures, 2 appendice