BACKGROUND: Stochastic models are commonly employed in the system and synthetic biology to study the effects of stochastic fluctuations emanating from reactions involving species with low copy-numbers. Many important models feature complex dynamics, involving a state-space explosion, stiffness, and multimodality, that complicate the quantitative analysis needed to understand their stochastic behavior. Direct numerical analysis of such models is typically not feasible and generating many simulation runs that adequately approximate the model's dynamics may take a prohibitively long time. RESULTS: We propose a new memoization technique that leverages a population-based abstraction and combines previously generated parts of simulations, called segments, to generate new simulations more efficiently while preserving the original system's dynamics and its diversity. Our algorithm adapts online to identify the most important abstract states and thus utilizes the available memory efficiently. CONCLUSION: We demonstrate that in combination with a novel fully automatic and adaptive hybrid simulation scheme, we can speed up the generation of trajectories significantly and correctly predict the transient behavior of complex stochastic systems.

Esparza and Reiter have recently conducted a systematic comparative study of models of distributed computing consisting of a network of identical finite-state automata that cooperate to decide if the underlying graph of the network satisfies a given property. The study classifies models according to four criteria, and shows that twenty-four initially possible combinations collapse into seven equivalence classes with respect to their decision power, i.e. the properties that the automata of each class can decide. However, Esparza and Reiter only show (proper) inclusions between the classes, and so do not characterise their decision power. In this paper we do so for labelling properties, i.e. properties that depend only on the labels of the nodes, but not on the structure of the graph. In particular, majority (whether more nodes carry label a than b) is a labelling property. Our results show that only one of the seven equivalence classes identified by Esparza and Reiter can decide majority for arbitrary networks. We then study the expressive power of the classes on bounded-degree networks, and show that three classes can. In particular, we present an algorithm for majority that works for all bounded-degree networks under adversarial schedulers, i.e. even if the scheduler must only satisfy that every node makes a move infinitely often, and prove that no such algorithm can work for arbitrary networks.

We present a sound and complete method for the verification of qualitative liveness properties of replicated systems under stochastic scheduling. These are systems consisting of a finite-state program, executed by an unknown number of indistinguishable agents, where the next agent to make a move is determined by the result of a random experiment. We show that if a property of such a system holds, then there is always a witness in the shape of a Presburger stage graph : a finite graph whose nodes are Presburger-definable sets of configurations. Due to the high complexity of the verification problem (non-elementary), we introduce an incomplete procedure for the construction of Presburger stage graphs, and implement it on top of an SMT solver. The procedure makes extensive use of the theory of well-quasi-orders, and of the structural theory of Petri nets and vector addition systems. We apply our results to a set of benchmarks, in particular to a large collection of population protocols, a model of distributed computation extensively studied by the distributed computing community.

Computer science class enrollments have rapidly risen in the past decade. With current class sizes, standard approaches to grading and providing personalized feedback are no longer possible and new techniques become both feasible and necessary. In this paper, we present the third version of Automata Tutor, a tool for helping teachers and students in large courses on automata and formal languages. The second version of Automata Tutor supported automatic grading and feedback for finite-automata constructions and has already been used by thousands of users in dozens of countries. This new version of Automata Tutor supports automated grading and feedback generation for a greatly extended variety of new problems, including problems that ask students to create regular expressions, context-free grammars, pushdown automata and Turing machines corresponding to a given description, and problems about converting between equivalent models - e.g., from regular expressions to nondeterministic finite automata. Moreover, for several problems, this new version also enables teachers and students to automatically generate new problem instances. We also present the results of a survey run on a class of 950 students, which shows very positive results about the usability and usefulness of the tool.

Angluin et al. proved that population protocols compute exactly the predicates definable in Presburger arithmetic (PA), the first-order theory of addition. As part of this result, they presented a procedure that translates any formula $φ$ of quantifier-free PA with remainder predicates (which has the same expressive power as full PA) into a population protocol with $2^{O(\text{poly}(|φ|))}$ states that computes $φ$. More precisely, the number of states of the protocol is exponential in both the bit length of the largest coefficient in the formula, and the number of nodes of its syntax tree. In this paper, we prove that every formula $φ$ of quantifier-free PA with remainder predicates is computable by a leaderless population protocol with $O(\text{poly}(|φ|))$ states. Our proof is based on several new constructions, which may be of independent interest. Given a formula $φ$ of quantifier-free PA with remainder predicates, a first construction produces a succinct protocol (with $O(|φ|^3)$ leaders) that computes $φ$; this completes the work initiated in [STACS'18], where we constructed such protocols for a fragment of PA. For large enough inputs, we can get rid of these leaders. If the input is not large enough, then it is small, and we design another construction producing a succinct protocol with one leader that computes $φ$. Our last construction gets rid of this leader for small inputs.