An Analysis for Proving Probabilistic Termination of Biological Systems

In this paper we apply the abstract interpretation approach for approximating the behavior of biological systems, modeled specifically using the Chemical Ground Form calculus, a simple stochastic calculus rich enough to model the dynamics of biochemical reactions. The analysis is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting the multiplicity of reagents present in a solution, using intervals. For abstracting the probabilistic semantics, modeled as a Discrete-Time Markov Chain, we use a variant of Interval Markov Chains, where probabilistic and non-deterministic steps are combined together. The abstract probabilistic semantics is systematically derived from an abstract Labeled Transition System. The abstract probabilistic model safely approximates the set of concrete experiments and reports conservative lower and upper bounds for probabilistic termination

Abstract Interpretation for Probabilistic Termination of Biological Systems

In a previous paper the authors applied the Abstract Interpretation approach for approximating the probabilistic semantics of biological systems, modeled specifically using the Chemical Ground Form calculus. The methodology is based on the idea of representing a set of experiments, which differ only for the initial concentrations, by abstracting the multiplicity of reagents present in a solution, using intervals. In this paper, we refine the approach in order to address probabilistic termination properties. More in details, we introduce a refinement of the abstract LTS semantics and we abstract the probabilistic semantics using a variant of Interval Markov Chains. The abstract probabilistic model safely approximates a set of concrete experiments and reports conservative lower and upper bounds for probabilistic termination

The Computational Power of Beeps

In this paper, we study the quantity of computational resources (state machine states and/or probabilistic transition precision) needed to solve specific problems in a single hop network where nodes communicate using only beeps. We begin by focusing on randomized leader election. We prove a lower bound on the states required to solve this problem with a given error bound, probability precision, and (when relevant) network size lower bound. We then show the bound tight with a matching upper bound. Noting that our optimal upper bound is slow, we describe two faster algorithms that trade some state optimality to gain efficiency. We then turn our attention to more general classes of problems by proving that once you have enough states to solve leader election with a given error bound, you have (within constant factors) enough states to simulate correctly, with this same error bound, a logspace TM with a constant number of unary input tapes: allowing you to solve a large and expressive set of problems. These results identify a key simplicity threshold beyond which useful distributed computation is possible in the beeping model.Comment: Extended abstract to appear in the Proceedings of the International Symposium on Distributed Computing (DISC 2015

Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks

We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail

A Deductive Verification Infrastructure for Probabilistic Programs

This paper presents a quantitative program verification infrastructure for discrete probabilistic programs. Our infrastructure can be viewed as the probabilistic analogue of Boogie: its central components are an intermediate verification language (IVL) together with a real-valued logic. Our IVL provides a programming-language-style for expressing verification conditions whose validity implies the correctness of a program under investigation. As our focus is on verifying quantitative properties such as bounds on expected outcomes, expected run-times, or termination probabilities, off-the-shelf IVLs based on Boolean first-order logic do not suffice. Instead, a paradigm shift from the standard Boolean to a real-valued domain is required. Our IVL features quantitative generalizations of standard verification constructs such as assume- and assert-statements. Verification conditions are generated by a weakest-precondition-style semantics, based on our real-valued logic. We show that our verification infrastructure supports natural encodings of numerous verification techniques from the literature. With our SMT-based implementation, we automatically verify a variety of benchmarks. To the best of our knowledge, this establishes the first deductive verification infrastructure for expectation-based reasoning about probabilistic programs

A Deductive Verification Infrastructure for Probabilistic Programs

This paper presents a quantitative program verification infrastructure for discrete probabilistic programs. Our infrastructure can be viewed as the probabilistic analogue of Boogie: its central components are an intermediate verification language (IVL) together with a real-valued logic. Our IVL provides a programming-language-style for expressing verification conditions whose validity implies the correctness of a program under investigation. As our focus is on verifying quantitative properties such as bounds on expected outcomes, expected run-times, or termination probabilities, off-the-shelf IVLs based on Boolean first-order logic do not suffice. Instead, a paradigm shift from the standard Boolean to a real-valued domain is required. Our IVL features quantitative generalizations of standard verification constructs such as assume- and assert-statements. Verification conditions are generated by a weakest-precondition-style semantics, based on our real-valued logic. We show that our verification infrastructure supports natural encodings of numerous verification techniques from the literature. With our SMT-based implementation, we automatically verify a variety of benchmarks. To the best of our knowledge, this establishes the first deductive verification infrastructure for expectation-based reasoning about probabilistic programs