Logic and model checking for hidden Markov models

The branching-time temporal logic PCTL* has been introduced to specify quantitative properties over probability systems, such as discrete-time Markov chains. Until now, however, no logics have been defined to specify properties over hidden Markov models (HMMs). In HMMs the states are hidden, and the hidden processes produce a sequence of observations. In this paper we extend the logic PCTL* to POCTL*. With our logic one can state properties such as "there is at least a 90 percent probability that the model produces a given sequence of observations" over HMMs. Subsequently, we give model checking algorithms for POCTL* over HMMs

Stuttering equivalence is too slow!

Groote and Wijs recently described an algorithm for deciding stuttering equivalence and branching bisimulation equivalence, acclaimed to run in $\mathcal{O}(m \log n)$ time. Unfortunately, the algorithm does not always meet the acclaimed running time. In this paper, we present two counterexamples where the algorithms uses $\Omega(md)$ time. A third example shows that the correction is not trivial. In order to analyse the problem we present pseudocode of the algorithm, and indicate the time that can be spent on each part of the algorithm in order to meet the desired bound. We also propose fixes to the algorithm such that it indeed runs in $\mathcal{O}(m \log n)$ time.Comment: 11 page

A probabilistic extension of UML statecharts: specification and verification

This paper is the extended technical report that corresponds to a published paper [14]. This paper introduces means to specify system randomness within UML statecharts, and to verify probabilistic temporal properties over such enhanced statecharts which we call probabilistic UML statecharts. To achieve this, we develop a general recipe to extend a statechart semantics with discrete probability distributions, resulting in Markov decision processes as semantic models. We apply this recipe to the requirements-level UML semantics of [8]. Properties of interest for probabilistic statecharts are expressed in PCTL, a probabilistic variant of CTL for processes that exhibit both non-determinism and probabilities. Verification is performed using the model checker Prism. A model checking example shows the feasibility of the suggested approach

Linear-Time--Branching-Time Spectroscopy Accounting for Silent Steps

We provide the first generalized game characterization of van Glabbeek's linear-time--branching-time spectrum with silent steps. Thereby, one multi-dimensional energy game can be used to decide a wide array of behavioral equivalences between stability-respecting branching bisimiarity and weak trace equivalence in one go. To establish correctness, we relate attacker-winning energy budgets and distinguishing sublanguages of Hennessy--Milner logic characterized by eight dimensions of formula expressiveness. We outline how to derive exponential-time algorithms and divergence-preserving variants

A Near-Linear-Time Algorithm for Weak Bisimilarity on Markov Chains

This article improves the time bound for calculating the weak/branching bisimulation minimisation quotient on state-labelled discrete-time Markov chains from O(m n) to an expected-time O(m log? n), where n is the number of states and m the number of transitions. For these results we assume that the set of state labels AP is small (|AP| ? O(m/n log? n)). It follows the ideas of Groote et al. (ACM ToCL 2017) in combination with an efficient algorithm to handle decremental strongly connected components (Bernstein et al., STOC 2019)

Far-Infrared and Sub-Millimeter Observations and Physical Models of the Reflection Nebula Ced 201

ISO [C II] 158 micron, [O I] 63 micron, and H_2 9 and 17 micron observations are presented of the reflection nebula Ced 201, which is a photon-dominated region illuminated by a B9.5 star with a color temperature of 10,000 K (a cool PDR). In combination with ground based [C I] 609 micron, CO, 13CO, CS and HCO+ data, the carbon budget and physical structure of the reflection nebula are constrained. The obtained data set is the first one to contain all important cooling lines of a cool PDR, and allows a comparison to be made with classical PDRs. To this effect one- and three-dimensional PDR models are presented which incorporate the physical characteristics of the source, and are aimed at understanding the dominant heating processes of the cloud. The contribution of very small grains to the photo-electric heating rate is estimated from these models and used to constrain the total abundance of PAHs and small grains. Observations of the pure rotational H_2 lines with ISO, in particular the S(3) line, indicate the presence of a small amount of very warm, approximately 330 K, molecular gas. This gas cannot be accommodated by the presented models.Comment: 32 pages, 7 figures, in LaTeX. To be published in Ap

Deglaciation of Fennoscandia

To provide a new reconstruction of the deglaciation of the Fennoscandian Ice Sheet, in the form of calendar-year time-slices, which are particularly useful for ice sheet modelling, we have compiled and synthesized published geomorphological data for eskers, ice-marginal formations, lineations, marginal meltwater channels, striae, ice-dammed lakes, and geochronological data from radiocarbon, varve, optically-stimulated luminescence, and cosmogenic nuclide dating. This 25 is summarized as a deglaciation map of the Fennoscandian Ice Sheet with isochrons marking every 1000 years between 22 and 13 cal kyr BP and every hundred years between 11.6 and final ice decay after 9.7 cal kyr BP. Deglaciation patterns vary across the Fennoscandian Ice Sheet domain, reflecting differences in climatic and geomorphic settings as well as ice sheet basal thermal conditions and terrestrial versus marine margins. For example, the ice sheet margin in the high-precipitation coastal setting of the western sector responded sensitively to climatic variations leaving a detailed record of prominent moraines and ice-marginal deposits in many fjords and coastal valleys. Retreat rates across the southern sector differed between slow retreat of the terrestrial margin in western and southern Sweden and rapid retreat of the calving ice margin in the Baltic Basin. Our reconstruction is consistent with much of the published research. However, the synthesis of a large amount of existing and new data support refined reconstructions in some areas. For example, we locate the LGM extent of the ice sheet in northwestern Russia further east than previously suggested and conclude that it occurred at a later time than the rest of the ice sheet, at around 17-15 cal kyr BP, and propose a slightly different chronology of moraine formation over southern Sweden based on improved correlations of moraine segments using new LiDAR data and tying the timing of moraine formation to Greenland ice core cold stages. Retreat rates vary by as much as an order of magnitude in different sectors of the ice sheet, with the lowest rates on the high-elevation and maritime Norwegian margin. Retreat rates compared to the climatic information provided by the Greenland ice core record show a general correspondence between retreat rate and climatic forcing, although a close match between retreat rate and climate is unlikely because of other controls, such as topography and marine versus terrestrial margins. Overall, the time slice reconstructions of Fennoscandian Ice Sheet deglaciation from 22 to 9.7 cal kyr BP provide an important dataset for understanding the contexts that underpin spatial and temporal patterns in retreat of the Fennoscandian Ice Sheet, and are an important resource for testing and refining ice sheet models

Probabilistic Bisimulation: Naturally on Distributions

In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a long-standing open problem concerning the representation of memoryless continuous time by memory-full continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems

Signal Transduction Pathways in the Pentameric Ligand-Gated Ion Channels

The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant sites in the extracellular (EC) domain of the bacterial pLGIC from Gloeobacter violaceus (GLIC). One site is at the C-loop region, where the NQN mutation (D91N, E177Q, and D178N) eliminated inter-subunit salt bridges in the open-channel GLIC structure and thereby shifted the channel activation to a higher agonist concentration. The other site is below the C-loop, where binding of the anesthetic ketamine inhibited GLIC currents in a concentration dependent manner. To understand how a perturbation signal in the EC domain, either resulting from the NQN mutation or ketamine binding, is transduced to the channel gate, we have used the Perturbation-based Markovian Transmission (PMT) model to determine dynamic responses of the GLIC channel and signaling pathways upon initial perturbations in the EC domain of GLIC. Despite the existence of many possible routes for the initial perturbation signal to reach the channel gate, the PMT model in combination with Yen's algorithm revealed that perturbation signals with the highest probability flow travel either via the β1-β2 loop or through pre-TM1. The β1-β2 loop occurs in either intra- or inter-subunit pathways, while pre-TM1 occurs exclusively in inter-subunit pathways. Residues involved in both types of pathways are well supported by previous experimental data on nAChR. The direct coupling between pre-TM1 and TM2 of the adjacent subunit adds new insight into the allosteric signaling mechanism in pLGICs. © 2013 Mowrey et al

Frontmatter: Mining Android User Interfaces at Scale

We introduce Frontmatter: the largest open-access dataset containing user interface models of about 160,000 Android apps. Frontmatter opens the door for comprehensive mining of mobile user interfaces, jumpstarting empirical research at a large scale, addressing questions such as "How many travel apps require registration?", "Which apps do not follow accessibility guidelines?", "Does the user interface correspond to the description?", and many more. The Frontmatter UI analysis tool and the Frontmatter dataset are available under an open-source license