Computational Complexity of Atomic Chemical Reaction Networks

Informally, a chemical reaction network is "atomic" if each reaction may be interpreted as the rearrangement of indivisible units of matter. There are several reasonable definitions formalizing this idea. We investigate the computational complexity of deciding whether a given network is atomic according to each of these definitions. Our first definition, primitive atomic, which requires each reaction to preserve the total number of atoms, is to shown to be equivalent to mass conservation. Since it is known that it can be decided in polynomial time whether a given chemical reaction network is mass-conserving, the equivalence gives an efficient algorithm to decide primitive atomicity. Another definition, subset atomic, further requires that all atoms are species. We show that deciding whether a given network is subset atomic is in $\textsf{NP}$, and the problem "is a network subset atomic with respect to a given atom set" is strongly $\textsf{NP}$-$\textsf{Complete}$. A third definition, reachably atomic, studied by Adleman, Gopalkrishnan et al., further requires that each species has a sequence of reactions splitting it into its constituent atoms. We show that there is a $\textbf{polynomial-time algorithm}$ to decide whether a given network is reachably atomic, improving upon the result of Adleman et al. that the problem is $\textbf{decidable}$. We show that the reachability problem for reachably atomic networks is $\textsf{Pspace}$-$\textsf{Complete}$. Finally, we demonstrate equivalence relationships between our definitions and some special cases of another existing definition of atomicity due to Gnacadja

Interrupt Timed Automata: verification and expressiveness

We introduce the class of Interrupt Timed Automata (ITA), a subclass of hybrid automata well suited to the description of timed multi-task systems with interruptions in a single processor environment. While the reachability problem is undecidable for hybrid automata we show that it is decidable for ITA. More precisely we prove that the untimed language of an ITA is regular, by building a finite automaton as a generalized class graph. We then establish that the reachability problem for ITA is in NEXPTIME and in PTIME when the number of clocks is fixed. To prove the first result, we define a subclass ITA- of ITA, and show that (1) any ITA can be reduced to a language-equivalent automaton in ITA- and (2) the reachability problem in this subclass is in NEXPTIME (without any class graph). In the next step, we investigate the verification of real time properties over ITA. We prove that model checking SCL, a fragment of a timed linear time logic, is undecidable. On the other hand, we give model checking procedures for two fragments of timed branching time logic. We also compare the expressive power of classical timed automata and ITA and prove that the corresponding families of accepted languages are incomparable. The result also holds for languages accepted by controlled real-time automata (CRTA), that extend timed automata. We finally combine ITA with CRTA, in a model which encompasses both classes and show that the reachability problem is still decidable. Additionally we show that the languages of ITA are neither closed under complementation nor under intersection

Model-driven engineering of an openCypher engine: using graph queries to compile graph queries

Graph database systems are increasingly adapted for storing and processing heterogeneous network-like datasets. Many challenging applications with near real-time requirements - such as financial fraud detection, on-the-fly model validation and root cause analysis - can be formalised as graph problems and tackled with graph databases efficiently. However, as no standard graph query language has yet emerged, users are subjected to the possibility of vendor lock-in. The openCypher group aims to define an open specification for a declarative graph query language. However, creating an openCypher-compatible query engine requires significant research and engineering efforts. Meanwhile, model-driven language workbenches support the creation of domain-specific languages by providing high-level tools to create parsers, editors and compilers. In this paper, we present an approach to build a compiler and optimizer for openCypher using model-driven technologies, which allows developers to define declarative optimization rules

Data science

Even though it has only entered public perception relatively recently, the term "data science" already means many things to many people. This chapter explores both top-down and bottom-up views on the field, on the basis of which we define data science as "a unique blend of principles and methods from analytics, engineering, entrepreneurship and communication that aim at generating value from the data itself". The chapter then discusses the disciplines that contribute to this "blend", briefly outlining their contributions and giving pointers for readers interested in exploring their backgrounds further

Understanding scientific study via process modeling

This paper argues that scientific studies distinguish themselves from other studies by a combination of their processes, their (knowledge) elements and the roles of these elements. This is supported by constructing a process model. An illustrative example based on Newtonian mechanics shows how scientific knowledge is structured according to the process model. To distinguish scientific studies from research and scientific research, two additional process models are built for such processes. We apply these process models: (1) to argue that scientific progress should emphasize both the process of change and the content of change; (2) to chart the major stages of scientific study development; and (3) to define “science”