We propose analyzing conditional reasoning by appeal to a notion of intervention on a simulation program, formalizing and subsuming a number of approaches to conditional thinking in the recent AI literature. Our main results include a series of axiomatizations, allowing comparison between this framework and existing frameworks (normality-ordering models, causal structural equation models), and a complexity result establishing NP-completeness of the satisfiability problem. Perhaps surprisingly, some of the basic logical principles common to all existing approaches are invalidated in our causal simulation approach. We suggest that this additional flexibility is important in modeling some intuitive examples.

We present a consequence-based calculus for concept subsumption and classification in the description logic ALCHOIQ, which extends ALC with role hierarchies, inverse roles, number restrictions, and nominals. By using standard transformations, our calculus extends to SROIQ, which covers all of OWL 2 DL except for datatypes. A key feature of our calculus is its pay-as-you-go behaviour: unlike existing algorithms, our calculus is worst-case optimal for all the well-known proper fragments of ALCHOIQ, albeit not for the full logic.

In this paper, we propose a variant of Answer Set Programming (ASP) with evaluable functions that extends their application to sets of objects, something that allows a fully logical treatment of aggregates. Formally, we start from the syntax of First Order Logic with equality and the semantics of Quantified Equilibrium Logic with evaluable functions (QELF). Then, we proceed to incorporate a new kind of logical term, intensional set (a construct commonly used to denote the set of objects characterised by a given formula), and to extend QELF semantics for this new type of expression. In our extended approach, intensional sets can be arbitrarily used as predicate or function arguments or even nested inside other intensional sets, just as regular first-order logical terms. As a result, aggregates can be naturally formed by the application of some evaluable function (count, sum, maximum, etc) to a set of objects expressed as an intensional set. This approach has several advantages. First, while other semantics for aggregates depend on some syntactic transformation (either via a reduct or a formula translation), the QELF interpretation treats them as regular evaluable functions, providing a compositional semantics and avoiding any kind of syntactic restriction. Second, aggregates can be explicitly defined now within the logical language by the simple addition of formulas that fix their meaning in terms of multiple applications of some (commutative and associative) binary operation. For instance, we can use recursive rules to define sum in terms of integer addition. Last, but not least, we prove that the semantics we obtain for aggregates coincides with the one defined by Gelfond and Zhang for the Alog language, when we restrict to that syntactic fragment. (Under consideration for acceptance in TPLP)

Logic Programs with Ordered Disjunction (LPOD) is an extension of standard answer set programs to handle preference using the construct of ordered disjunction, and CR-Prolog2 is an extension of standard answer set programs with consistency restoring rules and LPOD-like ordered disjunction. We present reductions of each of these languages into the standard ASP language, which gives us an alternative way to understand the extensions in terms of the standard ASP language.

We present a probabilistic extension of action language BC+. Just like BC+ is defined as a high-level notation of answer set programs for describing transition systems, the proposed language, which we call pBC+, is defined as a high-level notation of LPMLN programs---a probabilistic extension of answer set programs. We show how probabilistic reasoning about transition systems, such as prediction, postdiction, and planning problems, as well as probabilistic diagnosis for dynamic domains, can be modeled in pBC+ and computed using an implementation of LPMLN.

Evolutionary Biologists have long struggled with the challenge of developing analysis workflows in a flexible manner, thus facilitating the reuse of phylogenetic knowledge. An evolutionary biology workflow can be viewed as a plan which composes web services that can retrieve, manipulate, and produce phylogenetic trees. The Phylotastic project was launched two years ago as a collaboration between evolutionary biologists and computer scientists, with the goal of developing an open architecture to facilitate the creation of such analysis workflows. While composition of web services is a problem that has been extensively explored in the literature, including within the logic programming domain, the incarnation of the problem in Phylotastic provides a number of additional challenges. Along with the need to integrate preferences and formal ontologies in the description of the desired workflow, evolutionary biologists tend to construct workflows in an incremental manner, by successively refining the workflow, by indicating desired changes (e.g., exclusion of certain services, modifications of the desired output). This leads to the need of successive iterations of incremental replanning, to develop a new workflow that integrates the requested changes while minimizing the changes to the original workflow. This paper illustrates how Phylotastic has addressed the challenges of creating and refining phylogenetic analysis workflows using logic programming technology and how such solutions have been used within the general framework of the Phylotastic project.

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model-reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. Multiscale modeling benefits from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects, we define semantics-preserving implementation and semantics-approximating model reduction transformations, and we outline a "meta-hierarchy" for organizing declarative models and the mathematical methods that can fruitfully manipulate them.

We show how a bi-directional grammar can be used to specify and verbalise answer set programs in controlled natural language. We start from a program specification in controlled natural language and translate this specification automatically into an executable answer set program. The resulting answer set program can be modified following certain naming conventions and the revised version of the program can then be verbalised in the same subset of natural language that was used as specification language. The bi-directional grammar is parametrised for processing and generation, deals with referring expressions, and exploits symmetries in the data structure of the grammar rules whenever these grammar rules need to be duplicated. We demonstrate that verbalisation requires sentence planning in order to aggregate similar structures with the aim to improve the readability of the generated specification. Without modifications, the generated specification is always semantically equivalent to the original one; our bi-directional grammar is the first one that allows for semantic round-tripping in the context of controlled natural language processing. This paper is under consideration for acceptance in TPLP.

The standard approach in AI is to take a set of positive examples and a set of negative examples. We seek for a function that says "YES" for the positive examples given, and "NO" for the negative examples given. Using the function found, we begin to predict the right answer for examples which we do not know whether are positive or negative. In essence, the standard approach in AI represents an approximation. What is sought for is an approximation function. It is usually sought for in a given set of functions.

We generalize, by a progressive procedure, the notions of conjunction and disjunction of two conditional events to the case of $n$ conditional events. In our coherence-based approach, conjunctions and disjunctions are suitable conditional random quantities. We define the notion of negation, by verifying De Morgan's Laws. We also show that conjunction and disjunction satisfy the associative and commutative properties, and a monotonicity property. Then, we give some results on coherence of prevision assessments for some families of compounded conditionals; in particular we examine the Fr\'echet-Hoeffding bounds. Moreover, we study the reverse probabilistic inference from the conjunction $\mathcal{C}_{n+1}$ of $n+1$ conditional events to the family $\{\mathcal{C}_{n},E_{n+1}|H_{n+1}\}$. We consider the relation with the notion of quasi-conjunction and we examine in detail the coherence of the prevision assessments related with the conjunction of three conditional events. Based on conjunction, we also give a characterization of p-consistency and of p-entailment, with applications to several inference rules in probabilistic nonmonotonic reasoning. Finally, we examine some non p-valid inference rules; then, we illustrate by an example two methods which allow to suitably modify non p-valid inference rules in order to get inferences which are p-valid.