A Novel Hybrid Logic-ODE Modeling Approach to Overcome Knowledge Gaps

Mathematical modeling allows using different formalisms to describe, investigate, and understand biological processes. However, despite the advent of high-throughput experimental techniques, quantitative information is still a challenge when looking for data to calibrate model parameters. Furthermore, quantitative formalisms must cope with stiffness and tractability problems, more so if used to describe multicellular systems. On the other hand, qualitative models may lack the proper granularity to describe the underlying kinetic processes. We propose a hybrid modeling approach that integrates ordinary differential equations and logical formalism to describe distinct biological layers and their communication. We focused on a multicellular system as a case study by applying the hybrid formalism to the well-known Delta-Notch signaling pathway. We used a differential equation model to describe the intracellular pathways while the cell–cell interactions were defined by logic rules. The hybrid approach herein employed allows us to combine the pros of different modeling techniques by overcoming the lack of quantitative information with a qualitative description that discretizes activation and inhibition processes, thus avoiding complexity.

Plan recognition in dynamic 2-D environments

We look at the relatively unexplored problem of plan recognition applied to motion in 2-D environments where all moving objects are modelled as circles. Golog is a well-known high level logical language for solving planning problems and specifying agent controllers. Few studies have applied Golog to plan recognition. We use some of the features of this language, but its standard interpreter is adapted to solving plan recognition problems. This thesis makes several other contributions. First, plan recognition procedures are formulated as finite automata and expressed as Golog programs. Second, we elaborate a logical formalism for reasoning about depth and motion from an observer's viewpoint. We not only expand on this situation calculus based formalism, but also apply it to tackle plan recognition problems in the traffic domain. The proposed approach is implemented and thoroughly tested on recognizing simple behaviours such as left turns, right turns, and overtaking.

Plan recognition in dynamic 2-D environments

We look at the relatively unexplored problem of plan recognition applied to motion in 2-D environments where all moving objects are modelled as circles. Golog is a well-known high level logical language for solving planning problems and specifying agent controllers. Few studies have applied Golog to plan recognition. We use some of the features of this language, but its standard interpreter is adapted to solving plan recognition problems. This thesis makes several other contributions. First, plan recognition procedures are formulated as finite automata and expressed as Golog programs. Second, we elaborate a logical formalism for reasoning about depth and motion from an observer's viewpoint. We not only expand on this situation calculus based formalism, but also apply it to tackle plan recognition problems in the traffic domain. The proposed approach is implemented and thoroughly tested on recognizing simple behaviours such as left turns, right turns, and overtaking.

Labelled cyclic proofs for separation logic

Separation logic (SL) is a logical formalism for reasoning about programs that use pointers to mutate data structures. It is successful for program verification as an assertion language to state properties about memory heaps using Hoare triples. Most of the proof systems and verification tools for ${\textrm{SL}}$ focus on the decidable but rather restricted symbolic heaps fragment. Moreover, recent proof systems that go beyond symbolic heaps are purely syntactic or labelled systems dedicated to some fragments of ${\textrm{SL}}$ and they mainly allow either the full set of connectives, or the definition of arbitrary inductive predicates, but not both. In this work, we present a labelled proof system, called ${\textrm{G}_{\textrm{SL}}}$, that allows both the definition of cyclic proofs with arbitrary inductive predicates and the full set of SL connectives. We prove its soundness and show that we can derive in ${\textrm{G}_{\textrm{SL}}}$ the built-in rules for data structures of another non-cyclic labelled proof system and also that ${\textrm{G}_{\textrm{SL}}}$ is strictly more powerful than that system.

The Influence of the Test Operator on the Expressive Power of PDL-like Logics

Berman and Paterson proved that test-free propositional dynamic logic (PDL) is weaker than PDL. One would raise questions: does a similar result also hold for extensions of PDL? For example, is test-free converse-PDL (CPDL) weaker than CPDL? In what circumstances the test operator can be eliminated without reducing the expressive power of a PDL-based logical formalism? These problems have not yet been studied. As the description logics $\mathcal{ALC}_{trans}$ and $\mathcal{ALC}_{reg}$ are, respectively, variants of test-free PDL and PDL, there is a concept of $\mathcal{ALC}_{reg}$ that is not equivalent to any concept of $\mathcal{ALC}_{trans}$. Generalizing this, we prove that there is a concept of $\mathcal{ALC}_{reg}$ that is not equivalent to any concept of the logic that extends $\mathcal{ALC}_{trans}$ with inverse roles, nominals, qualified number restrictions, the universal role and local reflexivity of roles. We also provide some results for the case with RBoxes and TBoxes. One of them states that tests can be eliminated from TBoxes of the deterministic Horn fragment of $\mathcal{ALC}_{reg}$.

Logical modelling and analysis of cellular regulatory networks with GINsim 3.0

The logical formalism is well adapted to model large cellular networks, for which detailed kinetic data are scarce. This tutorial focuses on this well-established qualitative framework. Relying on GINsim (release 3.0), a software implementing this formalism, we guide the reader step by step towards the definition, the analysis and the simulation of a four-node model of the mammalian p53-Mdm2 network.

Computational logic: its origins and applications

Computational logic is the use of computers to establish facts in a logical formalism. Originating in nineteenth century attempts to understand the nature of mathematical reasoning, the subject now comprises a wide variety of formalisms, techniques and technologies. One strand of work follows the ‘logic for computable functions (LCF) approach’ pioneered by Robin Milner, where proofs can be constructed interactively or with the help of users’ code (which does not compromise correctness). A refinement of LCF, called Isabelle, retains these advantages while providing flexibility in the choice of logical formalism and much stronger automation. The main application of these techniques has been to prove the correctness of hardware and software systems, but increasingly researchers have been applying them to mathematics itself.

Constraint-Based Modeling in Systems Biology

The idea of constraint-based modeling in systems biology is to describe a biological system by a set of constraints, i.e., by pieces of partial information about its structure and dynamics. Using constraint-based reasoning one may then draw conclusions about the possible system behaviors.In this talk, we will focus on constraint-based modeling techniques for regulatory networks starting from the discrete logical formalism of René Thomas. In this framework, logic and constraints arise at two different levels. On the one hand, Boolean or multi-valued logic formulae provide a natural way to represent the structure of a regulatory network, which is given by positive and negative interactions (i.e., activation and inhibition) between the network components. On the other hand, temporal logic formulae (e.g. CTL) may be used to reason about the dynamics of the system, represented by a state transition graph or Kripke model.

Fenomenologi-Ekonomi Islam: Lit Review atas Epistemologi Ekonomi Islam Masudul Alam Choudhury

Islamic economics is difference with the positivism economics and others. It is a established-concessus among Muslim-economists. Albeit some scholars are still sceptical toward Islamic economics as a complete-science. To respond this assumption, various Islamic scholars who are concern in formulating the epistemology of Islamic Economics. Turast written by classical muslim scholars studied intensively. And also Masudul Alam Choudhury who have intensively research the epistemology of Islamic economics with uniqueness form of epistemology—named by the phenomenology of Islamic economics. This paper examine radically the essensy of Masudul Alam Choudhury. It is to identify the construction of Islamic economics metodology offered by Choudhury. Keywords : Phenomenology, Unity of Knowledge, Islamic Economics, Phenomenology methodology and logical formalism.

Reconstructing Arguments

Traditional logical reconstruction of arguments aims at assessing the validity of ordinary language arguments. It involves several tasks: extracting argumentations from texts, breaking up complex argumentations into individual arguments, framing arguments in standard form, as well as formalizing arguments and showing their validity with the help of a logical formalism. These tasks are guided by a multitude of partly antagonistic goals, they interact in various feedback loops, and they are intertwined with the development of theories of valid inference and adequate formalization. This paper explores how the method of reflective equilibrium can be used for modelling the complexity of such reconstructions and for justifying the various steps involved. The proposed approach is illustrated and tested in a detailed reconstruction of the beginning of Anselm’s De casu diaboli.