Probabilistic reasoning with a bayesian DNA device based on strand displacement

We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a specific molecular signal (evidence). The program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different DNA complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded DNA species whose relative proportion represents the application of Bayes? Law: the conditional probability of the disease given the signal. The models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro

Towards an Effective Decision Procedure for LTL formulas with Constraints

This paper presents an ongoing work that is part of a more wide-ranging project whose final scope is to define a method to validate LTL formulas w.r.t. a program written in the timed concurrent constraint language tccp, which is a logic concurrent constraint language based on the concurrent constraint paradigm of Saraswat. Some inherent notions to tccp processes are non-determinism, dealing with partial information in states and the monotonic evolution of the information. In order to check an LTL property for a process, our approach is based on the abstract diagnosis technique. The concluding step of this technique needs to check the validity of an LTL formula (with constraints) in an effective way. In this paper, we present a decision method for the validity of temporal logic formulas (with constraints) built by our abstract diagnosis technique.Comment: Part of WLPE 2013 proceedings (arXiv:1308.2055

Probabilistic Dynamic Logic of Phenomena and Cognition

The purpose of this paper is to develop further the main concepts of Phenomena Dynamic Logic (P-DL) and Cognitive Dynamic Logic (C-DL), presented in the previous paper. The specific character of these logics is in matching vagueness or fuzziness of similarity measures to the uncertainty of models. These logics are based on the following fundamental notions: generality relation, uncertainty relation, simplicity relation, similarity maximization problem with empirical content and enhancement (learning) operator. We develop these notions in terms of logic and probability and developed a Probabilistic Dynamic Logic of Phenomena and Cognition (P-DL-PC) that relates to the scope of probabilistic models of brain. In our research the effectiveness of suggested formalization is demonstrated by approximation of the expert model of breast cancer diagnostic decisions. The P-DL-PC logic was previously successfully applied to solving many practical tasks and also for modelling of some cognitive processes.Comment: 6 pages, WCCI 2010 IEEE World Congress on Computational Intelligence July, 18-23, 2010 - CCIB, Barcelona, Spain, IJCNN, IEEE Catalog Number: CFP1OUS-DVD, ISBN: 978-1-4244-6917-8, pp. 3361-336

Abstract Diagnosis for Timed Concurrent Constraint programs

The Timed Concurrent Constraint Language (tccp in short) is a concurrent logic language based on the simple but powerful concurrent constraint paradigm of Saraswat. In this paradigm, the notion of store-as-value is replaced by the notion of store-as-constraint, which introduces some differences w.r.t. other approaches to concurrency. In this paper, we provide a general framework for the debugging of tccp programs. To this end, we first present a new compact, bottom-up semantics for the language that is well suited for debugging and verification purposes in the context of reactive systems. We also provide an abstract semantics that allows us to effectively implement debugging algorithms based on abstract interpretation. Given a tccp program and a behavior specification, our debugging approach automatically detects whether the program satisfies the specification. This differs from other semiautomatic approaches to debugging and avoids the need to provide symptoms in advance. We show the efficacy of our approach by introducing two illustrative examples. We choose a specific abstract domain and show how we can detect that a program is erroneous.Comment: 16 page

Abduction in Well-Founded Semantics and Generalized Stable Models

Abductive logic programming offers a formalism to declaratively express and solve problems in areas such as diagnosis, planning, belief revision and hypothetical reasoning. Tabled logic programming offers a computational mechanism that provides a level of declarativity superior to that of Prolog, and which has supported successful applications in fields such as parsing, program analysis, and model checking. In this paper we show how to use tabled logic programming to evaluate queries to abductive frameworks with integrity constraints when these frameworks contain both default and explicit negation. The result is the ability to compute abduction over well-founded semantics with explicit negation and answer sets. Our approach consists of a transformation and an evaluation method. The transformation adjoins to each objective literal $O$ in a program, an objective literal $not(O)$ along with rules that ensure that $not(O)$ will be true if and only if $O$ is false. We call the resulting program a {\em dual} program. The evaluation method, \wfsmeth, then operates on the dual program. \wfsmeth{} is sound and complete for evaluating queries to abductive frameworks whose entailment method is based on either the well-founded semantics with explicit negation, or on answer sets. Further, \wfsmeth{} is asymptotically as efficient as any known method for either class of problems. In addition, when abduction is not desired, \wfsmeth{} operating on a dual program provides a novel tabling method for evaluating queries to ground extended programs whose complexity and termination properties are similar to those of the best tabling methods for the well-founded semantics. A publicly available meta-interpreter has been developed for \wfsmeth{} using the XSB system.Comment: 48 pages; To appear in Theory and Practice in Logic Programmin