Representation of probabilistic scientific knowledge

This article is available through the Brunel Open Access Publishing Fund. Copyright © 2013 Soldatova et al; licensee BioMed Central Ltd.The theory of probability is widely used in biomedical research for data analysis and modelling. In previous work the probabilities of the research hypotheses have been recorded as experimental metadata. The ontology HELO is designed to support probabilistic reasoning, and provides semantic descriptors for reporting on research that involves operations with probabilities. HELO explicitly links research statements such as hypotheses, models, laws, conclusions, etc. to the associated probabilities of these statements being true. HELO enables the explicit semantic representation and accurate recording of probabilities in hypotheses, as well as the inference methods used to generate and update those hypotheses. We demonstrate the utility of HELO on three worked examples: changes in the probability of the hypothesis that sirtuins regulate human life span; changes in the probability of hypotheses about gene functions in the S. cerevisiae aromatic amino acid pathway; and the use of active learning in drug design (quantitative structure activity relation learning), where a strategy for the selection of compounds with the highest probability of improving on the best known compound was used. HELO is open source and available at https://github.com/larisa-soldatova/HELO.This work was partially supported by grant BB/F008228/1 from the UK Biotechnology & Biological Sciences Research Council, from the European Commission under the FP7 Collaborative Programme, UNICELLSYS, KU Leuven GOA/08/008 and ERC Starting Grant 240186

How much of commonsense and legal reasoning is formalizable? A review of conceptual obstacles

Fifty years of effort in artificial intelligence (AI) and the formalization of legal reasoning have produced both successes and failures. Considerable success in organizing and displaying evidence and its interrelationships has been accompanied by failure to achieve the original ambition of AI as applied to law: fully automated legal decision-making. The obstacles to formalizing legal reasoning have proved to be the same ones that make the formalization of commonsense reasoning so difficult, and are most evident where legal reasoning has to meld with the vast web of ordinary human knowledge of the world. Underlying many of the problems is the mismatch between the discreteness of symbol manipulation and the continuous nature of imprecise natural language, of degrees of similarity and analogy, and of probabilities

GenePath: a System for Automated Construction of Genetic Networks from Mutant Data

Motivation: Genetic pathways are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. Results: We have developed GenePath, an intelligent assistant that mimics expert geneticists in the analysis of genetic data. GenePath employs expert-defined patterns to uncover gene relations from the data, and uses these relations as constraints that guide the search for a plausible genetic network. GenePath provides formalism to genetic data analysis, facilitates the consideration of all the available data in a consistent and systematic manner, and aids in the examination of the large number of possible consequences of a planned experiment. It also provides an explanation mechanism that traces back every finding to the pertinent data. GenePath was successfully tested on several genetic problems. Availability: GenePath can be accessed at http://genepath.org. Supplementary information: Supplementary material is available at http://genepath.org/bi-supp

Adaptive Process Management in Cyber-Physical Domains

The increasing application of process-oriented approaches in new challenging cyber-physical domains beyond business computing (e.g., personalized healthcare, emergency management, factories of the future, home automation, etc.) has led to reconsider the level of flexibility and support required to manage complex processes in such domains. A cyber-physical domain is characterized by the presence of a cyber-physical system coordinating heterogeneous ICT components (PCs, smartphones, sensors, actuators) and involving real world entities (humans, machines, agents, robots, etc.) that perform complex tasks in the “physical” real world to achieve a common goal. The physical world, however, is not entirely predictable, and processes enacted in cyber-physical domains must be robust to unexpected conditions and adaptable to unanticipated exceptions. This demands a more flexible approach in process design and enactment, recognizing that in real-world environments it is not adequate to assume that all possible recovery activities can be predefined for dealing with the exceptions that can ensue. In this chapter, we tackle the above issue and we propose a general approach, a concrete framework and a process management system implementation, called SmartPM, for automatically adapting processes enacted in cyber-physical domains in case of unanticipated exceptions and exogenous events. The adaptation mechanism provided by SmartPM is based on declarative task specifications, execution monitoring for detecting failures and context changes at run-time, and automated planning techniques to self-repair the running process, without requiring to predefine any specific adaptation policy or exception handler at design-time

An embodied conversational agent for intelligent web interaction on pandemic crisis communication

In times of crisis, an effective communication mechanism is paramount in providing accurate and timely information to the community. In this paper we study the use of an intelligent embodied conversational agent (EGA) as the front end interface with the public for a Crisis Communication Network Portal (CCNet). The proposed system, CCNet, is an integration of the intelligent conversation agent, AINI, and an Automated Knowledge Extraction Agent (AKEA). AKEA retrieves first hand information from relevant sources such as government departments and news channels. In this paper, we compare the interaction of AINI against two popular search engines, two question answering systems and two conversational systems