Argumentation in biology : exploration and analysis through a gene expression use case

Argumentation theory conceptualises the human practice of debating. Implemented as computational argumentation it enables a computer to perform a virtual debate. Using existing knowledge from research into argumentation theory, this thesis investigates the potential of computational argumentation within biology. As a form of non-monotonic reasoning, argumentation can be used to tackle inconsistent and incomplete information - two common problems for the users of biological data. Exploration of argumentation shall be conducted by examining these issues within one biological subdomain: in situ gene expression information for the developmental mouse. Due to the complex and often contradictory nature of biology, occasionally it is not apparent whether or not a particular gene is involved in the development of a particular tissue. Expert biological knowledge is recorded, and used to generate arguments relating to this matter. These arguments are presented to the user in order to help him/her decide whether or not the gene is expressed. In order to do this, the notion of argumentation schemes has been borrowed from philosophy, and combined with ideas and technologies from arti cial intelligence. The resulting conceptualisation is implemented and evaluated in order to understand the issues related to applying computational argumentation within biology. Ultimately, this work concludes with a discussion of Argudas - a real world tool developed for the biological community, and based on the knowledge gained during this work

The ss-semantics approach; theory and applications

AbstractThis paper is a general overview of an approach to the semantics of logic programs whose aim is to find notions of models which really capture the operational semantics, and are, therefore, useful for defining program equivalences and for semantics-based program analysis. The approach leads to the introduction of extended interpretations which are more expressive than Herbrand interpretations. The semantics in terms of extended interpretations can be obtained as a result of both an operational (top-down) and a fixpoint (bottom-up) construction. It can also be characterized from the model-theoretic viewpoint, by defining a set of extended models which contains standard Herbrand models. We discuss the original construction modeling computed answer substitutions, its compositional version, and various semantics modeling more concrete observables. We then show how the approach can be applied to several extensions of positive logic programs. We finally consider some applications, mainly in the area of semantics-based program transformation and analysis

Dagstuhl News January - December 2001

"Dagstuhl News" is a publication edited especially for the members of the Foundation "Informatikzentrum Schloss Dagstuhl" to thank them for their support. The News give a summary of the scientific work being done in Dagstuhl. Each Dagstuhl Seminar is presented by a small abstract describing the contents and scientific highlights of the seminar as well as the perspectives or challenges of the research topic

Constructive Reasoning for Semantic Wikis

One of the main design goals of social software, such as wikis, is to support and facilitate interaction and collaboration. This dissertation explores challenges that arise from extending social software with advanced facilities such as reasoning and semantic annotations and presents tools in form of a conceptual model, structured tags, a rule language, and a set of novel forward chaining and reason maintenance methods for processing such rules that help to overcome the challenges. Wikis and semantic wikis were usually developed in an ad-hoc manner, without much thought about the underlying concepts. A conceptual model suitable for a semantic wiki that takes advanced features such as annotations and reasoning into account is proposed. Moreover, so called structured tags are proposed as a semi-formal knowledge representation step between informal and formal annotations. The focus of rule languages for the Semantic Web has been predominantly on expert users and on the interplay of rule languages and ontologies. KWRL, the KiWi Rule Language, is proposed as a rule language for a semantic wiki that is easily understandable for users as it is aware of the conceptual model of a wiki and as it is inconsistency-tolerant, and that can be efficiently evaluated as it builds upon Datalog concepts. The requirement for fast response times of interactive software translates in our work to bottom-up evaluation (materialization) of rules (views) ahead of time – that is when rules or data change, not when they are queried. Materialized views have to be updated when data or rules change. While incremental view maintenance was intensively studied in the past and literature on the subject is abundant, the existing methods have surprisingly many disadvantages – they do not provide all information desirable for explanation of derived information, they require evaluation of possibly substantially larger Datalog programs with negation, they recompute the whole extension of a predicate even if only a small part of it is affected by a change, they require adaptation for handling general rule changes. A particular contribution of this dissertation consists in a set of forward chaining and reason maintenance methods with a simple declarative description that are efficient and derive and maintain information necessary for reason maintenance and explanation. The reasoning methods and most of the reason maintenance methods are described in terms of a set of extended immediate consequence operators the properties of which are proven in the classical logical programming framework. In contrast to existing methods, the reason maintenance methods in this dissertation work by evaluating the original Datalog program – they do not introduce negation if it is not present in the input program – and only the affected part of a predicate’s extension is recomputed. Moreover, our methods directly handle changes in both data and rules; a rule change does not need to be handled as a special case. A framework of support graphs, a data structure inspired by justification graphs of classical reason maintenance, is proposed. Support graphs enable a unified description and a formal comparison of the various reasoning and reason maintenance methods and define a notion of a derivation such that the number of derivations of an atom is always finite even in the recursive Datalog case. A practical approach to implementing reasoning, reason maintenance, and explanation in the KiWi semantic platform is also investigated. It is shown how an implementation may benefit from using a graph database instead of or along with a relational database

An overview of artificial intelligence and robotics. Volume 1: Artificial intelligence. Part C: Basic AI topics

Readily understandable overviews of search oriented problem solving, knowledge representation, and computational logic are provided. Mechanization, automation and artificial intelligence are discussed as well as how they interrelate

A unifying approach for queries and updates in deductive databases

This dissertation presents a unifying approach to process (recursive) queries and updates in a deductive database. To improve query performance, a combined top-down and bottom-up evaluation method is used to compile rules into iterative programs that contain relational algebra operators. This method is based on the lemma resolution that retains previous results to guarantee termination.Due to locality in database processing, it is desirable to materialize frequently used queries against views of the database. Unfortunately, if updates are allowed, maintaining materialized view tables becomes a major problem. We propose to materialize views incrementally, as queries are being answered. Hence views in our approach are only partially materialized. For such views, we design algorithms to perform updates only when the underlying view tables are actually affected.We compare our approach to two conventional methods for dealing with views: total materialization and query-modification. The first method materializes the entire view when it is defined while the second recomputes the view on the fly without maintaining any physical view tables. We demonstrate that our approach is a compromise between these two methods and performs better than either one in many situations.It is also desirable to be able to update views just like updating base tables. However, view updates are inherently ambiguous and the semantics of update propagation on recursively defined views were not well understood in the past. Using dynamic logic programming and lemma resolution, we are able to define the semantics of recursive view updates. These are expressed in the form of update translators specified by the database administrator when the view is defined. To guarantee completeness, we identify a subset of safe update translators. We prove that this subset of translators always terminate and are complete

Belief systems for persuasive discourse planning

This thesis is concerned with the problem of construction of the logical structure of a persuasive discourse. A persuasive discourse can be defined as a monodirectional form of communication, generated by a speaker in order to convince a hearer about the validity (or fallacy) of a specific belief The construction of the structure of a persuasive discourse is realized, in this work, through the adoption of two basic elements: a belief system and a planning system. The planning system is used as a tool for the automatic generation of the discourse structure (or plan), obtained through the decomposition of the assigned (communicative) goals of persuasion, aimed at producing specific effects on the hearer’s beliefs. The belief system is adopted in order to endow the planning process with a formal language of beliefs for the representation of such goals, and with the mechanisms which govern the propagation of their (expected) effects on the rest of the hearer's belief state. The main results presented consist of the formalization of a paradigm for specification of belief systems, and of a method — whose correctness is formally proved — for their integration with planning systems. The formalization of a belief system for discourse structure representation (defined in accordance with the theoretical paradigm) is also given, together with the description of its implementation and integration with a specific planner, which resulted in the actual completion of a system for the automatic generation of persuasive discourse plans