Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics

A conceptual architecture for semantic web services development and deployment

Several extensions of the Web Services Framework (WSF) have been proposed. The combination with Semantic Web technologies introduces a notion of semantics, which can enhance scalability through automation. Service composition to processes is an equally important issue. Ontology technology – the core of the Semantic Web – can be the central building block of an extension endeavour. We present a conceptual architecture for ontology-based Web service development and deployment. The development of service-based software systems within the WSF is gaining increasing importance. We show how ontologies can integrate models, languages, infrastructure, and activities within this architecture to support reuse and composition of semantic Web services

Four domains of complexity

In this short paper, which reflects on one of my contributions to the systems literature in 1992 (Pluralism and the Legitimation of Systems Science), I discuss the context at that time. Systems scientists were embroiled in a paradigm war, which threatened to fragment the systems research community. This is relevant, not only to understanding my 1992 contribution, but also because the same paradigms are evident in the complexity science community, and therefore it potentially faces the same risk of fragmentation. Having explained the context, I then go on to discuss my proposed solution to the paradigm war: that there are four domains of complexity, three of which reflect the competing paradigms. The problem comes when researchers say that inquiry into just one of these domains is valid. However, when we recognise all four as part of a new theory of complexity, we can view them as complementary. The four domains are natural world complexity, or “what is” (where the ideal of inquiry is truth); social world complexity, or the complexity of “what ought to be” in relation to actual or potential action (where the ideal of inquiry is rightness); subjective world complexity, or the complexity of what any individual (the self or another) is thinking, intending or feeling (where the ideal of inquiry is understanding subjectivity); and the complexity of interactions between elements of the other domains of complexity in the context of research and intervention practice. Following a discussion of the relevance of this theory for complexity scientists, I end the paper with a final critical reflection on my 1992 paper, pointing to some theoretical assumptions and terminology that I would, in retrospect, revise

A Boxology of Design Patterns for Hybrid Learning and Reasoning Systems

We propose a set of compositional design patterns to describe a large variety of systems that combine statistical techniques from machine learning with symbolic techniques from knowledge representation. As in other areas of computer science (knowledge engineering, software engineering, ontology engineering, process mining and others), such design patterns help to systematize the literature, clarify which combinations of techniques serve which purposes, and encourage re-use of software components. We have validated our set of compositional design patterns against a large body of recent literature.Comment: 12 pages,55 reference

Comparing knowledge sources for nominal anaphora resolution

We compare two ways of obtaining lexical knowledge for antecedent selection in other-anaphora and definite noun phrase coreference. Specifically, we compare an algorithm that relies on links encoded in the manually created lexical hierarchy WordNet and an algorithm that mines corpora by means of shallow lexico-semantic patterns. As corpora we use the British National Corpus (BNC), as well as the Web, which has not been previously used for this task. Our results show that (a) the knowledge encoded in WordNet is often insufficient, especially for anaphor-antecedent relations that exploit subjective or context-dependent knowledge; (b) for other-anaphora, the Web-based method outperforms the WordNet-based method; (c) for definite NP coreference, the Web-based method yields results comparable to those obtained using WordNet over the whole dataset and outperforms the WordNet-based method on subsets of the dataset; (d) in both case studies, the BNC-based method is worse than the other methods because of data sparseness. Thus, in our studies, the Web-based method alleviated the lexical knowledge gap often encountered in anaphora resolution, and handled examples with context-dependent relations between anaphor and antecedent. Because it is inexpensive and needs no hand-modelling of lexical knowledge, it is a promising knowledge source to integrate in anaphora resolution systems