Semantic networks

AbstractA semantic network is a graph of the structure of meaning. This article introduces semantic network systems and their importance in Artificial Intelligence, followed by I. the early background; II. a summary of the basic ideas and issues including link types, frame systems, case relations, link valence, abstraction, inheritance hierarchies and logic extensions; and III. a survey of ‘world-structuring’ systems including ontologies, causal link models, continuous models, relevance, formal dictionaries, semantic primitives and intersecting inference hierarchies. Speed and practical implementation are briefly discussed. The conclusion argues for a synthesis of relational graph theory, graph-grammar theory and order theory based on semantic primitives and multiple intersecting inference hierarchies

Systems level analysis of transgenerational spermatogenic inheritance predicts biomarkers and underlying pathways

Transgenerational spermatogenic inheritance of adult male acquired CNS gene expression characteristics has recently been discovered using a Drosophila systems model. In this novel mode of inheritance, transcriptomic alteration induced by the neuroactive drug pentylenetetrazole (PTZ) has been found to leak to future generations. Here, the available microarray gene expression data pertaining to CNS and/or testis of exposed F0 and the resulting F1 and F2 generations has been pooled and analyzed in an unbiased manner at four levels, namely, biological processes and pathways, protein interactome networks, miRNA-targets, and microarray expression profile similarities. Enrichment for processes related to translation, energy metabolism, cell proliferation, cell differentiation, secretion, central nervous system development, germ cell development, gamete generation, wing development, nutrition etc. was observed. Also, ribosome, oxidative phosphorylation and, to a lesser extent, wingless signaling pathway showed overrepresentation. In the proteomic interactome map, the cell cycle gene Ras85D exhibited overinteraction. In miRNA-target network, the fly transgenerational genes showed overrepresentation of mir-315 targets. Transcriptomic matching revealed overlap of transgenerational set with genes related to epigenetic drug treatment, stem cells, Myc targets and miRNA targets. Many of the findings were consistent with the existing epigenetic evidence in complex mammalian traits. Converging evidence suggests that ribosomal RNA and proteins may serve as candidate biomarkers of transgenerational environmental effect. A compelling systems biology frame-work integrative of transgenerational epigenetic inheritance is suggested. Nutrient, circulating peptide hormone, Myc, Wnt, and stem cell signaling pathways constitute the frame-work. The analysis has implications in explaining missing heritability in complex traits including common human disorders. The fly model offers an excellent opportunity to understand somatic and germline communication, and epigenetic memory formation and its retention across generations in molecular details

An Object-Oriented Approach to Knowledge Representation in a Biomedical Domain

An object-oriented approach has been applied to the different stages involved in developing a knowledge base about insulin metabolism. At an early stage the separation of terminological and assertional knowledge was made. The terminological component was developed by medical experts and represented in CORE. An object-oriented knowledge acquisition process was applied to the assertional knowledge. A frame description is proposed which includes features like states and events, inheritance and collaboration. States and events are formalized with qualitative calculus. The terminological knowledge was very useful in the development of the assertional component. It assisteed in understanding the problem domain, and in the implementation stage, it assisted in building good inheritance hierarchies

Software-Architecture Recovery from Machine Code

In this paper, we present a tool, called Lego, which recovers object-oriented software architecture from stripped binaries. Lego takes a stripped binary as input, and uses information obtained from dynamic analysis to (i) group the functions in the binary into classes, and (ii) identify inheritance and composition relationships between the inferred classes. The information obtained by Lego can be used for reengineering legacy software, and for understanding the architecture of software systems that lack documentation and source code. Our experiments show that the class hierarchies recovered by Lego have a high degree of agreement---measured in terms of precision and recall---with the hierarchy defined in the source code

Evaluating Knowledge Representation and Reasoning Capabilites of Ontology Specification Languages

The interchange of ontologies across the World Wide Web (WWW) and the cooperation among heterogeneous agents placed on it is the main reason for the development of a new set of ontology specification languages, based on new web standards such as XML or RDF. These languages (SHOE, XOL, RDF, OIL, etc) aim to represent the knowledge contained in an ontology in a simple and human-readable way, as well as allow for the interchange of ontologies across the web. In this paper, we establish a common framework to compare the expressiveness of "traditional" ontology languages (Ontolingua, OKBC, OCML, FLogic, LOOM) and "web-based" ontology languages. As a result of this study, we conclude that different needs in KR and reasoning may exist in the building of an ontology-based application, and these needs must be evaluated in order to choose the most suitable ontology language(s)

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology