52,613 research outputs found
Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences
Coding information is the main source of heterogeneity
(non-randomness) in the sequences of bacterial genomes. This
information can be naturally modeled by analysing cluster structures in the ``in-phase'' triplet distributions of relatively short genomic fragments (200-400bp). We found a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties.
The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic ``pure'' types of this model, observed in nature: ``parallel triangles'', ``perpendicular triangles'',
degenerated case and the flower-like type. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea).
All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site:
http://www.ihes.fr/~zinovyev/7clusters
The finding can be readily introduced into any software for gene prediction, sequence alignment or bacterial genomes classification
An agent-driven semantical identifier using radial basis neural networks and reinforcement learning
Due to the huge availability of documents in digital form, and the deception
possibility raise bound to the essence of digital documents and the way they
are spread, the authorship attribution problem has constantly increased its
relevance. Nowadays, authorship attribution,for both information retrieval and
analysis, has gained great importance in the context of security, trust and
copyright preservation. This work proposes an innovative multi-agent driven
machine learning technique that has been developed for authorship attribution.
By means of a preprocessing for word-grouping and time-period related analysis
of the common lexicon, we determine a bias reference level for the recurrence
frequency of the words within analysed texts, and then train a Radial Basis
Neural Networks (RBPNN)-based classifier to identify the correct author. The
main advantage of the proposed approach lies in the generality of the semantic
analysis, which can be applied to different contexts and lexical domains,
without requiring any modification. Moreover, the proposed system is able to
incorporate an external input, meant to tune the classifier, and then
self-adjust by means of continuous learning reinforcement.Comment: Published on: Proceedings of the XV Workshop "Dagli Oggetti agli
Agenti" (WOA 2014), Catania, Italy, Sepember. 25-26, 201
Extending the Modern Synthesis: The evolution of ecosystems
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis
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
Neurocognitive Informatics Manifesto.
Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given
Semantic distillation: a method for clustering objects by their contextual specificity
Techniques for data-mining, latent semantic analysis, contextual search of
databases, etc. have long ago been developed by computer scientists working on
information retrieval (IR). Experimental scientists, from all disciplines,
having to analyse large collections of raw experimental data (astronomical,
physical, biological, etc.) have developed powerful methods for their
statistical analysis and for clustering, categorising, and classifying objects.
Finally, physicists have developed a theory of quantum measurement, unifying
the logical, algebraic, and probabilistic aspects of queries into a single
formalism. The purpose of this paper is twofold: first to show that when
formulated at an abstract level, problems from IR, from statistical data
analysis, and from physical measurement theories are very similar and hence can
profitably be cross-fertilised, and, secondly, to propose a novel method of
fuzzy hierarchical clustering, termed \textit{semantic distillation} --
strongly inspired from the theory of quantum measurement --, we developed to
analyse raw data coming from various types of experiments on DNA arrays. We
illustrate the method by analysing DNA arrays experiments and clustering the
genes of the array according to their specificity.Comment: Accepted for publication in Studies in Computational Intelligence,
Springer-Verla
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