Kolmogorov Complexity in perspective. Part II: Classification, Information Processing and Duality

We survey diverse approaches to the notion of information: from Shannon entropy to Kolmogorov complexity. Two of the main applications of Kolmogorov complexity are presented: randomness and classification. The survey is divided in two parts published in a same volume. Part II is dedicated to the relation between logic and information system, within the scope of Kolmogorov algorithmic information theory. We present a recent application of Kolmogorov complexity: classification using compression, an idea with provocative implementation by authors such as Bennett, Vitanyi and Cilibrasi. This stresses how Kolmogorov complexity, besides being a foundation to randomness, is also related to classification. Another approach to classification is also considered: the so-called "Google classification". It uses another original and attractive idea which is connected to the classification using compression and to Kolmogorov complexity from a conceptual point of view. We present and unify these different approaches to classification in terms of Bottom-Up versus Top-Down operational modes, of which we point the fundamental principles and the underlying duality. We look at the way these two dual modes are used in different approaches to information system, particularly the relational model for database introduced by Codd in the 70's. This allows to point out diverse forms of a fundamental duality. These operational modes are also reinterpreted in the context of the comprehension schema of axiomatic set theory ZF. This leads us to develop how Kolmogorov's complexity is linked to intensionality, abstraction, classification and information system.Comment: 43 page

Soft peer review: social software and distributed scientific evaluation

The debate on the prospects of peer-review in the Internet age and the increasing criticism leveled against the dominant role of impact factor indicators are calling for new measurable criteria to assess scientific quality. Usage-based metrics offer a new avenue to scientific quality assessment but face the same risks as first generation search engines that used unreliable metrics (such as raw traffic data) to estimate content quality. In this article I analyze the contribution that social bookmarking systems can provide to the problem of usage-based metrics for scientific evaluation. I suggest that collaboratively aggregated metadata may help fill the gap between traditional citation-based criteria and raw usage factors. I submit that bottom-up, distributed evaluation models such as those afforded by social bookmarking will challenge more traditional quality assessment models in terms of coverage, efficiency and scalability. Services aggregating user-related quality indicators for online scientific content will come to occupy a key function in the scholarly communication system

Query-Based Sampling using Only Snippets

Query-based sampling is a popular approach to model the content of an uncooperative server. It works by sending queries to the server and downloading the returned documents in the search results in full. This sample of documents then represents the server’s content. We present an approach that uses the document snippets as samples instead of downloading entire documents. This yields more stable results at the same amount of bandwidth usage as the full document approach. Additionally, we show that using snippets does not necessarily incur more latency, but can actually save time

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

Mapping for the Masses: Accessing Web 2.0 through Crowdsourcing

The authors describe how we are harnessing the power of web 2.0 technologies to create new approaches to collecting, mapping, and sharing geocoded data. The authors begin with GMapCreator that lets users fashion new maps using Google Maps as a base. The authors then describe MapTube that enables users to archive maps and demonstrate how it can be used in a variety of contexts to share map information, to put existing maps into a form that can be shared, and to create new maps from the bottom-up using a combination of crowdcasting, crowdsourcing, and traditional broadcasting. The authors conclude by arguing that such tools are helping to define a neogeography that is essentially "mapping for the masses,'' while noting that there are many issues of quality, accuracy, copyright, and trust that will influence the impact of these tools on map-based communication

Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

Query-Based Sampling using Snippets

Query-based sampling is a commonly used approach to model the content of servers. Conventionally, queries are sent to a server and the documents in the search results returned are downloaded in full as representation of the server’s content. We present an approach that uses the document snippets in the search results as samples instead of downloading the entire documents. We show this yields equal or better modeling performance for the same bandwidth consumption depending on collection characteristics, like document length distribution and homogeneity. Query-based sampling using snippets is a useful approach for real-world systems, since it requires no extra operations beyond exchanging queries and search results

Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/