Conceptual biology, hypothesis discovery, and text mining: Swanson's legacy

Innovative biomedical librarians and information specialists who want to expand their roles as expert searchers need to know about profound changes in biology and parallel trends in text mining. In recent years, conceptual biology has emerged as a complement to empirical biology. This is partly in response to the availability of massive digital resources such as the network of databases for molecular biologists at the National Center for Biotechnology Information. Developments in text mining and hypothesis discovery systems based on the early work of Swanson, a mathematician and information scientist, are coincident with the emergence of conceptual biology. Very little has been written to introduce biomedical digital librarians to these new trends. In this paper, background for data and text mining, as well as for knowledge discovery in databases (KDD) and in text (KDT) is presented, then a brief review of Swanson's ideas, followed by a discussion of recent approaches to hypothesis discovery and testing. 'Testing' in the context of text mining involves partially automated methods for finding evidence in the literature to support hypothetical relationships. Concluding remarks follow regarding (a) the limits of current strategies for evaluation of hypothesis discovery systems and (b) the role of literature-based discovery in concert with empirical research. Report of an informatics-driven literature review for biomarkers of systemic lupus erythematosus is mentioned. Swanson's vision of the hidden value in the literature of science and, by extension, in biomedical digital databases, is still remarkably generative for information scientists, biologists, and physicians. © 2006Bekhuis; licensee BioMed Central Ltd

Collaborative development of the Arrowsmith two node search interface designed for laboratory investigators.

Arrowsmith is a unique computer-assisted strategy designed to assist investigators in detecting biologically-relevant connections between two disparate sets of articles in Medline. This paper describes how an inter-institutional consortium of neuroscientists used the UIC Arrowsmith web interface http://arrowsmith.psych.uic.edu in their daily work and guided the development, refinement and expansion of the system into a suite of tools intended for use by the wider scientific community

Thouless-Anderson-Palmer equation for analog neural network with temporally fluctuating white synaptic noise

Effects of synaptic noise on the retrieval process of associative memory neural networks are studied from the viewpoint of neurobiological and biophysical understanding of information processing in the brain. We investigate the statistical mechanical properties of stochastic analog neural networks with temporally fluctuating synaptic noise, which is assumed to be white noise. Such networks, in general, defy the use of the replica method, since they have no energy concept. The self-consistent signal-to-noise analysis (SCSNA), which is an alternative to the replica method for deriving a set of order parameter equations, requires no energy concept and thus becomes available in studying networks without energy functions. Applying the SCSNA to stochastic network requires the knowledge of the Thouless-Anderson-Palmer (TAP) equation which defines the deterministic networks equivalent to the original stochastic ones. The study of the TAP equation which is of particular interest for the case without energy concept is very few, while it is closely related to the SCSNA in the case with energy concept. This paper aims to derive the TAP equation for networks with synaptic noise together with a set of order parameter equations by a hybrid use of the cavity method and the SCSNA.Comment: 13 pages, 3 figure

Textpresso for Neuroscience: Searching the Full Text of Thousands of Neuroscience Research Papers

Textpresso is a text-mining system for scientific literature. Its two major features are access to the full text of research papers and the development and use of categories of biological concepts as well as categories that describe or relate objects. A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. Here we describe Textpresso for Neuroscience, part of the core Neuroscience Information Framework (NIF). The Textpresso site currently consists of 67,500 full text papers and 131,300 abstracts. We show that using categories in literature can make a pure keyword query more refined and meaningful. We also show how semantic queries can be formulated with categories only. We explain the build and content of the database and describe the main features of the web pages and the advanced search options. We also give detailed illustrations of the web service developed to provide programmatic access to Textpresso. This web service is used by the NIF interface to access Textpresso. The standalone website of Textpresso for Neuroscience can be accessed at http://www.textpresso.org/neuroscience

Social reference: Aggregating online usage of scientific literature in CiteULike for clustering academic resources

Citation-based methods have been widely studied and employed for clustering academic resources and mapping science. Although effective, these methods suffer from citation delay. In this study, we extend reference and citation analysis to a broader notion from social perspective. We coin the term "social reference" to refer to the references of literatures in social academic web environment. We propose clustering methods using social reference information from CiteULike. We experiment for journal clustering and author clustering using social reference and compare with citation-based methods. Our experiments indicate: first, social reference implies connections among literatures which are as effective as citation in clustering academic resources; second, in practical settings, social reference-based clustering methods are not as effective as citation-based ones due to the sparseness of social reference data, but they can outperform in clustering new resources that have few citation. © 2011 Authors

Quantum Information Dynamics and Open World Science

One of the fundamental insights of quantum mechanics is that complete knowledge of the state of a quantum system is not possible. Such incomplete knowledge of a physical system is the norm rather than the exception. This is becoming increasingly apparent as we apply scientific methods to increasingly complex situations. Empirically intensive disciplines in the biological, human, and geosciences all operate in situations where valid conclusions must be drawn, but deductive completeness is impossible. This paper argues that such situations are emerging examples of {it Open World} Science. In this paradigm, scientific models are known to be acting with incomplete information. Open World models acknowledge their incompleteness, and respond positively when new information becomes available. Many methods for creating Open World models have been explored analytically in quantitative disciplines such as statistics, and the increasingly mature area of machine learning. This paper examines the role of quantum theory and quantum logic in the underpinnings of Open World models, examining the importance of structural features of such as non-commutativity, degrees of similarity, induction, and the impact of observation. Quantum mechanics is not a problem around the edges of classical theory, but is rather a secure bridgehead in the world of science to come