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

Maximizing Activity in Ising Networks via the TAP Approximation

A wide array of complex biological, social, and physical systems have recently been shown to be quantitatively described by Ising models, which lie at the intersection of statistical physics and machine learning. Here, we study the fundamental question of how to optimize the state of a networked Ising system given a budget of external influence. In the continuous setting where one can tune the influence applied to each node, we propose a series of approximate gradient ascent algorithms based on the Plefka expansion, which generalizes the na\"{i}ve mean field and TAP approximations. In the discrete setting where one chooses a small set of influential nodes, the problem is equivalent to the famous influence maximization problem in social networks with an additional stochastic noise term. In this case, we provide sufficient conditions for when the objective is submodular, allowing a greedy algorithm to achieve an approximation ratio of $1-1/e$. Additionally, we compare the Ising-based algorithms with traditional influence maximization algorithms, demonstrating the practical importance of accurately modeling stochastic fluctuations in the system