Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined

Prospects for large-scale financial systems simulation

As the 21st century unfolds, we find ourselves having to control, support, manage or otherwise cope with large-scale complex adaptive systems to an extent that is unprecedented in human history. Whether we are concerned with issues of food security, infrastructural resilience, climate change, health care, web science, security, or financial stability, we face problems that combine scale, connectivity, adaptive dynamics, and criticality. Complex systems simulation is emerging as the key scientific tool for dealing with such complex adaptive systems. Although a relatively new paradigm, it is one that has already established a track record in fields as varied as ecology (Grimm and Railsback, 2005), transport (Nagel et al., 1999), neuroscience (Markram, 2006), and ICT (Bullock and Cliff, 2004). In this report, we consider the application of simulation methodologies to financial systems, assessing the prospects for continued progress in this line of research

@Note: a workbench for biomedical text mining

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists’ needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stopword removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open-source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.Fundação para a Ciência e a Tecnologia (FCT

Generalized topographic block model

Co-clustering leads to parsimony in data visualisation with a number of parameters dramatically reduced in comparison to the dimensions of the data sample. Herein, we propose a new generalized approach for nonlinear mapping by a re-parameterization of the latent block mixture model. The densities modeling the blocks are in an exponential family such that the Gaussian, Bernoulli and Poisson laws are particular cases. The inference of the parameters is derived from the block expectation–maximization algorithm with a Newton–Raphson procedure at the maximization step. Empirical experiments with textual data validate the interest of our generalized model