Good Learning and Implicit Model Enumeration

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Algorithmic Statistics

While Kolmogorov complexity is the accepted absolute measure of information content of an individual finite object, a similarly absolute notion is needed for the relation between an individual data sample and an individual model summarizing the information in the data, for example, a finite set (or probability distribution) where the data sample typically came from. The statistical theory based on such relations between individual objects can be called algorithmic statistics, in contrast to classical statistical theory that deals with relations between probabilistic ensembles. We develop the algorithmic theory of statistic, sufficient statistic, and minimal sufficient statistic. This theory is based on two-part codes consisting of the code for the statistic (the model summarizing the regularity, the meaningful information, in the data) and the model-to-data code. In contrast to the situation in probabilistic statistical theory, the algorithmic relation of (minimal) sufficiency is an absolute relation between the individual model and the individual data sample. We distinguish implicit and explicit descriptions of the models. We give characterizations of algorithmic (Kolmogorov) minimal sufficient statistic for all data samples for both description modes--in the explicit mode under some constraints. We also strengthen and elaborate earlier results on the ``Kolmogorov structure function'' and ``absolutely non-stochastic objects''--those rare objects for which the simplest models that summarize their relevant information (minimal sufficient statistics) are at least as complex as the objects themselves. We demonstrate a close relation between the probabilistic notions and the algorithmic ones.Comment: LaTeX, 22 pages, 1 figure, with correction to the published journal versio

Inductive queries for a drug designing robot scientist

It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments