Using ILP to Identify Pathway Activation Patterns in Systems Biology

We show a logical aggregation method that, combined with propositionalization methods, can construct novel structured biological features from gene expression data. We do this to gain understanding of pathway mechanisms, for instance, those associated with a particular disease. We illustrate this method on the task of distinguishing between two types of lung cancer; Squamous Cell Carcinoma (SCC) and Adenocarcinoma (AC). We identify pathway activation patterns in pathways previously implicated in the development of cancers. Our method identified a model with comparable predictive performance to the winning algorithm of a recent challenge, while providing biologically relevant explanations that may be useful to a biologist

Fast relational learning using bottom clause propositionalization with artificial neural networks

Relational learning can be described as the task of learning first-order logic rules from examples. It has enabled a number of new machine learning applications, e.g. graph mining and link analysis. Inductive Logic Programming (ILP) performs relational learning either directly by manipulating first-order rules or through propositionalization, which translates the relational task into an attribute-value learning task by representing subsets of relations as features. In this paper, we introduce a fast method and system for relational learning based on a novel propositionalization called Bottom Clause Propositionalization (BCP). Bottom clauses are boundaries in the hypothesis search space used by ILP systems Progol and Aleph. Bottom clauses carry semantic meaning and can be mapped directly onto numerical vectors, simplifying the feature extraction process. We have integrated BCP with a well-known neural-symbolic system, C-IL2P, to perform learning from numerical vectors. C-IL2P uses background knowledge in the form of propositional logic programs to build a neural network. The integrated system, which we call CILP++, handles first-order logic knowledge and is available for download from Sourceforge. We have evaluated CILP++ on seven ILP datasets, comparing results with Aleph and a well-known propositionalization method, RSD. The results show that CILP++ can achieve accuracy comparable to Aleph, while being generally faster, BCP achieved statistically significant improvement in accuracy in comparison with RSD when running with a neural network, but BCP and RSD perform similarly when running with C4.5. We have also extended CILP++ to include a statistical feature selection method, mRMR, with preliminary results indicating that a reduction of more than 90 % of features can be achieved with a small loss of accuracy

LazyBum: Decision tree learning using lazy propositionalization

Propositionalization is the process of summarizing relational data into a tabular (attribute-value) format. The resulting table can next be used by any propositional learner. This approach makes it possible to apply a wide variety of learning methods to relational data. However, the transformation from relational to propositional format is generally not lossless: different relational structures may be mapped onto the same feature vector. At the same time, features may be introduced that are not needed for the learning task at hand. In general, it is hard to define a feature space that contains all and only those features that are needed for the learning task. This paper presents LazyBum, a system that can be considered a lazy version of the recently proposed OneBM method for propositionalization. LazyBum interleaves OneBM's feature construction method with a decision tree learner. This learner both uses and guides the propositionalization process. It indicates when and where to look for new features. This approach is similar to what has elsewhere been called dynamic propositionalization. In an experimental comparison with the original OneBM and with two other recently proposed propositionalization methods (nFOIL and MODL, which respectively perform dynamic and static propositionalization), LazyBum achieves a comparable accuracy with a lower execution time on most of the datasets.status: Published onlin

On the algebra of quasi-shuffles

For any commutative algebra R the shuffle product on the tensor module T(R) can be deformed to a new product. It is called the quasi-shuffle algebra, or stuffle algebra, and denoted T q (R). We show that if R is the polynomial algebra, then T q (R) is free for some algebraic structure called Commutative TriDendriform (CTD-algebras). This result is part of a structure theorem for CTD-bialgebras which are associative as coalgebras and whose primitive part is commutative. In other words, there is a good triple of operads (As, CTD, Com) analogous to (Com, As, Lie). In the last part we give a similar interpretation of the quasi-shuffle algebra in the noncommutative setting