On the Error Resilience of Ordered Binary Decision Diagrams

Ordered Binary Decision Diagrams (OBDDs) are a data structure that is used in an increasing number of fields of Computer Science (e.g., logic synthesis, program verification, data mining, bioinformatics, and data protection) for representing and manipulating discrete structures and Boolean functions. The purpose of this paper is to study the error resilience of OBDDs and to design a resilient version of this data structure, i.e., a self-repairing OBDD. In particular, we describe some strategies that make reduced ordered OBDDs resilient to errors in the indexes, that are associated to the input variables, or in the pointers (i.e., OBDD edges) of the nodes. These strategies exploit the inherent redundancy of the data structure, as well as the redundancy introduced by its efficient implementations. The solutions we propose allow the exact restoring of the original OBDD and are suitable to be applied to classical software packages for the manipulation of OBDDs currently in use. Another result of the paper is the definition of a new canonical OBDD model, called {\em Index-resilient Reduced OBDD}, which guarantees that a node with a faulty index has a reconstruction cost $O(k)$, where $k$ is the number of nodes with corrupted index

Active templates: Manipulating pointers with pictures

Active templates are a semi-automatic visual mechanism for generating algorithms for manipulating pointer-based data structures. The programmer creates a picture showing the affected part of a data structure before and after a general-case manipulation. Code for the operation is compiled directly from the picture, which also provides the development environment with enough information to generate, automatically, a series of templates for other similar pictures, each describing a different configuration which the data structure may possess. The programmer completes the algorithm by creating matching after-pictures for each of these cases. At every stage, most of the picture-generation is automatic. Much of the tedious detail of conventional pointer-based data-structure manipulation, such as maintenance of current pointers, is unnecessary in a system based on active templates

The pharmacophore kernel for virtual screening with support vector machines

We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-points pharmacophores present in the 3D structures of molecul es, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approa ches. Experimental results suggest that this new approach outperforms state-of-the-art algorithms based on the 2D structure of mol ecules for the detection of inhibitors of several drug targets

A Defence of Cartesian Materialism

One of the principal tasks Dennett sets himself in "Consciousness Explained" is to demolish the Cartesian theatre model of phenomenal consciousness, which in its contemporary garb takes the form of Cartesian materialism: the idea that conscious experience is a process of presentation realized in the physical materials of the brain. The now standard response to Dennett is that, in focusing on Cartesian materialism, he attacks an impossibly naive account of consciousness held by no one currently working in cognitive science or the philosophy of mind. Our response is quite different. We believe that, once properly formulated, Cartesian materialism is no straw man. Rather, it is an attractive hypothesis about the relationship between the computational architecture of the brain and phenomenal consciousness, and hence one that is worthy of further exploration. Consequently, our primary aim in this paper is to defend Cartesian materialism from Dennett's assault. We do this by showing that Dennett's argument against this position is founded on an implicit assumption (about the relationship between phenomenal experience and information coding in the brain), which while valid in the context of classical cognitive science, is not forced on connectionism

A new approach to collaborative frameworks using shared objects

Multi-user graphical applications currently require the creation of a set of interface objects to maintain each participating display. The concept of shared objects allows a single object instance to be used in multiple contexts concurrently. This provides a novel way of reducing collaborative overheads by requiring the maintenance of only a single set of interface objects. The paper presents the concept of a shared-object collaborative framework and illustrates how the concept can be incorporated into an existing object-oriented toolkit