Biomedical subjects

Pierre Mahé

Publications and source records attributed to Pierre Mahé.

2 recordsLinked to original sources

PubMedDate not supplied

Graph kernels for molecular structure-activity relationship analysis with support vector machines.

The support vector machine algorithm together with graph kernel functions has recently been introduced to model structure-activity relationships (SAR) of molecules from their 2D structure, without the need for explicit molecular descriptor computation. We propose two extensions to this approach with the double goal to reduce the computational burden associated with the model and to enhance its predictive accuracy: description of the molecules by a Morgan index process and definition of a second-order Markov model for random walks on 2D structures. Experiments on two mutagenicity data sets validate the proposed extensions, making this approach a possible complementary alternative to other modeling strategies.

Algorithms↗

PubMedDate not supplied

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-point pharmacophores present in the 3D structures of molecules, 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 approaches. Experimental results suggest that this new approach is competitive with state-of-the-art algorithms based on the 2D structure of molecules for the detection of inhibitors of several drug targets.

Algorithms↗