Wladimiro Diaz-Villanueva

Discrimination and selection of new potential antibacterial compounds using simple topological descriptors

The aim of the work was to discriminate between antibacterial and non-antibacterial drugs by topological methods and to select new potential antibacterial agents from among new structures. The method used for antibacterial activity selection was a linear discriminant analysis (LDA). It is possible to obtain a QSAR interpretation of the information contained in the discriminant function. We make use of the pharmacological distribution diagrams (PDDs) as a visualizing technique for the identification and selection of new antibacterial agents.

Artificial neural networks and linear discriminant analysis: a valuable combination in the selection of new antibacterial compounds.

A set of topological descriptors has been used to discriminate between antibacterial and nonantibacterial drugs. Topological descriptors are simple integers calculated from the molecular structure represented in SMILES format. The methods used for antibacterial activity discrimination were linear discriminant analysis (LDA) and artificial neural networks of a multilayer perceptron (MLP) type. The following plot frequency distribution diagrams were used: a function of the number of drugs within a value interval of the discriminant function and the output value of the neural network versus these values. Pharmacological distribution diagrams (PDD) were used as a visualizing technique for the identification of antibacterial agents. The results confirmed the discriminative capacity of the topological descriptors proposed. The combined use of LDA and MLP in the guided search and the selection of new structures with theoretical antibacterial activity proved highly effective, as shown by the in vitro activity and toxicity assays conducted.

Drugs and nondrugs: an effective discrimination with topological methods and artificial neural networks.

A set of topological and structural descriptors has been used to discriminate general pharmacological activity. To that end, we selected a group of molecules with proven pharmacological activity including different therapeutic categories, and another molecule group without any activity. As a method for pharmacological activity discrimination, an artificial neural network was used, dividing molecules into active and inactive, to train the network and externally validate it. The following plot frequency distribution diagrams were used: a function of the number of drugs within a value interval, and the output value of the neural network versus these values. Pharmacological distribution diagrams (PDD) were used as a visualizing technique for the identification of drug and nondrug molecules. The results confirmed the discriminative capacity of the topological descriptors proposed.

A Linear Cost Algorithm to Compute the Discrete Gabor Transform

In this paper, we propose an alternative efficient method to calculate the Gabor coefficients of a signal given a synthesis window with a support of size much lesser than the length of the signal. The algorithm uses the canonical dual of the window (which does not need to be calculated beforehand) and achieves a computational cost that is linear with the signal length in both analysis and synthesis. This is done by exploiting the block structure of the matrices and using an ad hoc Cholesky decomposition of the Gabor frame matrix.

Image Recognition through Incremental Discriminative Common Vectors

An incremental approach to the discriminative common vector (DCV) method for image recognition is presented. Two different but equivalent ways of computing both common vectors and corresponding subspace projections have been considered in the particular context in which new training data becomes available and learned subspaces may need continuous updating. The two algorithms are based on either scatter matrix eigendecomposition or difference subspace orthonormalization as with the original DCV method. The proposed incremental methods keep the same good properties than the original one but with a dramatic decrease in computational burden when used in this kind of dynamic scenario. Extensive experimentation assessing the properties of the proposed algorithms using several publicly available image databases has been carried out.

Incremental Generalized Discriminative Common Vectors for Image Classification

Subspace-based methods have become popular due to their ability to appropriately represent complex data in such a way that both dimensionality is reduced and discriminativeness is enhanced. Several recent works have concentrated on the discriminative common vector (DCV) method and other closely related algorithms also based on the concept of null space. In this paper, we present a generalized incremental formulation of the DCV methods, which allows the update of a given model by considering the addition of new examples even from unseen classes. Having efficient incremental formulations of well-behaved batch algorithms allows us to conveniently adapt previously trained classifiers without the need of recomputing them from scratch. The proposed generalized incremental method has been empirically validated in different case studies from different application domains (faces, objects, and handwritten digits) considering several different scenarios in which new data are continuously added at different rates starting from an initial model.

Fast Approximated Discriminative Common Vectors Using Rank-One SVD Updates

An efficient incremental approach to the discriminative common vector (DCV) method for dimensionality reduction and classification is presented. The proposal consists of a rank-one update along with an adaptive restriction on the rank of the null space which leads to an approximate but convenient solution. The algorithm can be implemented very efficiently in terms of matrix operations and space complexity, which enables its use in large-scale dynamic application domains. Deep comparative experimentation using publicly available high dimensional image datasets has been carried out in order to properly assess the proposed algorithm against several recent incremental formulations.

Null space based image recognition using incremental eigendecomposition

An incremental approach to the discriminative common vector (DCV) method for image recognition is considered. Discriminative projections are tackled in the particular context in which new training data becomes available and learned subspaces may need continuous updating. Starting from incremental eigendecomposition of scatter matrices, an efficient updating rule based on projections and orthogonalization is given. The corresponding algorithm has been empirically assessed and compared to its batch counterpart. The same good properties and performance results of the original method are kept but with a dramatic decrease in the computation needed.

Efficient Dimensionality Reduction on Undersampled Problems through Incremental Discriminative Common Vectors

An efficient incremental approach to the discriminative common vector (DCV) method for dimensionality reduction and classification is presented. Starting from the original batch method, an incremental formulation is given. The main idea is to minimize both matrix operations and space constraints. To this end, an straightforward per sample correction is obtained enabling the possibility of setting up an efficient online algorithm. The performance results and the same good properties than the original method are preserved but with a very significant decrease in computational burden when used in dynamic contexts. Extensive experimentation assessing the properties of the proposed algorithms with regard to previously proposed ones using several publicly available high dimensional databases has been carried out.

A comparative study using different topological representations in pattern recognition based drug activity characterization

The use of certain machine learning and pattern recognition tools for automated pharmacological drug design has been recently introduced. Different families of learning algorithms have been applied to the task of associating observed chemical properties and pharmacological activities to certain kinds of representations of the candidate compounds. In this work, several families of molecular descriptors are considered in order to establish the appropriateness of these families for a particularly challenging drug design task consisting of characterizing the analgesic properties of a relatively large number of compounds. As a second goal, the composite use of descriptors from different families and a first attempt to select the best attributes from these families is considered. As a conclusion, relatively good discrimination results can be obtained by combining the best descriptors of the different families considered.