A Study of Structure-Carcinogenicity Relationship for 86 Compounds from NTP Data Base Using Topological Indices as Descriptors

Abstract

86 compounds from NTP carcinogenic potency data base have been used to derive neural network models. Compounds were described with topological indices. Carcinogenicity has been given as a binary quantity - a compound is carcinogenic or non carcinogenic. Several models have been tested with a recognition ability test and with the leave-one-out cross validation method. For the best model the ratio between correct and wrong classifications was 70/30. Furthermore, the model has been used to classify 17 compounds not used for setting of the models. The predicted carcinogenic classes and the neighbors in the neural network influencing the predictions have been discussed.     

N-亚硝基化合物结构-致癌活性的相关性研究

Ｎ－亚硝基化合物结构－致癌活性的相关性研究许禄,姚瑜元（中国科学院长春应用化学研究所应用谱学开放实验室,长春,１３００２２）关键词Ｎ－亚硝基化合物,半经验量化方法,构效关系目前已发现的Ｎ－亚硝基化合物约３００种中多数具有致癌活性。化学家和生物学家对该...     

Validation of counter propagation neural network models for predictive toxicology according to the OECD principles: a case study

The OECD has proposed five principles for validation of QSAR models used for regulatory purposes. Here we present a case study investigating how these principles can be applied to models based on Kohonen and counter propagation neural networks. The study is based on a counter propagation network model that has been built using toxicity data in fish fathead minnow for 541 compounds. The study demonstrates that most, if not all, of the OECD criteria may be met when modeling using this neural network approach.     

Validation of counter propagation neural network models for predictive toxicology according to the OECD principles: a case study

The OECD has proposed five principles for validation of QSAR models used for regulatory purposes. Here we present a case study investigating how these principles can be applied to models based on Kohonen and counter propagation neural networks. The study is based on a counter propagation network model that has been built using toxicity data in fish fathead minnow for 541 compounds. The study demonstrates that most, if not all, of the OECD criteria may be met when modeling using this neural network approach.     

Dynamic modelling of milk ultrafiltration by artificial neural network

Artificial neural networks (ANNs) have been used to dynamically model crossflow ultrafiltration of milk. It aims to predict permeate flux, total hydraulic resistance and the milk components rejection (protein, fat, lactose, ash and total solids) as a function of transmembrane pressure and processing time. Dynamic modelling of ultrafiltration performance of colloidal systems (such as milk) is very important for designing of a new process and better understanding of the present process. Such processes show complex non-linear behaviour due to unknown interactions between compounds of a colloidal system, thus the theoretical approaches were not being able to successfully model the process. In this work, emphasis has been focused on intelligent selection of training data, using few training data points and small network. Also it has been tried to test the ANN ability to predict new data that may not be originally available. Two neural network models were constructed to predict the flux/total resistance and rejection during ultrafiltration of milk. The results showed that there is an excellent agreement between the validation data (not used in training) and modelled data, with average errors less than 1%. Also the trained networks are able to accurately capture the non-linear dynamics of milk ultrafiltration even for a new condition that has not been used in the training process.     

Comparison of criteria used to access carcinogenicity in CPANN QSAR models versus the knowledge-based expert system Toxtree

The primary goal of this study was to describe and compare the criteria used to assess carcinogenic activity. The statistically-based predictive quantitative structure–activity relationship (QSAR) models based on the counter propagation artificial neural network (CPANN) algorithm, and knowledge-based expert systems based on a decision tree structural alert (SA) approach (Toxtree application), were considered. The integration of the QSAR (CPANN models) and SAR (Toxtree SA application) approach contributed to the mechanistic understanding of the QSAR model considered. The mapping technique inherent to CPANN Kohonen enables us to relate the similarities or dissimilarities within a congeneric set of chemicals with particular SAs for carcinogenicity. The focus of our investigations was the similarities and dissimilarities of the features used in the QSAR and SAR methods. Due to the complexity of the carcinogenic endpoint, the integration of different approaches allows the models to be improved and provides a valuable technique for evaluating the safety of chemicals.     

An elastic network model to identify characteristic stress response genes

Exposing eukaryotic cells to a toxic compound and subsequent gene expression profiling may allow the prediction of selected toxic effects based on changes in gene expression. This objective is complicated by the observation that compounds with different modes of toxicity cause similar changes in gene expression and that a global stress response affects many genes. We developed an elastic network model of global stress response with nodes representing genes which are connected by edges of graded coexpression. The expression of only few genes have to be known to model the global stress response of all but a few atypical responder genes. Those required genes and the atypical response genes are shown to be good biomarker for tox predictions. In total, 138 experiments and 13 different compounds were used to train models for different toxicity classes. The deduced biomarkers were shown to be biologically plausible. A neural network was trained to predict the toxic effects of compounds from profiling experiments. On a validation data set of 189 experiments with 16 different compounds the accuracy of the predictions was assessed: 14 out of 16 compounds have been classified correctly. Derivation of model based biomarkers through the elastic network approach can naturally be extended to other areas beyond toxicology since subtle signals against a broad response background are common in biological studies.     

Application of artificial neural network to determination of active principle ingredient in pharmaceutical quality control based on near infrared spectroscopy

In the construction of a neural network, most attentions have been paid to the selection of the architecture, the selection of the learning parameters and the network validation while the selection of input variables shared little. This study focused on the selection of input variables by various data pre-treatment for constructing ANN models. The results showed that the validation results differed from each other when different data-pretreatment methods combined with near-infrared spectroscopy (NIRS) to build a model using artificial neural network (ANN) for quality control of paracetamol in coldrex. And wavelet coefficients after orthogonal signal correction (OSC) in the ANN models reduced RMSEP by up to 77% compared to ANN models using derivatives combined with PCA pretreatment. The selection of input variables has potent to improve the calibration ability of ANN, and the model can be used for pressure reduction of quality control in the pharmaceutical industry.     

Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks

In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, Delta(solv)G degrees , has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the Delta(solv)G degrees in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R = 0.9985, standard deviation S = 0.68 kJ mol(-1), and mean absolute error MAE = 0.46 kJ mol(-1). The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the basis of a nontrivial combination of their chemical structure and target property.