Cheminformatics - QSAR

2011-09-15T17:48:00.000-07:00

A comprehensive and detailed essay about Y-Scrambling/Y-Randomization.

(A)

Y-Randomization – A Useful Tool in QSAR Validation, or Folklore? - Christoph Rücker, Gerta Rücker, and Markus Meringer

(B)

J Chem Inf Model. 2007 Nov-Dec;47(6):2345-57. Epub 2007 Sep 20.

y-Randomization and its variants in QSPR/QSAR.

Rücker C, Rücker G, Meringer M.

Source

Biozentrum, University of Basel, 4056 Basel, Switzerland. christoph.ruecker@uni-bayreuth.de

Cheminformatics

2011-07-20T07:26:00.000-07:00

Cheminformatics for development of new materials (by Ricardo Stefani - in portuguese)

Quimioinformatica

View more presentations from Ricardo Stefani

comp.ai.neural-nets FAQ, Part 1 of 7: Introduction

2011-07-19T05:32:00.000-07:00

Neural Networks FAQ

comp.ai.neural-nets FAQ, Part 1 of 7: Introduction

The Importance of Being Earnest: Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models - Tropsha - 2003 - QSAR & Combinatorial Science - Wiley Online Library

2011-06-10T10:39:00.000-07:00

The Importance of Being Earnest:

Validation is the Absolute Essential for Successful Application and Interpretation of QSPR Models

Alexander Tropsha1,†, Paola Gramatica2, Vijay K. Gombar3
Article first published online: 16 APR 2003

Abstract

This paper emphasizes the importance of rigorous validation as a crucial, integral component of Quantitative Structure Property Relationship (QSPR) model development. We consider some examples of published QSPR models, which in spite of their high fitted accuracy for the training sets and apparent mechanistic appeal, fail rigorous validation tests, and, thus, may lack practical utility as reliable screening tools. We present a set of simple guidelines for developing validated and predictive QSPR models. To this end, we discuss several validation strategies including (1) randomization of the modelled property, also called Y-scrambling, (2) multiple leave-many-out cross-validations, and (3) external validation using rational division of a dataset into training and test sets. We also highlight the need to establish the domain of model applicability in the chemical space to flag molecules for which predictions may be unreliable, and discuss some algorithms that can be used for this purpose. We advocate the broad use of these guidelines in the development of predictive QSPR models.

DOI: 10.1002/qsar.200390007
Copyright © 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Extreme Learning Machine Survey

2011-06-06T07:45:00.000-07:00

A Risk Assessment Perspective of Current Practice in Characterizing Uncertainties in QSAR Regression Predictions - Sahlin - 2011 - Molecular Informatics - Wiley Online Library

2011-05-18T08:56:00.000-07:00

A Risk Assessment Perspective of Current Practice in Characterizing Uncertainties in QSAR Regression Predictions - Sahlin - 2011 - Molecular Informatics - Wiley Online Library

Best Practices for QSAR Modelling

2011-03-29T08:04:00.001-07:00

Interesting papers about the validation and predictivity of QSAR Models:

Validation and Predictivity of QSAR Models - Hugo Kubinyi (lecture slides)

Best Practices for QSAR Model Development, Validation, and Exploitation - Alexander Tropsha - (2010), Best Practices for QSAR Model Development, Validation, and Exploitation. Molecular Informatics, 29: 476–488. doi: 10.1002/minf.201000061

Which MATLAB functions benefit from multithreaded computation?

2011-01-21T23:19:00.001-08:00

http://www.mathworks.com/support/solutions/en/data/1-4PG4AN/?solution=1-4PG4AN

GA Multiple response models

2010-08-17T12:02:00.001-07:00

“An important characteristic of the GA–VSS method is that a single model is not necessarily obtained but the result usually is a population of acceptable models; this characteristic, sometimes considered a disadvantage, provides an opportunity to make an evaluation of the relationships with the response from different points of view. A theoretical disadvantage is that the absolute best model could be not present in the final population. However, after a
careful selection of the best models, ! consensus analysis can be performed contemporarily using the selected models and estimating the response as weighted average of the responses of the single models.”

Molecular Descriptors for Chemoinformatics,
Volumes I & II
Roberto Todeschini
Viviana Consonni

Data pre-processing - Normalization

2009-10-14T11:30:00.000-07:00

Dogra, Shaillay K., "Normalization." From QSARWorld--A Strand Life Sciences Web Resource.
http://www.qsarworld.com/qsar-statistics-normalization.php

Normalization

Most of the computed descriptors differ in the scales in which their values lie. One may need to normalize them before proceeding with further statistical analysis. This mostly depends on the subsequent Machine Learning algorithms that one wants to run on the data.

Algorithms like Decision Trees, Regression Forest, Decision Forest and Naïve Bayes do not require normalized data as input. For Linear Regression, normalization is a recommended step. For Neural Networks – classification or regression, Support Vector Machines – classification or regression, normalization of data is required.

In context of cheminformatics, a standard way to normalize data is by mean shifting and auto-scaling. This makes the mean of a thus transformed descriptor column as 0 and the standard deviation as 1.

Mean Shifting

Most of the computed descriptors differ in the scales in which their values lie. One may thus want to normalize them before proceeding with further statistical analysis. As part of normalization, each value for a given descriptor (all values in a column) is adjusted or shifted by the mean value. As a result, the new mean value becomes 0. This happens for all the descriptors and they thus now have the same mean value 0. Hence, mean, as a measure of central location of the distribution of values, for all the descriptors, is now the same. However, the 'spread' or the 'variation' in the data, about the mean, is still the same as in the original data. This can now be taken care of by scaling the values with the standard deviation.

This is best illustrated with an example. Consider these numbers: 1, 2, 3, 4, and 5. The total of these numbers is 15 and the mean is 3. Adjusting each value by the mean value gives the transformed numbers as: -2, -1, 0, 1, and 2. The new total is 0 and thus the new mean is 0. However, note that the standard deviation is still the same as original (√2). This can now be taken care of by scaling the values with standard deviation in order to make the new standard deviation as 1.

Autoscaling

For a given set of values, the standard deviation can be made to be unit by scaling (dividing) all the values by the original standard deviation. This is a standard step in normalization of data.

Say, the values are - 1, 2, 3, 4 and 5. The standard deviation is √2. Now, dividing each value by the standard deviation gives us the transformed data as - 1/√2, √2, 3/√2, 2√2 and 5/√2. The new standard deviation for this set of values is 1.

(The above principle is better demonstrated algebraically).

A value x belonging to a distribution with mean 'x_mean' and standard deviation 's' can be transformed to a standard score, or z-score, in the following manner:

z = (x - x_mean)/s

The mean of standard scores is zero. When values are standardized, the units in which they are expressed are equal to the standard deviation, s. For the standardized scores, the standard deviation becomes 1. (Variance is also 1). The interpretation of the standard-score of a given value is in terms of the number of standard deviations the value is above or below the mean (of the distribution of standardized scores).

So, the standardization of a set of values involves two steps. First, the mean is subtracted from every value, which shifts the central location of the distribution to 0. Then the thus mean-shifted values are divided by the standard deviation, s. This now makes the standard deviation as 1.

Some Interesting Links about CUDA Programming

2009-10-14T06:53:00.000-07:00

Getting started with CUDA
CUDA Tutorial
HPCWire.com
multicoreinfo.com

Videos

Scalable Parallel Programming with CUDA on Manycore GPUs
Stanford University Computer Systems Colloquium (EE 380).
John Nickolls - NVIDIA

Model Applicability

2009-10-14T05:56:00.000-07:00

Dogra, Shaillay K., "Model Applicability" From QSARWorld--A Strand Life Sciences Web Resource.
http://www.qsarworld.com/insilico-chemistry-model-applicability.php

When using a model for predicting the value(s) for some unknown compound(s), assessment of the applicability of the model, in context of the compound(s) under study, is necessary. This can be assessed with different approaches, all of which in some sense try to assess whether the structure-, chemical-, or descriptor-based properties of the ‘unknown’ compound lie in similar ‘space’ as those for the compounds that were part of the training set used for building the model. This is an issue because the basic assumption of QSAR modeling is that similar compounds have similar activity/property and hence, given an unknown compound, we shall be able to predict its activity/property with confidence if it is ‘similar’ to the compounds that were used for building the model.

Whether the compound(s) under study is ‘similar’ to the training set compounds can be assessed in various ways:

1) Structure-based similarity: Tanimoto coefficient values, obtained by comparing MACCS fingerprints, can be used to assess structural similarity. If any of the training set compound has a Tanimoto coefficient value > 0.85 when compared against the compound under study, the same can be taken as an indication of high structural similarity and it can be believed that the given model is applicable for this case.

2)Descriptor-based similarity: Similarity of the compound under study against the compounds in the training set can also be estimated by computing the distances (Euclidean) of the descriptors, that were used in training the model, between the unknown compound(s) and the training set compounds. This distance should lie between 0 to ∞ and possibly, the lesser the distance the better it is.

3) Chemical Space: Comparing the ‘chemical space’ of the ‘unknown’ compounds against the compounds in the training set (used for building the model) can be another way to assess model applicability. What can be done here is to run a Principal Components Analysis (PCA) on the descriptors used in the model, for both the training set and the ‘unknown’ compounds, and then launch a plot on the first two components. In the figure below, the training set compounds are shown in red while the ‘unknown’ compounds, for which the predictions need to be made, are depicted in green. Thus, at a glance it can be visualized if the ‘unknown’ compounds belong to the same distribution or ‘space’ as the ones used for deriving the model (and decide for or against using the given model).

4) Statistical Measures: The model can anyway be used for predicting the values for the ‘unknown’ compounds. The predicted values usually also have a measure of statistical significance associated with them.

In case of regression models (prediction of a continuous value), this measure is in terms of standard error. A simple interpretation of the standard error is that, according to the model, the predicted value lies in an interval bound by +/- standard error with a 95% confidence. Say, the predicted value is x and the associated standard error is y, then the value is estimated to lie in x-y to x+y interval with a 95% confidence. (This however does not imply that there exists some interval wherein the confidence could be 100%).

In case of classification models (prediction of a categorical value), the statistical significance is in terms of confidence measure. This lies in a 0-1 scale and can be interpreted as the % confidence that the underlying algorithm (in the model) has when it is predicting some given compound to belong to a particular class. Say, if an ‘unknown’ compound is called by the model to belong to a particular class, and the model associates a confidence measure of 0.90 with that prediction, this implies that the algorithm is 90% confident about making this prediction. In other words, statistically, in the long run, when the algorithm makes large enough such predictions, 90% of them would turn out to be correct.

Cheminformatics - Definition

2008-10-13T18:46:00.000-07:00

Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery. These methods can also be used in chemical and allied industries in various other forms.