lazar toxicity predictions

lazar Frequently Asked Questions

I find multiple entries with different values for the same compound in the list of neighbors. Where do they come from and what is their impact on the prediction?

Multiple entries for the same structure originate from different biological experiments. lazar can use the information from multiple experiments to improve predictions, by considering each measurement as a separate example. This has the effect, that the impact of a neighbor on the prediction is increased, if repeated measurements give the same (classification) or very similar (regression) values, and decreased if the measurements differ a lot.

I get different values, if I repeat a prediction for the same compound and endpoint. Why?

This may happen for regression predictions only. lazar uses the random forest algorithm from R's Caret package to build local QSAR models. This algorithm uses random internal training set splits for parameter optimisations. This randomness can lead to models with slightly different parameters (and thus predictions) for the same set of neighbors.

The lazar program's interface has changed, and I am not sure how to use the information given with regard to its confidence. In the former version I would consider a confidence value higher than 0.025 as reliable, but now there is no such parameter in the prediction results.

In the past many users had problems to interpret the confidence level, for this reason we provide now the probabilities that the prediction belongs to one of the two classes. In contrast to the confidence level, these numbers can be interpreted as real probabilities ranging from 0 to 1.

Reliable prediction have a high probability for the predicted class and a low probability for the other one. Unreliable predictions have similar values for both classes, and are caused by a lot of contradictory activities of similar compounds.

Probabilities are calculated from the activities and similarities of neighbors, please make sure to inspect the neighbors list for any inconsistencies that might affect the prediction.

How can I use lazar locally on my computer

If you are familiar with docker, you can use one of our docker images to run lazar locally:

lazar docker image

nano-lazar docker image

If you want to install lazar/nano-lazar without docker you should know how to use UNIX/Linux and the Ruby programming language. Source code and brief installation instructions for the GUIs is available at:

lazar gui source code

nano-lazar gui source code

You can also use just the libraries from the command line:

lazar|nano-lazar lib

Documentation is available at:

gem

lazar depends on a couple of external libraries and programs, that could be difficult to install. Due to limited resources we cannot provide support, please use the docker version if you cannot manage it on your own.