Generates a k Nearest Neighbor (kNN) regression model using similarity and activity data of aligned molecules.
This node has been deprecated and replaced by the Forge Build Machine Learning node.
The kNN methodology is a well-known and robust distance learning approach where the activity for each new compound is predicted as the weighted average activity of its k nearest neighbors in the training set.
The similarity between the molecules is calculated using Cresset's field/shape similarity method or by using the 2D circular fingerprint methods ECFP4, ECFP6, FCFP4, or FCFP6. This model can be used within the "Forge Score k Nearest Neighbor (kNN)" node with fscore to predict an activity value for newly designed molecules.
Please refer to the Forge manual for a detailed description of the science behind kNN models in Forge and the corresponding model building options.
The molecules must be pre-aligned if Cresset's field/shape similarity method is being used - the falign program or Forge Align node are ideal for this.
This node wraps the Forge Build executable 'fbuild', which must be installed with a valid license for this node to work. If this is installed in the default location on Windows, then it should be found automatically. Otherwise, you must either set the 'Cresset Home' preference or the CRESSET_HOME environment variable to the base Cresset software install directory. You may also set the 'fbuild Path' preference or the CRESSET_FORGEBUILD_EXE environment variable to point directly at the executable itself.
The Forge Build k Nearest Neighbor (kNN) node can be configured to use additional resources to perform calculations. The time taken for the node to run will be drastically reduced using the Cresset's Engine Broker. To use this facility either set the 'Cresset Engine Broker' preference or the CRESSET_BROKER environment variable to point to the location of your local Engine Broker. If you do not currently have the Cresset Engine Broker then contact Cresset (email@example.com) for pricing on local and cloud based brokers.
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
A zipped version of the software site can be downloaded here.
Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.Try NodePit Runner!
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to firstname.lastname@example.org, follow @NodePit on Twitter or botsin.space/@nodepit on Mastodon.
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.