How can I contact you ? Your server/site bounces and won’t redirect email.

VisuMap allows you to plug-in your own distance functions to characterize dissimilarities. For those standard metrics, like jaccard distance, there are free ready-to-use plugin modules.

The size of the dataset used is only 171 compounds.

Hi James,

Thanks for the clarification. Yes, I am aware that VisuMap requires DirectX library but since my machines are all linux-based, I can only run it using Windows that is under VMWare. I had actually also asked my graduate student to try the software and she mentioned that the 3D navigation control is rather good.

I will be looking more into the clustering algorithms next. However, as I had mentioned in my previous post, I am not an expert in visualization software. I am still learning how to best utilize such software for research, in particular in QSAR research. Thus I hope readers don’t really treat these posts as reviews on the software but rather treat them as just personal observations of an amateur using the software. I will welcome comments from readers and yourself on how to more effectively use such software and correctly any inaccuracies that may inadvertently arise.

For most mapping algorithms in VisuMap the dataset size is limited
to 5000 to 10000 data points. If you have more data points, you
should use one of the integrated clustering algorithms to
reduced dataset size to a more manageable size. For instance,
you can easily reduce a dataset with 1 million data point to
few thousands clusters with the self-organizing map within few hours.

You can also use the clustering services to color data points
automatically according the their clusters

It should also be pointed out that mapping algorithms like Sammon map and PCA emphasize on the global inter-cluster structure, whereas other mapping algorithms (like the RPM and CCA) emphasize more on the details within clusters.