Faster Substructure Search in the CDK

The CDK uses the UniversalIsomorphismTester to perform graph and subgraph isomorphism. However it’s not very efficient and this shows when performing substructure searches over large collections. A quick test where I compared the CDK code to OpenBabel’s obgrep showed that the CDK is nearly forty times slower than OpenBabel. Improvements in this code will enhance SMARTS matching, pharmacophore searching, fingerprinting and descriptors.

The Ullman algorithm is a well known method to perform subgraph isomorphism and even though more than thirty years old, is still used in many applications. I implemented this algorithm, based on the C++ implementation in VFLib, to see whether it’d do better than the method currently used in the CDK.

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Computational Research and Software in Academia

This paper by Prof. Tim Pederson in the Journal of Computational Linguistics highlights the need for authors of computational linguistics papers to release working software that can be used to reproduce results in their papers.

While the paper focuses on the field of computational linguistics (CL), the discussion is perfectly applicable to other fields that publish computational research. Given my background in cheminformatics, which is heavily dependent on the use of computational tools, the points raised in the paper very applicable. For example, Prof. Pederson states

While we have table after table of results to pore over, we usually don’t have access to the software that would allow us to reproduce those results.

He also highlights four points on how to produce software to reproduce the results of research.  In this post, I wanted to highlight some aspects that have bugged me in the past and I think are important for transparency in computational research.

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Faster Fingerprinting

In my last post I had reported some timing measurements for various operations. One of them was fingerprinting using the path-based hashing Fingerprinter class in the CDK. As reported, it took nearly 4 minutes to process a 1000-molecule subset of ZINC. Not good.

So I spent a little time last night hacking on the code, primarily making the search for unique paths a little faster. Happily, my latest commit (in 1.2.x, should be merged into trunk soon) allows the fingerprinter to process 1000 molecules in approximately 59s – a 4X speed up.

In terms of behavior, the new code gets the exact same paths as the old code, the only difference being that the order of atoms in the path can be reversed. Since the fingerprint is generated by hashing “path strings”, this means that the fingerprints from the new code will differ slightly from the old code. So if you’re working witha bunch of fingerprints calculated with the old code, you should probably regenarate them with the new code.

CDK Performance Measurements

As part of a larger project, I’ve been doing some profiling on various aspects of the CDK, focusing on core cheminformatics operations. I’m using the excellent YourKit profiler to do the tests. They tests are run on a Macbook Pro (2.16GHz) with 1GB RAM, using the latest trunk version of the CDK and JDK 1.5.

The test data is a 1000-molecule subset take from the ZINC collection. The operations I’ve been looking at are

The test harness  simply reads the 1000 molecules one by one and performs the operation in question. For certain tasks which are not atomic in nature, the code does a little more but the timing is measured only for the operation under study. In all cases, things like loading molecules from disk are not measured. The whole process is repeated 10 times and the times reported are the average of the 10 runs. A brief overview of the results:

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