A Fully Reversible Data Transform Technique Enhancing Data Compression of SMILES Data

Abstract

Abstract. The requirement to efficiently store and process SMILES data used in Chemoinformatics creates a demand for efficient techniques to compress this data. General-purpose transforms and compressors are available to transform and compress this type of data to a certain extent, however, these techniques are not specific to SMILES data. We develop a transform specific to SMILES data that can be used alongside other general-purpose compressors as a preprocessor and post-processor to improve the compression of SMILES data. We test our transform with six other general-purpose compressors and also compare our results with another transform on our SMILES data corpus, we also compare our results with untransformed data.Keywords: SMILES, Data Transform, Data Compression. IntroductionThe Simplified Molecular Input Line Entry System (SMILES) language was developed to represent two-dimensional molecular structures in a concise and compact way allowing for storage and processing improvements. General-purpose compressors allow for further reductions in storage and processing costs [23], [8].With the continuous expansion of chemical databases [15] and the need for efficient storage and searching of molecular structure representations, such as SMILES [23], [8], storage and processing costs of these representations need to be further improved.Data can be transformed by exploiting the specific information contained in the data to its advantage. Transformed data can be used alongside general-purpose compression techniques to further improve compression results [21], [4], [20].We make the following contributions in this paper:• We present our SMILES-specific transform designed to enhance the compression of SMILES data when used with other general-purpose compressors.• We provide results from using general-purpose compression techniques on a breakdown of different SMILES transform scenarios and a combination of techniques used in our SMILES transforms.