Molecule mining

Molecule mining is the process of data mining, or extracting and discovering patterns, as applied to molecules. Since molecules may be represented by molecular graphs, this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances. One way to do this is chemical similarity metrics, which has a long tradition in the field of cheminformatics.

Typical approaches to calculate chemical similarities use chemical fingerprints, but this loses the underlying information about the molecule topology. Mining the molecular graphs directly avoids this problem. So does the inverse QSAR problem which is preferable for vectorial mappings.

Coding(Molecule_i,Molecule_j≠i)

Kernel methods

• Marginalized graph kernel ^[1]
• Optimal assignment kernel ^{[2] [3] [4]}
• Pharmacophore kernel ^[5]
• C++ (and R) implementation combining
  • the marginalized graph kernel between labeled graphs ^[1]
  • extensions of the marginalized kernel ^[6]
  • Tanimoto kernels ^[7]
  • graph kernels based on tree patterns ^[8]
  • kernels based on pharmacophores for 3D structure of molecules ^[5]

Maximum common graph methods

• MCS-HSCS ^[9] (Highest Scoring Common Substructure (HSCS) ranking strategy for single MCS)
• Small Molecule Subgraph Detector (SMSD) ^[10] - is a Java-based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure). ^[11]

Coding(Molecule_i)

Molecular query methods

• Warmr ^{[12] [13]}
• AGM ^{[14] [15]}
• PolyFARM ^[16]
• FSG ^{[17] [18]}
• MolFea ^[19]
• MoFa/MoSS ^{[20] [21] [22]}
• Gaston ^[23]
• LAZAR ^[24]
• ParMol ^[25] (contains MoFa, FFSM, gSpan, and Gaston)
• optimized gSpan ^{[26] [27]}
• SMIREP ^[28]
• DMax ^[29]
• SAm/AIm/RHC ^[30]
• AFGen ^[31]
• gRed ^[32]
• G-Hash ^[33]

Methods based on special architectures of neural networks

• BPZ ^{[34] [35]}
• ChemNet ^[36]
• CCS ^{[37] [38]}
• MolNet ^[39]
• Graph machines ^[40]

See also

• Molecular Query Language
• Chemical graph theory
• Chemical space
• QSAR
• ADME
• partition coefficient

References

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2. H. Fröhlich, J. K. Wegner, A. Zell, Optimal Assignment Kernels For Attributed Molecular Graphs, The 22nd International Conference on Machine Learning (ICML 2005), Omnipress, Madison, WI, USA, 2005, 225-232. PDF
3. Fröhlich H., Wegner J. K., Zell A. (2006). "Kernel Functions for Attributed Molecular Graphs - A New Similarity Based Approach To ADME Prediction in Classification and Regression". QSAR Comb. Sci. 25 (4): 317–326. doi:10.1002/qsar.200510135.
4. H. Fröhlich, J. K. Wegner, A. Zell, Assignment Kernels For Chemical Compounds, International Joint Conference on Neural Networks 2005 (IJCNN'05), 2005, 913-918. CiteSeer
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9. Wegner J. K., Fröhlich H., Mielenz H., Zell A. (2006). "Data and Graph Mining in Chemical Space for ADME and Activity Data Sets". QSAR Comb. Sci. 25 (3): 205–220. doi:10.1002/qsar.200510009.
10. Rahman S. A., Bashton M., Holliday G. L., Schrader R., Thornton J. M. (2009). "Small Molecule Subgraph Detector (SMSD) toolkit". Journal of Cheminformatics. 1 (1): 12. doi: 10.1186/1758-2946-1-12 . PMC   2820491 . PMID   20298518.
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15. A. Inokuchi, T. Washio, K. Nishimura, H. Motoda, A Fast Algorithm for Mining Frequent Connected Subgraphs, IBM Research, Tokyo Research Laboratory, 2002.
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20. T. Meinl, C. Borgelt, M. R. Berthold, Discriminative Closed Fragment Mining and Perfect Extensions in MoFa, Proceedings of the Second Starting AI Researchers Symposium (STAIRS 2004), 2004.
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22. Meinl, T.; Berthold, M. R. (2004). "Hybrid fragment mining with MoFa and FSG" (PDF). 2004 IEEE International Conference on Systems, Man and Cybernetics (IEEE Cat. No. 04CH37583). Vol. 5. pp. 4559–4564. doi:10.1109/ICSMC.2004.1401250. ISBN   0-7803-8567-5. S2CID   3248671.
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37. A. M. Bianucci; Micheli, Alessio; Sperduti, Alessandro; Starita, Antonina (2000). "Application of Cascade Correlation Networks for Structures to Chemistry". Applied Intelligence. 12 (1–2): 117–146. doi:10.1023/A:1008368105614. S2CID   10031212.
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Further reading

• Schölkopf, B., K. Tsuda and J. P. Vert: Kernel Methods in Computational Biology, MIT Press, Cambridge, MA, 2004.
• R.O. Duda, P.E. Hart, D.G. Stork, Pattern Classification, John Wiley & Sons, 2001. ISBN   0-471-05669-3
• Gusfield, D., Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997. ISBN   0-521-58519-8
• R. Todeschini, V. Consonni, Handbook of Molecular Descriptors, Wiley-VCH, 2000. ISBN   3-527-29913-0

External links

• Small Molecule Subgraph Detector (SMSD) - is a Java-based software library for calculating Maximum Common Subgraph (MCS) between small molecules.
• 5th International Workshop on Mining and Learning with Graphs, 2007
• Overview for 2006
• Molecule mining (basic chemical expert systems)
• ParMol and master thesis documentation - Java - Open source - Distributed mining - Benchmark algorithm library
• TU München - Kramer group
• Molecule mining (advanced chemical expert systems)
• DMax Chemistry Assistant - commercial software
• AFGen - Software for generating fragment-based descriptors