moss.html

A program to find frequent molecular substructures and discriminative fragments in a database of mol

<pre>
1,O-C,2,1,17,100.0,0,0.0
2,C12(-C(-C-C-C-2)-C2-C(-C-C-1)-C1-C(-C-C-2)-C-C-C-C-1)-C,18,21,17,100.0,0,0.0
</pre>
<p>in the file <tt>steroids.sub</tt>. The found substructures are
depicted in the table below.</p>
<p><table border=1 cellpadding=4>
<tr><th>id</th><th>fragment</th><th>SMILES description</th></tr>
<tr><td>1</td><td><img src="common_1.png"></td>
              <td>OC</td></tr>
<tr><td>2</td><td><img src="common_3.png"></td>
              <td>C12(C(CCC2)C2C(CC1)C1C(CC2)CCCC1)C</td></tr>
</table></p>
<p>As can be seen, the second found substructure contains the third
and the fourth ring, which are present in all molecules, but differ
slightly. For the fourth ring (on the right) this is obvious, since
it is an aromatic ring in most molecules, but not in molecules
k, p, and q. However, this also leads to a difference in the third
ring, since the bond that is shared by the third and fourth ring is
an aromatic bond if the fourth ring is aromatic, but only a single
bond in the three other cases.</p>

<p>Note that in this case the second substructure cannot be found
in exactly this form in all fragments, but only approximately.
Nevertheless it can be useful and may provide a deeper insight into
the structural properties of the molecules in the dataset.</p>

<p>Note also that in the first run the part of the third ring that
is identical in all molecules (all bonds with the exception of the
one that is shared by the third and fourth ring) is not part of the
fragment, since ring mining requires that a ring must be present as
a whole. Since the ring cannot be closed in the same way in all
molecules, it has to be left out completely. If, however, ring mining
is deactivated (by <i>not</i> specifying the option <tt>-R</tt> or
by setting "Ring extensions" to "none") these common ring bonds will
be part of a found fragment, which then contains a partial ring.</p>

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<h3><a name="publ">Publications</a></h3>

<p>Details about the algorithm underlying the MoSS program can be found
in these papers:</p>

<p><ul>
<li><b><a name="borgelt_2005">
    On Canonical Forms for Frequent Graph Mining</a></b><br>
    Christian Borgelt<br>
    <i>Workshop on Mining Graphs, Trees, and Sequences
       (MGTS'05 at PKDD'05, Porto, Portugal)</i>, 1-12.<br>
    ECML/PKDD'05 Organization Committee, Porto, Portugal 2005.<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/mgts_05.pdf">mgts_05.pdf</a> (210 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/mgts_05.ps.gz">mgts_05.ps.gz</a> (152 kb)
    (12 pages)</li>
<li><b>MoSS: A Program for Molecular Substructure Mining</b><br>
    Christian Borgelt, Thorsten Meinl, and Michael R. Berthold<br>
    <i>Workshop Open Source Data Mining Software
       (OSDM'05, Chicago, IL)</i>, 6--15.<br>
    ACM Press, New York, NY, USA 2005.<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/moss_ecs.pdf">moss_ecs.pdf</a> (247 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/moss_ecs.ps.gz">moss_ecs.ps.gz</a> (160 kb)
    (10 pages)</li>
<li><b><a name="borgelt_et_al_2004">Advanced Pruning Strategies to
    Speed Up Mining Closed Molecular Fragments</a></b><br>
    Christian Borgelt, Thorsten Meinl, and Michael R. Berthold.<br>
    <i>Proc. IEEE Conf. on Systems, Man and Cybernetics
    (SMC 2004, The Hague, Netherlands)</i>, on CD-ROM.<br>
    IEEE Press, Piscataway, NJ, USA 2004<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/smc_04.pdf">smc_04.pdf</a> (122 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/smc_04.ps.gz">smc_04.ps.gz</a> (65 kb)
    (6 pages)</li>
<li><b><a name="hofer_et_al_2004">Large Scale Mining
    of Molecular Fragments with Wildcards</a></b><br>
    Heiko Hofer, Christian Borgelt and Michael R. Berthold.<br>
    <it>Intelligent Data Analysis 8:495-504.<br>
    IOS Press, Amsterdam, Netherlands 2004<br>
    (10 pages)</li>
<li><b><a name="Meinl_et_al_2004">Mining Fragments
    with Fuzzy Chains in Molecular Databases</a></b><br>
    Thorsten Meinl, Christian Borgelt, and Michael R. Berthold.<br>
    <i>Proc. 2nd Int. Workshop on Mining Graphs, Trees and Sequences
    (MGTS 2004, Pisa, Italy)</i>, 49-60.<br>
    University of Pisa, Pisa, Italy 2004<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/mgts_04.pdf">mgts_04.pdf</a> (546 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/mgts_04.ps.gz">mgts_04.ps.gz</a> (211 kb)
    (12 pages)</li>
<li><b>Discriminative Closed Fragment Mining
       and Perfect Extensions in MoFa</b><br>
    Thorsten Meinl, Christian Borgelt, and Michael R. Berthold<br>
    <i>Proc. 2nd Starting AI Researchers' Symposium
       (STAIRS 2004, Valencia, Spain)</i>, 3-14<br>
    IOS Press, Amsterdam, Netherlands 2004<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/stairs_04.pdf">stairs_04.pdf</a> (382 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/stairs_04.ps.gz">stairs_04.ps.gz</a> (205 kb)
    (12 pages)</li>
<li><b>Finding Discriminative Molecular Fragments</b><br>
    Christian Borgelt, Heiko Hofer, and Michael Berthold<br>
    <i>Workshop Information Mining - Navigating Large Heterogeneous Spaces
    of Multimedia Information</i><br>
    German Conference on Artificial Intelligence,
    Hamburg, Germany 2003<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/wsim_03.pdf">wsim_03.pdf</a> (303 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/wsim_03.ps.gz">wsim_03.ps.gz</a> (143 kb)
    (13 pages)</li>
<li><b>Large Scale Mining of Molecular Fragments with Wildcards</b><br>
    Heiko Hofer, Christian Borgelt, and Michael Berthold.<br>
    <i>Proc. 5th International Symposium on Intelligent Data Analysis</i>
    (IDA 2003, Berlin, Germany), 380-389.<br>
    Springer-Verlag, Heidelberg, Germany 2003<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/ida_03.pdf">ida_03.pdf</a> (187 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/ida_03.ps.gz">ida_03.ps.gz</a> (125 kb)
    (10 pages)</li>
<li><b><a name="borgelt_and_berthold_2002">Mining Molecular Fragments:
       Finding Relevant Substructures of Molecules</a></b><br>
    Christian Borgelt and Michael R. Berthold<br>
    <i>IEEE International Conference on Data Mining</i>
    (ICDM 2002, Maebashi, Japan), 51-58<br>
    IEEE Press, Piscataway, NJ, USA 2002<br>
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/icdm_02.pdf">icdm_02.pdf</a> (112 kb)
    <a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/papers/icdm_02.ps.gz">icdm_02.ps.gz</a> (69 kb)
    (8 pages)</li>
</ul></p>

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<h3><a name="download">Download</a></h3>

<p><a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/moss.html">
Download page</a> with most recent version.</p>

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<h3><a name="copying">Copying</a></h3>

<p>This program is free software;
you can redistribute it and/or modify it under the terms of the
<a href="http://www.fsf.org/copyleft/lesser.html">
GNU Lesser (Library) General Public License</a> 
as published by the <a href="http://www.fsf.org">
Free Software Foundation</a>.</p>

<p>This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
<a href="http://www.fsf.org/copyleft/lesser.html">
GNU Lesser (Library) General Public License</a> for more details.</p>

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<h3><a name="contact">Contact</a></h3>

<table border=0 cellpadding=0 cellspacing=0>
<tr><td valign=top>E-mail:</td><td width=10></td>
    <td><a href="mailto:[e-mail]">
        [e-mail]</a></td></tr>
<tr><td valign=top>Snail mail: <font color="white">Old</font></td><td></td>
    <td><a href="http://www.softcomputing.es/cv_html/cv_cborgelt.html">
        Christian Borgelt</a><br>
        <a href="http://www.softcomputing.es/ru_html/ru_ida.htm"> 
        Intelligent Data Analysis and Graphical Models Research Unit</a><br>
        <a href="http://www.softcomputing.es/">
        European Center for Soft Computing</a><br>
        Edificio Cientifico-Tecnol&oacute;gico, 3<sup>a</sup> Planta<br>
        c/ Gonzalo Guti&eacute;rrez Quir&oacute;s s/n<br>
        33600 Mieres<br>
        Asturias, Spain</td></tr>
<tr><td>Phone:</td><td></td>
    <td>[phone]</td></tr>
<tr><td>Fax:</td><td></td>
    <td>[phone]</td></tr>
</table>

<p></p>

<table border=0 cellpadding=0 cellspacing=0>
<tr><td valign=top>Old E-mail:</td><td width=10></td>
    <td><a href="mailto:[e-mail]">
        [e-mail]</a><br>
        <a href="mailto:[e-mail]">
        [e-mail]</a></td></tr>
<tr><td valign=top>Old Snail mail:</td><td></td>
    <td><a href="http://fuzzy.cs.uni-magdeburg.de/~borgelt/index.html">
        Christian Borgelt</a><br>
        <a href="http://fuzzy.cs.uni-magdeburg.de/index.html">
        Working Group Neural Networks and Fuzzy Systems</a><br>
        <a href="http://www-iik.cs.uni-magdeburg.de/iik.html"> 
        Department of Knowledge Processing and Language Engineering</a><br>
        <a href="http://www.cs.uni-magdeburg.de/">
        School of Computer Science</a><br>
        <a href="http://www.uni-magdeburg.de/">
        Otto-von-Guericke-University of Magdeburg</a><br>
        Universit&auml;tsplatz 2<br>
        D-39106 Magdeburg<br>
        Germany</td></tr>
</table>

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<h3><a name="links">Useful Links</a></h3>

<ul>
<li><a href="http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html">
    SMILES Tutorial by Daylight, Inc.</a></li>
<li><a href="http://www.daylight.com/daycgi_tutorials/depict.cgi">
    Molecule renderer by Daylight, Inc. (for SMILES format)</a></li>
</ul>

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<address>&copy; 2002&ndash;2006
<a href="mailto:[e-mail]">Christian Borgelt</a>
</address>
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