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    <article-meta>
      <title-group>
        <article-title>SMURFF: a High-Performance Framework for Matrix Factorization Methods (extended abstract)</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Tom Vander Aa</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Imen Chakroun</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Thomas J. Ashby</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jaak Simm</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Adam Arany</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Yves Moreau</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Thanh Le Van</string-name>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jose Felipe Golib Dzib</string-name>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jorg Wegner</string-name>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Vladimir Chupakhin</string-name>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Hugo Ceulemans</string-name>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Roel Wuyts</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Wilfried Verachtert</string-name>
          <xref ref-type="aff" rid="aff1">1</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>ESAT-STADIUS, KU Leuven</institution>
          ,
          <addr-line>Leuven</addr-line>
          ,
          <country country="BE">Belgium</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>ExaScience Life Lab at imec</institution>
          ,
          <addr-line>Leuven</addr-line>
          ,
          <country country="BE">Belgium</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>Janssen Pharmaceutica</institution>
          ,
          <addr-line>Beerse</addr-line>
          ,
          <country country="BE">Belgium</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>This is a 2-page condensed abstract of the paper published at [1]. Bayesian Matrix Factorization Matrix factorization is a common machine learning technique for recommender systems, like books for Amazon or movies for Net ix [2]. The Bayesian Matrix Factorization (BMF) variant is especially powerful because it produces good results and is relatively robust against over tting. As sketched in Figure 1, the idea of these methods is to approximate the usermovie rating matrix R as a product of two low-rank matrices U and V such that R U V . In this way U and V are constructed from the known ratings in R, which is usually very sparsely lled. The recommendations can be made from the approximation U V which is dense. High-Performance Matrix Factorization with SMURFF While BMF is powerful, it is computationally very intensive and thus more challenging to implement for large datasets. In this work we present SMURFF a high-performance featurerich framework to compose and construct di erent Bayesian matrix-factorization methods, namely:</p>
      </abstract>
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  <body>
    <sec id="sec-1">
      <title>-</title>
      <p>N</p>
      <p>M
R
=</p>
      <p>K
U
x</p>
      <p>M</p>
      <p>V
 ≪ 
 ≪ 
R is very sparse</p>
      <p>K
Copyright c 2019 for this paper by its authors. Use permitted under Creative
Commons License Attribution 4.0 International (CC BY 4.0).</p>
      <p>
        Authors Suppressed Due to Excessive Length
{ BPMF, the basic version [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ];
{ Macau, adding support for high-dimensional side information to the
factorization [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ];
{ GFA, doing Group Factor Analysis [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ].
      </p>
      <p>
        Applications of SMURFF The framework has been used very successfully in
drug discovery. Here a key problem is the identi cation of candidate molecules
that a ect proteins associated with diseases [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ]. SMURFF with Macau has been
used to predict compound-on-protein activity on a matrix with more than one
million compounds (rows) and several thousand proteins (columns) [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ]. Chemical
ngerprints were used for the compounds, in both dense and sparse formats. This
has led to important new insights and potential new compounds to be used in
drug discovery.
      </p>
      <p>
        Getting SMURFF SMURFF is available as open-source [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ] and can be used both
on a supercomputer and on a desktop or laptop machine. Documentation and
several examples are provided as Jupyter notebooks using SMURFF's high-level
Python API.
      </p>
    </sec>
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