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  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>ORCID ID:</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Challenge-based learning in Computational Biology and Data Science</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Emilio Serrano?</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Martin Molina</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Daniel Manrique??</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Javier Bajo</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>emilioserra</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>mmolina</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>dmanrique</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>jbajog@ .upm.es</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Department of Arti cial Intelligence, Universidad Politecnica de Madrid</institution>
          ,
          <country country="ES">Spain</country>
        </aff>
      </contrib-group>
      <volume>000</volume>
      <fpage>0</fpage>
      <lpage>0001</lpage>
      <abstract>
        <p>Data Science is an interdisciplinary eld devoted to extract knowledge from large amounts of data. There is a great variety of programs that address the teaching of this eld with a growing demand of professionals. However, data science pedagogy tends to emphasize general aspects of data and the use of tools instead of the its scienti c dimension. This position paper describes an ongoing educational innovation project for the use of the Challenge-based Learning approach to teach and learn Data Science. In this approach, students work on solving complex and real world problems while the learning is obtained by iterating through three main phases: engage, investigate, and act.</p>
      </abstract>
      <kwd-group>
        <kwd>Challenge-based learning</kwd>
        <kwd>active learning</kwd>
        <kwd>experiential learning</kwd>
        <kwd>project based learning</kwd>
        <kwd>data science</kwd>
        <kwd>computational biology</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>Introduction</title>
      <p>
        Data science (DS) is an interdisciplinary eld devoted to identify patterns and
extract knowledge by mining large amounts of structured and unstructured data.
Among others, DS includes: machine learning, data processing, statistical
research, and their related methods. This science has become a revolution that
has changed our manner of doing business, health, politics, education and
innovation [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]. Scienti c breakthroughs will be increasingly assisted by advanced
computing capabilities and DS methods that help researchers manipulate and
explore massive datasets [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ].
      </p>
      <p>
        Challenge-based learning (CBL) is a new learning approach created by Apple
Inc. in collaboration with teachers and leaders in the education community. CBL
is \an engaging, multidisciplinary approach that starts with standards-based
content and lets students leverage the technology they use in their daily lives
to solve complex, real-world problems" [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ]. In CBL, students work with other
students, their teachers, and experts in their communities and around the world
to develop deeper knowledge of the subjects they are studying.
      </p>
      <p>
        Data science is in a privileged position with respect to other branches of
knowledge to articulate learning through experiences and challenges [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ]. The
Kaggle platform [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ] periodically releases a series of competitions on real problems
such as \Predicting a Biological Response" [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ]; which o ered 20,000$ to the
best predictive model that linked a biological response of molecules to their
chemical properties. These public competitions have the potential to involve
actively the student in a real, signi cant, and related problematic situation;
including a framework for the implementation of a solution to the challenge.
      </p>
      <p>
        This position paper presents an ongoing educational innovation project
focusing on using the CBL approach in a DS course, as part of a Computational
Biology master degree at the Technical University of Madrid (UPM). Students
will work on challenges at the level of a Kaggle competition with special
preference for active and multidisciplinary problems. Based on the 2016 update for
the CBL framework proposed by Apple Inc. [
        <xref ref-type="bibr" rid="ref12">12</xref>
        ], students will learn by following
three main phases: engage, investigate, and act.
      </p>
      <p>The paper outline is as follows: after describing the background of the
presented innovation project in section 2, the project details are given in section
3. These include the scope and students' pro le, the project goals, the
timeline and educational resources, the evaluation, resulting products, and di usion
plan. Section 4 explains the expected contribution to the improvement of
learning quality. Finally, section 5 concludes and presents future lines of research and
work.
2</p>
    </sec>
    <sec id="sec-2">
      <title>Background</title>
      <p>
        The great diversity of applications and the growing demand of experts in the DS
eld has made courses, books and manuals in DS proliferate [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ]. The standard
pedagogical method that we can appreciate in these courses consists of four
steps:
1. The explanation of the di erent machine learning branches (supervised,
unsupervised, and by reinforcement).
2. The detail of some learning paradigms under some of these branches; such
as decision trees or arti cial neural networks.
3. The illustration of these paradigms using toy datasets such as Weather or
      </p>
      <p>
        Iris [
        <xref ref-type="bibr" rid="ref21">21</xref>
        ].
4. Assignments with a straightforward application of the ideas previously
exposed using some DS framework such as Weka [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ] or Caret [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ].
      </p>
      <p>
        We executed an educational innovation project last year, where the
limitations of this standard pedagogical approach were revealed [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ]. Instead, an
experiential learning (EL) method was successfully adopted in a Deep Learning
course, included in the Master in Data Science (EIT Digital Master School),
o ered at UPM.
      </p>
      <p>
        EL brings real life experiences into the classroom which must be integrated
with the goals and objectives of the discipline theory [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ]. The students re ecting
on their product is a fundamental part of EL [
        <xref ref-type="bibr" rid="ref20">20</xref>
        ]. Di erent learning approaches
based on the Kolb cycle [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ] were proposed, applied, and evaluated in the deep
learning course within the frame of the educational innovation project. According
to this cycle, e ective learning involves: having a concrete experience, observation
of and re ection on that experience, the formation of abstract concepts (analysis)
and generalizations (conclusions), and testing them by active experimentation,
resulting in new experiences (iterations in the cycle).
      </p>
      <p>
        Some of the results of this previous project [
        <xref ref-type="bibr" rid="ref17">17</xref>
        ] were presented in a position
paper for an international conference [
        <xref ref-type="bibr" rid="ref18">18</xref>
        ], a Spanish conference paper [
        <xref ref-type="bibr" rid="ref19">19</xref>
        ], and
software tool to complement JupyterHub for Teaching1.
3
      </p>
    </sec>
    <sec id="sec-3">
      <title>Project details</title>
      <p>
        This section explains the ongoing project details [
        <xref ref-type="bibr" rid="ref16">16</xref>
        ] to allow interested
professors to extrapolate our case to their speci c environment. In this new project,
the CBL approach is studied in a new course with di erent students' pro les.
3.1
      </p>
      <sec id="sec-3-1">
        <title>Scope and students' pro le</title>
        <p>The project will be developed with students attending the master in
Computational Biology, o ered by the Computer Science School at the UPM. More
speci cally, in the module of \Knowledge representation and acquisition".</p>
        <p>The pro le of these Computational Biology students is multidisciplinary,
belonging part of them to the world of biology and part of them to branches of
information technology. Data science and CBL provide an exceptional framework
to establish synergies between these two main pro les, e.g. applying computer
science techniques to biology or vice-versa. In this vein, one of the requisites of
the challenges will be to include both pro les in each work group.</p>
        <p>Students will also have the opportunity to apply the knowledge acquired from
other master's modules such as \Statistical Analysis and Data Visualization" or
\Machine Learning" to real world problems. The results of this project will be
directly applicable to other modules, whether of this master degree or of the
master in Data Science (EIT Digital Master School)2, and also in courses of the
Bachelor Degree in Computer Engineering3 such as \Data Mining".
3.2</p>
      </sec>
      <sec id="sec-3-2">
        <title>Goals</title>
        <p>
          The goals of the presented project are the following:
{ G1. Development of methods for CBL in Data Science and Computational
Biology. This goal includes the instantiation of methodologies and general
frameworks of CBL to the speci c eld to be treated. Among these
frameworks, we can point out: the 2016 update for the CBL framework proposed
by Apple Inc [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ]; and the \Challenge Based Learning" report carried out
        </p>
        <sec id="sec-3-2-1">
          <title>1 https://jupyterhub-deploy-teaching.readthedocs.io 2 http://www.fi.upm.es/?id=masterdatascience 3 https://www.fi.upm.es/?id=gradoingenieriainformatica&amp;idioma=english</title>
          <p>
            by the Monterrey Institute of Technology and Higher Education in 2016 [
            <xref ref-type="bibr" rid="ref6">6</xref>
            ].
          </p>
          <p>
            The phases of the Apple Inc framework are depicted in Fig. 1.
{ G2. Study of speci c challenges in the eld of Data Science and
Computational Biology. Application of the explored, extended, and instantiated
methods in O1 to Data Science. This goal addresses the selection of concrete
challenges and for a speci c student pro le. The students will work on a
challenge at the Kaggle competition level with special preference for active
and multidisciplinary problems. Examples of past competitions that t the
students' pro le are \Predicting a Biological Response", \Merck Molecular
Activity Challenge", \Shelter Animal Outcomes", \Leaf Classi cation", or
\Zoo Animal Classi cation".
{ G3. Integration and documentation of tools for the support of CBL in the
course of "Representation and Acquisition of Knowledge". This goal includes
the analysis and documentation of tools available to support the CBL in this
speci c module. Although Kaggle has a working environment, Kaggle
Kernels4, this framework will be combined with other tools, preferably free and
open source, that meet the needs of the CBL. Among others and according
to the 2016 update for the ABR framework proposed by Apple Inc. [
            <xref ref-type="bibr" rid="ref12">12</xref>
            ],
          </p>
        </sec>
        <sec id="sec-3-2-2">
          <title>4 https://www.kaggle.com/kernels</title>
          <p>students will need: a calendar, space for collaboration, and storage of
documents. Project management tools such as Trello5 and Asana6 as well as free
alternatives will be considered.
3.3</p>
        </sec>
      </sec>
      <sec id="sec-3-3">
        <title>Timeline and educational resources</title>
        <p>The following three major tasks will be addressed with a clear correspondence
to the three goals explained above:
{ T1. Developing of methods for CBL in Data Science and Computational</p>
        <p>Biology.
{ T2. Analyzing and selecting speci c challenges in the eld of Data Science
and Computational Biology.
{ T3. Integrating and documenting tools for the support of CBL in the
Representation and Acquisition of Knowledge.</p>
        <p>
          The project kicks-o on February 15, 2018 and an ends on November 15,
2018, giving 9 months of project numbered from 1 to 9. In an iterative and
incremental approach such as the Scrum methodology [
          <xref ref-type="bibr" rid="ref14 ref15">15, 14</xref>
          ], the following
timeline is proposed in Fig. 2.
        </p>
        <p>As shown in Fig. 2, three iterations are considered for each task. This allows
the tasks results to feed back to previous tasks. Moreover, there is an overlap
into the di erent tasks as expected in an iterative and incremental approach.</p>
        <p>The following educational resources will be used:
{ Scienti c repositories available in the UPM as ScienceDirect7.
{ The Institutional Teaching Platform of the UPM (Moodle)8.
{ Data repositories and contests websites in Data Science such as Kaggle.
{ Resources of the Department of Arti cial Intelligence as web servers.</p>
        <sec id="sec-3-3-1">
          <title>5 https://trello.com/</title>
        </sec>
        <sec id="sec-3-3-2">
          <title>6 https://asana.com</title>
        </sec>
        <sec id="sec-3-3-3">
          <title>7 www.sciencedirect.com</title>
        </sec>
        <sec id="sec-3-3-4">
          <title>8 moodle.upm.es</title>
          <p>3.4</p>
        </sec>
      </sec>
      <sec id="sec-3-4">
        <title>Evaluation</title>
        <p>
          The evaluation of the project will be carried out through the generation of an
e-portfolio by the students attending the module under study. The e-portfolio
is a digital collection of evidence which includes: demonstrations, resources, and
achievements obtained by students. According to the CBL framework proposed
by Apple Inc [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ], the following sections will be evaluated:
{ Report of the great ideas to investigate.
{ The proposal of the challenge, the essential question to answer and the
motivation about the signi cance of the challenge.
{ Guiding issues, questions that will guide the search for a solution.
{ Learning plan and schedule.
{ Research report, in Jupyter IPython notebook format9 or alternative to
ensure the reproducibility and repeatability of the results achieved.
{ Proposed solution, presentation including prototypes, concepts, and expert
feedback.
{ Implementation and evaluation plans.
{ Evaluation results.
{ Final presentations.
{ Journals with personal and group experience.
        </p>
        <p>{ Final re ections on what was learned.
3.5</p>
      </sec>
      <sec id="sec-3-5">
        <title>Resulting products</title>
        <p>This section describes the tangible products resulting from the project
(methodological guides, reports, educational resources, etcetera) with a description of
their potential for internal and external transfer. The following deliverables will
be elaborated:
{ D1. Report on methods for CBL in Computational Biology and Data Science.
{ D2. Report on the analysis and selection of appropriate challenges for the
learning of Computational Biology and Data Science.
{ D3. Manual of tools for the support to the CBL in the Representation and</p>
        <p>Acquisition of Knowledge.
{ D4. Report on the evaluation of results based on e-portfolios created by
students.
{ D5. Journal and conference papers for the dissemination of results.</p>
        <p>As described in section 3.1 these deliverables have an internal transfer in the
UPM to other modules of the master for which it is proposed, other masters, and
other degrees. These products can also be a competitive advantage in the
organization of massive open online courses (MOOCs) by presenting a pedagogical
prescriptions.</p>
        <sec id="sec-3-5-1">
          <title>9 jupyter.org</title>
          <p>The main di usion materials generated in the project will be the deliverables 3,
4 and 5 explained in section 3.5. There will also be contemplated:
{ the construction of a website that collects all the deliverables,
{ news for di usion at the UPM,
{ microblogging posts (Twitter) in the department and the school,
{ radio interviews to disseminate educational innovation.
4</p>
        </sec>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>Contribution to the improvement of teaching quality</title>
      <p>Thanks to the application of the CBL approach, a signi cant improvement of
learning and teaching quality is expected. Among others, this improvement will
be re ected in:
1. A deeper understanding of Data Science for Computational Biology, allowing
to diagnose and analyze problems before proposing solutions.
2. A greater commitment to involve the student both in the de nition of the
Data Science problem to be addressed and in the solution that will be
developed to solve it.
3. Development of skills to investigate, create models, materialize them, and
work collaboratively and multidisciplinary.
4. A closer approach to the reality of their profession, establishing relationships
with specialists in the Kaggle platform that contribute to their professional
growth.
5. Strengthening the connection between what they learn in the Master's and
what they perceive in the professional world.
6. Development of high-level communication skills, through the use of social
tools such as Kaggle forums and media production techniques, to create and
share the solutions developed by them.</p>
      <p>
        Moreover, this teaching innovation project [
        <xref ref-type="bibr" rid="ref16">16</xref>
        ] will be aligned with the results
obtained from our previous project using EL in Data Science [
        <xref ref-type="bibr" rid="ref17 ref18">17, 18</xref>
        ]. Therefore,
the same bene ts obtained in the Deep Learning course are expected in the
\Knowledge representation and acquisition" module. Among others, the student
will:
1. learn to select relevant information about how learning paradigms work and
the information they o er, instead of considering them as black boxes where
the model built has no relevance and only quality metrics are studied;
2. learn to study the details and data of the concrete problem and to obtain
good understanding of the data;
3. perceive the iterative nature of DS, by building di erent prediction models
considering the data and results from previous models;
4. and, research on new methods and their extension or variation for new and
challenging problems, instead of just applying well-known solutions to
wellknown problems.
      </p>
    </sec>
    <sec id="sec-5">
      <title>Conclusion and future works</title>
      <p>This position paper has presented an ongoing educational research project to
use the challenge-based learning approach for DS in the context of a master
in Computational Biology. The paper has revised the background, including a
number of shortcomings repeated in current DS courses, and the results obtained
in a previous project, based on considering experiential learning for DS. The
ongoing project details have been presented: the scope and students' pro les,
goals, timeline, teaching resources, evaluation, resulting products, and di usion
plan. The project details allow interested professors to extrapolate our case to
their speci c environment and audience.</p>
      <p>The contribution to the improvement of the teaching quality of the project
has also been explored, highlighting a deeper understanding of Data Science for
Computational Biology. This allows students to diagnose and analyze problems
before proposing solutions. DS is not only about data and tools to manage
them as classic DS courses may suggest. DS is more about \science" and the
scienti c questions we can answer with data. Therefore, a major advantage in
using CBL for DS is that teachers do not present the answers before students
ask the scienti c questions by themselves.</p>
      <p>Our main future works include to create a survey on the acceptance and
quality of challenges proposed, to study new theoretical frameworks for applying
CBL in DS, and the exploration (or implementation) of software tools to develop
e-portfolios. Moreover, two students have been hired to assist in the search and
development of speci c challenges for Computational Biology.</p>
    </sec>
    <sec id="sec-6">
      <title>Acknowledgments</title>
      <p>This research work is supported by the Universidad Politecnica de Madrid under
the education innovation project \Aprendizaje basado en retos para la Biolog a
Computacional y la Ciencia de Datos", code IE1718.1003; and by the the Spanish
Ministry of Economy, Indystry and Competitiveness under the R&amp;D project
Datos 4.0: Retos y soluciones (TIN2016-78011-C4-4-R, AEI/FEDER, UE).</p>
    </sec>
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