Mining Abstractions in Scientific Workflows

251 Pages·2015·5.08 MB·English

Departamento de Inteligencia Artificial
Escuela T´ecnica Superior de Ingenieros Inform´aticos
PhD Thesis
Mining Abstractions in Scientific
Workflows
Author: Daniel Garijo Verdejo
Supervisors: Prof. Dr. Oscar Corcho
Prof. Dra. Yolanda Gil
December, 2015
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TribunalnombradoporelSr. RectorMagfco. delaUniversidadPolit´ecnicadeMadrid,
el d´ıa 30 de octubre de 2015
Presidente: Dra. Asunci´on G´omez P´erez
Vocal: Dr. Jose Manuel G´omez P´erez
Vocal: Dr. Malcolm Atkinson
Vocal: Dr. Rafael Tolosana
Secretario: Dr. Mark Wilkinson
Suplente: Dr. Mariano Fern´andez L´opez
Suplente: Dra. Bel´en D´ıaz Agudo
Realizado el acto de defensa y lectura de la Tesis el d´ıa 3 de diciembre de 2015 en la
Facultad de Inform´atica
Calificac´ıon:
EL PRESIDENTE VOCAL 1 VOCAL 2
VOCAL 3 EL SECRETARIO
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A mis padres
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Acknowledgements
Finally, after five years, I can finally say that I see light at the end of the
tunnel. Maybe the other side is still a bit cloudy at the moment, but the
important thing is to have arrived here. And, honestly, I think I wouldn’t
have made it to this point without all the people who have been by my side
during these years.
First, I would like to thank my supervisors Oscar Corcho and Yolanda Gil
for guiding me whenever I got stuck and for having the patience to answer
allmyquestions. Furthermore,thankstotheirhelp,togetherwithAsunci´on
G´omez P´erez’s advice, I was granted the FPU (Formaci´on de Profesorado
Universitario)scholarshipfromtheMinisteriodeCienciaeInnovaci´on. This
scholarship has funded the internships and the research described on this
document, and I am very grateful for having had the opportunity to enjoy
it.
I would also like to thank my family, specially my parents (Francisco Javier
and Mar´ıa Felisa) and my sister Elisa for all their support, advice and
suggestions during this period. Even from the distance!
Next up are my lab mates, who have helped me with the figures (Mar´ıa
Poveda, I really think you could write a thesis just by doing cool figures),
logos (Idafen Santana, also responsible for our soccer team), technical sup-
port (Miguel Angel Garc´ıa and Rau´l Alc´azar), advice for the thesis (Andr´es
Garc´ıa and Esther Lozano) or just cheering me up when hanging out with
them (Dani, Freddy, Carlos, Pablo, Julia, Boris, Alejandro, Olga and Vic-
tor). In this regard, I am also very grateful to my friends Sergio, Paloma,
David, Cristina and Javier for being always available to have a chat with a
beer and discuss things totally unrelated to this thesis.
IalsoowespecialthankstoPaoloMissierandKhalidBelhajjame, whohave
provided very valuable feedback with very little time for doing the review.
Next, Varun Ratnakar has always been crucial for some of the technical
parts described in this thesis. Varun is one of the best working colleagues
one could ever ask for.
And finally, I want to thank all the collaborators and projects pals I have
interacted with during these years, from the w4Ever team (with Carole,
Jun, Graham, Rau´l, Piotr, Stian, Khalid, Kristina, Lourdes, Susana, Pique)
to the people I have met during my internships at the ISI (Dirk, John,
Matheus, Felix, Zori).
Abstract
Scientific workflows have been adopted in the last decade to represent the
computational methods used in in silico scientific experiments and their
associated research products. Scientific workflows have demonstrated to be
usefulforsharingandreproducingscientificexperiments, allowingscientists
to visualize, debug and save time when re-executing previous work. How-
ever, scientific workflows may be difficult to understand and reuse. The
large amount of available workflows in repositories, together with their het-
erogeneity and lack of documentation and usage examples may become an
obstacle for a scientist aiming to reuse the work from other scientists. Fur-
thermore, giventhatitisoftenpossibletoimplementamethodusingdiffer-
ent algorithms or techniques, seemingly disparate workflows may be related
at a higher level of abstraction, based on their common functionality. In
this thesis we address the issue of reusability and abstraction by exploring
how workflows relate to one another in a workflow repository, mining ab-
stractions that may be helpful for workflow reuse. In order to do so, we
propose a simple model for representing and relating workflows and their
executions, we analyze the typical common abstractions that can be found
in workflow repositories, we explore the current practices of users regarding
workflowreuseandwedescribeamethodfordiscoveringusefulabstractions
for workflows based on existing graph mining techniques. Our results ex-
pose the common abstractions and practices of users in terms of workflow
reuse, and show how our proposed abstractions have potential to become
useful for users designing new workflows.
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