ISSSB'12 ECML/PKDD 2012 Workshop on
Learning and Discovery in
Symbolic Systems Biology
University of Bristol, UK
24 September 2012
* * * *   LDSSB'12   * * * *

Symbolic Systems Biology is a rapidly emerging field involving the application of formal logic-based methods to Systems Biology and Bioinformatics. In contrast to traditional numerical methods, symbolic techniques offer the advantages of being able to directly formalise and exploit biological knowledge in a way that facilitates integration of data across different levels of biological abstraction. Last year saw major developments in this field with the release of a new book and the convening of a first international symposium:

As a result of these developments, it is becoming clear that several symbolic approaches can be usefully deployed in various biological applications - especially in those where information is stored in graph-based formalisms (such as metabolic networks, signalling pathways, genetic interactions, and food webs). Such techniques include

  • formal logics (e.g., Boolean, classical and modal logics)
  • computational logic (e.g., constraint, answer set and logic programming)
  • graphical models (e.g., Bayes and Petri Nets)
  • synthetic inference (e.g., abductive, inductive and analogical reasoning)
  • formal methods (e.g., model checking, pi-calculus and hybrid logic)
  • qualitatitive reasoning and equation discovery

The main aim of the workshop is to explore how machine learning and knowledge discovery techniques can be used within such formalisms in order to further the practical utility of Symbolic Systems Biology. In principle, the ability to support diverse modes of logical inference ought to constitute a major advantage of symbolic methods that would allow them to add significant value over purely numerical methods. The Workshop will aim to explore the theoretical and practical aspects of this claim. Specific topics of interest include

  • theory and practice of machine learning and knowledge discovery for symbolic systems biology
  • integration of numerical and symbolic techniques
  • abductive and inductive hypothesis generation and evaluation
  • real-world applications and/or theoretical developments
  • methods for biological network repair and reconstruction
  • applications of forward, backward, and meta-reasoning

A secondary aim is to identify ways in which purely symbolic methods have been or could be combined with numerical techniques and applied to emerging problems in experimental and synthetic biology. We believe it is important to promote a dialogue between qualitative and quantitative practitioners in order to better handle real world noise and uncertainty. Within the context of machine learning, this raises the issue of how to combine structural and parameter learning.

Finally, we wish to provide a forum to discuss recent developments within symbolic system biology that enhance the power or usability of its constituent approaches. We especially welcome any efforts to make symbolic systems biology more accessible and useful to biologists with no specific background in formal methods.

09.00Welcome Address
09.05Invited Talk
Equation Discovery for Systems Biology: Saso Dzeroski
Biocircuit Design with Equation Discovery: Jovan Tanevski, Nikola Simidjievski and Saso Dzeroski
Towards a logic-based method to infer provenance-aware molecular networks: Zahira Aslaoui-Errafi, Sarah Cohen-Boulakia, Christine Froidevaux, Pauline Gloaguen, Anne Poupon, Adrien Rougny and Meriem Yahiaoui
Abducing Biological Regulatory Networks from Process Hitting models: Maxime Folschette, Loic Pauleve, Katsumi Inoue, Morgan Magnin and Olivier RouxPDF
Logical Modeling of Cancer and Chemoprevention: Antonis Kakas, Sotiris Lazarou, Christiana Neophytou and Andreas Constantinou
Towards a graphical rule editor for the pathway logic assistant: Amna Abbas, Carolyn Talcott, Merrill Knapp and Oliver RayPPT
Learning a Causal Network from Temporal Cancer Gene Expression Data: A Logical Abduction Approach: Hiroaki Watanabe, Stephen Muggleton, Richard Currie, Pooja Jain, Dianhuan Lin, Jianzhong Chen, Michael Sternberg, Charles Baxter, Jose Domingo Salazar and Stuart Dunbar
Learning Monadic and Dyadic Relations: Three Case Studies in Systems Biology: Michiel Stock, Tapio Pahikkala, Antti Airola, Tapio Salakoski, Bernard De Baets and Willem Waegeman
Ongoing Work on Applying Multi-clause ILP to Identify Metabolic Control Points: Dianhuan Lin, Jianzhong Chen, Hiroaki Watanabe, Pooja Jain, Charles Baxter, Richard Currie, Jose Domingo Salazar, Stuart Dunbar, Mark Earll, Michael Sternberg and Stephen Muggleton
Towards automatic construction and corroboration of food webs: Alireza Tamaddoni-Nezhad, Ghazal Afroozi Milani, David Bohan, Stuart Dunbar, Alan Raybould and Stephen Muggleton
Symbolic Systems Biology: a Roadmap: Oliver Ray and Marcus TindallPPT
16.30ECML/PKDD'12 Conference Opening

Submissions should be made through EasyChair system through this link.


The pre-workshop proceedings are available as a PDF

Apr 06call for papers
Jun 29
Jul 13
paper submission deadline
Jul 20
Jul 29
acceptance notification
Jul 31early registration deadline
Aug 03
Aug 10
Aug 15
camera-ready deadline
Sep 24workshop

Registration should be made through the ECML PKDD 2012 conference site at this link. As with all workshops at this event, participants will need to register for the main conference.

Oliver Ray (University of Bristol, UK)
Katsumi Inoue (National Institute of Informatics, Japan)
Andrew Phillips (Microsoft Research, UK)
Anne Siegel (University of Rennes, France)
Carolyn Talcott (SRI International, USA)
Celine Rouveirol (University of Paris 13, France)
Henning Christiansen (University of Roskilde, Denmark)
Katsumi Inoue (National Institute of Informatics, Japan)
Marcus Tindall (University of Reading, UK)
Mark Craven (University of Wisconsin, USA)
Oliver Ray (University of Bristol, UK)
Ross King (University of Manchester, UK)
Saso Dzersoki (Jozef Stefan Institute, Slovenia)
Sriram Iyengar (University of Texas, USA)
Stephen Muggleton (Imperial College London, UK)
Torsten Schaub (University of Potsdam, Germany)
img Last year's symposium aimed at establishing a research community in Symbolic Systems Biology:

The First International Symposium on Symbolic Systems Biology: Approaches and Applications
O. Ray, K. Inoue, and K. Horimoto (Chairs)
Shonan, Japan, 2011
img A very recent book that collects together several techniques in the area of symbolic systems biology:

Symbolic Systems Biology: Theory and Methods
M.Sriram Iyengar (Ed.)
Jones and Bartlett Learning, 2011
img A related conference exploring the use of Machine Learning in Systems Biology (but with no explicit focus on symbolic or logical methods):

5th International Workshop on Machine Learning in Systems Biology
S, Kramer and N. Lawrence (Chairs)
Vienna, Austria, 2011
img Another conference exploring the use of both algebraic/symbolic and numeric methods in Biology:

2010 Conference on Algebraic and Numeric Biology
K. Horimoto, M. Nakatsui and N. Popov (Chairs)
Hagenberg, Austria, 2010
img An earlier book that includes several biological applications of symbolic methods in biological applications:

Elements of Computational Systems Biology
H. Lodhi and S. Muggleton (Eds.)
John Wiley and Sons, 2009
img An earlier Schloss Dagstuhl seminar focusing on the use of formal methods in molecular biology:

Formal Methods in Molecular Biology
R. Breitling, D. Gilbert, M. Heiner and C. Priami (Chairs)
Dagstuhl, Germany, 2009
(c) Oliver Ray, last updated 23/09/2012