Christian Theil Have, M.Sc., Ph.D. I am now at The Novo Nordisk Foundation Center for Basic Metabolic research.

Research

Research interests

Events

• CICLOPS 2013

My PhD project

My PhD project was supervised by Henning Christiansen and was part of the LoSt research project.

My thesis entitled, "Efficient Probabilistic Logic programming for Biological Sequence Analysis" is available here.

Available software

• BANpipe - A logic-based scripting language designed to model complex compositions of time consuming analyses.
• Constrained Hidden Markov Models in PRISM
• Various stuff on github

Publications

Reviewed publications

• Christian Theil Have, Sine Zambach and Henning Christiansen. Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes. BMC Bioinformatics 14: 118 (2013)
• Christian Theil Have. Efficient Probabilistic Logic programming for Biological Sequence Analysis. 2013. Ph.D. thesis. pdf.
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen and Matthieu Petit. A declarative pipeline language for complex data analysis. In proc. of 22nd International Symposium on Logic-Based Program Synthesis and Transformation LOPSTR 2012. LNCS Vol. 7844. preprint pdf
• Neng-Fa Zhou and Christian Theil Have. Efficient tabling of structured data with enhanced hash-consing. TPLP 12(4-5): 547-563 (2012). pdf on arxiv.
• Christian Theil Have and Henning Christiansen. Efficient tabling of structured data using indexing and program transformation. In proc. PADL 2012, LNCS 7149. 2012. pdf.
• Christian Theil Have, Constraints and Global Optimization for Gene Prediction Overlap Resolution. Proc. WCB11 - Workshop on Constraint Based Methods for Bioinformatics.
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen and Matthieu Petit. Bayesian Annotation Networks for Complex Sequence Analysis. ICLP (Technical Communications) 2011: 220-230.
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• Christian Theil Have, Henning Christiansen. Modeling repeats in DNA using extended probabilistic regular expressions. Proc. 1st International Work-Conference on Linguistics, Biology and Computer Science: Interplays. IOS Press (to appear 2011). Tarragona, Spain, March 14-18, 2011.
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen and Matthieu Petit. Taming the Zoo of Discrete HMM Subspecies & some of their Relatives. Proc. 1st International Work-Conference on Linguistics, Biology and Computer Science: Interplays. IOS Press (to appear 2011). Tarragona, Spain, March 14-18, 2011.
• Kim Allan Hansen, Sine Zambach and Christian Theil Have. Ontology-based retrieval of bio-medical information based on microarray text corpora. ESSLLI student session 2010. Best poster award. (pdf).
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen and Matthieu Petit. The Viterbi Algorithm expressed in Constraint Handling Rules. Proceedings of CHR 2010, Seventh International Workshop on Constraint Handling Rules
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen, Matthieu Petit. (2010). Inference with constrained hidden Markov models in PRISM Theory and Practice of Logic Programming, 10, pp 449-464 doi:10.1017/S1471068410000219
• Henning Christiansen, Christian Theil Have, Ole Torp Lassen, Matthieu Petit. A Constraint Model for Constrained Hidden Markov Models: a first Biological Application WCB09, Workshop on Constraint Based Methods for Bioinformatics, Associated to CP 2009. Lisbon, Portugal, September 20, 2009 (pdf)
• Christian Theil Have. Stochastic Definite Clause Grammars. International Conference: Recent Advances in Natural Language Processing 2009. RANLP 2009, Recent Advances in Natural Language Processing Bulgaria, September 14-17, 2009 (pdf).
• Christian Theil Have, Logic-Statistic Models with Constraints for Biological Sequence Analysis, ICLP'09, International Conference of Logic Programming 2009 (pdf)
• Henning Christiansen, Christian Theil Have, Knut Tveitane. From use cases to UML class diagrams using logic grammars and constraints.
  G. Angelova, K. Bontcheva, R. Mitkov, N. Nicolov, N. Nikolov (eds.): International Conference: Recent Advances in Natural Language Processing: Proceedings Proc. RANLP 2007, Recent Advances in Natural Language Processing. Shoumen, Bulgaria: INCOMA Ltd., pp. 128-132 (2007). (pdf).
• Henning Christiansen, Christian Theil Have, Knut Tveitane. Reasoning about Use Cases using Logic Grammars and Constraints. Proceedings of the 4th International Workshop on Constraints and Language Processing, CSLP 2007. pp. 40-52. Computer Science Research Report 113, Roskilde University, 2007.

Unpublished papers and reports

• Master thesis: Stochastic Definite Clause Grammars
• Project report (ITU): Content Recognition of Business Cards
• Project report (ITU): A Small Natural Language Interpreter in Prolog
• Project report (ITU): Sleipner: An Extensible and Adaptive Framework for Load Balancing using Multicasting.

Teaching

• (spring 2013) Databases. Co-taught with Henning Christiansen
• (autumn 2012) The web of data and XML. Co-taught with John Gallagher
• (autumn 2011) Introduction to programming
• (autumn 2009) KIIS: Kunstig Intelligens og Intelligente Systemer (Artificial Intelligence and Intelligent Systems).

Courses

• (May 2009) Course on Rule-based Programming by Thom Frühwirth (Venice Rule Course 2009) in Venice, Italy.
• (July 2009) Cross discipline course on Nano-Bio-IT, Tsinghua University, Beijing, China.
• Autumn 2009: Introduction to Molecular Biology and Genetics, Copenhagen University
• Autumn 2009: Biological Sequence Analysis, Copenhagen University
• Autumn 2009: Phd reading group on data mining, IT-University of Copenhagen
• (June 2010) Statistical and Machine Learning Methods in Computational Biology
• September 2011. INTERNATIONAL SUMMER SCHOOL IN Language and Speech Technologies

Links

• B-Prolog
• Constraint Handling Rules
• Logtalk
• PRISM