Publications


Machine Learning and Bioinformatics

18
E.A.M. Andrews and A.J. Bonner. Explaining Genetic Knockout Effects Using Cost-Based Abduction. In Proceedings of the Twenty-Second International Joint Conference on Articial Intelligence (IJCAI 11), Barcelona, Spain, July 16-22, 2011, pp 1635-1640.

17
G.W. Bassel, H. Lan, D.J. Gibbs, T. Gerjets, A.J. Bonner, M.J. Holdsworth, N.J. Provart. A genome-wide network model capturing seed germination reveals co-ordinated regulation of plant cellular phase transitions. Proceedings of the National Academy of Sciences (PNAS), 7 June 2011, 108(23):9709-9714.

16
E.A.M. Andrews and A.J. Bonner. Finding MAPs using strongly equivalent high-order recurrent symmetric connectionist networks. Cognitive Systems Research, April 2012, 14(1):50-59. Special Issue on Modeling and Application of Cognitive Systems.

15
R. Min, L. van der Maaten, Z. Yuan, A. Bonner and Z. Zhang. A Deep Supervised t-Distributed Embedding. In Proceedings of the 27th International Conference on Machine Learning (ICML 2010), Haifa, Israel, June 21-24, 2010, pp 791-798.

14
J. Li, R. Min, A. Bonner, and Z. Zhang. A probabilistic framework to improve microRNA target prediction by incorporating proteomics data. Journal of Bioinformatics and Computational Biology, December 2009, 7(6):955-972.

13
E. Shenouda and A.J. Bonner. Finding MAPs using High Order Recurrent Networks. In Proceedings of the 16th International Conference on Neural Information Processing, Bangkok, Thailand, Dec 1-5, 2009, pp 100-109.

12
R. Min, D.A. Stanley, Z. Yuan, A. Bonner, and Z. Zhang. A Deep Non-Linear Feature Mapping for Large-Margin kNN Classification. In Proceedings of the IEEE International Conference on Data Mining (ICDM), Miami, Florida, Dec 6-9, 2009, pp 357-366.

11
R. Min, R. Kuang, A. Bonner, and Z. Zhang. Learning Random-Walk Kernels for Protein Remote Homology Identication and Motif Discovery. In Proceedings of the 2009 SIAM International Conference on Data Mining (SDM09), Sparks, Nevada, April/May 2009, pages 133-144.

10
R. Min, A. Bonner, J. Li, and Z. Zhang. Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classication. Journal of Computational Biology, March 2009, 16(3):457-474.

9
E. Andrews, Q. Morris, and A.J. Bonner. Neural Networks Approaches for Discovering the Learnable Correlation between Gene Function and Gene Expression in Mouse. Neurocomputing, October 2008, 71(16-18):3168-3175.

8
H. Lan, R. Carson, N.J. Provart, A.J. Bonner. Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements. BMC Bioinformatics, September 2007, 8:358.

7
R. Min, A. Bonner, Z. Zhang. Modifying kernels using label information improves SVM classification performance. In Proceedings of the 2007 International Conference on Machine Learning and Applications (ICMLA'07), Cincinnati, Ohio, December 13-15, 2007, pp 13-18.

6
E.A. Shenouda, Q. Morris and A.J. Bonner. Connectionist Approaches for Predicting Mouse Gene Function from Gene Expression. In Proceedings of the 13th International Conference on Neural Information Processing, Hong Kong, October 3-6, 2006, pages 280-289.

5
A.J. Bonner and H. Liu. Towards the Prediction of Protein Abundance from Tandem Mass Spectrometry Data. In Proceedings of the Sixth SIAM International Conference on Data Mining (SDM'06), Bethesda, MD, April 20-22, 2006, pages 599-603. Complete technical report.

4
A.J. Bonner and H. Liu. Canonical Correlation, an Approximation, and the Prediction of Protein Abundance. Appears in Proceedings of the Eighth Workshop on Mining Scientific and Engineering Datasets (MSD'05), Newport Beach, CA, April 23, 2005, pages 29-38. Workshop held in conjunction with the Fifth SIAM International Conference on Data Mining (SDM'05).

3
A.J. Bonner and H. Liu. Predicting Protein Levels from Tandem Mass Spectrometry Data. Presented at the NIPS'04 Workshop on New Problems and Methods in Computational Biology, Whistler, British Columbia, Canada, December 16, 2004.

2
A.J. Bonner and H. Liu. Comparison of Discrimination Methods for Peptide Classification in Tandem Mass Spectrometry. Appears in Proceedings of the IEEE 2004 Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'04), La Jolla, CA, October 7-8, 2004, pages 160-167.

1
M. Trochesset and A.J. Bonner. Clustering Labeled Data and Cross-Validation for Classificatfion with Few Positives in Yeast. Appears in Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD'04) Seattle, WA, USA, August 22, 2004.

Theses:

4
Renqiang Min. Machine Learning Approaches to Biological Sequence and Phenotype Data Analysis. PhD thesis, Department of Computer Science, University of Toronto, October 2010.

3
Lan Hui. Comparison and Evaluation of Statistical-Learning Methods for Gene Function Prediction in Arabidopsis thaliana. MSc thesis, Department of Computer Science, University of Toronto, September 2005.

2
Han Liu. Development and Evaluation of Methods for Predicting Protein Levels from Tandem Mass Spectrometry Data. MSc thesis, Department of Computer Science, University of Toronto, January 2005.

1
Miles Trochesset. Statistical Learning of Gene Annotations in Saccharomyces Cerevisiae. MSc thesis, Department of Computer Science, University of Toronto, September 2004. Abstract

Genome Mapping

4
E. Harley, A.J. Bonner and N. Goodman. Uniform Integration of Genome Mapping Data using Intersection Graphs. Bioinformatics, 17(6): 487-495, June 2001. Abstract. Also available in Adobe PDF

3
E. Harley, A.J. Bonner and N. Goodman. Revealing Hidden Interval-Graph Structure in STS-Content Data. Bioinformatics, 15(4):278-285, April 1999. Abstract. Also available in Adobe PDF

2
E. Harley, A.J. Bonner and N. Goodman. Good Maps are Straight. In Proceedings, Fourth International Conference on Intelligent Systems for Molecular Biology (ISMB-96), Washington University, St. Louis, Missouri, June 1996, pages 88-97. AAAI Press. Abstract. Also available in Adobe PDF

1
E. Harley and A.J. Bonner. A Flexible Approach to Genome Map Assembly. In Proceedings, Second International Conference on Intelligent Systems for Molecular Biology (ISMB-94), Stanford University, August 1994, pages 161-169. AAAI Press. Abstract.

Theses:

2
Eric R. Harley. Graph Algorithms for Assembling Integrated Genome Maps. PhD thesis, Department of Computer Science, University of Toronto, 2003. Abstract

1
James R. Randall. Using Interval Graphs for Solving Map Assembly Problems. Master's thesis, Department of Computer Science, University of Toronto, 1997. Abstract

Workflow in Genome Laboratories

4
A.J. Bonner, A. Shrufi and S. Rozen. LabFlow-1: a Database Benchmark for High-Throughput Workflow Management. In Proceedings, Fifth International Conference on Extending Database Technology (EDBT), Avignon, France, March 1996, pages 463-478. Springer-Verlag, Lecture Notes in Computer Science, volume 1057. Abstract

3
A.J. Bonner, A. Shrufi and S. Rozen. Database Requirements for Workflow Management in a High-Throughput Genome Laboratory. Presented at the NSF Workshop on Workflow and Process Automation in Information Systems, Athens, Georgia, May 1996. Available in postscript and html.

2
A.J. Bonner, A. Shrufi and S. Rozen. Benchmarking Object-Oriented DBMSs for Workflow Management. Presented at the OOPSLA Workshop on Object Database Behavior, Benchmarks, and Performance, Austin, Texas, Oct 1995.

1
A.J. Bonner, A. Shrufi and S. Rozen. LabFlow-1: a Database Benchmark for High-Throughput Workflow Management. Technical Report. 53 pages. Abstract

Sequence Databases

7
G. Mecca and A.J. Bonner. Query Languages for Sequence Databases: Termination and Complexity. IEEE Transactions on Knowledge and Data Engineering (TKDE), 13(3): 519-525, May/June 2001. Available in PostScript and Adobe PDF. Abstract.

6
A.J. Bonner and G. Mecca. Querying Sequence Databases with Transducers. Acta Informatica, 36(7): 511-544, 2000. Abstract

5
A.J. Bonner and G. Mecca. Querying Sequence Databases with Transducers. In Proceedings of the Sixth International Workshop on Database Programming Languages (DBPL), Estes Park, Colorado, August 1997. Lecture Notes in Computer Science, volume 1369, Springer-Verlag, 1998, pages 118-135. Abstract

4
A.J. Bonner and G. Mecca. Sequence Datalog: Declarative String Manipulation in Databases. In Proceedings of the International Workshop on Logic in Databases (LID), San Miniato, Italy, July 1996. Springer-Verlag, Lecture Notes in Computer Science, volume 1154, 1996, pages 399-413. Abstract

3
A.J. Bonner and G. Mecca. Sequences, Datalog and Transducers. Journal of Computer and System Sciences (JCSS), 57(3): 234-259, December 1998. Special issue on the Fourteenth ACM Symposium on Principles of Database Systems (PODS'95). Abstract

2
G. Mecca and A.J. Bonner. Finite Query Languages for Sequence Databases. In Proceedings of the Fifth International Workshop on Database Programming Languages (DBPL), Gubbio, Umbria, Italy, September 1995. Springer-Verlag, Electronic Workshops in Computing. Abstract

1
G. Mecca and A.J. Bonner. Sequences, Datalog and Transducers. In Proceedings of the Fourteenth ACM Symposium on the Principles of Database Systems (PODS), San Jose, CA, May 1995, pages 23-35. Abstract

Theses:

1
Giansalvatore Mecca. From Datalog to Sequence Datalog: Languages and techniques for querying sequence databases. PhD thesis, Dipartimento di Informatica e Sistemistica, Universitá di Roma ``La Sapienza'', Via Salaria, 113 - 00198 Rome, Italy, February 1996.

Transaction Logic

12
A.J. Bonner. Workflow, Transactions, and Datalog. In Proceedings of the Eighteenth ACM Symposium on the Principles of Database Systems (PODS), Philadelphia, PA, May/June 1999, pages 294-305. A long version is under construction. Abstract. Also available in Adobe PDF

11
A.J. Bonner and M. Kifer. Results on Reasoning about Updates in Transaction Logic. In B. Freitag, H. Decker, M. Kifer and A. Voronkov, editors, Transactions and Change in Logic Databases, volume 1472 of Lecture Notes in Computer Science, pages 166-196. Springer-Verlag, Berlin, 1998. Abstract. Also available in Adobe PDF

10
A.J. Bonner and M. Kifer. The State of Change: A Survey. In B. Freitag, H. Decker, M. Kifer and A. Voronkov, editors, Transactions and Change in Logic Databases, volume 1472 of Lecture Notes in Computer Science, pages 1-36. Springer-Verlag, Berlin, 1998. Abstract. Also available in Adobe PDF

9
A.J. Bonner and M. Kifer. A Logic for Programming Database Transactions. In J. Chomicki and G. Saake, editors, Logics for Databases and Information Systems, chapter 5. Kluwer Academic Publishers, March 1998. Abstract. Also available in Adobe PDF

8
A.J. Bonner. Transaction Datalog: a Compositional Language for Transaction Programming. In Proceedings of the Sixth International Workshop on Database Programming Languages (DBPL), Estes Park, Colorado, August 1997. Lecture Notes in Computer Science, volume 1369, Springer-Verlag, 1998, pages 373-395. Long version. Abstract. Also available in Adobe PDF

7
A.J. Bonner and M. Kifer. Concurrency and Communication in Transaction Logic. In Proceedings of the Joint International Conference and Symposium on Logic Programming (JICSLP), Bonn, Germany, September 1996, pages 142-156. MIT Press. Abstract. Also available in Adobe PDF

6
A.J. Bonner and M. Kifer. An Overview of Transaction Logic. Theoretical Computer Science (TCS), 133:205-265, 1994. Special issue on the Workshop on Formal Methods in Databases and Software Engineering. Abstract

5
A.J. Bonner and M. Kifer. Applications of Transaction Logic to Knowledge Representation. In Proceedings of the International Conference on Temporal Logic (ICTL), Bonn, Germany, July 1994, pages 67-81. Springer-Verlag, Lecture Notes in Artificial Intelligence, volume 827, 1994. Abstract

4
A.J. Bonner, M. Kifer and M. Consens. Database Programming in Transaction Logic. In Proceedings of the Fourth International Workshop on Database Programming Languages (DBPL), New York City, Aug/Sept 1993. Springer-Verlag, Workshops in Computing, 1994, pages 309-337. Abstract

3
A.J. Bonner and M. Kifer. Transaction Logic Programming. In Proceedings of the Tenth International Conference on Logic Programming (ICLP), Budapest, Hungary, June 1993, pages 257-279. MIT Press. Abstract

2
A.J. Bonner and M. Kifer. Transaction Logic: An (Early) Exposé. In Proceedings of the Workshop on Formal Methods in Databases and Software Engineering, Montreal, Canada, May 1992, pages 1-23. Keynote address. Springer-Verlag, Workshops in Computing, April 1993. Abstract

1
A.J. Bonner and M. Kifer. Transaction Logic Programming. Technical Report CSRI-323, Computer Systems Research Institute, University of Toronto, 1995. 159 pages. Abstract

Theses:

4
Amalia Sleghal An Optimizing Interpreter for Concurrent Transaction Logic. Master's thesis, Department of Computer Science, University of Toronto, 2000. 85 pages. Abstract

3
Marcus V. Santos. Specifying, Executing and Reasoning about Actions and Plans Using Transaction Logic. PhD thesis, Department of Electronic Engineering, University of Sao Paulo, Sao Paulo, Brazil, 2000. Abstract.

2
Samuel Y.K. Hung. Implementation and Performance of Transaction Logic in Prolog. Master's thesis, Department of Computer Science, University of Toronto, 1996. 132 pages. Abstract

1
Dimitrios Lagkouvardos. Evaluation of Transaction Logic Programs. Master's thesis, Department of Computer Science, University of Toronto, 1994. 139 pages. Abstract

Hypothetical Reasoning and Intuitionistic Logic

10
A.J. Bonner. Intuitionistic Deductive Databases and the Polynomial Time Hierarchy. Journal of Logic Programming (JLP), 33(1):1-47, October 1997. Abstract

9
A.J. Bonner. A Logical Semantics for Hypothetical Rulebases with Deletion. Journal of Logic Programming (JLP), 32(2):119-170, August 1997. Abstract

8
A.J. Bonner. Hypothetical Reasoning with Intuitionistic Logic. In R. Demolombe and T. Imielinski, editors, Non-Standard Queries and Answers, chapter 8, pages 187-219. Oxford University Press, Studies in Logic and Computation, October 1994. Abstract

7
A.J. Bonner. Hypothetical Reasoning in Deductive Databases. PhD thesis, Department of Computer Science, Rutgers University, New Brunswick, NJ, USA, October 1991. 234 pages. Published as Rutgers Technical Report DCS-TR-283. Abstract

6
A.J. Bonner. Hypothetical Datalog: Complexity and Expressibility. Theoretical Computer Science (TCS), 76:3-51, 1990. Special issue on the Second International Conference on Database Theory (ICDT'88). Abstract

5
A.J. Bonner and L.T. McCarty. Adding Negation-as-Failure to Intuitionistic Logic Programming. In Proceedings of the North American Conference on Logic Programming (NACLP'90), Austin, Texas, Oct/Nov 1990, pages 681-703. MIT Press. Abstract

4
A.J. Bonner, L.T. McCarty, and K. Vadaparty. Expressing Database Queries with Intuitionistic Logic. In Proceedings of the North American Conference on Logic Programming (NACLP'89), Cleveland, Ohio, October 1989, pages 831-850. MIT Press. Abstract

3
A.J. Bonner. Hypothetical Datalog: Negation and Linear Recursion. In Proceedings of the Eighth ACM Symposium on the Principles of Database Systems (PODS'89), Philadelphia, PA, March 1989, pages 286-300. Abstract

2
A.J. Bonner. Hypothetical Datalog: Complexity and Expressibility. In Proceedings of the Second International Conference on Database Theory (ICDT'88), Aug/Sept 1988, Bruges, Belgium, pages 144-160. Springer-Verlag, Lecture Notes in Computer Science, volume 326. Abstract

1
A.J. Bonner. A Logic for Hypothetical Reasoning. The long version of a paper that appears in Proceedings, Seventh National Conference on Artificial Intelligence (AAAI-88), Saint Paul, Minnesota, August 1988, pages 480-484. Morgan Kaufmann. Abstract

Object-Oriented Databases

2
S. Abiteboul and A.J. Bonner. Objects and Views. In Proceedings of the ACM SIGMOD International Conference on Management of Data, Denver, Colorado, May 1991, pages 238-247. Long version. Abstract

1
George Charalabopoulos. Objects, Views, and F-Logic. Master's thesis, Department of Computer Science, University of Toronto, 1994. 140 pages. Abstract

Software Reuse

3
A.J. Bonner and T. Imielinski. Reusing and Modifying Rulebases by Predicate Substitution. Journal of Computer and System Sciences (JCSS), 54(1):136-166, February 1997. Special issue on the Eleventh ACM Symposium on Principles of Database Systems (PODS'92). Abstract

2
A.J. Bonner. The Complexity of Reusing and Modifying Rulebases. In Proceedings of the Eleventh ACM Symposium on the Principles of Database Systems (PODS'92), San Diego, CA, June 1992, pages 316-330. Abstract

1
A.J. Bonner and T. Imielinski. The Reuse and Modification of Rulebases by Predicate Substitution. In Proceedings, International Conference on Extending Database Technology (EDBT'90), Venice, Italy, March 1990, pages 437-451. Springer-Verlag, Lecture Notes in Computer Science, volume 416. Abstract

Signal Processing

1
J.N. Maksym, A.J. Bonner, C.A. Dent, and G.L. Hemphill. Machine Analysis of Acoustical Signals. Pattern Recognition, 16(6):615-625, 1983.

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