Proceedings of the First International Conference on Intelligent Systems for Molecular Biology
Edited by Lawrence Hunter, David Searls, and Jude Shavlik
July 6-9, 1993, Bethesda, Maryland. Published by The AAAI Press, Menlo Park, California. This proceedings is available in book format.
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Contents
Sponsors / iii
Program Committee / iv
Preface / ix
Lawrence Hunter, David Searls, and Jude Shavlik
Knowledge Discovery in GENBANK / 3
J. S. Aaronson, J. Haas, and G. C. Overton
Probabilistic Structure Calculations: A Three- Dimensional tRNA Structure from Sequence Correlation Data / 12
R. B. Altman
Database Techniques for Biological Materials and Methods / 21
K. Baclawski, R. Futrelle, N. Fridman, and M. J. Pescitelli
The Induction of Rules for Predicting Chemical Carcinogenesis in Rodents / 29
D. Bahler and D. Bristol
SENEX: A CLOS/CLIM Application for Molecular Pathology / 38
S. S. Ball and V. H. Mah
Using Dirichlet Mixture Priors to Derive Hidden Markov Models for Protein Families / 47
M. Brown, R. Hughey, A. Krogh, I. S. Mian, K. Sjölander, and D.
Haussler
FLASH: A Fast Look-Up Algorithm for String Homology / 56
A. Califano and I. Rigoutsos
Toward Multi-Strategy Parallel & Distributed Learning in Sequence Analysis / 65
P. K. Chan and S. J. Stolfo
Protein Structure Prediction: Selecting Salient Features from Large Candidate Pools / 74
K. J. Cherkauer and J. W. Shavlik
Protein Topology Prediction through Parallel Constraint Logic Programming / 83
D. A. Clark, C. J. Rawlings, J. Shirazi, A. Veron, and M. Reeve
Knowledge-Based Generation of Machine-Learning Experiments: Learning with DNA Crystallography Data / 92
D. Cohen, C. Kulikowski, and H. Berman
Representation for Discovery of Protein Motifs / 101
D. Conklin, S. Fortier, and J. Glasgow
Protein Secondary-Structure Modeling with Probabilistic Networks / 109
A. L. Delcher, S. Kasif, H. R. Goldberg, and W. Hsu
Comparison of Two Variations of Neural Network Approaches to the Prediction of Protein Folding Pattern / 118
I. Dubchak, S. R. Holbrook, and S. -H. Kim
Protein Classification Using Neural Networks / 127
E. A. Ferrán, B. Pflugfelder, and P. Ferrara
Pattern Recognition for Automated DNA Sequencing: I. On-Line Signal Conditioning and Feature Extraction for Basecalling / 136
J. B. Golden III, D. Torgersen, and C. Tibbetts
A Modular Learning Environment for Protein Modeling / 145
J. Gracy, L. Chiche and J. Sallantin
Integrating Order and Distance Relationships from Heterogeneous Maps / 154
M. Graves
Inference of Order in Genetic Systems / 163
J. N. Guidi and T. H. Roderick
PALM--A Pattern Language for Molecular Biology / 172
C. Helgesen and P. R. Sibbald
Grammatical Formalization of Metabolic Processes / 181
R. Hofestädt
Finding Relevant Biomolecular Features / 190
L. Hunter and T. Klein
Constructive Induction and Protein Tertiary Structure Prediction / 198
T. R. Ioerger, L. Rendell, and S. Surbramaniam
Representations of Metabolic Knowledge / 207
P. D. Karp and M. Riley
Protein Sequencing Experiment Planning Using Analogy / 216
B. Kettler and L. Darden
Detection of Correlations in tRNA Sequences with Structural Implications / 225
T. M. Klingler and D. Brutlag
Design of an Object-Oriented Database for Reverse Genetics / 234
K. J. Kochut, J. Arnold, J. A. Miller, and W. D. Potter
A Small Automaton for Word Recognition in DNA Sequences / 243
C. Lefèvre and J. -E Ikeda
Protein Secondary Structure Prediction Using Two-Level Case-Based Reasoning / 251
B. Leng, B. G. Buchanan, and H. B. Nicholas
MultiMap: An Expert System for Automated Genetic Linkage Mapping / 260
T. C. Matise, M. Perlin and A. Chakravarti
Constructing a Distributed Object-Oriented System with Logical Constraints for Fluorescence-Activated Cell Sorting / 266
T. Matsushima
Identification of Localized and Distributed Bottlenecks in Metabolic Pathways / 275
M. L. Mavrovouniotis
Discovering Sequence Similarity by the Algorithmic Significance Method / 284
A. Milosavljevic
Prediction of Primate Splice Junction Gene Sequences with a Cooperative Knowledge Acquisition System / 292
E. Mephu Nguifo and J. Sallantin
A Multi-Level Description Scheme of Protein Conformation / 301
K. Onizuka, K. Asai, M. Ishikawa, and S. T. C. Wong
Genetic Algorithms for DNA Sequence Assembly / 310
R. Parsons, S. Forrest, and C. Burks
Object-Oriented Knowledge Bases for the Analysis of Prokaryotic and Eukaryotic Genomes / 319
G. Perrière, F. Dorkeld, F. Rechenmann, and C. Gautier
Petri Net Representations in Metabolic Pathways / 328
V. N. Reddy, M. L. Mavrovouniotis, and M. N. Liebman
Minimizing Complexity in Cellular Automata Models of Self-Replication / 337
J. A. Reggia, H. -H. Chou, S. L. Armentrout, and Y. Peng
Building Large Knowledge Bases in Molecular Biology / 345
O. Schmeltzer, C. Médigue, P. Uvietta, F. Rechenmann, F. Dorkeld, G.
Perrière, and C. Gautier
Testing HIV Molecular Biology In In Silico Physiologies / 354
H. B. Sieburg, C. Baray, and K. Kunzelman
A Partial Digest Approach to Restriction Site Mapping / 362
S. S. Skiena and G. Sundaram
Identification of Human Gene Functional Regions Based on Oligonucleotide Composition / 371
V. V. Solovyev and C. B. Lawrence
A Service-Oriented Information Sources Database for the Biological Sciences / 380
G. K. Springer and T. B. Patrick
Computationally Efficient Cluster Representation in Molecular Sequence Megaclassification / 387
D. J. States, N. Harris, and L. Hunter
Hidden Markov Models and Iterative classers: Study of Their Equivalence and Possibilities / 395
H. Tanaka, K. Asai, M. Ishikawa, and A. Konagaya
Protein Structure Prediction System Based on Artificial Neural Networks / 402
J. Vanhala and K. Kaski
Pattern Discovery in Gene Regulation: Designing an Analysis Environment / 411
S. M. Veretnik and B. R. Schatz
Transmembrane Segment Prediction from Protein Sequence Data / 420
S. M. Weiss, D. M. Cohen and N. Indurkhya
Neural Networks for Molecular Sequence Classification / 429
C. Wu, M. Berry, Y-S. Fung, and J. McLarty
Automatic Derivation of Substructures Yields Novel Structural Building Blocks in Globular Proteins / 438
X. Zhang, J. S. Fetrow, W. A. Rennie, D. L. Waltz, and G. Berg
A Constraint Reasoning System for Automating Sequence-Specific Resonance Assignments from Multidimensional Protein NMR Spectra / 447
D. Zimmerman, C. Kulikowski, and G. T. Montelione