Automated Learning of a Detector for alpha-Helices in Protein Sequences via Genetic Programming

This appendix contains bibliographic references to publications concerning genetic programming. Some effort has been made to make it as complete as possible but, like every such list, this is practically impossible and the list quickly becomes out of date as the field progresses. Nevertheless we hope that this appendix will prove a useful reference. The list is sorted into principle subject area. Within subject areas, publications are sorted by date (but works by the same author are grouped together). Where on-line copies are available, the standard bibliographic reference is followed by the address of the on-line version using the Universal Reference Location (URL) format. Internet document servers are occasionally unavailable and are sometimes re-organized so documents may be moved to new URLs, therefore a degree of perseverance may be required to obtain on-line copies. A small number of non-genetic programming papers have been included either for their historical significance or general interest to practitioners of genetic programming. These are marked thus .

[1]  John R. Koza,et al.  A Genetic Approach to Finding a Controller to Back Up a Tractor-Trailer Truck , 1992, 1992 American Control Conference.

[2]  Astro Teller,et al.  Turing completeness in the language of genetic programming with indexed memory , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[3]  H. Chandler Database , 1985 .

[4]  Paul R. Cohen,et al.  Learning monitoring strategies: a difficult genetic programming application , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[5]  Astro Teller,et al.  Algorithm evolution for face recognition: what makes a picture difficult , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[6]  Thomas S. Huang,et al.  Evolvable 3D modeling for model-based object recognition systems , 1994 .

[7]  John R. Koza,et al.  Evolution of Both the Architecture and the Sequence of Work-Performing Steps of a Computer Program Using Genetic Programming with Architecture-Altering Operations , 1995 .

[8]  Hitoshi Iba,et al.  Temporal Data Processing Using Genetic Programming , 1995, ICGA.

[9]  John R. Koza,et al.  Evolution of Subsumption Using Genetic Programming , 1993 .

[10]  Kurt Dirk Bettenhausen,et al.  Self-Organizing Modelling of Biotechnological Batch and Fed-Batch Fermentations , 1995, EUROSIM.

[11]  Manuela M. Veloso,et al.  A Contolled Experiment: Evolution for Learning Difficult Image Classification , 1995, EPIA.

[12]  Peter J. Angeline,et al.  Genetic programming and emergent intelligence , 1994 .

[13]  Robert G. Reynolds,et al.  An Adaptive Inductive Logic Programming System Using Genetic Programming , 1995 .

[14]  John R. Koza,et al.  Gene Duplication to Enable Genetic Programming to Concurrently Evolve Both the Architecture and Work-Performing Steps of a Computer Program , 1995, IJCAI.

[15]  Byoung-Tak Zhang,et al.  Synthesis of sigma-pi neural networks by the breeder genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[16]  Simon Handley,et al.  Predicting Whether Or Not a 60-Base DNA Sequence Contains a Centrally-Located Splice Site Using Genetic Programming , 1995 .

[17]  Kwong-Sak Leung,et al.  Learning Programs in Different Paradigms using Genetic Programming , 1995, AI*IA.

[18]  Mark J. Willis,et al.  Using a tree structured genetic algorithm to perform symbolic regression , 1995 .

[19]  Frédéric Gruau,et al.  Automatic Definition of Modular Neural Networks , 1994, Adapt. Behav..

[20]  D. Walters,et al.  Genetically evolved receptor models: a computational approach to construction of receptor models. , 1994, Journal of medicinal chemistry.

[21]  John R. Koza,et al.  Simultaneous Discovery of Reusable Detectors and Subroutines Using Genetic Programming , 1993, ICGA.

[22]  Christian Jacob,et al.  Genetic L-System Programming , 1994, PPSN.

[23]  Robert G. Reynolds,et al.  A Programming Language for Artificial Development , 1995 .

[24]  Jason M. Daida,et al.  Extracting curvilinear features from synthetic aperture radar images of Arctic ice: algorithm discovery using the genetic programming paradigm , 1995, 1995 International Geoscience and Remote Sensing Symposium, IGARSS '95. Quantitative Remote Sensing for Science and Applications.

[25]  Rick L. Riolo,et al.  Automatic Discovery of Classification and Estimation Algorithms for Earth- Observation Satellite Imagery , 1995 .

[26]  Peter J. Angeline Evolutionary algorithms and emergent intelligence , 1993 .

[27]  Michael E. Papka,et al.  A genetic programming application in virtual reality , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[28]  Craig W. Reynolds An evolved, vision-based behavioral model of coordinated group motion , 1993 .

[29]  Lee Spector,et al.  Criticism, Culture, and the Automatic Generation of Artworks , 1994, AAAI.

[30]  John R. Koza,et al.  Genetic programming 2 - automatic discovery of reusable programs , 1994, Complex Adaptive Systems.

[31]  E. Howard,et al.  The Application of Genetic Programming to the Investigation of Short, Noisy, Chaotic Data Series , 1994, Evolutionary Computing, AISB Workshop.

[32]  M. Andrews,et al.  Genetic programming for the acquisition of double auction market strategies , 1994 .

[33]  K. A. Marko,et al.  Application of genetic programming to control of vehicle systems , 1992, Proceedings of the Intelligent Vehicles `92 Symposium.

[34]  Paul McIlroy,et al.  Exploring some Commercial Applications of Genetic Programming , 1995, Evolutionary Computing, AISB Workshop.

[35]  Frédéric Gruau,et al.  Genetic synthesis of Boolean neural networks with a cell rewriting developmental process , 1992, [Proceedings] COGANN-92: International Workshop on Combinations of Genetic Algorithms and Neural Networks.

[36]  T. R. Osborn,et al.  Genetic logic programming , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[37]  John R. Koza,et al.  Two Ways of Discovering the Size and Shape of a Computer Program to Solve a Problem , 1995, ICGA.

[38]  Christopher G. Langton,et al.  Artificial life II : video proceedings , 1992 .

[39]  M. Yanagiya,et al.  Efficient genetic programming based on binary decision diagrams , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[40]  Sandip Sen,et al.  Evolving Cooperation Strategies , 1995, ICMAS.

[41]  Jarmo T. Alander,et al.  An Indexed Bibliography of Genetic Algorithms , 1995 .

[42]  Howard Oakley,et al.  Two scientific applications of genetic programming: Stack filters and non-linear equation fitting to , 1994 .

[43]  Justinian P. Rosca,et al.  Causality in Genetic Programming , 1995, International Conference on Genetic Algorithms.

[44]  John R. Koza,et al.  Spontaneous Emergence of Self-Replicating and Evolutionarily Self-Improving Computer Programs , 1993 .

[45]  John R. Koza,et al.  A genetic approach to the truck backer upper problem and the inter-twined spiral problem , 1992, [Proceedings 1992] IJCNN International Joint Conference on Neural Networks.

[46]  John R. Koza,et al.  Evolving the Architecture of a Multi-part Program in Genetic Programming Using Architecture-Altering Operations , 1995, Evolutionary Programming.

[47]  Tomonori Sugiyama,et al.  Evolving Robot Strategy for Open Ended Game , 1993, Evo Workshops.

[48]  John R. Koza,et al.  Automatic Programming of Robots Using Genetic Programming , 1992, AAAI.

[49]  John R. Koza,et al.  Evolution of Food-Foraging Strategies for the Caribbean Anolis Lizard Using Genetic Programming , 1992, Adapt. Behav..

[50]  Craig W. Reynolds The Difficulty of Roving Eyes. , 1994 .

[51]  Dana H. Ballard,et al.  Genetic Programming with Adaptive Representations , 1994 .

[52]  David E. Goldberg,et al.  Evolvable Modeling: structural adaptation through hierarchical evolution for 3-D model-based vision* , 1993 .

[53]  Frédéric Gruau,et al.  Genetic Synthesis of Modular Neural Networks , 1993, ICGA.

[54]  Sandip Sen,et al.  Evolving Beharioral Strategies in Predators and Prey , 1995, Adaption and Learning in Multi-Agent Systems.

[55]  Byoung-Tak Zhang,et al.  Evolving Optimal Neural Networks Using Genetic Algorithms with Occam's Razor , 1993, Complex Syst..

[56]  Simon Handley The Prediction of the Degree of Exposure to Solvent of Amino Acid Residues Via Genetic Programming , 1994, ISMB.

[57]  Simon Handley Classifying Nucleic Acid Sub-Sequences as Introns or Exons Using Genetic Programming , 1995, ISMB.

[58]  John R. Koza,et al.  Automated Discovery of Protein Motifs With Genetic Programming , 1995 .

[59]  John R. Koza,et al.  Scalable learning in genetic programming using automatic function definition , 1994 .

[60]  Sandip Sen,et al.  Evolving a Team , 1995 .

[61]  Justinian P. Rosca,et al.  Learning by adapting representations in genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[62]  Hirofumi Doi,et al.  Evolutionary system: structures and functions. Disparity hypothesis and gene duplication , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[63]  David Andre Learning and upgrading rules for an OCR system using genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[64]  Simon Handley,et al.  The genetic planner: The automatic generation of plans for a mobile robot via genetic programming , 1993, Proceedings of 8th IEEE International Symposium on Intelligent Control.

[65]  John R. Koza,et al.  Architecture-Altering Operations for Evolving the Architecture of a Multi-Part Program in Genetic Programming , 1994 .

[66]  Byoung-Tak Zhang,et al.  Genetic Programming of Minimal Neural Nets Using Occam's Razor , 1993, ICGA.

[67]  Worthy N. Martin,et al.  Using genetic programming to evolve board evaluation functions , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[68]  D. P. Barnes,et al.  Evolving co-operation in autonomous robotic systems , 1994 .

[69]  Justinian P. Rosca,et al.  Hierarchical Self-Organization in Genetic programming , 1994, ICML.

[70]  James P. Rice,et al.  Finding an Impulse Response Function Using Genetic Programming , 1993, 1993 American Control Conference.

[71]  Henning Tolle,et al.  BioX++ – NEW RESULTS AND CONCEPTIONS CONCERNING THE INTELLIGENT CONTROL OF BIOTECHNOLOGICAL PROCESSES , 1995 .

[72]  Robert G. Reynolds,et al.  Genetic Programming Exploratory Power and the Discovery of Functions , 1995 .

[73]  M. Jiang,et al.  An adaptive function identification system , 1993, [1993] Proceedings IEEE International Conference on Developing and Managing Intelligent System Projects.

[74]  Ulrich Wilhelm Thonemann,et al.  Finding improved simulated annealing schedules with genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[75]  John R. Koza,et al.  Genetic programming II (videotape): the next generation , 1994 .

[76]  D. Burkhardt,et al.  Genetic programming of fuzzy logic production rules , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[77]  Frederick E. Petry,et al.  Regular language induction with genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[78]  Samy Bengio,et al.  Use of genetic programming for the search of a new learning rule for neural networks , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[79]  P. Walsh,et al.  Automatic Conversion of Programs from Serial to Parallel using Genetic Programming - The Paragen System , 1995, PARCO.

[80]  John R. Koza,et al.  Performance improvement of machine learning via automatic discovery of facilitating functions as applied to a problem of symbolic system identification , 1993, IEEE International Conference on Neural Networks.

[81]  David Andre The Automatic Programming of Agents that Learn Mental Models and Create Simple Plans of Action , 1995, IJCAI.

[82]  C. A. Grimes Application of genetic techniques to the planning of railway track maintenance work , 1995 .

[83]  Walter Alden Tackett,et al.  Genetic Programming for Feature Discovery and Image Discrimination , 1993, ICGA.

[84]  J. K. Kinnear,et al.  Advances in Genetic Programming , 1994 .

[85]  David Andre,et al.  Evolution of mapmaking: learning, planning, and memory using genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[86]  J. K. Kinnear,et al.  Alternatives in automatic function definition: a comparison of performance , 1994 .

[87]  WB Langdon Evolving Data Structures Using Genetic Programming , 1995 .

[88]  Astro Teller,et al.  PADO: Learning Tree Structured Algorithms for Orchestration into an Object Recognition System , 1995 .

[89]  Kurt Dirk Bettenhausen,et al.  Selbstorganisierende Generierung strukturierter Prozeßmodelle , 1995 .

[90]  Peter A. Whigham,et al.  Genetic Approaches to Learning Recursive Relations , 1994, Evo Workshops.

[91]  Frédéric Gruau,et al.  Genetic micro programming of neural networks , 1994 .

[92]  Michael L. Littman,et al.  Memoryless policies: theoretical limitations and practical results , 1994 .

[93]  Ken Sharman,et al.  Evolving signal processing algorithms by genetic programming , 1995 .

[94]  John R. Koza,et al.  A Hierarchical Approach to Learning the Boolean Multiplexer Function , 1990, FOGA.

[95]  John R. Koza,et al.  Genetic generation of both the weights and architecture for a neural network , 1991, IJCNN-91-Seattle International Joint Conference on Neural Networks.

[96]  Craig W. Reynolds An Evolved, Vision-Based Model of Obstacle Avoidance Behavior , 1994 .

[97]  Ari Juels,et al.  Stochastic Hillclimbing as a Baseline Method for , 1994 .

[98]  Lee Spector,et al.  Genetic Programming and AI Planning Systems , 1994, AAAI.

[99]  Eugene H. Spafford,et al.  Applying Genetic Programming to Intrusion Detection , 1995 .

[100]  Justinian P. Rosca,et al.  An Analysis of Hierarchical Genetic Programming , 1995 .

[101]  Lee Spector,et al.  Induction and Recapitulation of Deep Musical Structure , 1995, IJCAI 1995.

[102]  Kwong-Sak Leung,et al.  Combining genetic programming and inductive logic programming using logic grammars , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[103]  Frederick E. Petry,et al.  Solving Complex Problems with Genetic Algorithms , 1995, International Conference on Genetic Algorithms.

[104]  Justinian P. Rosca Proceedings of the Workshop on Genetic Programming: From Theory to Real-World Applications , 1995 .

[105]  Steven O. Kimbrough,et al.  Bargaining in a Three-Agent CoalitionS Game: An Application of Genetic Programming , 1995 .

[106]  Simon Handley,et al.  Automated learning of a detector for the cores of /spl alpha/-helices in protein sequences via genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[107]  Byoung-Tak Zhang,et al.  Effects of Occam's Razor in Evolving Sigma-Pi Neural Nets , 1994, PPSN.

[108]  John R. Koza,et al.  Genetic breeding of non-linear optimal control strategies for broom balancing , 1990 .

[109]  Hitoshi Iba,et al.  Evolutionary learning of predatory behaviors based on structured classifiers , 1993 .

[110]  M. Atkin,et al.  Genetric Programming to Learn an Agent''s Monitoring Strategy , 1993 .

[111]  Frédéric Gruau,et al.  The cellular development of neural networks: the interaction of learning and evolution , 1993 .

[112]  Akira Ito,et al.  The Emergence of Cooperation in a Society of Autonomous Agents - The Prisoner's Dilemma Game under the Disclosure of Contract Histories , 1995, ICMAS.

[113]  John R. Koza,et al.  Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming , 1994, ISMB.

[114]  John R. Koza Discovery of a Main Program and Reusable Subroutines Using Genetic Programming , 1993 .

[115]  Justinian P. Rosea Towards Automatic Discovery of Building Blocks in Genetic Programming , 1995 .

[116]  John R. Koza,et al.  Recognizing patterns in protein sequences using iteration-performing calculations in genetic programming , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[117]  H. D. Garis EVOLVING A REPLICATOR The Genetic Programming of Self Reproduction in Cellular Automata , 1993 .

[118]  John R. Koza,et al.  Evolution of a subsumption architecture that performs a wall following task for an autonomous mobile robot , 1994, COLT 1994.

[119]  Graham F. Spencer,et al.  Automatic Generation of Programs for Crawling and Walking , 1993, International Conference on Genetic Algorithms.

[120]  Peter Nordin,et al.  Genetic Programming Controlling a Miniature Robot , 1995 .

[121]  David Andre,et al.  Classifying protein segments as transmembrane domains using architecture-altering operations in genetic programming , 1996 .

[122]  H. de Garis CAM-Brain: the genetic programming of an artificial brain which grows/evolves at electronic speeds in a cellular automata machine , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[123]  Roger L. Wainwright,et al.  A simulation of adaptive agents in a hostile environment , 1995, SAC '95.

[124]  John R. Koza,et al.  A GENETIC APPROACH TO ECONOMETRIC MODELING , 1992 .

[125]  John R. Koza,et al.  Automated discovery of detectors and iteration-performing calculations to recognize patterns in protein sequences using genetic programming , 1994, 1994 Proceedings of IEEE Conference on Computer Vision and Pattern Recognition.

[126]  Kurt Dirk Bettenhausen,et al.  Self-organizing structured modelling of a biotechnological fed-batch fermentation by means of genetic programming , 1995 .

[127]  David Andre,et al.  Automatically defined features: the simultaneous evolution of 2-dimensional feature detectors and an algorithm for using them , 1994 .

[128]  Simon Handley,et al.  The automatic generation of plans for a mobile robot via genetic programming with automatically defined functions , 1994 .

[129]  Kwong-Sak Leung,et al.  An induction system that learns programs in different programming languages using genetic programming and logic grammars , 1995, Proceedings of 7th IEEE International Conference on Tools with Artificial Intelligence.

[130]  Thomas S. Ray,et al.  Is It Alive or Is It GA? , 1991, ICGA.

[131]  Patrick Tufts,et al.  Dynanfic Classifiers: Genetic Programnfing and Classifier Systems , 1995 .

[132]  Hitoshi Iba,et al.  Differentiable Chromosomes: The Genetic Programming of Switchable Shape-Genes , 1992, PPSN.

[133]  Stan Openshaw,et al.  Building New Spatial Interaction Models Using Genetic Programming , 1994 .

[134]  Brij Masand,et al.  Optimizing confidence of text classification by evolution of symbolic expressions , 1994 .

[135]  M. Veloso Program Evolution for Data Mining , 1995 .

[136]  William B. Langdon Data structures and genetic programming , 1995 .

[137]  John R. Koza Simultaneous discovery of detectors and a way of using the detectors via genetic programming , 1993, IEEE International Conference on Neural Networks.

[138]  Karl Sims,et al.  Artificial evolution for computer graphics , 1991, SIGGRAPH.

[139]  Jan Jannink,et al.  Cracking and co-evolving randomizers , 1994 .

[140]  Hitoshi Iba,et al.  Applying Evolvable Hardware to Autonomous Agents , 1994, PPSN.

[141]  Hideyuki Nakashima,et al.  Organic Programming for Multi-Agents , 1995, ICMAS.

[142]  Mark J. Willis,et al.  On the application of genetic programming to chemical process systems , 1995, Proceedings of 1995 IEEE International Conference on Evolutionary Computation.

[143]  Ming-Yi Lay Application of genetic programming in analyzing multiple steady states of dynamical systems , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[144]  Les M. Howard,et al.  The GA-P: A Genetic Algorithm and Genetic Programming Hybrid , 1995, IEEE Expert.

[145]  John R. Koza,et al.  Concept Formation and Decision Tree Induction Using the Genetic Programming Paradigm , 1990, PPSN.

[146]  Walter Alden Tackett,et al.  Mining the Genetic Program , 1995, IEEE Expert.

[147]  Jean-Arcady Meyer,et al.  Evolution and Co Evolution of Computer Programs to Control Independently Acting Agents , 1991 .

[148]  Kevin J. Lang Hill Climbing Beats Genetic Search on a Boolean Circuit Synthesis Problem of Koza's , 1995, ICML.

[149]  Donald H. Kraft,et al.  The use of genetic programming to build queries for information retrieval , 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

[150]  J. Koza Automatic Discovery Using Genetic Programming of an Unknown-Sized Detector of Protein Motifs Containing Repeatedly-Used Subexpressions , 1995 .

[151]  David Andre,et al.  The Evolution of Agents that Build Mental Models and Create Simple Plans Using Genetic Programming , 1995, ICGA.

[152]  Justinian P. Rosca,et al.  Towards a New Generation of Program Synthesis Approaches , 1995, SEKE.

[153]  S. Handley Predicting whether or not a nucleic acid sequence is an E. coli promoter region using genetic programming , 1995, Proceedings First International Symposium on Intelligence in Neural and Biological Systems. INBS'95.

[154]  David Rogers,et al.  Development of a genetic algorithm based biomechanical simulation of sagittal lifting tasks , 2005 .

[155]  Piero Mussio,et al.  Toward a Practice of Autonomous Systems , 1994 .