Machine Learning is one of the oldest and most intriguing areas of Ar tificial Intelligence. From the moment that computer visionaries first began to conceive the potential for general-purpose symbolic computa tion, the concept of a machine that could learn by itself has been an ever present goal. Today, although there have been many implemented com puter programs that can be said to learn, we are still far from achieving the lofty visions of self-organizing automata that spring to mind when we think of machine learning. We have established some base camps and scaled some of the foothills of this epic intellectual adventure, but we are still far from the lofty peaks that the imagination conjures up. Nevertheless, a solid foundation of theory and technique has begun to develop around a variety of specialized learning tasks. Such tasks in clude discovery of optimal or effective parameter settings for controlling processes, automatic acquisition or refinement of rules for controlling behavior in rule-driven systems, and automatic classification and di agnosis of items on the basis of their features. Contributions include algorithms for optimal parameter estimation, feedback and adaptation algorithms, strategies for credit/blame assignment, techniques for rule and category acquisition, theoretical results dealing with learnability of various classes by formal automata, and empirical investigations of the abilities of many different learning algorithms in a diversity of applica tion areas."

Machine Learning is one of the oldest and most intriguing areas of Ar tificial Intelligence. From the moment that computer visionaries first began to conceive the potential for general-purpose symbolic computa tion, the concept of a machine that could learn by itself has been an ever present goal. Today, although there have been many implemented com puter programs that can be said to learn, we are still far from achieving the lofty visions of self-organizing automata that spring to mind when we think of machine learning. We have established some base camps and scaled some of the foothills of this epic intellectual adventure, but we are still far from the lofty peaks that the imagination conjures up. Nevertheless, a solid foundation of theory and technique has begun to develop around a variety of specialized learning tasks. Such tasks in clude discovery of optimal or effective parameter settings for controlling processes, automatic acquisition or refinement of rules for controlling behavior in rule-driven systems, and automatic classification and di agnosis of items on the basis of their features. Contributions include algorithms for optimal parameter estimation, feedback and adaptation algorithms, strategies for credit/blame assignment, techniques for rule and category acquisition, theoretical results dealing with learnability of various classes by formal automata, and empirical investigations of the abilities of many different learning algorithms in a diversity of applica tion areas."

These proceedings contain papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI), held at the University of Pennsylvania in Philadelphia, Pennsylvania during September 12-13, 2009. WABI 2009 was the ninth annual conference in this series, which focuses on novel algorithms that address imp- tantproblemsingenomics, molecularbiology, andevolution.Theconference- phasizes research that describes computationally e?cient algorithms and data structures that have been implemented and tested in simulations and on real data. WABI is sponsored by the European Association for Theoretical C- puter Science (EATCS) and the International Society for Computational Bi- ogy (ISCB). WABI 2009 was supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics at the University of Pennsylvania. For the 2009 conference, 90 full papers were submitted for review by the Program Committee, and from this strong ?eld of submissions, 34 papers were chosen for presentation at the conference and publication in the proceedings. The ?nal programcovered a wide range of topics including gene interaction n- works, molecular phylogeny, RNA and protein structure, and genome evolutio