In this thesis, the reduction of neural networks is studied. A new, largely automatic method is developed for reducing a neural network, and its capabilities are analyzed and compared with current methods. An example is presented that is irreducible via existing techniques, but is reducible by the new method. Factors...
Biologists need tools to see the structural relationships encoded in biological sequences (strings). The Walking Tree heuristics calculate some of these relationships. I have designed and implemented graphic presentations which allow the biologist (user) to see these relations. This thesis contains background information on the biological sequences and some background...
Approximate string matching is commonly used to align genetic sequences (DNA
or RNA) to determine their shared characteristics. In contrast with the standard
dynamic programming methods which use local edit distance models, the Walking
Tree heuristic method was created to handle non-local changes, e.g., translocations,
inversions, and duplications, altogether and...
Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared
characteristics. Most genetic string matching methods are based on the edit-distance model, which does not provide
alignments for inversions and translocations. Recently, a heuristic called the Walking Tree Method [2, 3] has been...
The meaning of biological sequences is a central problem
of modern biology. Although string matching is well understood
in the edit-distance model, biological strings
with transpositions and inversions violate this model's
assumptions. To align biologically reasonable strings, we
proposed the Walking Tree Method [4,5,6,7,8], an
approximate string alignment method that...
Basic biological information is stored in strings of nucleic acids (DNA, RNA) or amino acids
(proteins). Teasing out the meaning of these strings is a central problem of modern biology. Matching and
aligning strings brings out their shared characteristics. Although string matching is well-understood in the
edit-distance model, biological strings...
A hybrid landscape optimization/simulation model called SafeD (Simulation and analysis of forests with episodic Disturbances) was built to address the needs of forest management planning in the Applegate River Watershed, southwestern Oregon (the Apple gate Project). There are two goals of the Applegate Project: 1) search for forest policies and...