New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

The high cost of inappropriate empiric treatment of presumed Clostridium difficile-associated diarrhea

The Center for Disease Control and Prevention (CDC) estimates that more than 2 million patients annually acquire an infection while hospitalized in U.S. hospitals for other health problems, and that 88,000 die as a direct or indirect result of these infections. Infection with Clostridium difficile is the most important common cause of health care associated infectious diarrhea in industrialized countries. The purpose of this study was to explore the cost of current treatment practice of beginning empiric metronidazole treatment for hospitalized patients with diarrhea prior to identification of an infectious agent. The records of 70 hospitalized patients were retrospectively analyzed to determine the pharmacologic treatment, laboratory testing, and radiographic studies ordered and the median cost for each of these was determined. All patients in the study were tested for C. difficile and concurrently started on empiric metronidazole. The median direct cost for metronidazole was $7.25 per patient (95% CI 5.00, 12.721). The median direct cost for laboratory charges was $468.00 (95% CI 339.26, 552.58) and for radiology the median direct cost was $970.00 (95% CI 738.00, 3406.91). Indirect costs, which are far greater than direct costs, were not studied. At St. Luke's, if every hospitalized patient with diarrhea was empirically treated with metronidazole at a median cost of $7.25, the annual direct cost is estimated to be over $9,000.00 plus uncalculated indirect costs. In the U.S., the estimated annual direct cost may be as much as $21,750,000.00, plus indirect costs. ^ An unexpected and significant finding of this study was the inconsistency in testing and treatment of patients with health care associated diarrhea. A best-practice model for C. difficile testing and treatment was not found in the literature review. In addition to the cost savings gained by not routinely beginning empiric treatment with metronidazole, significant savings and improvement in patient care may result from a more consistent approach to the diagnosis and treatment of all patients with health care associated diarrhea. A decision tree model for C. difficile testing and treatment is proposed, but further research is needed to evaluate the decision arms before a validated best practice model can be proposed. ^