A general model for finite-sample effects in training and testing of competing classifiers

The conventional wisdom in the field of statistical pattern recognition (SPR) is that the size of the finite test sample dominates the variance in the assessment of the performance of a classical or neural classifier. The present work shows that this result has only narrow applicability. In particular, when competing algorithms are compared, the finite training sample more commonly dominates this uncertainty. This general problem in SPR is analyzed using a formal structure recently developed for multivariate random-effects receiver operating characteristic (ROC) analysis. Monte Carlo trials within the general model are used to explore the detailed statistical structure of several representative problems in the subfield of computer-aided diagnosis in medicine. The scaling laws between variance of accuracy measures and number of training samples and number of test samples are investigated and found to be comparable to those discussed in the classic text of Fukunaga, but important interaction terms have been neglected by previous authors. Finally, the importance of the contribution of finite trainers to the uncertainties argues for some form of bootstrap analysis to sample that uncertainty. The leading contemporary candidate is an extension of the 0.632 bootstrap and associated error analysis, as opposed to the more commonly used cross-validation.     

Measuring the beauty of forests

Aesthetic considerations are increasingly being taken into account when forest management decisions are made, but more quantitative studies testing assumptions are needed. This study tests the assumption that mature forests are perceived as being more beautiful than young forests; it also tests the philosophical concept of ‘serious beauty’, which hypothesises that the more knowledge one has about the ecological functioning of an environment, the more beautiful it will seem. All tests were done in situ. University students (N = 334) rated the mature forest as more beautiful than the young forest. The young forest was rated as less than neutral in appearance, and the mature forest was rated as more beautiful than neutral. Male students rated the forest as more beautiful than the females did. No significant difference was seen between the ratings from before or after an ecology presentation. Thus we did not confirm the serious beauty hypothesis in this instance.     

A Wnt signaling pathway controls hox gene expression and neuroblast migration in C. elegans

Immunization regimens that induce a broadly reactive cytolytic T lymphocyte (CTL) response specific for lentiviral antigens have emerged as the leading candidates in efficacy trials conducted in both animal modelshumans. To date, lentivirus vaccination strategies have overlooked one such immunization strategy, namely the use of particulate antigens. To evaluate the efficacy of targeting antigen into the phagocytic pathway to elicit a cell-mediated immune response to lentiviral antigens, we initiated the first study of a particulate-based vaccination protocol using a large animal model system. Gradient-purified equine infectious anemia virus (EIAV) was covalently coupled to glutaraldehyde-activated iron oxide beads. In vitro studies demonstrated the effectiveness of the inactivated whole virus particulate to prime antigen presenting cells for the activationexpansion of virus-specific CD8(+) CTL. The in vivo effectiveness of the particulate antigen was evaluated by experimental immunization of ponies. Ponies receiving the viral particulate vaccinechallenged with infectious EIAV had a delayed progression to diseasea reduced viral load compared with infected ponies that had not been vaccinated. Interestingly, in vitro virus-specific CTL activity was detected in only one of four immunized animals at the day of challenge. The beneficial effects of the particulate vaccine regimen were not clearly associated with any in vitro measurable parameters of the virus-specific cellular or humoral immune responses elicited by the vaccine at the day of challenge. However, within 3 weeks after virus challenge, anamnestic humoral responses characterized by a rapid emergence of neutralizing activity in the seruma predominance of conformationally dependent epitopes recognized by virus-specific antibodies were observed in the vaccinates. Taken together, further studies are clearly warranted in large animal model systems using a particulate-based vaccine regimen considering the beneficial effects of this regimen in our studythe protective effects of particulate antigen delivery in the murine model.     

A probabilistic framework for detecting and identifying anomalies

This paper develops a probabilistic framework to detect and identify anomalies such as damage in structures. The framework is developed by introducing new terms and definitions with their corresponding mathematical formulation. An advantage of the new framework is that ill-conditioning in the identification problem is avoided and that a clear relation between measurements and modeling is established. Special results are then obtained in the form of bounds that allow for computationally efficient applications. An example application is then presented. The application is to detect and identify part-through cracks in a plate from surface strain measurements. In this application problem, the role of strain gauge size and measurement errors are considered and discussed.     

Alpha subunit contamination of human albumin preparations: interference in radioimmunoassy

Certain preparations of human serum albumin have been found to decrease the apparent titer of antisera to alpha subunit of human TSH (hTSH-alpha) and the sensitivity of the resultant radioimmunoassay for the immunologically common alpha subunit of the human glycoprotein hormones. Utilizing bovine serum albumin as the carrier protein, antisera to hTSH-alpha had 20-fold higher titers, and the resultant radioimmunoassay demonstrated 20-fold greater sensitivity for alpha subunit. Interference in the alpha immunoassay was not caused by protease since protease inhibitors did not eliminate it. Gel chromatography of human serum albumin revealed alph immunoactivity in an elution position identical to that of standard alpha subunit. Only certain human serum albumin preparations demonstrated interference in the radioimmunoassay because of the species specificity of the alpha subunit.A possible explanation for the alpha subunit contamination of human albumin preparations may be contamination of the serum source with placental blood, which contains large quantities of the alpha subunit of human chorionic gonadotropin.     

Improved Rooftop Detection in Aerial Images with Machine Learning

In this paper, we examine the use of machine learning to improve a rooftop detection process, one step in a vision system that recognizes buildings in overhead imagery. We review the problem of analyzing aerial images and describe an existing system that detects buildings in such images. We briefly review four algorithms that we selected to improve rooftop detection. The data sets were highly skewed and the cost of mistakes differed between the classes, so we used ROC analysis to evaluate the methods under varying error costs. We report three experiments designed to illuminate facets of applying machine learning to the image analysis task. One investigated learning with all available images to determine the best performing method. Another focused on within-image learning, in which we derived training and testing data from the same image. A final experiment addressed between-image learning, in which training and testing sets came from different images. Results suggest that useful generalization occurred when training and testing on data derived from images differing in location and in aspect. They demonstrate that under most conditions, naive Bayes exceeded the accuracy of other methods and a handcrafted classifier, the solution currently used in the building detection system.     

Hox gene expression in a single Caenorhabditis elegans cell is regulated by a caudal homolog and intercellular signals that inhibit wnt signaling

In Caenorhabditis elegans males, a row of epidermal precursor cells called seam cells generates a pattern of cuticular alae in anterior body regions and neural sensilla called rays in the posterior. The Hox gene mab-5 is required for two posterior seam cells, V5 and V6, to generate rays. In mab-5 mutant males, V5 and V6 do not generate sensory ray lineages but instead generate lineages that lead to alae. Here we show that two independent regulatory pathways can activate mab-5 expression in the V cells. First, the caudal homolog pal-1 turns on mab-5 in V6 during embryogenesis. Second, a Wnt signaling pathway is capable of activating mab-5 in the V cells during postembryonic development; however, during normal development Wnt signaling is inhibited by signals from neighboring V cells. The inhibition of this Wnt signaling pathway by lateral signals between the V cells limits the number of rays in the animal and also determines the position of the boundary between alae and rays.     

The beta-catenin homolog BAR-1 and LET-60 Ras coordinately regulate the Hox gene lin-39 during Caenorhabditis elegans vulval development

In C. elegans, the epithelial Pn.p cells adopt either a vulval precursor cell fate or fuse with the surrounding hypodermis (the F fate). Our results suggest that a Wnt signal transduced through a pathway involving the beta-catenin homolog BAR-1 controls whether P3.p through P8.p adopt the vulval precursor cell fate. In bar-1 mutants, P3.p through P8.p can adopt F fates instead of vulval precursor cell fates. The Wnt/bar-1 signaling pathway acts by regulating the expression of the Hox gene lin-39, since bar-1 is required for LIN-39 expression and forced lin-39 expression rescues the bar-1 mutant phenotype. LIN-39 activity is also regulated by the anchor cell signal/let-23 receptor tyrosine kinase/let-60 Ras signaling pathway. Our genetic and molecular experiments show that the vulval precursor cells can integrate the input from the BAR-1 and LET-60 Ras signaling pathways by coordinately regulating activity of the common target LIN-39 Hox.