Validation of Soft Classification Models using Partial Class Memberships: An Extended Concept of Sensitivity & Co. applied to the Grading of Astrocytoma Tissues

We use partial class memberships in soft classification to model uncertain labelling and mixtures of classes. Partial class memberships are not restricted to predictions, but may also occur in reference labels (ground truth, gold standard diagnosis) for training and validation data. Classifier performance is usually expressed as fractions of the confusion matrix, such as sensitivity, specificity, negative and positive predictive values. We extend this concept to soft classification and discuss the bias and variance properties of the extended performance measures. Ambiguity in reference labels translates to differences between best-case, expected and worst-case performance. We show a second set of measures comparing expected and ideal performance which is closely related to regression performance, namely the root mean squared error RMSE and the mean absolute error MAE. All calculations apply to classical crisp classification as well as to soft classification (partial class memberships and/or one-class classifiers). The proposed performance measures allow to test classifiers with actual borderline cases. In addition, hardening of e.g. posterior probabilities into class labels is not necessary, avoiding the corresponding information loss and increase in variance. We implement the proposed performance measures in the R package "softclassval", which is available from CRAN and at http://softclassval.r-forge.r-project.org. Our reasoning as well as the importance of partial memberships for chemometric classification is illustrated by a real-word application: astrocytoma brain tumor tissue grading (80 patients, 37000 spectra) for finding surgical excision borders. As borderline cases are the actual target of the analytical technique, samples which are diagnosed to be borderline cases must be included in the validation.Comment: The manuscript is accepted for publication in Chemometrics and Intelligent Laboratory Systems. Supplementary figures and tables are at the end of the pd

Theoretical Interpretations and Applications of Radial Basis Function Networks

Medical applications usually used Radial Basis Function Networks just as Artificial Neural Networks. However, RBFNs are Knowledge-Based Networks that can be interpreted in several way: Artificial Neural Networks, Regularization Networks, Support Vector Machines, Wavelet Networks, Fuzzy Controllers, Kernel Estimators, Instanced-Based Learners. A survey of their interpretations and of their corresponding learning algorithms is provided as well as a brief survey on dynamic learning algorithms. RBFNs' interpretations can suggest applications that are particularly interesting in medical domains

Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem

This paper builds upon the fundamental work of Niwa et al. [34], which provides the unique possibility to analyze the relative aggregation/folding propensity of the elements of the entire Escherichia coli (E. coli) proteome in a cell-free standardized microenvironment. The hardness of the problem comes from the superposition between the driving forces of intra- and inter-molecule interactions and it is mirrored by the evidences of shift from folding to aggregation phenotypes by single-point mutations [10]. Here we apply several state-of-the-art classification methods coming from the field of structural pattern recognition, with the aim to compare different representations of the same proteins gathered from the Niwa et al. data base; such representations include sequences and labeled (contact) graphs enriched with chemico-physical attributes. By this comparison, we are able to identify also some interesting general properties of proteins. Notably, (i) we suggest a threshold around 250 residues discriminating "easily foldable" from "hardly foldable" molecules consistent with other independent experiments, and (ii) we highlight the relevance of contact graph spectra for folding behavior discrimination and characterization of the E. coli solubility data. The soundness of the experimental results presented in this paper is proved by the statistically relevant relationships discovered among the chemico-physical description of proteins and the developed cost matrix of substitution used in the various discrimination systems.Comment: 17 pages, 3 figures, 46 reference

An examination of thermal features' relevance in the task of battery-fault detection

Uninterruptible power supplies (UPS), represented by lead-acid batteries, play an important role in various kinds of industries. They protect industrial technologies from being damaged by dangerous interruptions of an electric power supply. Advanced UPS monitoring performed by a complex battery management system (BMS) prevents the UPS from sustaining more serious damage due to its timely and accurate battery-fault detection based on voltage metering. This technique is very advanced and precise but also very expensive on a long-term basis. This article describes an experiment applying infrared thermographic measurements during a long term monitoring and fault detection in UPS. The assumption that the battery overheat implies its damaged state is the leading factor of our experiments. They are based on real measured data on various UPS battery sets and several statistical examinations confirming the high relevancy of the thermal features with mostly over 90% detection accuracy. Such a model can be used as a supplement for lead-acid battery based UPS monitoring to ensure their higher reliability under significantly lower maintenance costs.Web of Science82art. no. 18

Application of Fuzzy Cognitive Mapping in Livelihood Vulnerability Analysis

Feedback mechanisms are important in the analysis of vulnerability and resilience of social-ecological systems, as well as in the analysis of livelihoods, but how to evaluate systems with direct feedbacks has been a great challenge. We applied fuzzy cognitive mapping, a tool that allows analysis of both direct and indirect feedbacks and can be used to explore the vulnerabilities of livelihoods to identified hazards. We studied characteristics and drivers of rural livelihoods in the Great Limpopo Transfrontier Conservation Area in southern Africa to assess the vulnerability of inhabitants to the different hazards they face. The process involved four steps: (1) surveys and interviews to identify the major livelihood types; (2) description of specific livelihood types in a system format using fuzzy cognitive maps (FCMs), a semi-quantitative tool that models systems based on people’s knowledge; (3) linking variables and drivers in FCMs by attaching weights; and (4) defining and applying scenarios to visualize the effects of drought and changing park boundaries on cash and household food security. FCMs successfully gave information concerning the nature (increase or decrease) and magnitude by which a livelihood system changed under different scenarios. However, they did not explain the recovery path in relation to time and pattern (e.g., how long it takes for cattle to return to desired numbers after a drought). Using FCMs revealed that issues of policy, such as changing situations at borders, can strongly aggravate effects of climate change such as drought. FCMs revealed hidden knowledge and gave insights that improved the understanding of the complexity of livelihood systems in a way that is better appreciated by stakeholders

Art Neural Networks for Remote Sensing: Vegetation Classification from Landsat TM and Terrain Data

A new methodology for automatic mapping from Landsat Thematic Mapper (TM) and terrain data, based on the fuzzy ARTMAP neural network, is developed. System capabilities are tested on a challenging remote sensing classification problem, using spectral and terrain features for vegetation classification in the Cleveland National Forest. After training at the pixel level, system performance is tested at the stand level, using sites not seen during training. Results are compared to those of maximum likelihood classifiers, as well as back propagation neural networks and K Nearest Neighbor algorithms. ARTMAP dynamics are fast, stable, and scalable, overcoming common limitations of back propagation, which did not give satisfactory performance. Best results are obtained using a hybrid system based on a convex combination of fuzzy ARTMAP and maximum likelihood predictions. A prototype remote sensing example introduces each aspect of data processing and fuzzy ARTMAP classification. The example shows how the network automatically constructs a minimal number of recognition categories to meet accuracy criteria. A voting strategy improves prediction and assigns confidence estimates by training the system several times on different orderings of an input set.National Science Foundation (IRI 94-01659, SBR 93-00633); Office of Naval Research (N00014-95-l-0409, N00014-95-0657