Use of a probabilistic neural network to reduce costs of selecting construction rock

Rocks used as construction aggregate in temperate climates deteriorate to differing degrees because of repeated freezing and thawing. The magnitude of the deterioration depends on the rock's properties. Aggregate, including crushed carbonate rock, is required to have minimum geotechnical qualities before it can be used in asphalt and concrete. In order to reduce chances of premature and expensive repairs, extensive freeze-thaw tests are conducted on potential construction rocks. These tests typically involve 300 freeze-thaw cycles and can take four to five months to complete. Less time consuming tests that (1) predict durability as well as the extended freeze-thaw test or that (2) reduce the number of rocks subject to the extended test, could save considerable amounts of money. Here we use a probabilistic neural network to try and predict durability as determined by the freeze-thaw test using four rock properties measured on 843 limestone samples from the Kansas Department of Transportation. Modified freeze-thaw tests and less time consuming specific gravity (dry), specific gravity (saturated), and modified absorption tests were conducted on each sample. Durability factors of 95 or more as determined from the extensive freeze-thaw tests are viewed as acceptable—rocks with values below 95 are rejected. If only the modified freeze-thaw test is used to predict which rocks are acceptable, about 45% are misclassified. When 421 randomly selected samples and all four standardized and scaled variables were used to train aprobabilistic neural network, the rate of misclassification of 422 independent validation samples dropped to 28%. The network was trained so that each class (group) and each variable had its own coefficient (sigma). In an attempt to reduce errors further, an additional class was added to the training data to predict durability values greater than 84 and less than 98, resulting in only 11% of the samples misclassified. About 43% of the test data was classed by the neural net into the middle group—these rocks should be subject to full freeze-thaw tests. Thus, use of the probabilistic neural network would meanthat the extended test would only need be applied to 43% of the samples, and 11% of the rocks classed as acceptable would fail early.

GANN: Genetic algorithm neural networks for the detection of conserved combinations of features in DNA

Background: The multitude of motif detection algorithms developed to date have largely focused on the detection of patterns in primary sequence. Since sequence-dependent DNA structure and flexibility may also play a role in protein-DNA interactions, the simultaneous exploration of sequence-and structure-based hypotheses about the composition of binding sites and the ordering of features in a regulatory region should be considered as well. The consideration of structural features requires the development of new detection tools that can deal with data types other than primary sequence. Results: GANN ( available at http://bioinformatics.org.au/gann) is a machine learning tool for the detection of conserved features in DNA. The software suite contains programs to extract different regions of genomic DNA from flat files and convert these sequences to indices that reflect sequence and structural composition or the presence of specific protein binding sites. The machine learning component allows the classification of different types of sequences based on subsamples of these indices, and can identify the best combinations of indices and machine learning architecture for sequence discrimination. Another key feature of GANN is the replicated splitting of data into training and test sets, and the implementation of negative controls. In validation experiments, GANN successfully merged important sequence and structural features to yield good predictive models for synthetic and real regulatory regions. Conclusion: GANN is a flexible tool that can search through large sets of sequence and structural feature combinations to identify those that best characterize a set of sequences.

Real-Time Gene-Expression Extraction with Fast Classification (FC) Networks

Fast Classification (FC) networks were inspired by a biologically plausible mechanism for short term memory where learning occurs instantaneously. Both weights and the topology for an FC network are mapped directly from the training samples by using a prescriptive training scheme. Only two presentations of the training data are required to train an FC network. Compared with iterative learning algorithms such as Back-propagation (which may require many hundreds of presentations of the training data), the training of FC networks is extremely fast and learning convergence is always guaranteed. Thus FC networks may be suitable for applications where real-time classification is needed. In this paper, the FC networks are applied for the real-time extraction of gene expressions for Chlamydia microarray data. Both the classification performance and learning time of the FC networks are compared with the Multi-Layer Proceptron (MLP) networks and support-vector-machines (SVM) in the same classification task. The FC networks are shown to have extremely fast learning time and comparable classification accuracy.

An empirical study of Hoelfding Racing for model selction in K-nearest neighbor classification

Racing algorithms have recently been proposed as a general-purpose method for performing model selection in machine teaming algorithms. In this paper, we present an empirical study of the Hoeffding racing algorithm for selecting the k parameter in a simple k-nearest neighbor classifier. Fifteen widely-used classification datasets from UCI are used and experiments conducted across different confidence levels for racing. The results reveal a significant amount of sensitivity of the k-nn classifier to its model parameter value. The Hoeffding racing algorithm also varies widely in its performance, in terms of the computational savings gained over an exhaustive evaluation. While in some cases the savings gained are quite small, the racing algorithm proved to be highly robust to the possibility of erroneously eliminating the optimal models. All results were strongly dependent on the datasets used.

Neural networks

An overview of neural networks, covering multilayer perceptrons, radial basis functions, constructive algorithms, Kohonen and K-means unupervised algorithms, RAMnets, first and second order training methods, and Bayesian regularisation methods.

Topographic mappings and feed-forward neural networks

This thesis is a study of the generation of topographic mappings - dimension reducing transformations of data that preserve some element of geometric structure - with feed-forward neural networks. As an alternative to established methods, a transformational variant of Sammon's method is proposed, where the projection is effected by a radial basis function neural network. This approach is related to the statistical field of multidimensional scaling, and from that the concept of a 'subjective metric' is defined, which permits the exploitation of additional prior knowledge concerning the data in the mapping process. This then enables the generation of more appropriate feature spaces for the purposes of enhanced visualisation or subsequent classification. A comparison with established methods for feature extraction is given for data taken from the 1992 Research Assessment Exercise for higher educational institutions in the United Kingdom. This is a difficult high-dimensional dataset, and illustrates well the benefit of the new topographic technique. A generalisation of the proposed model is considered for implementation of the classical multidimensional scaling (¸mds}) routine. This is related to Oja's principal subspace neural network, whose learning rule is shown to descend the error surface of the proposed ¸mds model. Some of the technical issues concerning the design and training of topographic neural networks are investigated. It is shown that neural network models can be less sensitive to entrapment in the sub-optimal global minima that badly affect the standard Sammon algorithm, and tend to exhibit good generalisation as a result of implicit weight decay in the training process. It is further argued that for ideal structure retention, the network transformation should be perfectly smooth for all inter-data directions in input space. Finally, there is a critique of optimisation techniques for topographic mappings, and a new training algorithm is proposed. A convergence proof is given, and the method is shown to produce lower-error mappings more rapidly than previous algorithms.

Efficient training of RBF networks for classification.

Radial Basis Function networks with linear outputs are often used in regression problems because they can be substantially faster to train than Multi-layer Perceptrons. For classification problems, the use of linear outputs is less appropriate as the outputs are not guaranteed to represent probabilities. We show how RBFs with logistic and softmax outputs can be trained efficiently using the Fisher scoring algorithm. This approach can be used with any model which consists of a generalised linear output function applied to a model which is linear in its parameters. We compare this approach with standard non-linear optimisation algorithms on a number of datasets.

Efficient training of RBF networks for classification

Radial Basis Function networks with linear outputs are often used in regression problems because they can be substantially faster to train than Multi-layer Perceptrons. For classification problems, the use of linear outputs is less appropriate as the outputs are not guaranteed to represent probabilities. In this paper we show how RBFs with logistic and softmax outputs can be trained efficiently using algorithms derived from Generalised Linear Models. This approach is compared with standard non-linear optimisation algorithms on a number of datasets.

Mean field methods for classification with Gaussian processes

We discuss the Application of TAP mean field methods known from Statistical Mechanics of disordered systems to Bayesian classification with Gaussian processes. In contrast to previous applications, no knowledge about the distribution of inputs is needed. Simulation results for the Sonar data set are given.

Gaussian processes for classification: mean field algorithms:mean-field algorithms

We derive a mean field algorithm for binary classification with Gaussian processes which is based on the TAP approach originally proposed in Statistical Physics of disordered systems. The theory also yields an approximate leave-one-out estimator for the generalization error which is computed with no extra computational cost. We show that from the TAP approach, it is possible to derive both a simpler 'naive' mean field theory and support vector machines (SVM) as limiting cases. For both mean field algorithms and support vectors machines, simulation results for three small benchmark data sets are presented. They show 1. that one may get state of the art performance by using the leave-one-out estimator for model selection and 2. the built-in leave-one-out estimators are extremely precise when compared to the exact leave-one-out estimate. The latter result is a taken as a strong support for the internal consistency of the mean field approach.

Evolutionary neural networks : models and applications

The scaling problems which afflict attempts to optimise neural networks (NNs) with genetic algorithms (GAs) are disclosed. A novel GA-NN hybrid is introduced, based on the bumptree, a little-used connectionist model. As well as being computationally efficient, the bumptree is shown to be more amenable to genetic coding lthan other NN models. A hierarchical genetic coding scheme is developed for the bumptree and shown to have low redundancy, as well as being complete and closed with respect to the search space. When applied to optimising bumptree architectures for classification problems the GA discovers bumptrees which significantly out-perform those constructed using a standard algorithm. The fields of artificial life, control and robotics are identified as likely application areas for the evolutionary optimisation of NNs. An artificial life case-study is presented and discussed. Experiments are reported which show that the GA-bumptree is able to learn simulated pole balancing and car parking tasks using only limited environmental feedback. A simple modification of the fitness function allows the GA-bumptree to learn mappings which are multi-modal, such as robot arm inverse kinematics. The dynamics of the 'geographic speciation' selection model used by the GA-bumptree are investigated empirically and the convergence profile is introduced as an analytical tool. The relationships between the rate of genetic convergence and the phenomena of speciation, genetic drift and punctuated equilibrium arc discussed. The importance of genetic linkage to GA design is discussed and two new recombination operators arc introduced. The first, linkage mapped crossover (LMX) is shown to be a generalisation of existing crossover operators. LMX provides a new framework for incorporating prior knowledge into GAs.Its adaptive form, ALMX, is shown to be able to infer linkage relationships automatically during genetic search.

A smart sensing platform for the classification of ambulatory patterns

This paper describes an innovative sensing approach allowing capture, discrimination, and classification of transients automatically in gait. A walking platform is described, which offers an alternative design to that of standard force plates with advantages that include mechanical simplicity and less restriction on dimensions. The scope of the work is to investigate as an experiment the sensitivity of the distributive tactile sensing method with the potential to address flexibility on gait assessment, including patient targeting and the extension to a variety of ambulatory applications. Using infrared sensors to measure plate deflection, gait patterns are compared with stored templates using a pattern recognition algorithm. This information is input into a neural network to classify normal and affected walking events, with a classification accuracy of just under 90 per cent achieved. The system developed has potential applications in gait analysis and rehabilitation, whereby it can be used as a tool for early diagnosis of walking disorders or to determine changes between pre- and post-operative gait.

Learning task specific distributed paragraph representations using a 2-tier convolutional neural network

We introduce a type of 2-tier convolutional neural network model for learning distributed paragraph representations for a special task (e.g. paragraph or short document level sentiment analysis and text topic categorization). We decompose the paragraph semantics into 3 cascaded constitutes: word representation, sentence composition and document composition. Specifically, we learn distributed word representations by a continuous bag-of-words model from a large unstructured text corpus. Then, using these word representations as pre-trained vectors, distributed task specific sentence representations are learned from a sentence level corpus with task-specific labels by the first tier of our model. Using these sentence representations as distributed paragraph representation vectors, distributed paragraph representations are learned from a paragraph-level corpus by the second tier of our model. It is evaluated on DBpedia ontology classification dataset and Amazon review dataset. Empirical results show the effectiveness of our proposed learning model for generating distributed paragraph representations.

Regression analysis of ranked segment parameters for optic nerve head classification:a pilot study

Purpose: To determine whether curve-fitting analysis of the ranked segment distributions of topographic optic nerve head (ONH) parameters, derived using the Heidelberg Retina Tomograph (HRT), provide a more effective statistical descriptor to differentiate the normal from the glaucomatous ONH. Methods: The sample comprised of 22 normal control subjects (mean age 66.9 years; S.D. 7.8) and 22 glaucoma patients (mean age 72.1 years; S.D. 6.9) confirmed by reproducible visual field defects on the Humphrey Field Analyser. Three 10°-images of the ONH were obtained using the HRT. The mean topography image was determined and the HRT software was used to calculate the rim volume, rim area to disc area ratio, normalised rim area to disc area ratio and retinal nerve fibre cross-sectional area for each patient at 10°-sectoral intervals. The values were ranked in descending order, and each ranked-segment curve of ordered values was fitted using the least squares method. Results: There was no difference in disc area between the groups. The group mean cup-disc area ratio was significantly lower in the normal group (0.204 ± 0.16) compared with the glaucoma group (0.533 ± 0.083) (p < 0.001). The visual field indices, mean deviation and corrected pattern S.D., were significantly greater (p < 0.001) in the glaucoma group (-9.09 dB ± 3.3 and 7.91 ± 3.4, respectively) compared with the normal group (-0.15 dB ± 0.9 and 0.95 dB ± 0.8, respectively). Univariate linear regression provided the best overall fit to the ranked segment data. The equation parameters of the regression line manually applied to the normalised rim area-disc area and the rim area-disc area ratio data, correctly classified 100% of normal subjects and glaucoma patients. In this study sample, the regression analysis of ranked segment parameters method was more effective than conventional ranked segment analysis, in which glaucoma patients were misclassified in approximately 50% of cases. Further investigation in larger samples will enable the calculation of confidence intervals for normality. These reference standards will then need to be investigated for an independent sample to fully validate the technique. Conclusions: Using a curve-fitting approach to fit ranked segment curves retains information relating to the topographic nature of neural loss. Such methodology appears to overcome some of the deficiencies of conventional ranked segment analysis, and subject to validation in larger scale studies, may potentially be of clinical utility for detecting and monitoring glaucomatous damage. © 2007 The College of Optometrists.

Applications of Radial Basis Neural Networks for Area Forest

This paper proposes a new method using radial basis neural networks in order to find the classification and the recognition of trees species for forest inventories. This method computes the wood volume using a set of data easily obtained. The results that are obtained improve the used classic and statistical models.