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.

Normalized Gaussian Networks with Mixed Feature Data

With mixed feature data, problems are induced in modeling the gating network of normalized Gaussian (NG) networks as the assumption of multivariate Gaussian becomes invalid. In this paper, we propose an independence model to handle mixed feature data within the framework of NG networks. The method is illustrated using a real example of breast cancer data.

Seizure detection algorithm for neonates based on wave-sequence analysis

Objective: The description and evaluation of the performance of a new real-time seizure detection algorithm in the newborn infant. Methods: The algorithm includes parallel fragmentation of EEG signal into waves; wave-feature extraction and averaging; elementary, preliminary and final detection. The algorithm detects EEG waves with heightened regularity, using wave intervals, amplitudes and shapes. The performance of the algorithm was assessed with the use of event-based and liberal and conservative time-based approaches and compared with the performance of Gotman's and Liu's algorithms. Results: The algorithm was assessed on multi-channel EEG records of 55 neonates including 17 with seizures. The algorithm showed sensitivities ranging 83-95% with positive predictive values (PPV) 48-77%. There were 2.0 false positive detections per hour. In comparison, Gotman's algorithm (with 30 s gap-closing procedure) displayed sensitivities of 45-88% and PPV 29-56%; with 7.4 false positives per hour and Liu's algorithm displayed sensitivities of 96-99%, and PPV 10-25%; with 15.7 false positives per hour. Conclusions: The wave-sequence analysis based algorithm displayed higher sensitivity, higher PPV and a substantially lower level of false positives than two previously published algorithms. Significance: The proposed algorithm provides a basis for major improvements in neonatal seizure detection and monitoring. Published by Elsevier Ireland Ltd. on behalf of International Federation of Clinical Neurophysiology.

The parameterless self-organizing map algorithm

The parameterless self-organizing map (PLSOM) is a new neural network algorithm based on the self-organizing map (SOM). It eliminates the need for a learning rate and annealing schemes for learning rate and neighborhood size. We discuss the relative performance of the PLSOM and the SOM and demonstrate some tasks in which the SOM fails but the PLSOM performs satisfactory. Finally we discuss some example applications of the PLSOM and present a proof of ordering under certain limited conditions.

Genetic parameters and predicted response to selection for lean growth in an Australian commercial nucleus pig herd

Genetic parameters for performance traits in a pig population were estimated using a multi-trait derivative-free REML algorithm. The 2590 total data included 922 restrictively fed male and 1668 ad libitum fed female records. Estimates of heritability (standard error in parentheses) were 0.25 (0.03), 0.15 (0.03), and 0.30 (0.05) for lifetime daily gain, test daily gain, and P2-fat depth in males, respectively; and 0.27 (0.04) and 0.38 (0.05) for average daily gain and P2-fat depth in females, respectively. The genetic correlation between P2-fat depth and test daily gain in males was -0.17 (0.06) and between P2-fat and lifetime average daily gain in females 0.44 (0.09). Genetic correlations between sexes were 0.71 (0.11) for average daily gain and -0.30 (0.10) for P2-fat depth. Genetic response per standard deviation of selection on an index combining all traits was predicted at $AU120 per sow per year. Responses in daily gain and backfat were expected to be higher when using only male selection than when using only female selection. Selection for growth rate in males will improve growth rate and carcass leanness simultaneously.

The dynamics of a genetic algorithm for a simple learning problem

A formalism for describing the dynamics of Genetic Algorithms (GAs) using method s from statistical mechanics is applied to the problem of generalization in a perceptron with binary weights. The dynamics are solved for the case where a new batch of training patterns is presented to each population member each generation, which considerably simplifies the calculation. The theory is shown to agree closely to simulations of a real GA averaged over many runs, accurately predicting the mean best solution found. For weak selection and large problem size the difference equations describing the dynamics can be expressed analytically and we find that the effects of noise due to the finite size of each training batch can be removed by increasing the population size appropriately. If this population resizing is used, one can deduce the most computationally efficient size of training batch each generation. For independent patterns this choice also gives the minimum total number of training patterns used. Although using independent patterns is a very inefficient use of training patterns in general, this work may also prove useful for determining the optimum batch size in the case where patterns are recycled.

The primal sketch revisited: locating and representing edges in human vision via Gaussian-derivative filtering

Marr's work offered guidelines on how to investigate vision (the theory - algorithm - implementation distinction), as well as specific proposals on how vision is done. Many of the latter have inevitably been superseded, but the approach was inspirational and remains so. Marr saw the computational study of vision as tightly linked to psychophysics and neurophysiology, but the last twenty years have seen some weakening of that integration. Because feature detection is a key stage in early human vision, we have returned to basic questions about representation of edges at coarse and fine scales. We describe an explicit model in the spirit of the primal sketch, but tightly constrained by psychophysical data. Results from two tasks (location-marking and blur-matching) point strongly to the central role played by second-derivative operators, as proposed by Marr and Hildreth. Edge location and blur are evaluated by finding the location and scale of the Gaussian-derivative `template' that best matches the second-derivative profile (`signature') of the edge. The system is scale-invariant, and accurately predicts blur-matching data for a wide variety of 1-D and 2-D images. By finding the best-fitting scale, it implements a form of local scale selection and circumvents the knotty problem of integrating filter outputs across scales. [Supported by BBSRC and the Wellcome Trust]

A novel silicon membrane-based biosensing platform using distributive sensing strategy and artificial neural networks for feature analysis

A novel biosensing system based on a micromachined rectangular silicon membrane is proposed and investigated in this paper. A distributive sensing scheme is designed to monitor the dynamics of the sensing structure. An artificial neural network is used to process the measured data and to identify cell presence and density. Without specifying any particular bio-application, the investigation is mainly concentrated on the performance testing of this kind of biosensor as a general biosensing platform. The biosensing experiments on the microfabricated membranes involve seeding different cell densities onto the sensing surface of membrane, and measuring the corresponding dynamics information of each tested silicon membrane in the form of a series of frequency response functions (FRFs). All of those experiments are carried out in cell culture medium to simulate a practical working environment. The EA.hy 926 endothelial cell lines are chosen in this paper for the bio-experiments. The EA.hy 926 endothelial cell lines represent a particular class of biological particles that have irregular shapes, non-uniform density and uncertain growth behaviour, which are difficult to monitor using the traditional biosensors. The final predicted results reveal that the methodology of a neural-network based algorithm to perform the feature identification of cells from distributive sensory measurement has great potential in biosensing applications.

A constructive learning algorithm based on back-propagation

There are been a resurgence of interest in the neural networks field in recent years, provoked in part by the discovery of the properties of multi-layer networks. This interest has in turn raised questions about the possibility of making neural network behaviour more adaptive by automating some of the processes involved. Prior to these particular questions, the process of determining the parameters and network architecture required to solve a given problem had been a time consuming activity. A number of researchers have attempted to address these issues by automating these processes, concentrating in particular on the dynamic selection of an appropriate network architecture.The work presented here specifically explores the area of automatic architecture selection; it focuses upon the design and implementation of a dynamic algorithm based on the Back-Propagation learning algorithm. The algorithm constructs a single hidden layer as the learning process proceeds using individual pattern error as the basis of unit insertion. This algorithm is applied to several problems of differing type and complexity and is found to produce near minimal architectures that are shown to have a high level of generalisation ability.

Comparing methods to separate treatment from self-selection effects in an online banking setting

The literature discusses several methods to control for self-selection effects but provides little guidance on which method to use in a setting with a limited number of variables. The authors theoretically compare and empirically assess the performance of different matching methods and instrumental variable and control function methods in this type of setting by investigating the effect of online banking on product usage. Hybrid matching in combination with the Gaussian kernel algorithm outperforms the other methods with respect to predictive validity. The empirical finding of large self-selection effects indicates the importance of controlling for these effects when assessing the effectiveness of marketing activities.

The multiple pheromone Ant clustering algorithm

Ant Colony Optimisation algorithms mimic the way ants use pheromones for marking paths to important locations. Pheromone traces are followed and reinforced by other ants, but also evaporate over time. As a consequence, optimal paths attract more pheromone, whilst the less useful paths fade away. In the Multiple Pheromone Ant Clustering Algorithm (MPACA), ants detect features of objects represented as nodes within graph space. Each node has one or more ants assigned to each feature. Ants attempt to locate nodes with matching feature values, depositing pheromone traces on the way. This use of multiple pheromone values is a key innovation. Ants record other ant encounters, keeping a record of the features and colony membership of ants. The recorded values determine when ants should combine their features to look for conjunctions and whether they should merge into colonies. This ability to detect and deposit pheromone representative of feature combinations, and the resulting colony formation, renders the algorithm a powerful clustering tool. The MPACA operates as follows: (i) initially each node has ants assigned to each feature; (ii) ants roam the graph space searching for nodes with matching features; (iii) when departing matching nodes, ants deposit pheromones to inform other ants that the path goes to a node with the associated feature values; (iv) ant feature encounters are counted each time an ant arrives at a node; (v) if the feature encounters exceed a threshold value, feature combination occurs; (vi) a similar mechanism is used for colony merging. The model varies from traditional ACO in that: (i) a modified pheromone-driven movement mechanism is used; (ii) ants learn feature combinations and deposit multiple pheromone scents accordingly; (iii) ants merge into colonies, the basis of cluster formation. The MPACA is evaluated over synthetic and real-world datasets and its performance compares favourably with alternative approaches.

A decision support system for supplier selection and order allocation in stochastic, multi-stakeholder and multi-criteria environments

Integrated supplier selection and order allocation is an important decision for both designing and operating supply chains. This decision is often influenced by the concerned stakeholders, suppliers, plant operators and customers in different tiers. As firms continue to seek competitive advantage through supply chain design and operations they aim to create optimized supply chains. This calls for on one hand consideration of multiple conflicting criteria and on the other hand consideration of uncertainties of demand and supply. Although there are studies on supplier selection using advanced mathematical models to cover a stochastic approach, multiple criteria decision making techniques and multiple stakeholder requirements separately, according to authors' knowledge there is no work that integrates these three aspects in a common framework. This paper proposes an integrated method for dealing with such problems using a combined Analytic Hierarchy Process-Quality Function Deployment (AHP-QFD) and chance constrained optimization algorithm approach that selects appropriate suppliers and allocates orders optimally between them. The effectiveness of the proposed decision support system has been demonstrated through application and validation in the bioenergy industry.

Achievable performance gain of IEEE 802.11 multi-rate link adaptation algorithm with cross-layer design

Link quality-based rate adaptation has been widely used for IEEE 802.11 networks. However, network performance is affected by both link quality and random channel access. Selection of transmit modes for optimal link throughput can cause medium access control (MAC) throughput loss. In this paper, we investigate this issue and propose a generalised cross-layer rate adaptation algorithm. It considers jointly link quality and channel access to optimise network throughput. The objective is to examine the potential benefits by cross-layer design. An efficient analytic model is proposed to evaluate rate adaptation algorithms under dynamic channel and multi-user access environments. The proposed algorithm is compared to link throughput optimisation-based algorithm. It is found rate adaptation by optimising link layer throughput can result in large performance loss, which cannot be compensated by the means of optimising MAC access mechanism alone. Results show cross-layer design can achieve consistent and considerable performance gains of up to 20%. It deserves to be exploited in practical design for IEEE 802.11 networks.

ACARS:adaptive context - aware rate selection for DSRC in vehicular networks

Throughput plays a vital role for data transfer in Vehicular Networks which is useful for both safety and non-safety applications. An algorithm that adapts to mobile environment by using Context information has been proposed in this paper. Since one of the problems of existing rate adaptation algorithm is underutilization of link capacity in Vehicular environments, we have demonstrated that in wireless and mobile environments, vehicles can adapt to high mobility link condition and still perform better due to regular vehicles that will be out of communication range due to range checking and then de-congest the network thereby making the system perform better since fewer vehicles will contend for network resources. In this paper, we have design, implement and analyze ACARS, a more robust algorithm with significant increase in throughput performance and energy efficiency in the mist of high mobility of vehicles.

An Adaptive Genetic Algorithm with Dynamic Population Size for Optimizing Join Queries

The problem of finding the optimal join ordering executing a query to a relational database management system is a combinatorial optimization problem, which makes deterministic exhaustive solution search unacceptable for queries with a great number of joined relations. In this work an adaptive genetic algorithm with dynamic population size is proposed for optimizing large join queries. The performance of the algorithm is compared with that of several classical non-deterministic optimization algorithms. Experiments have been performed optimizing several random queries against a randomly generated data dictionary. The proposed adaptive genetic algorithm with probabilistic selection operator outperforms in a number of test runs the canonical genetic algorithm with Elitist selection as well as two common random search strategies and proves to be a viable alternative to existing non-deterministic optimization approaches.