Evaluation of pesticide toxicity: a hierarchical QSAR approach to model the acute aquatic toxicity and avian oral toxicity of pesticides

The thesis aimed to extract information relevant to the hazard and risk assessment of pesticides. In particular, quantitative structure-activity relationship (QSAR) approaches have been used to build up a mathematical model able to predict the aquatic acute toxicity, LC50, and the avian oral toxicity, LD50, for pesticides. Ecotoxicological values were collected from several databases, and screened according to quality criteria. A hierarchical QSAR approach was applied for the prediction of acute aquatic toxicity. Chemical structures were encoded into molecular descriptors by an automated, seamless procedure available within the OpenMolGRID system. Different linear and non-linear regression techniques were used to obtain reliable and thoroughly validated QSARs. The final model was developed by a counter-propagation neural network coupled with genetic algorithms for variable selection. The proposed QSAR is consistent with McFarland's principle for biological activity and makes use of seven molecular descriptors. The model was assessed thoroughly in test (R2 = 0.8) and validation sets (R2 = 0.72), the y-scrambling test and a sensitivity/stability test. The second endpoint considered in this thesis was avian oral toxicity. As previously, the chemical description of chemicals was generated automatically by the OpenMolGRID system. The best classification model was chosen on the basis of the performances on a validation set of 19 data points, and was obtained from a support vector machine using 94 data points and nine variables selected by genetic algorithms (Error Ratetraining = 0.021, Error Ratevalidation = 0.158). The model allowed for a mechanistic estimation of the toxicological action. In fact, several descriptors selected for the final classification model encode for the interaction of the pesticides with other molecules. The presence of hetero-atoms, e.g. sulphur atoms, is correlated with the toxicity, and the pool of descriptor selected is generally dependent from the 3D conformation of the structures. These suggest that, in the case of avian oral toxicity, pesticides probably exert their toxic action through the interaction with some macromolecule and/or protein of the biological system

Methods to Improve the Prediction Accuracy and Performance of Ensemble Models

The application of ensemble predictive models has been an important research area in predicting medical diagnostics, engineering diagnostics, and other related smart devices and related technologies. Most of the current predictive models are complex and not reliable despite numerous efforts in the past by the research community. The performance accuracy of the predictive models have not always been realised due to many factors such as complexity and class imbalance. Therefore there is a need to improve the predictive accuracy of current ensemble models and to enhance their applications and reliability and non-visual predictive tools. The research work presented in this thesis has adopted a pragmatic phased approach to propose and develop new ensemble models using multiple methods and validated the methods through rigorous testing and implementation in different phases. The first phase comprises of empirical investigations on standalone and ensemble algorithms that were carried out to ascertain their performance effects on complexity and simplicity of the classifiers. The second phase comprises of an improved ensemble model based on the integration of Extended Kalman Filter (EKF), Radial Basis Function Network (RBFN) and AdaBoost algorithms. The third phase comprises of an extended model based on early stop concepts, AdaBoost algorithm, and statistical performance of the training samples to minimize overfitting performance of the proposed model. The fourth phase comprises of an enhanced analytical multivariate logistic regression predictive model developed to minimize the complexity and improve prediction accuracy of logistic regression model. To facilitate the practical application of the proposed models; an ensemble non-invasive analytical tool is proposed and developed. The tool links the gap between theoretical concepts and practical application of theories to predict breast cancer survivability. The empirical findings suggested that: (1) increasing the complexity and topology of algorithms does not necessarily lead to a better algorithmic performance, (2) boosting by resampling performs slightly better than boosting by reweighting, (3) the prediction accuracy of the proposed ensemble EKF-RBFN-AdaBoost model performed better than several established ensemble models, (4) the proposed early stopped model converges faster and minimizes overfitting better compare with other models, (5) the proposed multivariate logistic regression concept minimizes the complexity models (6) the performance of the proposed analytical non-invasive tool performed comparatively better than many of the benchmark analytical tools used in predicting breast cancers and diabetics ailments. The research contributions to ensemble practice are: (1) the integration and development of EKF, RBFN and AdaBoost algorithms as an ensemble model, (2) the development and validation of ensemble model based on early stop concepts, AdaBoost, and statistical concepts of the training samples, (3) the development and validation of predictive logistic regression model based on breast cancer, and (4) the development and validation of a non-invasive breast cancer analytic tools based on the proposed and developed predictive models in this thesis. To validate prediction accuracy of ensemble models, in this thesis the proposed models were applied in modelling breast cancer survivability and diabetics’ diagnostic tasks. In comparison with other established models the simulation results of the models showed improved predictive accuracy. The research outlines the benefits of the proposed models, whilst proposes new directions for future work that could further extend and improve the proposed models discussed in this thesis

Socio-Economic Evaluation of the Potential for Australian Tree Species in the Philippines

Crop Production/Industries,

Property valuation with interpretable machine learning

Property valuation is an important task for various stakeholders, including banks, local authorities, property developers, and brokers. As a result of the characteristics of the real estate market, such as the infrequency of trades, limited supply, negotiated prices, and small submarkets with unique traits, there is no clear market value for properties. Traditionally property valuations are done by expert appraisers. Property valuation can also be done accurately with machine learning methods, but the lack of interpretability with accurate machine learning methods can limit the adoption of those methods. Interpretable machine learning methods could be a solution to this issue, but there are concerns related to the accuracy of these methods. This thesis aims to evaluate the feasibility of interpretable machine learning methods in property valuation by comparing a promising interpretable method to a more complex machine learning method that has had good results in property valuation previously. The promising interpretable method and the well-performed machine learning method are chosen based on previous literature. The two chosen methods, Extreme Gradient Boosting (XGB) and Explainable Boosting Machine (EBM) are compared in terms of prediction accuracy of properties in six big municipalities of Denmark. In addition to the accuracy comparison, the interpretability of the EBM is highlighted. The accuracy of the XGB method is better, even though there are no big differences between the two methods in individual municipalities. The interpretability of the EBM is good, as it is possible to understand, how the model makes predictions in general, and how individual predictions are made

Integrated assessment and valuation of ecosystem services - Guidelines and experiences

EU FP7 OpenNESS project deliverable D33 & D4

Introduction to machine and deep learning for medical physicists

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155469/1/mp14140_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155469/2/mp14140.pd

The evolution and dynamics of stocks on the Johannesburg Securities Exchange and their implications for equity investment management

[No subject] This thesis explores the dynamics of the Johannesburg Stock Exchange returns to understand how they impact stock prices. The introductory chapter renders a brief overview of financial markets in general and the Johannesburg Securities Exchange (JSE) in particular. The second chapter employs the fractal analysis technique, a method for estimating the Hurst exponent, to examine the JSE indices. The results suggest that the JSE is fractal in nature, implying a long-term predictability property. The results also indicate a logical system of variation of the Hurst exponent by firm size, market characteristics and sector grouping. The third chapter investigates the economic and political events that affect different market sectors and how they are implicated in the structural dynamics of the JSE. It provides some insights into the degree of sensitivity of different market sectors to positive and negative news. The findings demonstrate transient episodes of nonlinearity that can be attributed to economic events and the state of the market. Chapter 4 looks at the evolution of risk measurement and the distribution of returns on the JSE. There is evidence of fat tails and that the Student t-distribution is a better fit for the JSE returns than the Normal distribution. The Gaussian based Value-at-Risk model also proved to be an ineffective risk measurement tool under high market volatility. In Chapter 5 simulations are used to investigate how different agent interactions affect market dynamics. The results show that it is possible for traders to switch between trading strategies and this evolutionary switching of strategies is dependent on the state of the market. Chapter 6 shows the extent to which endogeneity affects price formation. To explore this relationship, the Poisson Hawkes model, which combines exogenous influences with self-excited dynamics, is employed. Evidence suggests that the level of endogeneity has been increasing rapidly over the past decade. This implies that there is an increasing influence of internal dynamics on price formation. The findings also demonstrate that market crashes are caused by endogenous dynamics and exogenous shocks merely act as catalysts. Chapter 7 presents the hybrid adaptive intelligent model for financial time series prediction. Given evidence of non-linearity, heterogeneous agents and the fractal nature of the JSE market, neural networks, fuzzy logic and fractal theory are combined, to obtain a hybrid adaptive intelligent model. The proposed system outperformed traditional models

Spatio-temporal Negotiation Protocols

Canonical problems are simplified representations of a class of real world problems. They allow researchers to compare algorithms in a standard setting which captures the most important challenges of the real world problems being modeled. In this dissertation, we focus on negotiating a collaboration in space and time, a problem with many important real world applications. Although technically a multi-issue negotiation, we show that the problem can not be represented in a satisfactory manner by previous models. We propose the Children in the Rectangular Forest (CRF) model as a possible canonical problem for negotiating spatio-temporal collaboration. In the CRF problem, two embodied agents are negotiating the synchronization of their movement for a portion of the path from their respective sources to destinations. The negotiation setting is zero initial knowledge and it happens in physical time. As equilibrium strategies are not practically possible, we are interested in strategies with bounded rationality, which achieve good performance in a wide range of practical negotiation scenarios. We design a number of negotiation protocols to allow agents to exchange their offers. The simple negotiation protocol can be enhanced by schemes in which the agents add additional information of the negotiation flow to aid the negotiation partner in offer formation. Naturally, the performance of a strategy is dependent on the strategy of the opponent and the iii characteristics of the scenario. Thus we develop a set of metrics for the negotiation scenario which formalizes our intuition of collaborative scenarios (where the agents’ interests are closely aligned) versus competitive scenarios (where the gain of the utility for one agent is paid off with a loss of utility for the other agent). Finally, we further investigate the sophisticated strategies which allow agents to learn the opponents while negotiating. We find strategies can be augmented by collaborativeness analysis: the approximate collaborativeness metric can be used to cut short the negotiation. Then, we discover an approach to model the opponent through Bayesian learning. We assume the agents do not disclose their information voluntarily: the learning needs to rely on the study of the offers exchanged during normal negotiation. At last, we explore a setting where the agents are able to perform physical action (movement) while the negotiation is ongoing. We formalize a method to represent and update the beliefs about the valuation function, the current state of negotiation and strategy of the opponent agent using a particle filter. By exploring a number of different negotiation protocols and several peer-to-peer negotiation based strategies, we claim that the CRF problem captures the main challenges of the real world problems while allows us to simplify away some of the computationally demanding but semantically marginal features of real world problems

Combining evolutionary algorithms and agent-based simulation for the development of urbanisation policies

Urban-planning authorities continually face the problem of optimising the allocation of green space over time in developing urban environments. To help in these decision-making processes, this thesis provides an empirical study of using evolutionary approaches to solve sequential decision making problems under uncertainty in stochastic environments. To achieve this goal, this work is underpinned by developing a theoretical framework based on the economic model of Alonso and the associated methodology for modelling spatial and temporal urban growth, in order to better understand the complexity inherent in this kind of system and to generate and improve relevant knowledge for the urban planning community. The model was hybridised with cellular automata and agent-based model and extended to encompass green space planning based on urban cost and satisfaction. Monte Carlo sampling techniques and the use of the urban model as a surrogate tool were the two main elements investigated and applied to overcome the noise and uncertainty derived from dealing with future trends and expectations. Once the evolutionary algorithms were equipped with these mechanisms, the problem under consideration was defined and characterised as a type of adaptive submodular. Afterwards, the performance of a non-adaptive evolutionary approach with a random search and a very smart greedy algorithm was compared and in which way the complexity that is linked with the configuration of the problem modifies the performance of both algorithms was analysed. Later on, the application of very distinct frameworks incorporating evolutionary algorithm approaches for this problem was explored: (i) an ‘offline’ approach, in which a candidate solution encodes a complete set of decisions, which is then evaluated by full simulation, and (ii) an ‘online’ approach which involves a sequential series of optimizations, each making only a single decision, and starting its simulations from the endpoint of the previous run