Particle Swarm Optimisation for learning Bayesian Networks

This paper discusses the potential of Particle Swarm Optimisation (PSO) for inducing Bayesian Networks (BNs). Specifically, we detail two methods which adopt the search and score approach to BN learning. The two algorithms are similar in that they both use PSO as the search algorithm, and the K2 metric to score the resulting network. The difference lies in the way networks are constructed. The CONstruct And Repair (CONAR) algorithm generates structures, validates, and repairs if required, and the REstricted STructure (REST) algorithm, only permits valid structures to be developed. Initial experiments indicate that these approaches produce promising results when compared to other BN learning strategies

Optimising Antibiotic Treatments with Multi-objective Population-based Algorithms

Antibiotic resistance is one of the major challenges that we are facing today. The frequent overuse of antibiotics is one of the main reasons for the development of resistance. A mathematical model of bacterial population dynamics is used, where drug administration and absorption mechanics are implemented to evaluate the fitness of automatically designed treatments. To maximise the probability of curing the host while minimising the total drug used we have explored treatments with different daily dosages and lengths. Two multi-objective population-based methods, a well-known evolutionary algorithm and a particle swarm optimisation algorithm are tuned and contrasted when solving the posed treatment design problem. The best solutions found by our approach suggest treatments ranging from five to seven days with a high initial dose, followed by lower doses, use lower amounts of the drug than the standard common practice of fixed daily dosages over ten days

Optimising Antibiotic Treatments using Evolutionary Algorithms

Antimicrobial resistance is one of the biggest threats to global health, food security, and development. Antibiotic overuse and misuse are the main drivers for the emergence of resistance. Studies in the medical sphere have indicated that shortened antibiotic treatments can be as effective as standard fixed-dose ones and have shown that an initial higher dose followed by a lower maintenance dose are more beneficial to patients with critical illnesses. It is crucial to optimise the use of existing antibiotics in order to improve medical outcomes, decrease toxicity and reduce the emergence of resistance. We formulate the design of antibiotic dosing regimens as a continuous optimisation problem and use several evolutionary algorithms as the search technique. Regimens are represented as vectors of real numbers encoding daily doses, which can vary across the treatment duration. A stochastic mathematical model of bacterial infections with tuneable resistance levels is used to evaluate the effectiveness of evolved regimens. The main objective is to minimise the treatment failure rate, subject to a constraint on the maximum total antibiotic used. We consider simulations with different levels of bacterial resistance; two ways of administering the drug (orally and intravenously); as well as coinfections with two strains of bacteria. The approach produced effective dosing regimens, with an average improvement in lowering the failure rate 30%, when compared with standard fixed-daily-dose regimens with the same total amount of antibiotic. A general pattern of an optimised treatment is found, where if 2x is the standard daily dose then the optimised treatment follows the 3x mg, followed by several 2x mg with a last dose of x mg. A noise handling technique is used to minimise the runtime of the experiments while maintaining the quality of treatments. The results of this work indicate that clinical studies confirming the effectiveness of this approach could be highly beneficial to future of antibiotic treatments

Depth Modulation in Radiotherapy

Intensity Modulated Radiotherapy (IMRT) has been a major field of research over the last thirty years and is today the standard in radiotherapy treatment of cancer. The introduction of IMRT into the clinical environment has greatly improved the ability of the treatment team to conform the radiation dose to the tumour volume. Alongside improvements in image guidance, IMRT has led to a reduction in side effects for patients and opened up the possibilities of dose escalation and hypofractionation. IMRT is however by no means perfect. IMRT and derivatives such as Volumated Arc Therapy (VMAT) are limited by the exit dose from the X-ray beams and deliver a significant amount of radiation dose to normal tissues. The much publicised alternative to IMRT is proton therapy. Proton therapy beams deposit dose over a narrow range resulting in minimal exit dose. The future of radiotherapy certainly involves a significant contribution from proton therapy but the availability to patients is likely to remain limited for a long time to come. The research in this thesis considers the possibility of further improving IMRT by modulating radiotherapy beams along their direction of travel as well as across their intensity, i.e. the so called ‘Depth Modulation’ of the thesis title. Although there are numerous possible ways to achieve depth modulation, this work proposes a combination of X-ray beams with electron beams of different energies with both modalities delivered with a conventional medical linear accelerator. The research in this thesis is concerned with developing a proof of principle for this method. It is to some extent a theoretical study, however at each step the possibility of practical implementation has been considered with the view that the method is only a viable proposition if it can be effectively implemented into clinical practice. The technique proposed in this work is to use electron beams delivered through X-ray MLC with a standard patient set up. To reduce scatter and photon contamination it is proposed to remove the scattering foils from the beamline and to employ optimisation of the electron and photon components to compensate for any remaining penumbra broadening. The research has shown that improvements to dosimetry through removal of the scattering foil would allow delivery without reducing the source to surface distance, making a single isocentre synergistic delivery for both the electron and photon components practical. Electron dose segments have been calculated using Monte Carlo radiation transport and a procedure to optimise dose for the combined photon and electron IMRT technique has been developed. Through development of the optimisation procedure the characteristics of the mixed modality technique have been examined. A number of findings are demonstrated such as the benefit of gaps between electron segments, the benefits of optimising for energy in three dimensions and the dependence of the cost function minimum on the electron to photon ratio. Through clinical examples it has been shown that for tumours close to the surface the mixed modality technique has the potential to reduce the dose to normal tissues, particular in the low dose wash. Calculations of relative malignant induction probability demonstrate that this reduction in dose has the potential to reduce the incidence of secondary cancer induction. Possible treatment sites for application of the technique include breast, head and neck, brain and sarcomas

Analysis of physiological signals using machine learning methods

Technological advances in data collection enable scientists to suggest novel approaches, such as Machine Learning algorithms, to process and make sense of this information. However, during this process of collection, data loss and damage can occur for reasons such as faulty device sensors or miscommunication. In the context of time-series data such as multi-channel bio-signals, there is a possibility of losing a whole channel. In such cases, existing research suggests imputing the missing parts when the majority of data is available. One way of understanding and classifying complex signals is by using deep neural networks. The hyper-parameters of such models have been optimised using the process of back propagation. Over time, improvements have been suggested to enhance this algorithm. However, an essential drawback of the back propagation can be the sensitivity to noisy data. This thesis proposes two novel approaches to address the missing data challenge and back propagation drawbacks: First, suggesting a gradient-free model in order to discover the optimal hyper-parameters of a deep neural network. The complexity of deep networks and high-dimensional optimisation parameters presents challenges to find a suitable network structure and hyper-parameter configuration. This thesis proposes the use of a minimalist swarm optimiser, Dispersive Flies Optimisation(DFO), to enable the selected model to achieve better results in comparison with the traditional back propagation algorithm in certain conditions such as limited number of training samples. The DFO algorithm offers a robust search process for finding and determining the hyper-parameter configurations. Second, imputing whole missing bio-signals within a multi-channel sample. This approach comprises two experiments, namely the two-signal and five-signal imputation models. The first experiment attempts to implement and evaluate the performance of a model mapping bio-signals from A toB and vice versa. Conceptually, this is an extension to transfer learning using CycleGenerative Adversarial Networks (CycleGANs). The second experiment attempts to suggest a mechanism imputing missing signals in instances where multiple data channels are available for each sample. The capability to map to a target signal through multiple source domains achieves a more accurate estimate for the target domain. The results of the experiments performed indicate that in certain circumstances, such as having a limited number of samples, finding the optimal hyper-parameters of a neural network using gradient-free algorithms outperforms traditional gradient-based algorithms, leading to more accurate classification results. In addition, Generative Adversarial Networks could be used to impute the missing data channels in multi-channel bio-signals, and the generated data used for further analysis and classification tasks

Optimal Multi-Drug Chemotherapy Control Scheme for Cancer Treatment. Design and development of a multi-drug feedback control scheme for optimal chemotherapy treatment for cancer. Evolutionary multi-objective optimisation algorithms were used to achieve the optimal parameters of the controller for effective treatment of cancer with minimum side effects.

Cancer is a generic term for a large group of diseases where cells of the body lose their normal mechanisms for growth so that they grow in an uncontrolled way. One of the most common treatments of cancer is chemotherapy that aims to kill abnormal proliferating cells; however normal cells and other organs of the patients are also adversely affected. In practice, it¿s often difficult to maintain optimum chemotherapy doses that can maximise the abnormal cell killing as well as reducing side effects. The most chemotherapy drugs used in cancer treatment are toxic agents and usually have narrow therapeutic indices, dose levels in which these drugs significantly kill the cancerous cells are close to the levels which sometime cause harmful toxic side effects. To make the chemotherapeutic treatment effective, optimum drug scheduling is required to balance between the beneficial and toxic side effects of the cancer drugs. Conventional clinical methods very often fail to find drug doses that balance between these two due to their inherent conflicting nature. In this investigation, mathematical models for cancer chemotherapy are used to predict the number of tumour cells and control the tumour growth during treatment. A feedback control method is used so as to maintain certain level of drug concentrations at the tumour sites. Multi-objective Genetic Algorithm (MOGA) is then employed to find suitable solutions where drug resistances and drug concentrations are incorporated with cancer cell killing and toxic effects as design objectives. Several constraints and specific goal values were set for different design objectives in the optimisation process and a wide range of acceptable solutions were obtained trading off among different conflicting objectives. Abstract v In order to develop a multi-objective optimal control model, this study used proportional, integral and derivative (PID) and I-PD (modified PID with Integrator used as series) controllers based on Martin¿s growth model for optimum drug concentration to treat cancer. To the best of our knowledge, this is the first PID/I-PD based optimal chemotherapy control model used to investigate the cancer treatment. It has been observed that some solutions can reduce the cancer cells up to nearly 100% with much lower side effects and drug resistance during the whole period of treatment. The proposed strategy has been extended for more drugs and more design constraints and objectives.Libyan Ministry of Higher Educatio

Parameters estimation for a mechanistic model of high dose irradiation damages using Nelder-Mead simplex method and genetic algorithm

Radiation therapy is one of the cancer cells treatments that use high-energy radiation to shrink tumors and kill cancer cells. Radiation therapy kills cancer cells by damaging their DNA directly or creates charged particles within the cells that can in turn damage the DNA. As a side effect of the treatment, the radiation therapy can also damage the normal cell that located at parts of our body. The main goals of radiation therapy are to maximise the damaging of tumors cell and minimise the damage of normal tissue cell. Hence, in this study, we adopt an existing model of high dose irradiation damage. The purpose of this study is to estimate the six parameters of the model which are involved. Two optimisation algorithms is used in order to estimate the parameters, there are Nelder-Mead simplex method and Genetic Algorithm. Both methods have to achieve the objective function which are to minimise the sum of square error (SSE) between the experimental data and simulation data. The performance of both algorithms are compared based on the computational time, number of iteration and value of sum of square error. The optimisation process is carried out using MATLAB programming built-in functions. The parameters estimation results shown that Nelder- Mead simplex method is more superior than Genetic Algorithm for this problem

Directed Intervention Crossover Approaches in Genetic Algorithms with Application to Optimal Control Problems

Genetic Algorithms (GAs) are a search heuristic modeled on the processes of evolution. They have been used to solve optimisation problems in a wide variety of fields. When applied to the optimisation of intervention schedules for optimal control problems, such as cancer chemotherapy treatment scheduling, GAs have been shown to require more fitness function evaluations than other search heuristics to find fit solutions. This thesis presents extensions to the GA crossover process, termed directed intervention crossover techniques, that greatly reduce the number of fitness function evaluations required to find fit solutions, thus increasing the effectiveness of GAs for problems of this type. The directed intervention crossover techniques use intervention scheduling information from parent solutions to direct the offspring produced in the GA crossover process towards more promising areas of a search space. By counting the number of interventions present in parents and adjusting the number of interventions for offspring schedules around it, this allows for highly fit solutions to be found in less fitness function evaluations. The validity of these novel approaches are illustrated through comparison with conventional GA crossover approaches for optimisation of intervention schedules of bio-control application in mushroom farming and cancer chemotherapy treatment. These involve optimally scheduling the application of a bio-control agent to combat pests in mushroom farming and optimising the timing and dosage strength of cancer chemotherapy treatments to maximise their effectiveness. This work demonstrates that significant advantages are gained in terms of both fitness function evaluations required and fitness scores found using the proposed approaches when compared with traditional GA crossover approaches for the production of optimal control schedules

Predicting breast cancer risk, recurrence and survivability

This thesis focuses on predicting breast cancer at early stages by using machine learning algorithms based on biological datasets. The accuracy of those algorithms has been improved to enable the physicians to enhance the success of treatment, thus saving lives and avoiding several further medical tests

Controller tuning by means of evolutionary multiobjective optimization: current trends and applications

Control engineering problems are generally multi-objective problems; meaning that there are several specifications and requirements that must be fulfilled. A traditional approach for calculating a solution with the desired trade-off is to define an optimisation statement. Multi-objective optimisation techniques deal with this problem from a particular perspective and search for a set of potentially preferable solutions; the designer may then analyse the trade-offs among them, and select the best solution according to his/her preferences. In this paper, this design procedure based on evolutionary multiobjective optimisation (EMO) is presented and significant applications on controller tuning are discussed. Throughout this paper it is noticeable that EMO research has been developing towards different optimisation statements, but these statements are not commonly used in controller tuning. Gaps between EMO research and EMO applications on controller tuning are therefore detected and suggested as potential trends for research.The first author is grateful for the hospitality and availability of the UTC at the University of Sheffield during his academic research stay at 2011; especially to Dr. P.J. Fleming for his valuable comments and insights in the development of this paper. This work was partially supported by Grant FPI-2010/19 and project PAID-2011/2732 from the Universitat Politecnica de Valencia and projects TIN2011-28082 and ENE2011-25900 from the Spanish Ministry of Economy and Competitiveness.Reynoso Meza, G.; Blasco Ferragud, FX.; Sanchís Saez, J.; Martínez Iranzo, MA. (2014). Controller tuning by means of evolutionary multiobjective optimization: current trends and applications. Control Engineering Practice. 28:58-73. https://doi.org/10.1016/j.conengprac.2014.03.003S58732