Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models

The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model the order of accumulation of such mutations during the progression, which eventually leads to the disease, by means of probabilistic graphic models, i.e., Bayesian Networks (BNs). We investigate how to perform the task of learning the structure of such BNs, according to experimental evidence, adopting a global optimization meta-heuristics. In particular, in this work we rely on Genetic Algorithms, and to strongly reduce the execution time of the inference -- which can also involve multiple repetitions to collect statistically significant assessments of the data -- we distribute the calculations using both multi-threading and a multi-node architecture. The results show that our approach is characterized by good accuracy and specificity; we also demonstrate its feasibility, thanks to a 84x reduction of the overall execution time with respect to a traditional sequential implementation

Improving generalisation of AutoML systems with dynamic fitness evaluations

A common problem machine learning developers are faced with is overfitting, that is, fitting a pipeline too closely to the training data that the performance degrades for unseen data. Automated machine learning aims to free (or at least ease) the developer from the burden of pipeline creation, but this overfitting problem can persist. In fact, this can become more of a problem as we look to iteratively optimise the performance of an internal cross-validation (most often \textit{k}-fold). While this internal cross-validation hopes to reduce this overfitting, we show we can still risk overfitting to the particular folds used. In this work, we aim to remedy this problem by introducing dynamic fitness evaluations which approximate repeated \textit{k}-fold cross-validation, at little extra cost over single \textit{k}-fold, and far lower cost than typical repeated \textit{k}-fold. The results show that when time equated, the proposed fitness function results in significant improvement over the current state-of-the-art baseline method which uses an internal single \textit{k}-fold. Furthermore, the proposed extension is very simple to implement on top of existing evolutionary computation methods, and can provide essentially a free boost in generalisation/testing performance.Comment: 19 pages, 4 figure

A simpler method of preprocessing MALDI-TOF MS data for differential biomarker analysis: stem cell and melanoma cancer studies

<p>Abstract</p> <p>Introduction</p> <p>Raw spectral data from matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) with MS profiling techniques usually contains complex information not readily providing biological insight into disease. The association of identified features within raw data to a known peptide is extremely difficult. Data preprocessing to remove uncertainty characteristics in the data is normally required before performing any further analysis. This study proposes an alternative yet simple solution to preprocess raw MALDI-TOF-MS data for identification of candidate marker ions. Two in-house MALDI-TOF-MS data sets from two different sample sources (melanoma serum and cord blood plasma) are used in our study.</p> <p>Method</p> <p>Raw MS spectral profiles were preprocessed using the proposed approach to identify peak regions in the spectra. The preprocessed data was then analysed using bespoke machine learning algorithms for data reduction and ion selection. Using the selected ions, an ANN-based predictive model was constructed to examine the predictive power of these ions for classification.</p> <p>Results</p> <p>Our model identified 10 candidate marker ions for both data sets. These ion panels achieved over 90% classification accuracy on blind validation data. Receiver operating characteristics analysis was performed and the area under the curve for melanoma and cord blood classifiers was 0.991 and 0.986, respectively.</p> <p>Conclusion</p> <p>The results suggest that our data preprocessing technique removes unwanted characteristics of the raw data, while preserving the predictive components of the data. Ion identification analysis can be carried out using MALDI-TOF-MS data with the proposed data preprocessing technique coupled with bespoke algorithms for data reduction and ion selection.</p

Training Neural Networks Through the Integration of Evolution and Gradient Descent

Neural networks have achieved widespread adoption due to both their applicability to a wide range of problems and their success relative to other machine learning algorithms. The training of neural networks is achieved through any of several paradigms, most prominently gradient-based approaches (including deep learning), but also through up-and-coming approaches like neuroevolution. However, while both of these neural network training paradigms have seen major improvements over the past decade, little work has been invested in developing algorithms that incorporate the advances from both deep learning and neuroevolution. This dissertation introduces two new algorithms that are steps towards the integration of gradient descent and neuroevolution for training neural networks. The first is (1) the Limited Evaluation Evolutionary Algorithm (LEEA), which implements a novel form of evolution where individuals are partially evaluated, allowing rapid learning and enabling the evolutionary algorithm to behave more like gradient descent. This conception provides a critical stepping stone to future algorithms that more tightly couple evolutionary and gradient descent components. The second major algorithm (2) is Divergent Discriminative Feature Accumulation (DDFA), which combines a neuroevolution phase, where features are collected in an unsupervised manner, with a gradient descent phase for fine tuning of the neural network weights. The neuroevolution phase of DDFA utilizes an indirect encoding and novelty search, which are sophisticated neuroevolution components rarely incorporated into gradient descent-based systems. Further contributions of this work that build on DDFA include (3) an empirical analysis to identify an effective distance function for novelty search in high dimensions and (4) the extension of DDFA for the purpose of discovering convolutional features. The results of these DDFA experiments together show that DDFA discovers features that are effective as a starting point for gradient descent, with significant improvement over gradient descent alone. Additionally, the method of collecting features in an unsupervised manner allows DDFA to be applied to domains with abundant unlabeled data and relatively sparse labeled data. This ability is highlighted in the STL-10 domain, where DDFA is shown to make effective use of unlabeled data

A prescription of methodological guidelines for comparing bio-inspired optimization algorithms

Bio-inspired optimization (including Evolutionary Computation and Swarm Intelligence) is a growing research topic with many competitive bio-inspired algorithms being proposed every year. In such an active area, preparing a successful proposal of a new bio-inspired algorithm is not an easy task. Given the maturity of this research field, proposing a new optimization technique with innovative elements is no longer enough. Apart from the novelty, results reported by the authors should be proven to achieve a significant advance over previous outcomes from the state of the art. Unfortunately, not all new proposals deal with this requirement properly. Some of them fail to select appropriate benchmarks or reference algorithms to compare with. In other cases, the validation process carried out is not defined in a principled way (or is even not done at all). Consequently, the significance of the results presented in such studies cannot be guaranteed. In this work we review several recommendations in the literature and propose methodological guidelines to prepare a successful proposal, taking all these issues into account. We expect these guidelines to be useful not only for authors, but also for reviewers and editors along their assessment of new contributions to the field.This work was supported by grants from the Spanish Ministry of Science (TIN2016-8113-R, TIN2017-89517-P and TIN2017-83132-C2- 2-R) and Universidad Politécnica de Madrid (PINV-18-XEOGHQ-19- 4QTEBP). Eneko Osaba and Javier Del Ser-would also like to thank the Basque Government for its funding support through the ELKARTEK and EMAITEK programs. Javier Del Ser-receives funding support from the Consolidated Research Group MATHMODE (IT1294-19) granted by the Department of Education of the Basque Government

Computer vision and optimization methods applied to the measurements of in-plane deformations

fi=vertaisarvioitu|en=peerReviewed

APIC: A method for automated pattern identification and classification

Machine Learning (ML) is a transformative technology at the forefront of many modern research endeavours. The technology is generating a tremendous amount of attention from researchers and practitioners, providing new approaches to solving complex classification and regression tasks. While concepts such as Deep Learning have existed for many years, the computational power for realising the utility of these algorithms in real-world applications has only recently become available. This dissertation investigated the efficacy of a novel, general method for deploying ML in a variety of complex tasks, where best feature selection, data-set labelling, model definition and training processes were determined automatically. Models were developed in an iterative fashion, evaluated using both training and validation data sets. The proposed method was evaluated using three distinct case studies, describing complex classification tasks often requiring significant input from human experts. The results achieved demonstrate that the proposed method compares with, and often outperforms, less general, comparable methods designed specifically for each task. Feature selection, data-set annotation, model design and training processes were optimised by the method, where less complex, comparatively accurate classifiers with lower dependency on computational power and human expert intervention were produced. In chapter 4, the proposed method demonstrated improved efficacy over comparable systems, automatically identifying and classifying complex application protocols traversing IP networks. In chapter 5, the proposed method was able to discriminate between normal and anomalous traffic, maintaining accuracy in excess of 99%, while reducing false alarms to a mere 0.08%. Finally, in chapter 6, the proposed method discovered more optimal classifiers than those implemented by comparable methods, with classification scores rivalling those achieved by state-of-the-art systems. The findings of this research concluded that developing a fully automated, general method, exhibiting efficacy in a wide variety of complex classification tasks with minimal expert intervention, was possible. The method and various artefacts produced in each case study of this dissertation are thus significant contributions to the field of ML

Variable selection and validation in multivariate modelling

Motivation Validation of variable selection and predictive performance is crucial in construction of robust multivariate models that generalize well, minimize overfitting and facilitate interpretation of results. Inappropriate variable selection leads instead to selection bias, thereby increasing the risk of model overfitting and false positive discoveries. Although several algorithms exist to identify a minimal set of most informative variables (i.e. the minimal-optimal problem), few can select all variables related to the research question (i.e. the all-relevant problem). Robust algorithms combining identification of both minimal-optimal and all-relevant variables with proper cross-validation are urgently needed. Results We developed the MUVR algorithm to improve predictive performance and minimize overfitting and false positives in multivariate analysis. In the MUVR algorithm, minimal variable selection is achieved by performing recursive variable elimination in a repeated double cross-validation (rdCV) procedure. The algorithm supports partial least squares and random forest modelling, and simultaneously identifies minimal-optimal and all-relevant variable sets for regression, classification and multilevel analyses. Using three authentic omics datasets, MUVR yielded parsimonious models with minimal overfitting and improved model performance compared with state-of-the-art rdCV. Moreover, MUVR showed advantages over other variable selection algorithms, i.e. Boruta and VSURF, including simultaneous variable selection and validation scheme and wider applicability