A tandem evolutionary algorithm for identifying causal rules from complex data

We propose a new evolutionary approach for discovering causal rules in complex classification problems from batch data. Key aspects include (a) the use of a hypergeometric probability mass function as a principled statistic for assessing fitness that quantifies the probability that the observed association between a given clause and target class is due to chance, taking into account the size of the dataset, the amount of missing data, and the distribution of outcome categories, (b) tandem age-layered evolutionary algorithms for evolving parsimonious archives of conjunctive clauses, and disjunctions of these conjunctions, each of which have probabilistically significant associations with outcome classes, and (c) separate archive bins for clauses of different orders, with dynamically adjusted order-specific thresholds. The method is validated on majority-on and multiplexer benchmark problems exhibiting various combinations of heterogeneity, epistasis, overlap, noise in class associations, missing data, extraneous features, and imbalanced classes. We also validate on a more realistic synthetic genome dataset with heterogeneity, epistasis, extraneous features, and noise. In all synthetic epistatic benchmarks, we consistently recover the true causal rule sets used to generate the data. Finally, we discuss an application to a complex real-world survey dataset designed to inform possible ecohealth interventions for Chagas disease

Genetic heterogeneity analysis using genetic algorithm and network science

Through genome-wide association studies (GWAS), disease susceptible genetic variables can be identified by comparing the genetic data of individuals with and without a specific disease. However, the discovery of these associations poses a significant challenge due to genetic heterogeneity and feature interactions. Genetic variables intertwined with these effects often exhibit lower effect-size, and thus can be difficult to be detected using machine learning feature selection methods. To address these challenges, this paper introduces a novel feature selection mechanism for GWAS, named Feature Co-selection Network (FCSNet). FCS-Net is designed to extract heterogeneous subsets of genetic variables from a network constructed from multiple independent feature selection runs based on a genetic algorithm (GA), an evolutionary learning algorithm. We employ a non-linear machine learning algorithm to detect feature interaction. We introduce the Community Risk Score (CRS), a synthetic feature designed to quantify the collective disease association of each variable subset. Our experiment showcases the effectiveness of the utilized GA-based feature selection method in identifying feature interactions through synthetic data analysis. Furthermore, we apply our novel approach to a case-control colorectal cancer GWAS dataset. The resulting synthetic features are then used to explain the genetic heterogeneity in an additional case-only GWAS dataset

A New Evolutionary Algorithm For Mining Noisy, Epistatic, Geospatial Survey Data Associated With Chagas Disease

The scientific community is just beginning to understand some of the profound affects that feature interactions and heterogeneity have on natural systems. Despite the belief that these nonlinear and heterogeneous interactions exist across numerous real-world systems (e.g., from the development of personalized drug therapies to market predictions of consumer behaviors), the tools for analysis have not kept pace. This research was motivated by the desire to mine data from large socioeconomic surveys aimed at identifying the drivers of household infestation by a Triatomine insect that transmits the life-threatening Chagas disease. To decrease the risk of transmission, our colleagues at the laboratory of applied entomology and parasitology have implemented mitigation strategies (known as Ecohealth interventions); however, limited resources necessitate the search for better risk models. Mining these complex Chagas survey data for potential predictive features is challenging due to imbalanced class outcomes, missing data, heterogeneity, and the non-independence of some features. We develop an evolutionary algorithm (EA) to identify feature interactions in Big Datasets with desired categorical outcomes (e.g., disease or infestation). The method is non-parametric and uses the hypergeometric PMF as a fitness function to tackle challenges associated with using p-values in Big Data (e.g., p-values decrease inversely with the size of the dataset). To demonstrate the EA effectiveness, we first test the algorithm on three benchmark datasets. These include two classic Boolean classifier problems: (1) the majority-on problem and (2) the multiplexer problem, as well as (3) a simulated single nucleotide polymorphism (SNP) disease dataset. Next, we apply the EA to real-world Chagas Disease survey data and successfully archived numerous high-order feature interactions associated with infestation that would not have been discovered using traditional statistics. These feature interactions are also explored using network analysis. The spatial autocorrelation of the genetic data (SNPs of Triatoma dimidiata) was captured using geostatistics. Specifically, a modified semivariogram analysis was performed to characterize the SNP data and help elucidate the movement of the vector within two villages. For both villages, the SNP information showed strong spatial autocorrelation albeit with different geostatistical characteristics (sills, ranges, and nuggets). These metrics were leveraged to create risk maps that suggest the more forested village had a sylvatic source of infestation, while the other village had a domestic/peridomestic source. This initial exploration into using Big Data to analyze disease risk shows that novel and modified existing statistical tools can improve the assessment of risk on a fine-scale

LITERATURE MINING SUSTAINS AND ENHANCES KNOWLEDGE DISCOVERY FROM OMIC STUDIES

Genomic, proteomic and other experimentally generated data from studies of biological systems aiming to discover disease biomarkers are currently analyzed without sufficient supporting evidence from the literature due to complexities associated with automated processing. Extracting prior knowledge about markers associated with biological sample types and disease states from the literature is tedious, and little research has been performed to understand how to use this knowledge to inform the generation of classification models from ‘omic’ data. Using pathway analysis methods to better understand the underlying biology of complex diseases such as breast and lung cancers is state-of-the-art. However, the problem of how to combine literature-mining evidence with pathway analysis evidence is an open problem in biomedical informatics research. This dissertation presents a novel semi-automated framework, named Knowledge Enhanced Data Analysis (KEDA), which incorporates the following components: 1) literature mining of text; 2) classification modeling; and 3) pathway analysis. This framework aids researchers in assigning literature-mining-based prior knowledge values to genes and proteins associated with disease biology. It incorporates prior knowledge into the modeling of experimental datasets, enriching the development process with current findings from the scientific community. New knowledge is presented in the form of lists of known disease-specific biomarkers and their accompanying scores obtained through literature mining of millions of lung and breast cancer abstracts. These scores can subsequently be used as prior knowledge values in Bayesian modeling and pathway analysis. Ranked, newly discovered biomarker-disease-biofluid relationships which identify biomarker specificity across biofluids are presented. A novel method of identifying biomarker relationships is discussed that examines the attributes from the best-performing models. Pathway analysis results from the addition of prior information, ultimately lead to more robust evidence for pathway involvement in diseases of interest based on statistically significant standard measures of impact factor and p-values. The outcome of implementing the KEDA framework is enhanced modeling and pathway analysis findings. Enhanced knowledge discovery analysis leads to new disease-specific entities and relationships that otherwise would not have been identified. Increased disease understanding, as well as identification of biomarkers for disease diagnosis, treatment, or therapy targets should ultimately lead to validation and clinical implementation

Principled design of evolutionary learning sytems for large scale data mining

Currently, the data mining and machine learning fields are facing new challenges because of the amount of information that is collected and needs processing. Many sophisticated learning approaches cannot simply cope with large and complex domains, because of the unmanageable execution times or the loss of prediction and generality capacities that occurs when the domains become more complex. Therefore, to cope with the volumes of information of the current realworld problems there is a need to push forward the boundaries of sophisticated data mining techniques. This thesis is focused on improving the efficiency of Evolutionary Learning systems in large scale domains. Specifically the objective of this thesis is improving the efficiency of the Bioinformatic Hierarchical Evolutionary Learning (BioHEL) system, a system designed with the purpose of handling large domains. This is a classifier system that uses an Iterative Rule Learning approach to generate a set of rules one by one using consecutive Genetic Algorithms. This system have shown to be very competitive so far in large and complex domains. In particular, BioHEL has obtained very important results when solving protein structure prediction problems and has won related merits, such as being placed among the best algorithms for this purpose at the Critical Assessment of Techniques for Protein Structure Prediction (CASP) in 2008 and 2010, and winning the bronze medal at the HUMIES Awards for Human-competitive results in 2007. However, there is still a need to analyse this system in a principled way to determine how the current mechanisms work together to solve larger domains and determine the aspects of the system that can be improved towards this aim. To fulfil the objective of this thesis, the work is divided in two parts. In the first part of the thesis exhaustive experimentation was carried out to determine ways in which the system could be improved. From this exhaustive analysis three main weaknesses are pointed out: a) the problem-dependancy of parameters in BioHEL's fitness function, which results in having a system difficult to set up and which requires an extensive preliminary experimentation to determine the adequate values for these parameters; b) the execution time of the learning process, which at the moment does not use any parallelisation techniques and depends on the size of the training sets; and c) the lack of global supervision over the generated solutions which comes from the usage of the Iterative Rule Learning paradigm and produces larger rule sets in which there is no guarantee of minimality or maximal generality. The second part of the thesis is focused on tackling each one of the weaknesses abovementioned to have a system capable of handling larger domains. First a heuristic approach to set parameters within BioHEL's fitness function is developed. Second a new parallel evaluation process that runs on General Purpose Graphic Processing Units was developed. Finally, post-processing operators to tackle the generality and cardinality of the generated solutions are proposed. By means of these enhancements we managed to improve the BioHEL system to reduce both the learning and the preliminary experimentation time, increase the generality of the final solutions and make the system more accessible for end-users. Moreover, as the techniques discussed in this thesis can be easily extended to other Evolutionary Learning systems we consider them important additions to the research in this field towards tackling large scale domains

Knowledge extraction from biomedical data using machine learning

PhD ThesisThanks to the breakthroughs in biotechnologies that have occurred during the recent years, biomedical data is accumulating at a previously unseen pace. In the field of biomedicine, decades-old statistical methods are still commonly used to analyse such data. However, the simplicity of these approaches often limits the amount of useful information that can be extracted from the data. Machine learning methods represent an important alternative due to their ability to capture complex patterns, within the data, likely missed by simpler methods. This thesis focuses on the extraction of useful knowledge from biomedical data using machine learning. Within the biomedical context, the vast majority of machine learning applications focus their e↵ort on the generation and validation of prediction models. Rarely the inferred models are used to discover meaningful biomedical knowledge. The work presented in this thesis goes beyond this scenario and devises new methodologies to mine machine learning models for the extraction of useful knowledge. The thesis targets two important and challenging biomedical analytic tasks: (1) the inference of biological networks and (2) the discovery of biomarkers. The first task aims to identify associations between di↵erent biological entities, while the second one tries to discover sets of variables that are relevant for specific biomedical conditions. Successful solutions for both problems rely on the ability to recognise complex interactions within the data, hence the use of multivariate machine learning methods. The network inference problem is addressed with FuNeL: a protocol to generate networks based on the analysis of rule-based machine learning models. The second task, the biomarker discovery, is studied with RGIFE, a heuristic that exploits the information extracted from machine learning models to guide its search for minimal subsets of variables. The extensive analysis conducted for this dissertation shows that the networks inferred with FuNeL capture relevant knowledge complementary to that extracted by standard inference methods. Furthermore, the associations defined by FuNeL are discovered - 6 - more pertinent in a disease context. The biomarkers selected by RGIFE are found to be disease-relevant and to have a high predictive power. When applied to osteoarthritis data, RGIFE confirmed the importance of previously identified biomarkers, whilst also extracting novel biomarkers with possible future clinical applications. Overall, the thesis shows new e↵ective methods to leverage the information, often remaining buried, encapsulated within machine learning models and discover useful biomedical knowledge.European Union Seventh Framework Programme (FP7/2007- 2013) that funded part of this work under the “D-BOARD” project (grant agreement number 305815)

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Untangling hotel industry’s inefficiency: An SFA approach applied to a renowned Portuguese hotel chain

The present paper explores the technical efficiency of four hotels from Teixeira Duarte Group - a renowned Portuguese hotel chain. An efficiency ranking is established from these four hotel units located in Portugal using Stochastic Frontier Analysis. This methodology allows to discriminate between measurement error and systematic inefficiencies in the estimation process enabling to investigate the main inefficiency causes. Several suggestions concerning efficiency improvement are undertaken for each hotel studied.info:eu-repo/semantics/publishedVersio