Optimality-based Analysis of XCSF Compaction in Discrete Reinforcement Learning

Learning classifier systems (LCSs) are population-based predictive systems that were originally envisioned as agents to act in reinforcement learning (RL) environments. These systems can suffer from population bloat and so are amenable to compaction techniques that try to strike a balance between population size and performance. A well-studied LCS architecture is XCSF, which in the RL setting acts as a Q-function approximator. We apply XCSF to a deterministic and stochastic variant of the FrozenLake8x8 environment from OpenAI Gym, with its performance compared in terms of function approximation error and policy accuracy to the optimal Q-functions and policies produced by solving the environments via dynamic programming. We then introduce a novel compaction algorithm (Greedy Niche Mass Compaction - GNMC) and study its operation on XCSF's trained populations. Results show that given a suitable parametrisation, GNMC preserves or even slightly improves function approximation error while yielding a significant reduction in population size. Reasonable preservation of policy accuracy also occurs, and we link this metric to the commonly used steps-to-goal metric in maze-like environments, illustrating how the metrics are complementary rather than competitive

Predicting the Difficulty of Pure, Strict, Epistatic Models: Metrics for Simulated Model Selection

Background: Algorithms designed to detect complex genetic disease associations are initially evaluated using simulated datasets. Typical evaluations vary constraints that influence the correct detection of underlying models (i.e. number of loci, heritability, and minor allele frequency). Such studies neglect to account for model architecture (i.e. the unique specification and arrangement of penetrance values comprising the genetic model), which alone can influence the detectability of a model. In order to design a simulation study which efficiently takes architecture into account, a reliable metric is needed for model selection. Results: We evaluate three metrics as predictors of relative model detection difficulty derived from previous works: (1) Penetrance table variance (PTV), (2) customized odds ratio (COR), and (3) our own Ease of Detection Measure (EDM), calculated from the penetrance values and respective genotype frequencies of each simulated genetic model. We evaluate the reliability of these metrics across three very different data search algorithms, each with the capacity to detect epistatic interactions. We find that a model’s EDM and COR are each stronger predictors of model detection success than heritability. Conclusions: This study formally identifies and evaluates metrics which quantify model detection difficulty. We utilize these metrics to intelligently select models from a population of potential architectures. This allows for an improved simulation study design which accounts for differences in detection difficulty attributed to model architecture. We implement the calculation and utilization of EDM and COR into GAMETES, an algorithm which rapidly and precisely generates pure, strict, n-locus epistatic models

Information Extraction on Para-Relational Data.

Para-relational data (such as spreadsheets and diagrams) refers to a type of nearly relational data that shares the important qualities of relational data but does not present itself in a relational format. Para-relational data often conveys highly valuable information and is widely used in many different areas. If we can convert para-relational data into the relational format, many existing tools can be leveraged for a variety of interesting applications, such as data analysis with relational query systems and data integration applications. This dissertation aims to convert para-relational data into a high-quality relational form with little user assistance. We have developed four standalone systems, each addressing a specific type of para-relational data. Senbazuru is a prototype spreadsheet database management system that extracts relational information from a large number of spreadsheets. Anthias is an extension of the Senbazuru system to convert a broader range of spreadsheets into a relational format. Lyretail is an extraction system to detect long-tail dictionary entities on webpages. Finally, DiagramFlyer is a web-based search system that obtains a large number of diagrams automatically extracted from web-crawled PDFs. Together, these four systems demonstrate that converting para-relational data into the relational format is possible today, and also suggest directions for future systems.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/120853/1/chenzhe_1.pd

The intersection of evolutionary computation and explainable AI.

In the past decade, Explainable Artificial Intelligence (XAI) has attracted a great interest in the research community, motivated by the need for explanations in critical AI applications. Some recent advances in XAI are based on Evolutionary Computation (EC) techniques, such as Genetic Programming. We call this trend EC for XAI. We argue that the full potential of EC methods has not been fully exploited yet in XAI, and call the community for future efforts in this field. Likewise, we find that there is a growing concern in EC regarding the explanation of population-based methods, i.e., their search process and outcomes. While some attempts have been done in this direction (although, in most cases, those are not explicitly put in the context of XAI), we believe that there are still several research opportunities and open research questions that, in principle, may promote a safer and broader adoption of EC in real-world applications. We call this trend XAI within EC. In this position paper, we briefly overview the main results in the two above trends, and suggest that the EC community may play a major role in the achievement of XAI

Novice-Centric Visualizations for Machine Learning

This thesis focuses on visualizations for machine learning tasks. More specifically, we create a taxonomy for existing machine learning visualizations, and design a system to help machine learning novices perform labelling tasks. There are many mature visualizations to help people understand the performance of current classifiers, including scatterplots, confusion matrices and ROC curves. However, most machine learning researchers are unaware of the visualization possibilities that exist, and many published visualizations are too task-oriented or dataset-oriented to be easily applied to other tasks. This thesis defines a taxonomy for machine learning visualizations in three dimensions: the data displayed, the advanced features to add for a specific task, and the goal of the visualizations. This taxonomy seeks to help machine learning researchers select a better visualization method to analyze their data. Previous machine learning tools focus on presenting comprehensive information to experts, treating machine learning as a black-box for end-users, or explaining the reason behind the prediction in a simple and clear way. However, to build a machine learning system, one needs to label data first, and a lot of machine learning novices want to build a classifier themselves simply by labelling data. This inspired our idea to design and implement the Label-and-Learn system, which includes five visualizations to help users better understand their data, the likelihood of the classifier's success, and to improve their user experience. To evaluate the utility of our Label-and-Learn system, we ran user studies to compare the visualization system and traditional system in the quality of the labels, the user's mental model about the task, and the user experience. The results from the experiment show that visualizations have no negative effect on the quality of the labels, but do improve the user's mental model and the user experience. The success of the Label-and-Learn system should inspire further research in using visualizations to improve the user experience of data labelling in machine learning tasks

Efficient Training Set Use For Blood Pressure Prediction in a Large Scale Learning Classifier System

ABSTRACT We define a machine learning problem to forecast arterial blood pressure. Our goal is to solve this problem with a large scale learning classifier system. Because learning classifiers systems are extremely computationally intensive and this problem's eventually large training set will be very costly to execute, we address how to use less of the training set while not negatively impacting learning accuracy. Our approach is to allow competition among solutions which have not been evaluated on the entire training set. The best of these solutions are then evaluated on more of the training set while their offspring start off being evaluated on less of the training set. To keep selection fair, we divide competing solutions according to how many training examples they have been tested on

Contributions to the study of Austism Spectrum Brain conectivity

164 p.Autism Spectrum Disorder (ASD) is a largely prevalent neurodevelopmental condition with a big social and economical impact affecting the entire life of families. There is an intense search for biomarkers that can be assessed as early as possible in order to initiate treatment and preparation of the family to deal with the challenges imposed by the condition. Brain imaging biomarkers have special interest. Specifically, functional connectivity data extracted from resting state functional magnetic resonance imaging (rs-fMRI) should allow to detect brain connectivity alterations. Machine learning pipelines encompass the estimation of the functional connectivity matrix from brain parcellations, feature extraction and building classification models for ASD prediction. The works reported in the literature are very heterogeneous from the computational and methodological point of view. In this Thesis we carry out a comprehensive computational exploration of the impact of the choices involved while building these machine learning pipelines

Analysis of mass spectrometry data from the secretome of an explant model of articular cartilage exposed to pro-inflammatory and anti-inflammatory stimuli using machine learning

Background: Osteoarthritis (OA) is an inflammatory disease of synovial joints involving the loss and degeneration of articular cartilage. The gold standard for evaluating cartilage loss in OA is the measurement of joint space width on standard radiographs. However, in most cases the diagnosis is made well after the onset of the disease, when the symptoms are well established. Identification of early biomarkers of OA can facilitate earlier diagnosis, improve disease monitoring and predict responses to therapeutic interventions. Methods: This study describes the bioinformatic analysis of data generated from high throughput proteomics for identification of potential biomarkers of OA. The mass spectrometry data was generated using a canine explant model of articular cartilage treated with the pro-inflammatory cytokine interleukin 1 β (IL-1β). The bioinformatics analysis involved the application of machine learning and network analysis to the proteomic mass spectrometry data. A rule based machine learning technique, BioHEL, was used to create a model that classified the samples into their relevant treatment groups by identifying those proteins that separated samples into their respective groups. The proteins identified were considered to be potential biomarkers. Protein networks were also generated; from these networks, proteins pivotal to the classification were identified. Results: BioHEL correctly classified eighteen out of twenty-three samples, giving a classification accuracy of 78.3% for the dataset. The dataset included the four classes of control, IL-1β, carprofen, and IL-1β and carprofen together. This exceeded the other machine learners that were used for a comparison, on the same dataset, with the exception of another rule-based method, JRip, which performed equally well. The proteins that were most frequently used in rules generated by BioHEL were found to include a number of relevant proteins including matrix metalloproteinase 3, interleukin 8 and matrix gla protein. Conclusions: Using this protocol, combining an in vitro model of OA with bioinformatics analysis, a number of relevant extracellular matrix proteins were identified, thereby supporting the application of these bioinformatics tools for analysis of proteomic data from in vitro models of cartilage degradation

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)