Browsing by Author "Akova, Ferit"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    A non-parametric Bayesian model for joint cell clustering and cluster matching: identification of anomalous sample phenotypes with random effects
    (Springer (Biomed Central Ltd.), 2014) Dundar, Murat; Akova, Ferit; Yerebakan, Halid Z.; Rajwa, Bartek; Department of Computer & Information Science, School of Science
    BACKGROUND: Flow cytometry (FC)-based computer-aided diagnostics is an emerging technique utilizing modern multiparametric cytometry systems.The major difficulty in using machine-learning approaches for classification of FC data arises from limited access to a wide variety of anomalous samples for training. In consequence, any learning with an abundance of normal cases and a limited set of specific anomalous cases is biased towards the types of anomalies represented in the training set. Such models do not accurately identify anomalies, whether previously known or unknown, that may exist in future samples tested. Although one-class classifiers trained using only normal cases would avoid such a bias, robust sample characterization is critical for a generalizable model. Owing to sample heterogeneity and instrumental variability, arbitrary characterization of samples usually introduces feature noise that may lead to poor predictive performance. Herein, we present a non-parametric Bayesian algorithm called ASPIRE (anomalous sample phenotype identification with random effects) that identifies phenotypic differences across a batch of samples in the presence of random effects. Our approach involves simultaneous clustering of cellular measurements in individual samples and matching of discovered clusters across all samples in order to recover global clusters using probabilistic sampling techniques in a systematic way. RESULTS: We demonstrate the performance of the proposed method in identifying anomalous samples in two different FC data sets, one of which represents a set of samples including acute myeloid leukemia (AML) cases, and the other a generic 5-parameter peripheral-blood immunophenotyping. Results are evaluated in terms of the area under the receiver operating characteristics curve (AUC). ASPIRE achieved AUCs of 0.99 and 1.0 on the AML and generic blood immunophenotyping data sets, respectively. CONCLUSIONS: These results demonstrate that anomalous samples can be identified by ASPIRE with almost perfect accuracy without a priori access to samples of anomalous subtypes in the training set. The ASPIRE approach is unique in its ability to form generalizations regarding normal and anomalous states given only very weak assumptions regarding sample characteristics and origin. Thus, ASPIRE could become highly instrumental in providing unique insights about observed biological phenomena in the absence of full information about the investigated samples.
  • Thumbnail Image
    Item
    A nonparametric Bayesian perspective for machine learning in partially-observed settings
    (2014-07-31) Akova, Ferit; Dundar, Mehmet Murat; Qi, Yuan Alan
    Robustness and generalizability of supervised learning algorithms depend on the quality of the labeled data set in representing the real-life problem. In many real-world domains, however, we may not have full knowledge of the underlying data-generating mechanism, which may even have an evolving nature introducing new classes continually. This constitutes a partially-observed setting, where it would be impractical to obtain a labeled data set exhaustively defined by a fixed set of classes. Traditional supervised learning algorithms, assuming an exhaustive training library, would misclassify a future sample of an unobserved class with probability one, leading to an ill-defined classification problem. Our goal is to address situations where such assumption is violated by a non-exhaustive training library, which is a very realistic yet an overlooked issue in supervised learning. In this dissertation we pursue a new direction for supervised learning by defining self-adjusting models to relax the fixed model assumption imposed on classes and their distributions. We let the model adapt itself to the prospective data by dynamically adding new classes/components as data demand, which in turn gradually make the model more representative of the entire population. In this framework, we first employ suitably chosen nonparametric priors to model class distributions for observed as well as unobserved classes and then, utilize new inference methods to classify samples from observed classes and discover/model novel classes for those from unobserved classes. This thesis presents the initiating steps of an ongoing effort to address one of the most overlooked bottlenecks in supervised learning and indicates the potential for taking new perspectives in some of the most heavily studied areas of machine learning: novelty detection, online class discovery and semi-supervised learning.