Supervised Machine Learning Under Test-Time Resource Constraints: A Trade-off Between Accuracy and Cost

The past decade has witnessed how the field of machine learning has established itself as a necessary component in several multi-billion-dollar industries. The real-world industrial setting introduces an interesting new problem to machine learning research: computational resources must be budgeted and cost must be strictly accounted for during test-time. A typical problem is that if an application consumes x additional units of cost during test-time, but will improve accuracy by y percent, should the additional x resources be allocated? The core of this problem is a trade-off between accuracy and cost. In this thesis, we examine components of test-time cost, and develop different strategies to manage this trade-off. We first investigate test-time cost and discover that it typically consists of two parts: feature extraction cost and classifier evaluation cost. The former reflects the computational efforts of transforming data instances to feature vectors, and could be highly variable when features are heterogeneous. The latter reflects the effort of evaluating a classifier, which could be substantial, in particular nonparametric algorithms. We then propose three strategies to explicitly trade-off accuracy and the two components of test-time cost during classifier training. To budget the feature extraction cost, we first introduce two algorithms: GreedyMiser and Anytime Representation Learning (AFR). GreedyMiser employs a strategy that incorporates the extraction cost information during classifier training to explicitly minimize the test-time cost. AFR extends GreedyMiser to learn a cost-sensitive feature representation rather than a classifier, and turns traditional Support Vector Machines (SVM) into test- time cost-sensitive anytime classifiers. GreedyMiser and AFR are evaluated on two real-world data sets from two different application domains, and both achieve record performance. We then introduce Cost Sensitive Tree of Classifiers (CSTC) and Cost Sensitive Cascade of Classifiers (CSCC), which share a common strategy that trades-off the accuracy and the amortized test-time cost. CSTC introduces a tree structure and directs test inputs along different tree traversal paths, each is optimized for a specific sub-partition of the input space, extracting different, specialized subsets of features. CSCC extends CSTC and builds a linear cascade, instead of a tree, to cope with class-imbalanced binary classification tasks. Since both CSTC and CSCC extract different features for different inputs, the amortized test-time cost is greatly reduced while maintaining high accuracy. Both approaches out-perform the current state-of-the-art on real-world data sets. To trade-off accuracy and high classifier evaluation cost of nonparametric classifiers, we propose a model compression strategy and develop Compressed Vector Machines (CVM). CVM focuses on the nonparametric kernel Support Vector Machines (SVM), whose test-time evaluation cost is typically substantial when learned from large training sets. CVM is a post-processing algorithm which compresses the learned SVM model by reducing and optimizing support vectors. On several benchmark data sets, CVM maintains high test accuracy while reducing the test-time evaluation cost by several orders of magnitude

Deep Machine Learning with Spatio-Temporal Inference

Deep Machine Learning (DML) refers to methods which utilize hierarchies of more than one or two layers of computational elements to achieve learning. DML may draw upon biomemetic models, or may be simply biologically-inspired. Regardless, these architectures seek to employ hierarchical processing as means of mimicking the ability of the human brain to process a myriad of sensory data and make meaningful decisions based on this data. In this dissertation we present a novel DML architecture which is biologically-inspired in that (1) all processing is performed hierarchically; (2) all processing units are identical; and (3) processing captures both spatial and temporal dependencies in the observations to organize and extract features suitable for supervised learning. We call this architecture Deep Spatio-Temporal Inference Network (DeSTIN). In this framework, patterns observed in pixel data at the lowest layer of the hierarchy are organized and fit to generalizations using decomposition algorithms. Subsequent spatial layers draw upon previous layers, their own temporal observations and beliefs, and the observations and beliefs of parent nodes to extract features suitable for supervised learning using standard classifiers such as feedforward neural networks. Hence, DeSTIN is viewed as an unsupervised feature extraction scheme in the sense that rather than relying on human engineering to determine features for a particular problem, DeSTIN naturally constructs features of interest by representing salient regularities in the patterns observed. Detailed discussion and analysis of the DeSTIN framework is provided, including focus on its key components of generalization through online clustering and temporal inference. We present a variety of implementation details, including static and dynamic learning formulations, and function approximation methods. Results on standardized datasets of handwritten digits as well as face and optic nerve detection are presented, illustrating the efficacy of the proposed approach

Graph-Based Approaches to Protein StructureComparison - From Local to Global Similarity

The comparative analysis of protein structure data is a central aspect of structural bioinformatics. Drawing upon structural information allows the inference of function for unknown proteins even in cases where no apparent homology can be found on the sequence level. Regarding the function of an enzyme, the overall fold topology might less important than the specific structural conformation of the catalytic site or the surface region of a protein, where the interaction with other molecules, such as binding partners, substrates and ligands occurs. Thus, a comparison of these regions is especially interesting for functional inference, since structural constraints imposed by the demands of the catalyzed biochemical function make them more likely to exhibit structural similarity. Moreover, the comparative analysis of protein binding sites is of special interest in pharmaceutical chemistry, in order to predict cross-reactivities and gain a deeper understanding of the catalysis mechanism. From an algorithmic point of view, the comparison of structured data, or, more generally, complex objects, can be attempted based on different methodological principles. Global methods aim at comparing structures as a whole, while local methods transfer the problem to multiple comparisons of local substructures. In the context of protein structure analysis, it is not a priori clear, which strategy is more suitable. In this thesis, several conceptually different algorithmic approaches have been developed, based on local, global and semi-global strategies, for the task of comparing protein structure data, more specifically protein binding pockets. The use of graphs for the modeling of protein structure data has a long standing tradition in structural bioinformatics. Recently, graphs have been used to model the geometric constraints of protein binding sites. The algorithms developed in this thesis are based on this modeling concept, hence, from a computer scientist's point of view, they can also be regarded as global, local and semi-global approaches to graph comparison. The developed algorithms were mainly designed on the premise to allow for a more approximate comparison of protein binding sites, in order to account for the molecular flexibility of the protein structures. A main motivation was to allow for the detection of more remote similarities, which are not apparent by using more rigid methods. Subsequently, the developed approaches were applied to different problems typically encountered in the field of structural bioinformatics in order to assess and compare their performance and suitability for different problems. Each of the approaches developed during this work was capable of improving upon the performance of existing methods in the field. Another major aspect in the experiments was the question, which methodological concept, local, global or a combination of both, offers the most benefits for the specific task of protein binding site comparison, a question that is addressed throughout this thesis

Generative-Discriminative Low Rank Decomposition for Medical Imaging Applications

In this thesis, we propose a method that can be used to extract biomarkers from medical images toward early diagnosis of abnormalities. Surge of demand for biomarkers and availability of medical images in the recent years call for accurate, repeatable, and interpretable approaches for extracting meaningful imaging features. However, extracting such information from medical images is a challenging task because the number of pixels (voxels) in a typical image is in order of millions while even a large sample-size in medical image dataset does not usually exceed a few hundred. Nevertheless, depending on the nature of an abnormality, only a parsimonious subset of voxels is typically relevant to the disease; therefore various notions of sparsity are exploited in this thesis to improve the generalization performance of the prediction task. We propose a novel discriminative dimensionality reduction method that yields good classification performance on various datasets without compromising the clinical interpretability of the results. This is achieved by combining the modelling strength of generative learning framework and the classification performance of discriminative learning paradigm. Clinical interpretability can be viewed as an additional measure of evaluation and is also helpful in designing methods that account for the clinical prior such as association of certain areas in a brain to a particular cognitive task or connectivity of some brain regions via neural fibres. We formulate our method as a large-scale optimization problem to solve a constrained matrix factorization. Finding an optimal solution of the large-scale matrix factorization renders off-the-shelf solver computationally prohibitive; therefore, we designed an efficient algorithm based on the proximal method to address the computational bottle-neck of the optimization problem. Our formulation is readily extended for different scenarios such as cases where a large cohort of subjects has uncertain or no class labels (semi-supervised learning) or a case where each subject has a battery of imaging channels (multi-channel), \etc. We show that by using various notions of sparsity as feasible sets of the optimization problem, we can encode different forms of prior knowledge ranging from brain parcellation to brain connectivity

A hybrid algorithm for Bayesian network structure learning with application to multi-label learning

We present a novel hybrid algorithm for Bayesian network structure learning, called H2PC. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. The algorithm is based on divide-and-conquer constraint-based subroutines to learn the local structure around a target variable. We conduct two series of experimental comparisons of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning. First, we use eight well-known Bayesian network benchmarks with various data sizes to assess the quality of the learned structure returned by the algorithms. Our extensive experiments show that H2PC outperforms MMHC in terms of goodness of fit to new data and quality of the network structure with respect to the true dependence structure of the data. Second, we investigate H2PC's ability to solve the multi-label learning problem. We provide theoretical results to characterize and identify graphically the so-called minimal label powersets that appear as irreducible factors in the joint distribution under the faithfulness condition. The multi-label learning problem is then decomposed into a series of multi-class classification problems, where each multi-class variable encodes a label powerset. H2PC is shown to compare favorably to MMHC in terms of global classification accuracy over ten multi-label data sets covering different application domains. Overall, our experiments support the conclusions that local structural learning with H2PC in the form of local neighborhood induction is a theoretically well-motivated and empirically effective learning framework that is well suited to multi-label learning. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available.Comment: arXiv admin note: text overlap with arXiv:1101.5184 by other author