Bayesian mixed-effects inference on classification performance in hierarchical data sets

Classification algorithms are frequently used on data with a natural hierarchical structure. For instance, classifiers are often trained and tested on trial-wise measurements, separately for each subject within a group. One important question is how classification outcomes observed in individual subjects can be generalized to the population from which the group was sampled. To address this question, this paper introduces novel statistical models that are guided by three desiderata. First, all models explicitly respect the hierarchical nature of the data, that is, they are mixed-effects models that simultaneously account for within-subjects (fixed-effects) and across-subjects (random-effects) variance components. Second, maximum-likelihood estimation is replaced by full Bayesian inference in order to enable natural regularization of the estimation problem and to afford conclusions in terms of posterior probability statements. Third, inference on classification accuracy is complemented by inference on the balanced accuracy, which avoids inflated accuracy estimates for imbalanced data sets. We introduce hierarchical models that satisfy these criteria and demonstrate their advantages over conventional methods usingMCMC implementations for model inversion and model selection on both synthetic and empirical data. We envisage that our approach will improve the sensitivity and validity of statistical inference in future hierarchical classification studies. © 2012

Tree models: a Bayesian perspective

Submitted in partial fulfilment of the requirements for the degree of Master of Philosophy at Queen Mary, University of London, November 2006Classical tree models represent an attempt to create nonparametric models which have good predictive powers as well a simple structure readily comprehensible by non- experts. Bayesian tree models have been created by a team consisting of Chipman, George and McCulloch and second team consisting of Denison, Mallick and Smith. Both approaches employ Green's Reversible Jump Markov Chain Monte Carlo tech- nique to carry out a more e®ective search than the `greedy' methods used classically. The aim of this work is to evaluate both types of Bayesian tree models from a Bayesian perspective and compare them

Bayesian machine learning methods for predicting protein-peptide interactions and detecting mosaic structures in DNA sequences alignments

Short well-defined domains known as peptide recognition modules (PRMs) regulate many important protein-protein interactions involved in the formation of macromolecular complexes and biochemical pathways. High-throughput experiments like yeast two-hybrid and phage display are expensive and intrinsically noisy, therefore it would be desirable to target informative interactions and pursue in silico approaches. We propose a probabilistic discriminative approach for predicting PRM-mediated protein-protein interactions from sequence data. The model suffered from over-fitting, so Laplacian regularisation was found to be important in achieving a reasonable generalisation performance. A hybrid approach yielded the best performance, where the binding site motifs were initialised with the predictions of a generative model. We also propose another discriminative model which can be applied to all sequences present in the organism at a significantly lower computational cost. This is due to its additional assumption that the underlying binding sites tend to be similar.It is difficult to distinguish between the binding site motifs of the PRM due to the small number of instances of each binding site motif. However, closely related species are expected to share similar binding sites, which would be expected to be highly conserved. We investigated rate variation along DNA sequence alignments, modelling confounding effects such as recombination. Traditional approaches to phylogenetic inference assume that a single phylogenetic tree can represent the relationships and divergences between the taxa. However, taxa sequences exhibit varying levels of conservation, e.g. due to regulatory elements and active binding sites, and certain bacteria and viruses undergo interspecific recombination. We propose a phylogenetic factorial hidden Markov model to infer recombination and rate variation. We examined the performance of our model and inference scheme on various synthetic alignments, and compared it to state of the art breakpoint models. We investigated three DNA sequence alignments: one of maize actin genes, one bacterial (Neisseria), and the other of HIV-1. Inference is carried out in the Bayesian framework, using Reversible Jump Markov Chain Monte Carlo

PHYSTAT-LHC Workshop on Statistical Issues for LHC Physics

A PHYSTAT workshop on the topic of Statistical issues for LHC physics was held at CERN. The workshop focused on issues related to discovery that we hope will be relevant to the LHC. These proceedings contain written versions of nearly all the talks, several of which were given by professional statisticians. The talks varied from general overviews, to those describing searches for specific particles. The treatment of background uncertainties figured prominently. Many of the talks describing search strategies for new effects should be of interest not only to particle physicists but also to scientists in other fields

Advances and Applications of Dezert-Smarandache Theory (DSmT) for Information Fusion (Collected Works), Vol. 4

The fourth volume on Advances and Applications of Dezert-Smarandache Theory (DSmT) for information fusion collects theoretical and applied contributions of researchers working in different fields of applications and in mathematics. The contributions (see List of Articles published in this book, at the end of the volume) have been published or presented after disseminating the third volume (2009, http://fs.unm.edu/DSmT-book3.pdf) in international conferences, seminars, workshops and journals. First Part of this book presents the theoretical advancement of DSmT, dealing with Belief functions, conditioning and deconditioning, Analytic Hierarchy Process, Decision Making, Multi-Criteria, evidence theory, combination rule, evidence distance, conflicting belief, sources of evidences with different importance and reliabilities, importance of sources, pignistic probability transformation, Qualitative reasoning under uncertainty, Imprecise belief structures, 2-Tuple linguistic label, Electre Tri Method, hierarchical proportional redistribution, basic belief assignment, subjective probability measure, Smarandache codification, neutrosophic logic, Evidence theory, outranking methods, Dempster-Shafer Theory, Bayes fusion rule, frequentist probability, mean square error, controlling factor, optimal assignment solution, data association, Transferable Belief Model, and others. More applications of DSmT have emerged in the past years since the apparition of the third book of DSmT 2009. Subsequently, the second part of this volume is about applications of DSmT in correlation with Electronic Support Measures, belief function, sensor networks, Ground Moving Target and Multiple target tracking, Vehicle-Born Improvised Explosive Device, Belief Interacting Multiple Model filter, seismic and acoustic sensor, Support Vector Machines, Alarm classification, ability of human visual system, Uncertainty Representation and Reasoning Evaluation Framework, Threat Assessment, Handwritten Signature Verification, Automatic Aircraft Recognition, Dynamic Data-Driven Application System, adjustment of secure communication trust analysis, and so on. Finally, the third part presents a List of References related with DSmT published or presented along the years since its inception in 2004, chronologically ordered

Multivariate EEG feature analysis and its application on brain death determination and brain computer interface

埼玉工業大学201

Effective techniques for handling incomplete data using decision trees

Decision Trees (DTs) have been recognized as one of the most successful formalisms for knowledge representation and reasoning and are currently applied to a variety of data mining or knowledge discovery applications, particularly for classification problems. There are several efficient methods to learn a DT from data. However, these methods are often limited to the assumption that data are complete. In this thesis, some contributions to the field of machine learning and statistics that solve the problem of extracting DTs for learning and classification tasks from incomplete databases are presented. The methodology underlying the thesis blends together well-established statistical theories with the most advanced techniques for machine learning and automated reasoning with uncertainty. The first contribution is the extensive simulations which study the impact of missing data on predictive accuracy of existing DTs which can cope with missing values, when missing values are in both the training and test sets or when they are in either of the two sets. All simulations are performed under missing completely at random, missing at random and informatively missing mechanisms and for different missing data patterns and proportions. The proposal of a simple, novel, yet effective proposed procedure for training and testing using decision trees in the presence of missing data is the next contribution. Original and simple splitting criteria for attribute selection in tree building are put forward. The proposed technique is evaluated and validated in empirical tests over many real world application domains. In this work, the proposed algorithm maintains (sometimes exceeds) the outstanding accuracy of multiple imputation, especially on datasets containing mixed attributes and purely nominal attributes. Also, the proposed algorithm greatly improves in accuracy for IM data. Another major advantage of this method over multiple imputation is the important saving in computational resources due to it simplicity. The next contribution is the proposal of three versions of simple probabilistic techniques that could be used for classifying incomplete vectors using decision trees based on complete data. The proposed procedure is superficially similar to that of fractional cases but more effective. The experimental results demonstrate that these approaches can achieve comparative quality to sophisticated algorithms like multiple imputation and therefore are applicable to all kinds of datasets. Finally, novel uses of two proposed ensemble procedures for handling incomplete training and test data are proposed and discussed. The algorithms combine the two best approaches either with resampling (REMIMIA) or without resampling (EMIMIA) of the training data before growing the decision trees. Experiments are used to evaluate and validate the success of the proposed ensemble methods with respect to individual missing data techniques in the form of empirical tests. EMIMIA attains the highest overall level of prediction accuracy

Deep Learning for Abstraction, Control and Monitoring of Complex Cyber-Physical Systems

Cyber-Physical Systems (CPS) consist of digital devices that interact with some physical components. Their popularity and complexity are growing exponentially, giving birth to new, previously unexplored, safety-critical application domains. As CPS permeate our daily lives, it becomes imperative to reason about their reliability. Formal methods provide rigorous techniques for verification, control and synthesis of safe and reliable CPS. However, these methods do not scale with the complexity of the system, thus their applicability to real-world problems is limited. A promising strategy is to leverage deep learning techniques to tackle the scalability issue of formal methods, transforming unfeasible problems into approximately solvable ones. The approximate models are trained over observations which are solutions of the formal problem. In this thesis, we focus on the following tasks, which are computationally challenging: the modeling and the simulation of a complex stochastic model, the design of a safe and robust control policy for a system acting in a highly uncertain environment and the runtime verification problem under full or partial observability. Our approaches, based on deep learning, are indeed applicable to real-world complex and safety-critical systems acting under strict real-time constraints and in presence of a significant amount of uncertainty.Cyber-Physical Systems (CPS) consist of digital devices that interact with some physical components. Their popularity and complexity are growing exponentially, giving birth to new, previously unexplored, safety-critical application domains. As CPS permeate our daily lives, it becomes imperative to reason about their reliability. Formal methods provide rigorous techniques for verification, control and synthesis of safe and reliable CPS. However, these methods do not scale with the complexity of the system, thus their applicability to real-world problems is limited. A promising strategy is to leverage deep learning techniques to tackle the scalability issue of formal methods, transforming unfeasible problems into approximately solvable ones. The approximate models are trained over observations which are solutions of the formal problem. In this thesis, we focus on the following tasks, which are computationally challenging: the modeling and the simulation of a complex stochastic model, the design of a safe and robust control policy for a system acting in a highly uncertain environment and the runtime verification problem under full or partial observability. Our approaches, based on deep learning, are indeed applicable to real-world complex and safety-critical systems acting under strict real-time constraints and in presence of a significant amount of uncertainty

Speaker Recognition in Unconstrained Environments

Speaker recognition is applied in smart home devices, interactive voice response systems, call centers, online banking and payment solutions as well as in forensic scenarios. This dissertation is concerned with speaker recognition systems in unconstrained environments. Before this dissertation, research on making better decisions in unconstrained environments was insufficient. Aside from decision making, unconstrained environments imply two other subjects: security and privacy. Within the scope of this dissertation, these research subjects are regarded as both security against short-term replay attacks and privacy preservation within state-of-the-art biometric voice comparators in the light of a potential leak of biometric data. The aforementioned research subjects are united in this dissertation to sustain good decision making processes facing uncertainty from varying signal quality and to strengthen security as well as preserve privacy. Conventionally, biometric comparators are trained to classify between mated and non-mated reference,--,probe pairs under idealistic conditions but are expected to operate well in the real world. However, the more the voice signal quality degrades, the more erroneous decisions are made. The severity of their impact depends on the requirements of a biometric application. In this dissertation, quality estimates are proposed and employed for the purpose of making better decisions on average in a formalized way (quantitative method), while the specifications of decision requirements of a biometric application remain unknown. By using the Bayesian decision framework, the specification of application-depending decision requirements is formalized, outlining operating points: the decision thresholds. The assessed quality conditions combine ambient and biometric noise, both of which occurring in commercial as well as in forensic application scenarios. Dual-use (civil and governmental) technology is investigated. As it seems unfeasible to train systems for every possible signal degradation, a low amount of quality conditions is used. After examining the impact of degrading signal quality on biometric feature extraction, the extraction is assumed ideal in order to conduct a fair benchmark. This dissertation proposes and investigates methods for propagating information about quality to decision making. By employing quality estimates, a biometric system's output (comparison scores) is normalized in order to ensure that each score encodes the least-favorable decision trade-off in its value. Application development is segregated from requirement specification. Furthermore, class discrimination and score calibration performance is improved over all decision requirements for real world applications. In contrast to the ISOIEC 19795-1:2006 standard on biometric performance (error rates), this dissertation is based on biometric inference for probabilistic decision making (subject to prior probabilities and cost terms). This dissertation elaborates on the paradigm shift from requirements by error rates to requirements by beliefs in priors and costs. Binary decision error trade-off plots are proposed, interrelating error rates with prior and cost beliefs, i.e., formalized decision requirements. Verbal tags are introduced to summarize categories of least-favorable decisions: the plot's canvas follows from Bayesian decision theory. Empirical error rates are plotted, encoding categories of decision trade-offs by line styles. Performance is visualized in the latent decision subspace for evaluating empirical performance regarding changes in prior and cost based decision requirements. Security against short-term audio replay attacks (a collage of sound units such as phonemes and syllables) is strengthened. The unit-selection attack is posed by the ASVspoof 2015 challenge (English speech data), representing the most difficult to detect voice presentation attack of this challenge. In this dissertation, unit-selection attacks are created for German speech data, where support vector machine and Gaussian mixture model classifiers are trained to detect collage edges in speech representations based on wavelet and Fourier analyses. Competitive results are reached compared to the challenged submissions. Homomorphic encryption is proposed to preserve the privacy of biometric information in the case of database leakage. In this dissertation, log-likelihood ratio scores, representing biometric evidence objectively, are computed in the latent biometric subspace. Conventional comparators rely on the feature extraction to ideally represent biometric information, latent subspace comparators are trained to find ideal representations of the biometric information in voice reference and probe samples to be compared. Two protocols are proposed for the the two-covariance comparison model, a special case of probabilistic linear discriminant analysis. Log-likelihood ratio scores are computed in the encrypted domain based on encrypted representations of the biometric reference and probe. As a consequence, the biometric information conveyed in voice samples is, in contrast to many existing protection schemes, stored protected and without information loss. The first protocol preserves privacy of end-users, requiring one public/private key pair per biometric application. The latter protocol preserves privacy of end-users and comparator vendors with two key pairs. Comparators estimate the biometric evidence in the latent subspace, such that the subspace model requires data protection as well. In both protocols, log-likelihood ratio based decision making meets the requirements of the ISOIEC 24745:2011 biometric information protection standard in terms of unlinkability, irreversibility, and renewability properties of the protected voice data