Tree structures are ubiquitous in data across many domains, and many datasets are naturally modelled by unobserved tree structures. In this paper, first we review the theory of random fragmentation processes [Bertoin, 2006], and a number of existing methods for modelling trees, including the popular nested Chinese restaurant process (nCRP). Then we define a general class of probability distributions over trees: the Dirichlet fragmentation process (DFP) through a novel combination of the theory of Dirichlet processes and random fragmentation processes. This DFP presents a stick-breaking construction, and relates to the nCRP in the same way the Dirichlet process relates to the Chinese restaurant process. Furthermore, we develop a novel hierarchical mixture model with the DFP, and empirically compare the new model to similar models in machine learning. Experiments show the DFP mixture model to be convincingly better than existing state-of-the-art approaches for hierarchical clustering and density modelling. The process of random fragmentation is common to many areas, such as the degradation of large polymer chains in chemistry, or the evolution of phylogenetic trees in biology. An elegant mathematical tool for describing such phenomena is the fragmentation process (FP) [Bertoin, 2006]. As a concrete example of a FP, consider a stick of unit length.

Traditional Kalman filter (KF) is derived under the well-known minimum mean square error (MMSE) criterion, which is optimal under Gaussian assumption. However, when the signals are non-Gaussian, especially when the system is disturbed by some heavy-tailed impulsive noises, the performance of KF will deteriorate seriously. To improve the robustness of KF against impulsive noises, we propose in this work a new Kalman filter, called the maximum correntropy Kalman filter (MCKF), which adopts the robust maximum correntropy criterion (MCC) as the optimality criterion, instead of using the MMSE. Similar to the traditional KF, the state mean and covariance matrix propagation equations are used to give prior estimations of the state and covariance matrix in MCKF. A novel fixed-point algorithm is then used to update the posterior estimations. A sufficient condition that guarantees the convergence of the fixed-point algorithm is given. Illustration examples are presented to demonstrate the effectiveness and robustness of the new algorithm.

We study the restless bandit associated with an extremely simple scalar Kalman filter model in discrete time. Under certain assumptions, we prove that the problem is indexable in the sense that the Whittle index is a non-decreasing function of the relevant belief state. In spite of the long history of this problem, this appears to be the first such proof. We use results about Schur-convexity and mechanical words, which are particular binary strings intimately related to palindromes.

Consider a classification problem where we do not have access to labels for individual training examples, but only have average labels over subpopulations. We give practical examples of this setup and show how such a classification task can usefully be analyzed as a weakly supervised clustering problem. We propose three approaches to solving the weakly supervised clustering problem, including a latent variables model that performs well in our experiments. We illustrate our methods on an analysis of aggregated elections data and an industry data set that was the original motivation for this research.

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.

The Singleton Property (SP) approach has been proposed for representing and querying metadata about RDF triples such as provenance, time, location, and evidence. In this approach, one singleton property is created to uniquely represent a relationship in a particular context, and in general, generates a large property hierarchy in the schema. It has become the subject of important questions from Semantic Web practitioners. Can an existing reasoner recognize the singleton property triples? And how? If the singleton property triples describe a data triple, then how can a reasoner infer this data triple from the singleton property triples? Or would the large property hierarchy affect the reasoners in some way? We address these questions in this paper and present our study about the reasoning aspects of the singleton properties. We propose a simple mechanism to enable existing reasoners to recognize the singleton property triples, as well as to infer the data triples described by the singleton property triples. We evaluate the effect of the singleton property triples in the reasoning processes by comparing the performance on RDF datasets with and without singleton properties. Our evaluation uses as benchmark the LUBM datasets and the LUBM-SP datasets derived from LUBM with temporal information added through singleton properties.

Characterizing the phase transitions of convex optimizations in recovering structured signals or data is of central importance in compressed sensing, machine learning and statistics. The phase transitions of many convex optimization signal recovery methods such as $\ell_1$ minimization and nuclear norm minimization are well understood through recent years' research. However, rigorously characterizing the phase transition of total variation (TV) minimization in recovering sparse-gradient signal is still open. In this paper, we fully characterize the phase transition curve of the TV minimization. Our proof builds on Donoho, Johnstone and Montanari's conjectured phase transition curve for the TV approximate message passing algorithm (AMP), together with the linkage between the minmax Mean Square Error of a denoising problem and the high-dimensional convex geometry for TV minimization.

In the Bayesian Reinforcement Learning (BRL) setting, agents try to maximise the collected rewards while interacting with their environment while using some prior knowledge that is accessed beforehand. Many BRL algorithms have already been proposed, but even though a few toy examples exist in the literature, there are still no extensive or rigorous benchmarks to compare them. The paper addresses this problem, and provides a new BRL comparison methodology along with the corresponding open source library. In this methodology, a comparison criterion that measures the performance of algorithms on large sets of Markov Decision Processes (MDPs) drawn from some probability distributions is defined. In order to enable the comparison of non-anytime algorithms, our methodology also includes a detailed analysis of the computation time requirement of each algorithm. Our library is released with all source code and documentation: it includes three test problems, each of which has two different prior distributions, and seven state-of-the-art RL algorithms. Finally, our library is illustrated by comparing all the available algorithms and the results are discussed.

Entity resolution (ER) is the task of identifying records belonging to the same entity (e.g. individual, group) across one or multiple databases. Ironically, it has multiple names: deduplication and record linkage, among others. In this paper we survey metrics used to evaluate ER results in order to iteratively improve performance and guarantee sufficient quality prior to deployment. Some of these metrics are borrowed from multi-class classification and clustering domains, though some key differences exist differentiating entity resolution from general clustering. Menestrina et al. empirically showed rankings from these metrics often conflict with each other, thus our primary motivation for studying them. This paper provides practitioners the basic knowledge to begin evaluating their entity resolution results.

Objective: Anemia is a frequent comorbidity in hemodialysis patients that can be successfully treated by administering erythropoiesis-stimulating agents (ESAs). ESAs dosing is currently based on clinical protocols that often do not account for the high inter- and intra-individual variability in the patient's response. As a result, the hemoglobin level of some patients oscillates around the target range, which is associated with multiple risks and side-effects. This work proposes a methodology based on reinforcement learning (RL) to optimize ESA therapy. Methods: RL is a data-driven approach for solving sequential decision-making problems that are formulated as Markov decision processes (MDPs). Computing optimal drug administration strategies for chronic diseases is a sequential decision-making problem in which the goal is to find the best sequence of drug doses. MDPs are particularly suitable for modeling these problems due to their ability to capture the uncertainty associated with the outcome of the treatment and the stochastic nature of the underlying process. The RL algorithm employed in the proposed methodology is fitted Q iteration, which stands out for its ability to make an efficient use of data. Results: The experiments reported here are based on a computational model that describes the effect of ESAs on the hemoglobin level. The performance of the proposed method is evaluated and compared with the well-known Q-learning algorithm and with a standard protocol. Simulation results show that the performance of Q-learning is substantially lower than FQI and the protocol. Conclusion: Although prospective validation is required, promising results demonstrate the potential of RL to become an alternative to current protocols.