Partially-Hidden Markov Models.

International audienceThis paper addresses the problem of Hidden Markov Models (HMM) training and inference when the training data are composed of feature vectors plus uncertain and imprecise labels. The "soft" labels represent partial knowledge about the possible states at each time step and the "softness" is encoded by belief functions. For the obtained model, called a Partially-Hidden Markov Model (PHMM), the training algorithm is based on the Evidential Expectation-Maximisation (E2M) algorithm. The usual HMM model is recovered when the belief functions are vacuous and the obtained model includes supervised, unsupervised and semi-supervised learning as special cases

Partially hidden Markov models for privacy-preserving modeling of indoor trajectories

Markov models are natural tools for modeling trajectories, following the principle that recent location history is predictive of near-future directions. In this work we study Markov models for describing and predicting human movement in indoor spaces, with the goal of modeling the movement on a coarse scale to protect the privacy of the individuals. Modern positioning devices, however, provide location information on a much more finer scale. To utilize this additional information we develop a novel family of partially hidden Markov models that couple each observed state with an auxiliary side information vector characterizing the movement within the coarse grid cell. We implement the model as a non-parametric Bayesian model and demonstrate it on real-world trajectory data collected in a hypermarket.Peer reviewe

Human activity learning and segmentation using partially hidden discriminative models

Learning and understanding the typical patterns in the daily activities and routines of people from low-level sensory data is an important problem in many application domains such as building smart environments, or providing intelligent assistance. Traditional approaches to this problem typically rely on supervised learning and generative models such as the hidden Markov models and its extensions. While activity data can be readily acquired from pervasive sensors, e.g. in smart environments, providing manual labels to support supervised training is often extremely expensive. In this paper, we propose a new approach based on semi-supervised training of partially hidden discriminative models such as the conditional random field (CRF) and the maximum entropy Markov model (MEMM). We show that these models allow us to incorporate both labeled and unlabeled data for learning, and at the same time, provide us with the flexibility and accuracy of the discriminative framework. Our experimental results in the video surveillance domain illustrate that these models can perform better than their generative counterpart, the partially hidden Markov model, even when a substantial amount of labels are unavailable.<br /

Computational identification and analysis of noncoding RNAs - Unearthing the buried treasures in the genome

The central dogma of molecular biology states that the genetic information flows from DNA to RNA to protein. This dogma has exerted a substantial influence on our understanding of the genetic activities in the cells. Under this influence, the prevailing assumption until the recent past was that genes are basically repositories for protein coding information, and proteins are responsible for most of the important biological functions in all cells. In the meanwhile, the importance of RNAs has remained rather obscure, and RNA was mainly viewed as a passive intermediary that bridges the gap between DNA and protein. Except for classic examples such as tRNAs (transfer RNAs) and rRNAs (ribosomal RNAs), functional noncoding RNAs were considered to be rare. However, this view has experienced a dramatic change during the last decade, as systematic screening of various genomes identified myriads of noncoding RNAs (ncRNAs), which are RNA molecules that function without being translated into proteins [11], [40]. It has been realized that many ncRNAs play important roles in various biological processes. As RNAs can interact with other RNAs and DNAs in a sequence-specific manner, they are especially useful in tasks that require highly specific nucleotide recognition [11]. Good examples are the miRNAs (microRNAs) that regulate gene expression by targeting mRNAs (messenger RNAs) [4], [20], and the siRNAs (small interfering RNAs) that take part in the RNAi (RNA interference) pathways for gene silencing [29], [30]. Recent developments show that ncRNAs are extensively involved in many gene regulatory mechanisms [14], [17]. The roles of ncRNAs known to this day are truly diverse. These include transcription and translation control, chromosome replication, RNA processing and modification, and protein degradation and translocation [40], just to name a few. These days, it is even claimed that ncRNAs dominate the genomic output of the higher organisms such as mammals, and it is being suggested that the greater portion of their genome (which does not encode proteins) is dedicated to the control and regulation of cell development [27]. As more and more evidence piles up, greater attention is paid to ncRNAs, which have been neglected for a long time. Researchers began to realize that the vast majority of the genome that was regarded as “junk,” mainly because it was not well understood, may indeed hold the key for the best kept secrets in life, such as the mechanism of alternative splicing, the control of epigenetic variations and so forth [27]. The complete range and extent of the role of ncRNAs are not so obvious at this point, but it is certain that a comprehensive understanding of cellular processes is not possible without understanding the functions of ncRNAs [47]

Active Learning with Multiple Views

Active learners alleviate the burden of labeling large amounts of data by detecting and asking the user to label only the most informative examples in the domain. We focus here on active learning for multi-view domains, in which there are several disjoint subsets of features (views), each of which is sufficient to learn the target concept. In this paper we make several contributions. First, we introduce Co-Testing, which is the first approach to multi-view active learning. Second, we extend the multi-view learning framework by also exploiting weak views, which are adequate only for learning a concept that is more general/specific than the target concept. Finally, we empirically show that Co-Testing outperforms existing active learners on a variety of real world domains such as wrapper induction, Web page classification, advertisement removal, and discourse tree parsing

Health Assessment of Composite Structures in Unconstrained Environments Using Partially Supervised Pattern Recognition Tools.

International audienceThe health assessment of composite structures from acoustic emission data is generally tackled by the use of clustering techniques. In this paper, the K-means clustering and the newly proposed Partially-Hidden Markov Model (PHMM) are exploited to analyse the data collected during mechanical tests on composite structures. The health assessment considered in this paper is made difficult by working in unconstrained environments. The presence of the noise is illustrated in several examples and is shown to distort strongly the results of clustering. A solution is proposed to filter out the noisy partition provided by the clustering methods. After filtering, the PHMM provides results which appeared closer to the expectations than the K-means. The PHMM offers the possibility to use uncertain and imprecise labels on the possible states, and thus covers supervised and unsupervised learning as special cases which makes it suitable for real applications