MOTIVATION: In recent years, gene expression studies have increasingly made use of high-throughput sequencing technology. In turn, research concerning the appropriate statistical methods for the analysis of digital gene expression (DGE) has flourished, primarily in the context of normalization and differential analysis. RESULTS: In this work, we focus on the question of clustering DGE profiles as a means to discover groups of co-expressed genes. We propose a Poisson mixture model using a rigorous framework for parameter estimation as well as the choice of the appropriate number of clusters. We illustrate co-expression analyses using our approach on two real RNA-seq datasets. A set of simulation studies also compares the performance of the proposed model with that of several related approaches developed to cluster RNA-seq or serial analysis of gene expression data. AVAILABILITY AND AND IMPLEMENTATION: The proposed method is implemented in the open-source R package HTSCluster, available on CRAN. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: RNA sequencing is now widely performed to study differential expression among experimental conditions. As tests are performed on a large number of genes, stringent false-discovery rate control is required at the expense of detection power. Ad hoc filtering techniques are regularly used to moderate this correction by removing genes with low signal, with little attention paid to their impact on downstream analyses. RESULTS: We propose a data-driven method based on the Jaccard similarity index to calculate a filtering threshold for replicated RNA sequencing data. In comparisons with alternative data filters regularly used in practice, we demonstrate the effectiveness of our proposed method to correctly filter lowly expressed genes, leading to increased detection power for moderately to highly expressed genes. Interestingly, this data-driven threshold varies among experiments, highlighting the interest of the method proposed here. AVAILABILITY: The proposed filtering method is implemented in the R package HTSFilter available on Bioconductor.

This paper is concerned with the selection of a generative model for supervised classification. Classical criteria for model selection assess the fit of a model rather than its ability to produce a low classification error rate. A new criterion, the Bayesian Entropy Criterion (BEC), is proposed. This criterion takes into account the decisional purpose of a model by minimizing the integrated classification entropy. It provides an interesting alternative to the cross-validated error rate which is computationally expensive. The asymptotic behavior of the BEC criterion is presented. Numerical experiments on both simulated and real data sets show that BEC performs better than the BIC criterion to select a model minimizing the classification error rate and provides analogous performance to the cross-validated error rate.

UTOMATED video surveillance addresses real-time observation of people and vehicles within a busy environment, leading to a description of their actions and interactions. The technical issues include moving object detection and tracking, object classification, human motion analysis, and activity understanding, touching on many of the core topics of computer vision, pattern analysis, and aritificial intelligence. Video surveillance has spawned large research projects in the United States, Europe, and Japan, and has been the topic of several international conferences and workshops in recent years. There are immediate needs for automated surveillance systems in commercial, law enforcement, and military applications. Mounting video cameras is cheap, but finding available human resources to observe the output is expensive. Although surveillance cameras are already prevalent in banks, stores, and parking lots, video data currently is used only “after the fact” as a forensic tool, thus losing its primary benefit as an active, real-time medium. What is needed is continuous 24-hour monitoring of surveillance video to alert security officers to a burglary in progress or to a suspicious individual loitering in the parking lot, while there is still time to prevent the crime. In addition to the obvious security applications, video surveillance technology has been proposed to measure traffic flow, detect accidents on highways, monitor pedestrian congestion in public spaces, compile consumer demographics in shopping malls and amusement parks, log routine maintainence tasks at nuclear facilities, and count endangered species. The numerous military applications include patrolling national borders, measuring the flow of refugees in troubled areas, monitoring peace treaties, and providing secure perimeters around bases and embassies. The 11 papers in this special section illustrate topics and techniques at the forefront of video surveillance research. These papers can be loosely organized into three categories. Detection and tracking involves real-time extraction of moving objects from video and continuous tracking over time to form persistent object trajectories. C. Stauffer and W.E.L. Grimson introduce unsupervised statistical learning techniques to cluster object trajectories produced by adaptive background subtraction into descriptions of normal scene activity. Viewpoint-specific trajectory descriptions from multiple cameras are combined into a common scene coordinate system using a calibration technique described by L. Lee, R. Romano, and G. Stein, who automatically determine the relative exterior orientation of overlapping camera views by observing a sparse set of moving objects on flat terrain. Two papers address the accumulation of noisy motion evidence over time. R. Pless, T. Brodský, and Y. Aloimonos detect and track small objects in aerial video sequences by first compensating for the self-motion of the aircraft, then accumulating residual normal flow to acquire evidence of independent object motion. L. Wixson notes that motion in the image does not always signify purposeful travel by an independently moving object (examples of such “motion clutter” are wind-blown tree branches and sun reflections off rippling water) and devises a flow-based salience measure to highlight objects that tend to move in a consistent direction over time. Human motion analysis is concerned with detecting periodic motion signifying a human gait and acquiring descriptions of human body pose over time. R. Cutler and L.S. Davis plot an object’s self-similarity across all pairs of frames to form distinctive patterns that classify bipedal, quadripedal, and rigid object motion. Y. Ricquebourg and P. Bouthemy track apparent contours in XT slices of an XYT sequence volume to robustly delineate and track articulated human body structure. I. Haritaoglu, D. Harwood, and L.S. Davis present W4, a surveillance system specialized to the task of looking at people. The W4 system can locate people and segment their body parts, build simple appearance models for tracking, disambiguate between and separately track multiple individuals in a group, and detect carried objects such as boxes and backpacks. Activity analysis deals with parsing temporal sequences of object observations to produce high-level descriptions of agent actions and multiagent interactions. In our opinion, this will be the most important area of future research in video surveillance. N.M. Oliver, B. Rosario, and A.P. Pentland introduce Coupled Hidden Markov Models (CHMMs) to detect and classify interactions consisting of two interleaved agent action streams and present a training method based on synthetic agents to address the problem of parameter estimation from limited real-world training examples. M. Brand and V. Kettnaker present an entropyminimization approach to estimating HMM topology and