Robust graphical modeling of gene networks using classical and alternative T-distributions

Graphical Gaussian models have proven to be useful tools for exploring network structures based on multivariate data. Applications to studies of gene expression have generated substantial interest in these models, and resulting recent progress includes the development of fitting methodology involving penalization of the likelihood function. In this paper we advocate the use of multivariate $t$-distributions for more robust inference of graphs. In particular, we demonstrate that penalized likelihood inference combined with an application of the EM algorithm provides a computationally efficient approach to model selection in the $t$-distribution case. We consider two versions of multivariate $t$-distributions, one of which requires the use of approximation techniques. For this distribution, we describe a Markov chain Monte Carlo EM algorithm based on a Gibbs sampler as well as a simple variational approximation that makes the resulting method feasible in large problems.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS410 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Reviving dormant ties in an online social network experiment

Social network users connect and interact with one another to fulfil different kinds of social and information needs. When interaction ceases between two users, we say that their tie becomes dormant. While there are different underlying rea-sons of dormant ties, it is important to find means to revive such ties so as to maintain vibrancy in the relationships. In this work, we thus focus on designing an online experiment to evaluate the effectiveness of personalized social messages to revive dormant ties. The experiment carefully selects users with dormant ties so that each user does not get mixed treat-ments and be affected by the responses of other users un-dergoing treatment. Our results show that personalized mes-sage content plays an important part in reviving dormant ties. Specifically, we find the message containing friend’s recent activity information is more effective than that containing inter-friend activity information. We observe that the quality of engagement of at least 50 % of the revived ties can effec-tively be restored to the level before the ties become dormant. We also observe that it is easier to revive dormant ties that involve users from the same country but not users with the same and different gender

Predicting response in mobile advertising with Hierarchical Importance-Aware Factorization Machine

Mobile advertising has recently seen dramatic growth, fu-eled by the global proliferation of mobile phones and devices. The task of predicting ad response is thus crucial for maxi-mizing business revenue. However, ad response data change dynamically over time, and are subject to cold-start situ-ations in which limited history hinders reliable prediction

Six Degrees of Francis Bacon: A Statistical Method for Reconstructing Large Historical Social Networks

In this paper we present a statistical method for inferring historical social networks from biographical documents as well as the scholarly aims for doing so. Existing scholarship on historical social networks is scattered across an unmanageable number of disparate books and articles. A researcher interested in how persons were connected to one another in our field of study, early modern Britain (c. 1500-1700), has no global, unified resource to which to turn. Manually building such a network is infeasible, since it would need to represent thousands of nodes and tens of millions of potential edges just to include the relations among the most prominent persons of the period. Our Six Degrees of Francis Bacon project takes up recent statistical techniques and digital tools to reconstruct and visualize the early modern social network. We describe in this paper the natural language processing tools and statistical graph learning techniques that we used to extract names and infer relations from the Oxford Dictionary of National Biography. We then explain the steps taken to test inferred relations against the knowledge of experts in order to improve the accuracy of the learning techniques. Our argument here is twofold: first, that the results of this process, a global visualization of Britain’s early modern social network, will be useful to scholars and students of the period; second, that the pipeline we have developed can, with local modifications, be reused by other scholars to generate networks for other historical or contemporary societies from biographical documents

Bovine Necrotic Vulvovaginitis Associated with Porphyromonas levii

An outbreak of bovine necrotic vulvovaginitis associated with Porphyromonas levii, an emerging animal and human pathogen, affected 32 cows on a dairy farm in the northeast of Israel. Five animals had to be culled. This report appears to be the first that associates P. levii with bovine necrotic vulvovagnitis

Detecting click fraud in online advertising: A data mining approach

National Research Foundation (NRF) Singapore under International Research Centres in Singapore Funding InitiativeSubmit request for dataset at https://larc.smu.edu.sg/buzzcity-mobile-advertisement-dataset</p

Structural covariance of the ventral visual stream predicts posttraumatic intrusion and nightmare symptoms: a multivariate data fusion analysis

Visual components of trauma memories are often vividly re-experienced by survivors with deleterious consequences for normal function. Neuroimaging research on trauma has primarily focused on threat-processing circuitry as core to trauma-related dysfunction. Conversely, limited attention has been given to visual circuitry which may be particularly relevant to posttraumatic stress disorder (PTSD). Prior work suggests that the ventral visual stream is directly related to the cognitive and affective disturbances observed in PTSD and may be predictive of later symptom expression. The present study used multimodal magnetic resonance imaging data (n = 278) collected two weeks after trauma exposure from the AURORA study, a longitudinal, multisite investigation of adverse posttraumatic neuropsychiatric sequelae. Indices of gray and white matter were combined using data fusion to identify a structural covariance network (SCN) of the ventral visual stream 2 weeks after trauma. Participant\u27s loadings on the SCN were positively associated with both intrusion symptoms and intensity of nightmares. Further, SCN loadings moderated connectivity between a previously observed amygdala-hippocampal functional covariance network and the inferior temporal gyrus. Follow-up MRI data at 6 months showed an inverse relationship between SCN loadings and negative alterations in cognition in mood. Further, individuals who showed decreased strength of the SCN between 2 weeks and 6 months had generally higher PTSD symptom severity over time. The present findings highlight a role for structural integrity of the ventral visual stream in the development of PTSD. The ventral visual stream may be particularly important for the consolidation or retrieval of trauma memories and may contribute to efficient reactivation of visual components of the trauma memory, thereby exacerbating PTSD symptoms. Potentially chronic engagement of the network may lead to reduced structural integrity which becomes a risk factor for lasting PTSD symptoms

Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome

The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured

Genetic causes of hypercalciuric nephrolithiasis

Renal stone disease (nephrolithiasis) affects 3–5% of the population and is often associated with hypercalciuria. Hypercalciuric nephrolithiasis is a familial disorder in over 35% of patients and may occur as a monogenic disorder that is more likely to manifest itself in childhood. Studies of these monogenic forms of hypercalciuric nephrolithiasis in humans, e.g. Bartter syndrome, Dent’s disease, autosomal dominant hypocalcemic hypercalciuria (ADHH), hypercalciuric nephrolithiasis with hypophosphatemia, and familial hypomagnesemia with hypercalciuria have helped to identify a number of transporters, channels and receptors that are involved in regulating the renal tubular reabsorption of calcium. Thus, Bartter syndrome, an autosomal disease, is caused by mutations of the bumetanide-sensitive Na–K–Cl (NKCC2) co-transporter, the renal outer-medullary potassium (ROMK) channel, the voltage-gated chloride channel, CLC-Kb, the CLC-Kb beta subunit, barttin, or the calcium-sensing receptor (CaSR). Dent’s disease, an X-linked disorder characterized by low molecular weight proteinuria, hypercalciuria and nephrolithiasis, is due to mutations of the chloride/proton antiporter 5, CLC-5; ADHH is associated with activating mutations of the CaSR, which is a G-protein-coupled receptor; hypophosphatemic hypercalciuric nephrolithiasis associated with rickets is due to mutations in the type 2c sodium–phosphate co-transporter (NPT2c); and familial hypomagnesemia with hypercalciuria is due to mutations of paracellin-1, which is a member of the claudin family of membrane proteins that form the intercellular tight junction barrier in a variety of epithelia. These studies have provided valuable insights into the renal tubular pathways that regulate calcium reabsorption and predispose to hypercalciuria and nephrolithiasis