A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes

The influence of DNA cis-regulatory elements on a gene's expression has been intensively studied. However, little is known about expressions driven by trans-acting DNA hotspots. DNA hotspots harboring copy number aberrations are recognized to be important in cancer as they influence multiple genes on a global scale. The challenge in detecting trans-effects is mainly due to the computational difficulty in detecting weak and sparse trans-acting signals amidst co-occuring passenger events. We propose an integrative approach to learn a sparse interaction network of DNA copy-number regions with their downstream targets in a breast cancer dataset. Information from this network helps distinguish copy-number driven from copy-number independent expression changes on a global scale. Our result further delineates cis- and trans-effects in a breast cancer dataset, for which important oncogenes such as ESR1 and ERBB2 appear to be highly copy-number dependent. Further, our model is shown to be efficient and in terms of goodness of fit no worse than other state-of the art predictors and network reconstruction models using both simulated and real data.Comment: Accepted at IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010

A new approach to hierarchical data analysis: Targeted maximum likelihood estimation for the causal effect of a cluster-level exposure

We often seek to estimate the impact of an exposure naturally occurring or randomly assigned at the cluster-level. For example, the literature on neighborhood determinants of health continues to grow. Likewise, community randomized trials are applied to learn about real-world implementation, sustainability, and population effects of interventions with proven individual-level efficacy. In these settings, individual-level outcomes are correlated due to shared cluster-level factors, including the exposure, as well as social or biological interactions between individuals. To flexibly and efficiently estimate the effect of a cluster-level exposure, we present two targeted maximum likelihood estimators (TMLEs). The first TMLE is developed under a non-parametric causal model, which allows for arbitrary interactions between individuals within a cluster. These interactions include direct transmission of the outcome (i.e. contagion) and influence of one individual's covariates on another's outcome (i.e. covariate interference). The second TMLE is developed under a causal sub-model assuming the cluster-level and individual-specific covariates are sufficient to control for confounding. Simulations compare the alternative estimators and illustrate the potential gains from pairing individual-level risk factors and outcomes during estimation, while avoiding unwarranted assumptions. Our results suggest that estimation under the sub-model can result in bias and misleading inference in an observational setting. Incorporating working assumptions during estimation is more robust than assuming they hold in the underlying causal model. We illustrate our approach with an application to HIV prevention and treatment

Structured Training for Neural Network Transition-Based Parsing

We present structured perceptron training for neural network transition-based dependency parsing. We learn the neural network representation using a gold corpus augmented by a large number of automatically parsed sentences. Given this fixed network representation, we learn a final layer using the structured perceptron with beam-search decoding. On the Penn Treebank, our parser reaches 94.26% unlabeled and 92.41% labeled attachment accuracy, which to our knowledge is the best accuracy on Stanford Dependencies to date. We also provide in-depth ablative analysis to determine which aspects of our model provide the largest gains in accuracy

Incorporating Intra-Class Variance to Fine-Grained Visual Recognition

Fine-grained visual recognition aims to capture discriminative characteristics amongst visually similar categories. The state-of-the-art research work has significantly improved the fine-grained recognition performance by deep metric learning using triplet network. However, the impact of intra-category variance on the performance of recognition and robust feature representation has not been well studied. In this paper, we propose to leverage intra-class variance in metric learning of triplet network to improve the performance of fine-grained recognition. Through partitioning training images within each category into a few groups, we form the triplet samples across different categories as well as different groups, which is called Group Sensitive TRiplet Sampling (GS-TRS). Accordingly, the triplet loss function is strengthened by incorporating intra-class variance with GS-TRS, which may contribute to the optimization objective of triplet network. Extensive experiments over benchmark datasets CompCar and VehicleID show that the proposed GS-TRS has significantly outperformed state-of-the-art approaches in both classification and retrieval tasks.Comment: 6 pages, 5 figure

Assessing the effect of advertising expenditures upon sales: a Bayesian structural time series model

We propose a robust implementation of the Nerlove--Arrow model using a Bayesian structural time series model to explain the relationship between advertising expenditures of a country-wide fast-food franchise network with its weekly sales. Thanks to the flexibility and modularity of the model, it is well suited to generalization to other markets or situations. Its Bayesian nature facilitates incorporating \emph{a priori} information (the manager's views), which can be updated with relevant data. This aspect of the model will be used to present a strategy of budget scheduling across time and channels.Comment: Published at Applied Stochastic Models in Business and Industry, https://onlinelibrary.wiley.com/doi/full/10.1002/asmb.246

Value at Risk models with long memory features and their economic performance

We study alternative dynamics for Value at Risk (VaR) that incorporate a slow moving component and information on recent aggregate returns in established quantile (auto) regression models. These models are compared on their economic performance, and also on metrics of first-order importance such as violation ratios. By better economic performance, we mean that changes in the VaR forecasts should have a lower variance to reduce transaction costs and should lead to lower exceedance sizes without raising the average level of the VaR. We find that, in combination with a targeted estimation strategy, our proposed models lead to improved performance in both statistical and economic terms