Structured penalized regression for drug sensitivity prediction

Large-scale {\it in vitro} drug sensitivity screens are an important tool in personalized oncology to predict the effectiveness of potential cancer drugs. The prediction of the sensitivity of cancer cell lines to a panel of drugs is a multivariate regression problem with high-dimensional heterogeneous multi-omics data as input data and with potentially strong correlations between the outcome variables which represent the sensitivity to the different drugs. We propose a joint penalized regression approach with structured penalty terms which allow us to utilize the correlation structure between drugs with group-lasso-type penalties and at the same time address the heterogeneity between omics data sources by introducing data-source-specific penalty factors to penalize different data sources differently. By combining integrative penalty factors (IPF) with tree-guided group lasso, we create the IPF-tree-lasso method. We present a unified framework to transform more general IPF-type methods to the original penalized method. Because the structured penalty terms have multiple parameters, we demonstrate how the interval-search Efficient Parameter Selection via Global Optimization (EPSGO) algorithm can be used to optimize multiple penalty parameters efficiently. Simulation studies show that IPF-tree-lasso can improve the prediction performance compared to other lasso-type methods, in particular for heterogenous data sources. Finally, we employ the new methods to analyse data from the Genomics of Drug Sensitivity in Cancer project.Comment: Zhao Z, Zucknick M (2020). Structured penalized regression for drug sensitivity prediction. Journal of the Royal Statistical Society, Series C. 19 pages, 6 figures and 2 table

Profiling user activities with minimal traffic traces

Understanding user behavior is essential to personalize and enrich a user's online experience. While there are significant benefits to be accrued from the pursuit of personalized services based on a fine-grained behavioral analysis, care must be taken to address user privacy concerns. In this paper, we consider the use of web traces with truncated URLs - each URL is trimmed to only contain the web domain - for this purpose. While such truncation removes the fine-grained sensitive information, it also strips the data of many features that are crucial to the profiling of user activity. We show how to overcome the severe handicap of lack of crucial features for the purpose of filtering out the URLs representing a user activity from the noisy network traffic trace (including advertisement, spam, analytics, webscripts) with high accuracy. This activity profiling with truncated URLs enables the network operators to provide personalized services while mitigating privacy concerns by storing and sharing only truncated traffic traces. In order to offset the accuracy loss due to truncation, our statistical methodology leverages specialized features extracted from a group of consecutive URLs that represent a micro user action like web click, chat reply, etc., which we call bursts. These bursts, in turn, are detected by a novel algorithm which is based on our observed characteristics of the inter-arrival time of HTTP records. We present an extensive experimental evaluation on a real dataset of mobile web traces, consisting of more than 130 million records, representing the browsing activities of 10,000 users over a period of 30 days. Our results show that the proposed methodology achieves around 90% accuracy in segregating URLs representing user activities from non-representative URLs

Accessibility-based reranking in multimedia search engines

Traditional multimedia search engines retrieve results based mostly on the query submitted by the user, or using a log of previous searches to provide personalized results, while not considering the accessibility of the results for users with vision or other types of impairments. In this paper, a novel approach is presented which incorporates the accessibility of images for users with various vision impairments, such as color blindness, cataract and glaucoma, in order to rerank the results of an image search engine. The accessibility of individual images is measured through the use of vision simulation filters. Multi-objective optimization techniques utilizing the image accessibility scores are used to handle users with multiple vision impairments, while the impairment profile of a specific user is used to select one from the Pareto-optimal solutions. The proposed approach has been tested with two image datasets, using both simulated and real impaired users, and the results verify its applicability. Although the proposed method has been used for vision accessibility-based reranking, it can also be extended for other types of personalization context

A Utility-Theoretic Approach to Privacy in Online Services

Online offerings such as web search, news portals, and e-commerce applications face the challenge of providing high-quality service to a large, heterogeneous user base. Recent efforts have highlighted the potential to improve performance by introducing methods to personalize services based on special knowledge about users and their context. For example, a user's demographics, location, and past search and browsing may be useful in enhancing the results offered in response to web search queries. However, reasonable concerns about privacy by both users, providers, and government agencies acting on behalf of citizens, may limit access by services to such information. We introduce and explore an economics of privacy in personalization, where people can opt to share personal information, in a standing or on-demand manner, in return for expected enhancements in the quality of an online service. We focus on the example of web search and formulate realistic objective functions for search efficacy and privacy. We demonstrate how we can find a provably near-optimal optimization of the utility-privacy tradeoff in an efficient manner. We evaluate our methodology on data drawn from a log of the search activity of volunteer participants. We separately assess users’ preferences about privacy and utility via a large-scale survey, aimed at eliciting preferences about peoples’ willingness to trade the sharing of personal data in returns for gains in search efficiency. We show that a significant level of personalization can be achieved using a relatively small amount of information about users

Clinical proteomics for precision medicine: the bladder cancer case

Precision medicine can improve patient management by guiding therapeutic decision based on molecular characteristics. The concept has been extensively addressed through the application of –omics based approaches. Proteomics attract high interest, as proteins reflect a “real-time” dynamic molecular phenotype. Focusing on proteomics applications for personalized medicine, a literature search was conducted to cover: a) disease prevention, b) monitoring/ prediction of treatment response, c) stratification to guide intervention and d) identification of drug targets. The review indicates the potential of proteomics for personalized medicine by also highlighting multiple challenges to be addressed prior to actual implementation. In oncology, particularly bladder cancer, application of precision medicine appears especially promising. The high heterogeneity and recurrence rates together with the limited treatment options, suggests that earlier and more efficient intervention, continuous monitoring and the development of alternative therapies could be accomplished by applying proteomics-guided personalized approaches. This notion is backed by studies presenting biomarkers that are of value in patient stratification and prognosis, and by recent studies demonstrating the identification of promising therapeutic targets. Herein, we aim to present an approach whereby combining the knowledge on biomarkers and therapeutic targets in bladder cancer could serve as basis towards proteomics- guided personalized patient management