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  1. Cancer is an umbrella term that includes a range of disorders, from those that are fast-growing and lethal to indolent lesions with low or delayed potential for progression to death. The treatment options, as well as treatment success, are highly dependent on the correct subtyping of individual patients. With the advancement of high-throughput platforms, we have the opportunity to differentiate among cancer subtypes from a holistic perspective that takes into consideration phenomena at different molecular levels (mRNA, methylation, etc.). This demands powerful integrative methods to leverage large multi-omics datasets for a better subtyping. Here we introduce Subtyping Multi-omics using a Randomized Transformation (SMRT), a new method for multi-omics integration and cancer subtyping. SMRT offers the following advantages over existing approaches: (i) the scalable analysis pipeline allows researchers to integrate multi-omics data and analyze hundreds of thousands of samples in minutes, (ii) the ability to integrate data types with different numbers of patients, (iii) the ability to analyze un-matched data of different types, and (iv) the ability to offer users a convenient data analysis pipeline through a web application. We also improve the efficiency of our ensemble-based, perturbation clustering to support analysis on machines with memory constraints. In an extensive analysis,more »we compare SMRT with eight state-of-the-art subtyping methods using 37 TCGA and two METABRIC datasets comprising a total of almost 12,000 patient samples from 28 different types of cancer. We also performed a number of simulation studies. We demonstrate that SMRT outperforms other methods in identifying subtypes with significantly different survival profiles. In addition, SMRT is extremely fast, being able to analyze hundreds of thousands of samples in minutes. The web application is available at http://SMRT.tinnguyen-lab.com . The R package will be deposited to CRAN as part of our PINSPlus software suite.« less
  2. Nonverbal interactions are a key component of human communication. Since robots have become significant by trying to get close to human beings, it is important that they follow social rules governing the use of space. Prior research has conceptualized personal space as physical zones which are based on static distances. This work examined how preferred interaction distance can change given different interaction scenarios. We conducted a user study using three different robot heights. We also examined the difference in preferred interaction distance when a robot approaches a human and, conversely, when a human approaches a robot. Factors included in quantitative analysis are the participants' gender, robot's height, and method of approach. Subjective measures included human comfort and perceived safety. The results obtained through this study shows that robot height, participant gender and method of approach were significant factors influencing measured proxemic zones and accordingly participant comfort. Subjective data showed that experiment respondents regarded robots in a more favorable light following their participation in this study. Furthermore, the NAO was perceived most positively by respondents according to various metrics and the PR2 Tall, most negatively.
  3. Abstract. This paper studies how to improve the accuracy of hydrologic models using machine-learning models as post-processors and presents possibilities to reduce the workload to create an accurate hydrologic model by removing the calibration step. It is often challenging to develop an accurate hydrologic model due to the time-consuming model calibration procedure and the nonstationarity of hydrologic data. Our findings show that the errors of hydrologic models are correlated with model inputs. Thus motivated, we propose a modeling-error-learning-based post-processor framework by leveraging this correlation to improve the accuracy of a hydrologic model. The key idea is to predict the differences (errors) between the observed values and the hydrologic model predictions by using machine-learning techniques. To tackle the nonstationarity issue of hydrologic data, a moving-window-based machine-learning approach is proposed to enhance the machine-learning error predictions by identifying the local stationarity of the data using a stationarity measure developed based on the Hilbert–Huang transform. Two hydrologic models, the Precipitation–Runoff Modeling System (PRMS) and the Hydrologic Modeling System (HEC-HMS), are used to evaluate the proposed framework. Two case studies are provided to exhibit the improved performance over the original model using multiple statistical metrics.