The central goal of human genetics is to understand the inherited basis of human variation in phenotypes, elucidating human physiology, evolution and disease. Rare mutations have been found underlying two thousand mendelian diseases; more recently, it has become possible to assess systematically the contribution of common SNPs to complex disease. The known role of copy-number alterations in sporadic genomic disorders, combined with emerging information about inherited copy-number variation, indicate the importance of systematically assessing copy-number variants (CNVs), including common copy-number polymorphisms (CNPs), in disease. Here we discuss evidence that CNVs affect phenotypes, directions for basic knowledge to support clinical study of CNVs, the challenge of genotyping CNPs in clinical cohorts, the use of SNPs as markers for CNPs and statistical challenges in testing CNVs for association with disease. Critical needs are high-resolution maps of common CNPs and techniques that accurately determine the allelic state of affected individuals.

Copy number variation in association studies of human disease

This paper provides an overview of the most significant existing methods for indoor positioning on a contemporary smartphone. The approaches include Wi-Fi and Bluetooth based positioning, magnetic field fingerprinting, map aided navigation using building floor plans, and aiding from self-contained sensors. Wi-Fi and Bluetooth based positioning methods considered in this survey are fingerprint approaches that determine a user's position using a database of radio signal strength measurements that were collected earlier at known locations. Magnetic field fingerprinting can be used in an information fusion algorithm to improve positioning. The map-matching algorithms include application of wall constraints, topological indoor maps, and building geometry for heading correction. Finally, methods for step counting, step length and direction estimation, orientation tracking, motion classification, transit mode detection, and floor change detection in multi-storey buildings are discussed.

A Survey of Selected Indoor Positioning Methods for Smartphones

Detecting outliers is a significant problem that has been studied in various research and application areas. Researchers continue to design robust schemes to provide solutions to detect outliers efficiently. In this survey, we present a comprehensive and organized review of the progress of outlier detection methods from 2000 to 2019. First, we offer the fundamental concepts of outlier detection and then categorize them into different techniques from diverse outlier detection techniques, such as distance-, clustering-, density-, ensemble-, and learning-based methods. In each category, we introduce some state-of-the-art outlier detection methods and further discuss them in detail in terms of their performance. Second, we delineate their pros, cons, and challenges to provide researchers with a concise overview of each technique and recommend solutions and possible research directions. This paper gives current progress of outlier detection techniques and provides a better understanding of the different outlier detection methods. The open research issues and challenges at the end will provide researchers with a clear path for the future of outlier detection methods.

Progress in Outlier Detection Techniques: A Survey

Robust and accurate indoor localization has been the goal of several research efforts over the past decade. Due to the ubiquitous availability of WiFi indoors, many indoor localization systems have been proposed relying on WiFi fingerprinting. However, due to the inherent noise and instability of the wireless signals, the localization accuracy usually degrades and is not robust to dynamic changes in the environment.We present WiDeep, a deep learning-based indoor localization system that achieves a fine-grained and robust accuracy in the presence of noise. Specifically, WiDeep combines a stacked denoising autoencoders deep learning model and a probabilistic framework to handle the noise in the received WiFi signal and capture the complex relationship between the WiFi APs signals heard by the mobile phone and its location. WiDeep also introduces a number of modules to address practical challenges such as avoiding over-training and handling heterogeneous devices.We evaluate WiDeep in two testbeds of different sizes and densities of access points. The results show that it can achieve a mean localization accuracy of 2.64m and 1.21m for the larger and the smaller testbeds, respectively. This accuracy outperforms the state-of-the-art techniques in all test scenarios and is robust to heterogeneous devices.

WiDeep: WiFi-based Accurate and Robust Indoor Localization System using Deep Learning

Indoor localization using mobile sensors has gained momentum lately. Most of the current systems rely on an extensive calibration step to achieve high accuracy. We propose SemanticSLAM , a novel unsupervised indoor localization scheme that bypasses the need for war-driving. SemanticSLAM leverages the idea that certain locations in an indoor environment have a unique signature on one or more phone sensors. Climbing stairs, for example, has a distinct pattern on the phone's accelerometer; a specific spot may experience an unusual magnetic interference while another may have a unique set of Wi-Fi access points covering it. SemanticSLAM uses these unique points in the environment as landmarks and combines them with dead-reckoning in a new Simultaneous Localization And Mapping (SLAM) framework to reduce both the localization error and convergence time. In particular, the phone inertial sensors are used to keep track of the user's path, while the observed landmarks are used to compensate for the accumulation of error in a unified probabilistic framework. Evaluation in two testbeds on Android phones shows that the system can achieve $0.53$ meters human median localization errors. In addition, the system can detect the location of landmarks with 0.83 meters median error. This is 62 percent better than a system that does not use SLAM. Moreover, SemanticSLAM has a 33 percent lower convergence time compared to the same systems. This highlights the promise of SemanticSLAM as an unconventional approach for indoor localization.

SemanticSLAM: Using Environment Landmarks for Unsupervised Indoor Localization

Ubiquity of Internet-connected and sensor-equipped portable devices sparked a new set of mobile computing applications that leverage the proliferating sensing capabilities of smartphones. For many of these applications, accurate estimation of the user heading, as compared to the phone heading, is of paramount importance. This is of special importance for many crowd-sensing applications, where the phone can be carried in arbitrary positions and orientations relative to the user body. Current state-of-the-art focus mainly on estimating the phone orientation, require the phone to be placed in a particular position, require user intervention, and/or do not work accurately indoors; which limits their ubiquitous usability in different applications.

In this paper we present Humaine, a novel system to reliably and accurately estimate the user orientation relative to the Earth coordinate system. Humaine requires no prior-configuration nor user intervention and works accurately indoors and outdoors for arbitrary cell phone positions and orientations relative to the user body. The system applies statistical analysis techniques to the inertial sensors widely available on today's cell phones to estimate both the phone and user orientation. Implementation of the system on different Android devices with 170 experiments performed at different indoor and outdoor testbeds shows that Humaine significantly outperforms the state-of-the-art in diverse scenarios, achieving a median accuracy of 15° averaged over a wide variety of phone positions. This is 558% better than the-state-of-the-art. The accuracy is bounded by the error in the inertial sensors readings and can be enhanced with more accurate sensors and sensor fusion.

It's the human that matters: accurate user orientation estimation for mobile computing applications

The problem of unsupervised outlier detection is challenging, especially when the structure of data is unknown. This paper presents a new density-based outlier detection technique that detects the top-n outliers. It overcomes the limitations of existing approaches, like low accuracy and high sensitivity to parameters. Our approach provides a score to each object called Dynamic-Window Outlier Factor (DWOF). DWOF improves Resolution-based Outlier Factor method (ROF) to consider varying-density clusters, which improves outliers’ ranking even when providing same outliers. Experiments show that DWOF’s average accuracy is better than existing approaches and less sensitive to its parameter.

DWOF: A Robust Density-Based Outlier Detection Approach

Integrative approaches that combine multiple forms of data can more accurately capture pathway associations and so provide a comprehensive understanding of the molecular mechanisms that cause complex diseases. Association analyses based on single nucleotide polymorphism (SNP) genotypes, copy number variant (CNV) genotypes, and gene expression profiles are the 3 most common paradigms used for gene set/pathway enrichment analyses. Many work has been done to leverage information from 2 types of data from these 3 paradigms. However, to the best of our knowledge, there is no work done before to integrate the 3 paradigms all together. In this article, we present an integrated analysis that combine SNP, CNV, and gene expression data to generate a single gene list. We present different methods to compare this gene list with the other 3 possible lists that result from the combinations of the following pairs of data: SNP genotype with gene expression, CNV genotype with gene expression, and SNP genotype with CNV genotype. The comparison is done using 3 different cancer datasets and 2 different methods of comparison. Our results show that integrating SNP, CNV, and gene expression data give better association results than integrating any pair of 3 data.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/cge.13092

Integrated analysis of SNP, CNV and gene expression data in genetic association studies.

Ubiquity of Internet-connected and sensor-equipped portable devices sparked a new set of mobile computing applications that leverage the proliferating sensing capabilities of smart-phones. For many of these applications, accurate estimation of the user heading, as compared to the phone heading, is of paramount importance. This is of special importance for many crowd-sensing applications, where the phone can be carried in arbitrary positions and orientations relative to the user body. Current state-of-the-art focus mainly on estimating the phone orientation, require the phone to be placed in a particular position, require user intervention, and/or do not work accurately indoors; which limits their ubiquitous usability in different applications. In this paper we present Humaine, a novel system to reliably and accurately estimate the user orientation relative to the Earth coordinate system. 
Humaine requires no prior-configuration nor user intervention and works accurately indoors and outdoors for arbitrary cell phone positions and orientations relative to the user body. The system applies statistical analysis techniques to the inertial sensors widely available on today's cell phones to estimate both the phone and user orientation. Implementation of the system on different Android devices with 170 experiments performed at different indoor and outdoor testbeds shows that Humaine significantly outperforms the state-of-the-art in diverse scenarios, achieving a median accuracy of $15^\circ$ averaged over a wide variety of phone positions. This is $558\%$ better than the-state-of-the-art. The accuracy is bounded by the error in the inertial sensors readings and can be enhanced with more accurate sensors and sensor fusion.

It's the Human that Matters: Accurate User Orientation Estimation for Mobile Computing Applications

Recently, there have been a wide range of mobile computing and crowd-sourcing applications that leverage the proliferating sensing capabilities of smartphones. Many of these place a paramount importance on accurate user heading estimation. Such applications include dead-reckoning-based localization and many crowd-sensing applications where the user typically carry her phone in arbitrary positions and orientations relative to her body and her transportation mode. However, there is no general solution available to estimate the user's heading as current state-of-the-art focus on improving the phone orientation estimation, require the phone to be placed in a particular position, require a fixed transportation mode, require user intervention, and/or do not work accurately indoors. In this paper we present Humaine, a novel ubiquitous system that reliably and accurately estimates the user orientation relative to the Earth coordinate system. Humaine works accurately whether the user is riding a vehicle or walking indoors/outdoors for arbitrary cell phone positions and orientations relative to the user body. Moreover, it requires no prior-configuration nor user intervention. The system intelligently fuses the different inertial sensors widely available in off-the-shelf smartphones and employs statistical analysis techniques to their measurements to estimate the user orientation. Implementation of the system on different Android devices with 300 experiments performed at different indoor and outdoor testbeds shows that Humaine significantly outperforms the state-of-the-art in diverse scenarios, achieving a median accuracy of 14ź and 16ź for indoor and outdoor pedestrian users and 20ź for in-vehicle users over a wide variety of phone positions. This is better than the-state-of-the-art by 523% and 594% for indoor and outdoor pedestrian users and 750% for in-vehicle users. This accuracy highlights the ubiquity of Humaine and its robustness against the various noise sources.

Rana Momtaz

Papers

It's the human that matters: accurate user orientation estimation for mobile computing applications

DWOF: A Robust Density-Based Outlier Detection Approach

Integrated analysis of SNP, CNV and gene expression data in genetic association studies.

It's the Human that Matters: Accurate User Orientation Estimation for Mobile Computing Applications

Humaine: a ubiquitous smartphone-based user heading estimation for mobile computing systems