An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery.

Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs

Visual Affect Around the World: A Large-scale Multilingual Visual Sentiment Ontology

Every culture and language is unique. Our work expressly focuses on the uniqueness of culture and language in relation to human affect, specifically sentiment and emotion semantics, and how they manifest in social multimedia. We develop sets of sentiment- and emotion-polarized visual concepts by adapting semantic structures called adjective-noun pairs, originally introduced by Borth et al. (2013), but in a multilingual context. We propose a new language-dependent method for automatic discovery of these adjective-noun constructs. We show how this pipeline can be applied on a social multimedia platform for the creation of a large-scale multilingual visual sentiment concept ontology (MVSO). Unlike the flat structure in Borth et al. (2013), our unified ontology is organized hierarchically by multilingual clusters of visually detectable nouns and subclusters of emotionally biased versions of these nouns. In addition, we present an image-based prediction task to show how generalizable language-specific models are in a multilingual context. A new, publicly available dataset of >15.6K sentiment-biased visual concepts across 12 languages with language-specific detector banks, >7.36M images and their metadata is also released.Comment: 11 pages, to appear at ACM MM'1

Mathematical practice, crowdsourcing, and social machines

The highest level of mathematics has traditionally been seen as a solitary endeavour, to produce a proof for review and acceptance by research peers. Mathematics is now at a remarkable inflexion point, with new technology radically extending the power and limits of individuals. Crowdsourcing pulls together diverse experts to solve problems; symbolic computation tackles huge routine calculations; and computers check proofs too long and complicated for humans to comprehend. Mathematical practice is an emerging interdisciplinary field which draws on philosophy and social science to understand how mathematics is produced. Online mathematical activity provides a novel and rich source of data for empirical investigation of mathematical practice - for example the community question answering system {\it mathoverflow} contains around 40,000 mathematical conversations, and {\it polymath} collaborations provide transcripts of the process of discovering proofs. Our preliminary investigations have demonstrated the importance of "soft" aspects such as analogy and creativity, alongside deduction and proof, in the production of mathematics, and have given us new ways to think about the roles of people and machines in creating new mathematical knowledge. We discuss further investigation of these resources and what it might reveal. Crowdsourced mathematical activity is an example of a "social machine", a new paradigm, identified by Berners-Lee, for viewing a combination of people and computers as a single problem-solving entity, and the subject of major international research endeavours. We outline a future research agenda for mathematics social machines, a combination of people, computers, and mathematical archives to create and apply mathematics, with the potential to change the way people do mathematics, and to transform the reach, pace, and impact of mathematics research.Comment: To appear, Springer LNCS, Proceedings of Conferences on Intelligent Computer Mathematics, CICM 2013, July 2013 Bath, U

An Open System for Social Computation

Part of the power of social computation comes from using the collective intelligence of humans to tame the aggregate uncertainty of (otherwise) low veracity data obtained from human and automated sources. We have witnessed a surge in development of social computing systems but, ironically, there have been few attempts to generalise across this activity so that creation of the underlying mechanisms themselves can be made more social. We describe a method for achieving this by standardising patterns of social computation via lightweight formal specifications (we call these social artifacts) that can be connected to existing internet architectures via a single model of computation. Upon this framework we build a mechanism for extracting provenance meta-data across social computations

An Open System for Social Computation

Part of the power of social computation comes from using the collective intelligence of humans to tame the aggregate uncertainty of (otherwise) low veracity data obtained from human and automated sources. We have witnessed a surge in development of social computing systems but, ironically, there have been few attempts to generalise across this activity so that creation of the underlying mechanisms themselves can be made more social. We describe a method for achieving this by standardising patterns of social computation via lightweight formal specifications (we call these social artifacts) that can be connected to existing internet architectures via a single model of computation. Upon this framework we build a mechanism for extracting provenance meta-data across social computations

T-Crowd: Effective Crowdsourcing for Tabular Data

Crowdsourcing employs human workers to solve computer-hard problems, such as data cleaning, entity resolution, and sentiment analysis. When crowdsourcing tabular data, e.g., the attribute values of an entity set, a worker's answers on the different attributes (e.g., the nationality and age of a celebrity star) are often treated independently. This assumption is not always true and can lead to suboptimal crowdsourcing performance. In this paper, we present the T-Crowd system, which takes into consideration the intricate relationships among tasks, in order to converge faster to their true values. Particularly, T-Crowd integrates each worker's answers on different attributes to effectively learn his/her trustworthiness and the true data values. The attribute relationship information is also used to guide task allocation to workers. Finally, T-Crowd seamlessly supports categorical and continuous attributes, which are the two main datatypes found in typical databases. Our extensive experiments on real and synthetic datasets show that T-Crowd outperforms state-of-the-art methods in terms of truth inference and reducing the cost of crowdsourcing