Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission. Here we introduce an epidemiological model where infectives leave the epidemic, either by recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by, can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, namely an application to influenza and an application to HIV. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions.Comment: 30 pages, 2 figure

High-resolution spectroscopy of V854 Cen in decline - Absorption and emission lines of C_2 molecules

High-resolution optical spectra of the R Coronae Borealis (RBC) star V854 Centauri in the early stages of a decline show, in addition to the features reported for other RCBs in decline, narrow absorption lines from the C_2 Phillips system. The low rotational temperature, T_rot = 1150K, of the C_2 ground electronic state suggests the cold gas is associated with the developing shroud of carbon dust. These absorption lines were not seen at a fainter magnitude on the rise from minimum light nor at maximum light. This is the first detection of cold gas around a RCB star.Comment: 5 pages, 5 figures, accepted for publication by Monthly Notices of the Royal Society of Astronom

Rich Tags: Cross-Repository Browsing

We present RichTags, a system for cross-site browsing and exploration of digital repositories. Categorical and faceted search across repositories is poorly supported, especially compared to the support of keyword search through internet search engines. We combine a variety of information retrieval techniques to determine categories of papers, to enable cross-repository browsing by category. The browsing and exploration of this metadata is achieved through a multi-faceted dynamic exploration interface. Social interaction features have also been added to enable cross-repository tagging, commenting and sharing of papers into groups. These social features are available via an API to enable future work to add plugins to pull comments back to the repositories

Deep Forward and Inverse Perceptual Models for Tracking and Prediction

We consider the problems of learning forward models that map state to high-dimensional images and inverse models that map high-dimensional images to state in robotics. Specifically, we present a perceptual model for generating video frames from state with deep networks, and provide a framework for its use in tracking and prediction tasks. We show that our proposed model greatly outperforms standard deconvolutional methods and GANs for image generation, producing clear, photo-realistic images. We also develop a convolutional neural network model for state estimation and compare the result to an Extended Kalman Filter to estimate robot trajectories. We validate all models on a real robotic system.Comment: 8 pages, International Conference on Robotics and Automation (ICRA) 201

Multi-sensor fire detection by fusing visual and non-visual flame features

This paper proposes a feature-based multi-sensor fire detector operating on ordinary video and long wave infrared (LWIR) thermal images. The detector automatically extracts hot objects from the thermal images by dynamic background subtraction and histogram-based segmentation. Analogously, moving objects are extracted from the ordinary video by intensity-based dynamic background subtraction. These hot and moving objects are then further analyzed using a set of flame features which focus on the distinctive geometric, temporal and spatial disorder characteristics of flame regions. By combining the probabilities of these fast retrievable visual and thermal features, we are able to detect the fire at an early stage. Experiments with video and LWIR sequences of lire and non-fire real case scenarios show good results in id indicate that multi-sensor fire analysis is very promising

Using pivots to explore heterogeneous collections: A case study in musicology

In order to provide a better e-research environment for musicologists, the musicSpace project has partnered with musicology’s leading data publishers, aggregated and enriched their data, and developed a richly featured exploratory search interface to access the combined dataset. There have been several significant challenges to developing this service, and intensive collaboration between musicologists (the domain experts) and computer scientists (who developed the enabling technologies) was required. One challenge was the actual aggregation of the data itself, as this was supplied adhering to a wide variety of different schemas and vocabularies. Although the domain experts expended much time and effort in analysing commonalities in the data, as data sources of increasing complexity were added earlier decisions regarding the design of the aggregated schema, particularly decisions made with reference to simpler data sources, were often revisited to take account of unanticipated metadata types. Additionally, in many domains a single source may be considered to be definitive for certain types of information. In musicology, this is essentially the case with the “works lists” of composers’ musical compositions given in Grove Music Online (http://www.oxfordmusiconline.com/public/book/omo_gmo), and so for musicSpace, we have mapped all sources to the works lists from Grove for the purposes of exploration, specifically to exploit the accuracy of its metadata in respect to dates of publication, catalogue numbers, and so on. Therefore, rather than mapping all fields from Grove to a central model, it would be far quicker (in terms of development time) to create a system to “pull-in” data from other sources that are mapped directly to the Grove works lists

musicSpace: integrating musicology's heterogeneous data sources

A significant barrier to the research endeavours of musicologists (and humanities scholars more generally) is the sheer amount of potentially relevant information that has accumulated over centuries. Whereas researchers once faced the daunting prospect of physically scouring through endless primary and secondary sources in order to answer the basic whats, wheres and whens of history, these sources and the data they contain are now increasingly available online. Yet the vast increase in the online availability of data, the heterogeneity of this data, the plethora of data providers, and, moreover, the inability of current search tools to manipulate metadata in useful and intelligent ways, means that extracting large tranches of basic factual information or running multi-part search queries is still enormously and needlessly time consuming. Accordingly, the musicSpace project is exploiting Semantic Web technologies (Berners-Lee et al., 2001) to develop a search interface that integrates access to musicology’s largest and most significant online resources. This will make previously intractable search queries tractable, thus allowing our users to spend their research time more efficiently and ultimately aiding the attainment of new knowledge. This brief paper gives an overview of our work

Orchestrating musical (meta)data to better address the real-world search queries of musicologists

The dispersal of musicology’s diverse array of primary and secondary sources across countless libraries and archives was once an enormous obstacle to conducting research, but this has largely been overcome by the digitisation and online publication of resources in recent years. Yet, while the research process has undoubtedly been revolutionised, the current situation is far from perfect, as the digitisation of resources has often been accompanied by their segregation—according to media type, date of publication, subject, language, copyright holder, etc.—into a myriad of discrete online repositories, often with little thought having been given to interoperability. Given that musicological research typically cuts across such artificial divisions, this segregation of data means that accessing basic factual information or running multi-part search queries remains endlessly complicated, needlessly time consuming, and sometimes impossible. This barrier to tractability is only exacerbated by the limited capabilities of currently deployed search interfaces. There is one seemingly obvious solution to this query dilemma: enable integrated real-time querying over all the available metadata from as many sources as possible, and allow users to use that metadata to guide their queries. This solution implies that all data that could feasibly be construed as useful, but which is buried in the records, is extracted in some way, and that there is an interaction approach that enables metadata to be explored effectively and allows for the formulation of rich compound queries. The musicSpace project has taken a dual approach towards realising this solution. At the back-end we are developing services to integrate and, where necessary, surface (meta)data from many of musicology’s most important online resources, including the British Library Music Collections catalogue, the British Library Sound Archive catalogue, Cecilia, Copac, Grove Music Online, Naxos Music Library, Répertoire International de Littérature Musicale (RILM), and Répertoire International des Sources Musicale (RISM) UK and Ireland. While at the front-end, in order to optimise the exploration of this integrated dataset, we are developing a modern web-based faceted browsing interface that utilises Semantic Web and Web2.0 technologies such as RDF and AJAX, and which is based on the existing ‘mSpace’ codebase. Our poster outlines the approach we have taken to importing, enriching and integrating the metadata provided by our data partners, and gives examples of the real-world musicological research questions that musicSpace has enabled

Discovery and exploration using musicSpace

Musicologists have to rely upon an extraordinarily heterogeneous body of primary and secondary research sources, even when conducting the most basic exploratory research. Although increasingly available online, data is nevertheless routinely catalogued or stored in numerous discrete databases according to media type (text, image, video, audio) and historical period (contemporary literature/sources, historical literature/sources), yet most musicological research cuts across these artificial divisions; researching Monteverdi’s madrigals, for example, could involve performing essentially the same search several times, because there are several relevant data sources (RISM, Grove, Naxos, RILM, BL Integrated Catalogue and BL Sound Archive). The musicSpace project seeks to integrate access to musicological data sources by providing a single search interface, thereby removing the need for search repetition and reducing inefficiency. The vast increase in on-hand data that comes with database integration both demands and allows for the development of far more sophisticated, intelligent and interactive user interfaces. Accordingly, musicSpace facilitates searching and encourages browsing by displaying search results and parameters using multiple panes, allowing instantaneous paradigmatic shifts in search focus, and employing a detailed subject ontology to enable the semi-automatic construction of complex searches. In this paper we present the musicSpace explorer interface and demonstrate its efficacy. We describe key technologies behind musicSpace to reflect on performance and scalability. In particular, however, we describe how we will be evaluating the system in use for research, and describe our longitudinal study to assess the impact of this integrated approach on artefact discovery and research query support