SurfelWarp: Efficient Non-Volumetric Single View Dynamic Reconstruction

We contribute a dense SLAM system that takes a live stream of depth images as input and reconstructs non-rigid deforming scenes in real time, without templates or prior models. In contrast to existing approaches, we do not maintain any volumetric data structures, such as truncated signed distance function (TSDF) fields or deformation fields, which are performance and memory intensive. Our system works with a flat point (surfel) based representation of geometry, which can be directly acquired from commodity depth sensors. Standard graphics pipelines and general purpose GPU (GPGPU) computing are leveraged for all central operations: i.e., nearest neighbor maintenance, non-rigid deformation field estimation and fusion of depth measurements. Our pipeline inherently avoids expensive volumetric operations such as marching cubes, volumetric fusion and dense deformation field update, leading to significantly improved performance. Furthermore, the explicit and flexible surfel based geometry representation enables efficient tackling of topology changes and tracking failures, which makes our reconstructions consistent with updated depth observations. Our system allows robots to maintain a scene description with non-rigidly deformed objects that potentially enables interactions with dynamic working environments.Comment: RSS 2018. The video and source code are available on https://sites.google.com/view/surfelwarp/hom

Using Links to prototype a Database Wiki

Both relational databases and wikis have strengths that make them attractive for use in collaborative applications. In the last decade, database-backed Web applications have been used extensively to develop valuable shared biological references called curated databases. Databases offer many advantages such as scalability, query optimization and concurrency control, but are not easy to use and lack other features needed for collaboration. Wikis have become very popular for early-stage biocuration projects because they are easy to use, encourage sharing and collaboration, and provide built-in support for archiving, history-tracking and annotation. However, curation projects often outgrow the limited capabilities of wikis for structuring and efficiently querying data at scale, necessitating a painful phase transition to a database-backed Web application. We perceive a need for a new class of general-purpose system, which we call a Database Wiki, that combines flexible wiki-like support for collaboration with robust database-like capabilities for structuring and querying data. This paper presents DBWiki, a design prototype for such a system written in the Web programming language Links. We present the architecture, typical use, and wiki markup language design for DBWiki and discuss features of Links that provided unique advantages for rapid Web/database application prototyping

A Data Transformation System for Biological Data Sources

Scientific data of importance to biologists in the Human Genome Project resides not only in conventional databases, but in structured files maintained in a number of different formats (e.g. ASN.1 and ACE) as well a.s sequence analysis packages (e.g. BLAST and FASTA). These formats and packages contain a number of data types not found in conventional databases, such as lists and variants, and may be deeply nested. We present in this paper techniques for querying and transforming such data, and illustrate their use in a prototype system developed in conjunction with the Human Genome Center for Chromosome 22. We also describe optimizations performed by the system, a crucial issue for bulk data

QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization. It is freely available for academic institutions at http://queryor.cribi.unipd.it/

SkiMap: An Efficient Mapping Framework for Robot Navigation

We present a novel mapping framework for robot navigation which features a multi-level querying system capable to obtain rapidly representations as diverse as a 3D voxel grid, a 2.5D height map and a 2D occupancy grid. These are inherently embedded into a memory and time efficient core data structure organized as a Tree of SkipLists. Compared to the well-known Octree representation, our approach exhibits a better time efficiency, thanks to its simple and highly parallelizable computational structure, and a similar memory footprint when mapping large workspaces. Peculiarly within the realm of mapping for robot navigation, our framework supports realtime erosion and re-integration of measurements upon reception of optimized poses from the sensor tracker, so as to improve continuously the accuracy of the map.Comment: Accepted by International Conference on Robotics and Automation (ICRA) 2017. This is the submitted version. The final published version may be slightly differen

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Closed-loop Bayesian Semantic Data Fusion for Collaborative Human-Autonomy Target Search

In search applications, autonomous unmanned vehicles must be able to efficiently reacquire and localize mobile targets that can remain out of view for long periods of time in large spaces. As such, all available information sources must be actively leveraged -- including imprecise but readily available semantic observations provided by humans. To achieve this, this work develops and validates a novel collaborative human-machine sensing solution for dynamic target search. Our approach uses continuous partially observable Markov decision process (CPOMDP) planning to generate vehicle trajectories that optimally exploit imperfect detection data from onboard sensors, as well as semantic natural language observations that can be specifically requested from human sensors. The key innovation is a scalable hierarchical Gaussian mixture model formulation for efficiently solving CPOMDPs with semantic observations in continuous dynamic state spaces. The approach is demonstrated and validated with a real human-robot team engaged in dynamic indoor target search and capture scenarios on a custom testbed.Comment: Final version accepted and submitted to 2018 FUSION Conference (Cambridge, UK, July 2018

A Survey on IT-Techniques for a Dynamic Emergency Management in Large Infrastructures

This deliverable is a survey on the IT techniques that are relevant to the three use cases of the project EMILI. It describes the state-of-the-art in four complementary IT areas: Data cleansing, supervisory control and data acquisition, wireless sensor networks and complex event processing. Even though the deliverable’s authors have tried to avoid a too technical language and have tried to explain every concept referred to, the deliverable might seem rather technical to readers so far little familiar with the techniques it describes