生醫分析系統之語意整合

[[abstract]]這計畫提議建立一個知識系統，允許生物醫學的研究人員透過以自然語言查詢方 式，綜合查詢複雜的生物資訊數據及影像訊息。我們的數據庫的目標是使數據的輸 入更有效率的，更有組織性，容易取回，及使操作和綜合變得容易。此系統以阿茲海 默症作為研究的對象。這一個知識系統與傳統知識系統的基本的區別在於它支援複雜 的數據組織和一個強大的查詢界面。 SemanticObjects 是由美國加州大學Irvine 分校和日本NEC 共同開發的一個物件 相關的平台，目的是為建造一物件知識系統。它允許使用者有效的組織及儲存生物學 模式和數據成階層式的複雜物件。使用者可利用結構性的自然語言來查詢及利用此知 識系統的數據。 最後，我們將迅速地把這個以SemanticObjects 為主的知識系統成為網站應用。這 使其它的研究人員可分享及獲得是項研究的結果。 我們提議的系統由以下的數個模組組成，a) 文字採礦模組，b) microarry/SNP 模 組，c) 基因網路模組，d)影像模組和e)實驗模組。 This proposal suggests building a knowledge system that allows biomedical researchers to synthesize complex bioinformatics information and images data via natural language query. The goal of our database is to facilitate efficient data entry, organization, retrieval, manipulation and integration. The Alzheimer』s Disease was chosen as our study case. A fundamental distinction of the biological database addressed in this research and the others is that it supports both complex data organization and a powerful querying facility. SemanticObjects is an object-relational platform that has been jointly developed by University of California, Irvine and NEC Soft, Japan as a tool for building object knowledge systems. It allows users to efficiently organize and store biological models and data as complex objects that are hierarchically structured. User can query and manipulate the data in Structured Natural Language (SNL). Finally, we will rapidly deploy this SemanticObjects database into a web application. This makes it easy for the research community to share the results obtained from proposed research. Our proposed system consists of: a) a text mining module, b) a microarry/SNP module, c) a gene network module, d) an image module, and e) a web laboratory module

Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM , which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development

VPS-SLAM: Visual Planar Semantic SLAM for Aerial Robotic Systems

Indoor environments have abundant presence of high-level semantic information which can provide a better understanding of the environment for robots to improve the uncertainty in their pose estimate. Although semantic information has proved to be useful, there are several challenges faced by the research community to accurately perceive, extract and utilize such semantic information from the environment. In order to address these challenges, in this paper we present a lightweight and real-time visual semantic SLAM framework running on board aerial robotic platforms. This novel method combines low-level visual/visual-inertial odometry (VO/VIO) along with geometrical information corresponding to planar surfaces extracted from detected semantic objects. Extracting the planar surfaces from selected semantic objects provides enhanced robustness and makes it possible to precisely improve the metric estimates rapidly, simultaneously generalizing to several object instances irrespective of their shape and size. Our graph-based approach can integrate several state of the art VO/VIO algorithms along with the state of the art object detectors in order to estimate the complete 6DoF pose of the robot while simultaneously creating a sparse semantic map of the environment. No prior knowledge of the objects is required, which is a significant advantage over other works. We test our approach on a standard RGB-D dataset comparing its performance with the state of the art SLAM algorithms. We also perform several challenging indoor experiments validating our approach in presence of distinct environmental conditions and furthermore test it on board an aerial robot. Video:https://vimeo.com/368217703Released Code:https://bitbucket.org/hridaybavle/semantic_slam.git

Generation of skill-specific maps from graph world models for robotic systems

With the increase in the availability of Building Information Models (BIM) and (semi-) automatic tools to generate BIM from point clouds, we propose a world model architecture and algorithms to allow the use of the semantic and geometric knowledge encoded within these models to generate maps for robot localization and navigation. When heterogeneous robots are deployed within an environment, maps obtained from classical SLAM approaches might not be shared between all agents within a team of robots, e.g. due to a mismatch in sensor type, or a difference in physical robot dimensions. Our approach extracts the 3D geometry and semantic description of building elements (e.g. material, element type, color) from BIM, and represents this knowledge in a graph. Based on queries on the graph and knowledge of the skills of the robot, we can generate skill-specific maps that can be used during the execution of localization or navigation tasks. The approach is validated with data from complex build environments and integrated into existing navigation frameworks.Comment: 8 page

Ring: a Unifying Meta-Model and Infrastructure for Smalltalk Source Code Analysis Tools

International audienceSource code management systems record different versions of code. Tool support can then compute deltas between versions. To ease version history analysis we need adequate models to represent source code entities. Now naturally the questions of their definition, the abstractions they use, and the APIs of such models are raised, especially in the context of a reflective system which already offers a model of its own structure. We believe that this problem is due to the lack of a powerful code meta-model as well as an infrastructure. In Smalltalk, often several source code meta-models coexist: the Smalltalk reflective API coexists with the one of the Refactoring Engine or distributed versioning system such as Monticello or Store. While having specific meta-models is an adequate engineered solution, it multiplies meta-models and it requires more maintenance efforts (e.g., duplication of tests, transformation between models), and more importantly hinders navigation tool reuse when meta-models do not offer polymorphic APIs. As a first step to provide an infrastructure to support history analysis, this article presents Ring, a unifying source code meta-model that can be used to support several activities and proposes a unified and layered approach to be the foundation for building an infrastructure for version and stream of change analyses. We re-implemented three tools based on Ring to show that it can be used as the underlying meta-model for remote and off-image browsing, scoping refactoring, and visualizing and analyzing changes. As a future work and based on Ring we will build a new generation of history analysis tools

A Database Approach for Modeling and Querying Video Data

Indexing video data is essential for providing content based access. In this paper, we consider how database technology can offer an integrated framework for modeling and querying video data. As many concerns in video (e.g., modeling and querying) are also found in databases, databases provide an interesting angle to attack many of the problems. From a video applications perspective, database systems provide a nice basis for future video systems. More generally, database research will provide solutions to many video issues even if these are partial or fragmented. From a database perspective, video applications provide beautiful challenges. Next generation database systems will need to provide support for multimedia data (e.g., image, video, audio). These data types require new techniques for their management (i.e., storing, modeling, querying, etc.). Hence new solutions are significant. This paper develops a data model and a rule-based query language for video content based indexing and retrieval. The data model is designed around the object and constraint paradigms. A video sequence is split into a set of fragments. Each fragment can be analyzed to extract the information (symbolic descriptions) of interest that can be put into a database. This database can then be searched to find information of interest. Two types of information are considered: (1) the entities (objects) of interest in the domain of a video sequence, (2) video frames which contain these entities. To represent these information, our data model allows facts as well as objects and constraints. We present a declarative, rule-based, constraint query language that can be used to infer relationships about information represented in the model. The language has a clear declarative and operational semantics. This work is a major revision and a consolidation of [12, 13].This is an extended version of the article in: 15th International Conference on Data Engineering, Sydney, Australia, 1999

Towards Complex Real-World Safety Factory Inspection: A High-Quality Dataset for Safety Clothing and Helmet Detection

Safety clothing and helmets play a crucial role in ensuring worker safety at construction sites. Recently, deep learning methods have garnered significant attention in the field of computer vision for their potential to enhance safety and efficiency in various industries. However, limited availability of high-quality datasets has hindered the development of deep learning methods for safety clothing and helmet detection. In this work, we present a large, comprehensive, and realistic high-quality dataset for safety clothing and helmet detection, which was collected from a real-world chemical plant and annotated by professional security inspectors. Our dataset has been compared with several existing open-source datasets, and its effectiveness has been verified applying some classic object detection methods. The results demonstrate that our dataset is more complete and performs better in real-world settings. Furthermore, we have released our deployment code to the public to encourage the adoption of our dataset and improve worker safety. We hope that our efforts will promote the convergence of academic research and industry, ultimately contribute to the betterment of society.Comment: 11 pages, 7 figure

Recaf: Java dialects as libraries

Mainstream programming languages like Java have limited support for language extensibility. Without mechanisms for syntactic abstraction, new programming styles can only be embedded in the form of libraries, limiting expressiveness. In this paper, we present Recaf, a lightweight tool for creating Java dialects; effectively extending Java with new language constructs and user defined semantics. The Recaf compiler generically transforms designated method bodies to code that is parameterized by a semantic factory (Object Algebra), defined in plain Java. The implementation of such a factory defines the desired runtime semantics. We applied our design to produce several examples from a diverse set of programming styles and two case studies: We define i) extensions for generators, asynchronous computations and asynchronous streams and ii) a Domain-Specific Language (DSL) for Parsing Expression Grammars (PEGs), in a few lines of code

Pedestrian Detection and Tracking in Video Surveillance System: Issues, Comprehensive Review, and Challenges

Pedestrian detection and monitoring in a surveillance system are critical for numerous utility areas which encompass unusual event detection, human gait, congestion or crowded vicinity evaluation, gender classification, fall detection in elderly humans, etc. Researchers’ primary focus is to develop surveillance system that can work in a dynamic environment, but there are major issues and challenges involved in designing such systems. These challenges occur at three different levels of pedestrian detection, viz. video acquisition, human detection, and its tracking. The challenges in acquiring video are, viz. illumination variation, abrupt motion, complex background, shadows, object deformation, etc. Human detection and tracking challenges are varied poses, occlusion, crowd density area tracking, etc. These results in lower recognition rate. A brief summary of surveillance system along with comparisons of pedestrian detection and tracking technique in video surveillance is presented in this chapter. The publicly available pedestrian benchmark databases as well as the future research directions on pedestrian detection have also been discussed

Automatic object classification for surveillance videos.

PhDThe recent popularity of surveillance video systems, specially located in urban scenarios, demands the development of visual techniques for monitoring purposes. A primary step towards intelligent surveillance video systems consists on automatic object classification, which still remains an open research problem and the keystone for the development of more specific applications. Typically, object representation is based on the inherent visual features. However, psychological studies have demonstrated that human beings can routinely categorise objects according to their behaviour. The existing gap in the understanding between the features automatically extracted by a computer, such as appearance-based features, and the concepts unconsciously perceived by human beings but unattainable for machines, or the behaviour features, is most commonly known as semantic gap. Consequently, this thesis proposes to narrow the semantic gap and bring together machine and human understanding towards object classification. Thus, a Surveillance Media Management is proposed to automatically detect and classify objects by analysing the physical properties inherent in their appearance (machine understanding) and the behaviour patterns which require a higher level of understanding (human understanding). Finally, a probabilistic multimodal fusion algorithm bridges the gap performing an automatic classification considering both machine and human understanding. The performance of the proposed Surveillance Media Management framework has been thoroughly evaluated on outdoor surveillance datasets. The experiments conducted demonstrated that the combination of machine and human understanding substantially enhanced the object classification performance. Finally, the inclusion of human reasoning and understanding provides the essential information to bridge the semantic gap towards smart surveillance video systems