Building characteristics are often absent in building stock datasets, particularly in regions most vulnerable to climate change and requiring effective disaster management strategies. Traditional machine learning approaches, while widely used to predict building attributes, typically neglect the spatial context of the data, leading to less accurate and reliable outcomes. To address these challenges, this paper introduces a novel algorithm, the Stacked Integration of Geospatial Hierarchical Typologies. This algorithm adapts a meta-learning framework to incorporate geospatial context into the predictive modeling process. We demonstrate the utility of the algorithm through two primary use cases: building use type classification and building height prediction. The algorithm consistently achieved or exceeded a 0.94 macro average F1 score across five geographically distinct countries for building use type classification. For building height prediction, it accurately predicted heights with a root mean square error of 3.01 in a comprehensive study using roughly 3.6 million buildings in Japan. These results underscore the benefits of integrating spatial hierarchies into machine learning models, enhancing both predictive accuracy and reliability in geospatial modeling. This work introduces a new algorithm to address the pervasive data sparsity issue in existing building stock datasets.

With the emergence of online social networks (OSNs), video recommendation has come to play a crucial role in mitigating the semantic gap between users and videos. Conventional approaches to video recommendation primarily focus on exploiting content features or simple user-video interactions to model the users’ preferences. Although these methods have achieved promising results, they fail to model the complex video context interdependency, which is obscure/hidden in heterogeneous auxiliary data from OSNs. In this paper, we study the problem of video recommendation in Heterogeneous Information Networks (HINs) due to its excellence in characterizing heterogeneous and complex context information. We propose a Context-Dependent Propagating Recommendation network (CDPRec) to obtain accurate video embedding and capture global context cues among videos in HINs. The CDPRec can iteratively propagate the contexts of a video along links in a graph-structured HIN and explore multiple types of dependencies among the surrounding video nodes. Then, each video is represented as the composition of the multimodal content feature and global dependency structure information using an attention network. The learned video embedding with sequential based recommendation are jointly optimized for the final rating prediction. Experimental results on real-world YouTube video recommendation scenarios demonstrate the effectiveness of the proposed methods compared with strong baselines.

The task of estimating the fundamental frequency of a monophonic sound recording, also known as pitch tracking, is fundamental to audio processing with multiple applications in speech processing and music information retrieval. To date, the best performing techniques, such as the pYIN algorithm, are based on a combination of DSP pipelines and heuristics. While such techniques perform very well on average, there remain many cases in which they fail to correctly estimate the pitch. In this paper, we propose a data-driven pitch tracking algorithm, CREPE, which is based on a deep convolutional neural network that operates directly on the time-domain waveform. We show that the proposed model produces state-of-the-art results, performing equally or better than pYIN. Furthermore, we evaluate the model's generalizability in terms of noise robustness. A pre-trained version of CREPE is made freely available as an open-source Python module for easy application.

On line analytical processing (OLAP) is an essential element of decision-support systems. However, OLAP queries can be biased and lead to perplexing and incorrect insights. In this demo, we present HypDB, the first system to detect, explain and resolve bias in OLAP queries. Our demonstration, shows several examples of OLAP queries from real world datasets that are biased and could lead to statistical anomalies such as Simpson's paradox. Then, we demonstrate step-by-step how HypDB: (1) detects whether an OLAP query is biased, (2) explains the root causes of the bias and reveals illuminating insights about the domain and the data collection process and (3) eliminates the bias via query rewriting and generates decision-support insights.

We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.

We developed a real-time, visual analytics tool for clinical decision support. The system expands the "recall of past experience" approach that a provider (physician) uses to formulate a course of action for a given patient. By utilizing Big-Data techniques, we enable the provider to recall all similar patients from an institution's electronic medical record (EMR) repository, to explore "what-if" scenarios, and to collect these evidence-based cohorts for future statistical validation and pattern mining.

This paper presents a new multi-level EDT scheme to reduce scan channels of scan-based SoC designs. Multi-level EDT requires trivial modification on existing EDT scheme with two-pass encoding. Experimental results show that this scheme can reduce channel count by up to 30% without penalty of test coverage and pattern count.

Computational and data-intensive science increasingly depends on a large Web Service infrastructure, as services that provide a broad array of functionality can be composed into workflows to address complex research questions. In this context, the goal of service registries is to offer accurate search and discovery functions to scientists. Their effectiveness, however, depends not only on the model chosen to annotate the services, but also on the level of abstraction chosen for the annotations. The work presented in this paper stems from the observation that current annotation models force users to think in terms of service interfaces, rather than of high-level functionality, thus reducing their effectiveness. To alleviate this problem,we introduce Functional Units (FU) as the elementary units of information used to describe a service. Using popular examples of services for the Life Sciences, we define FUs as configurations and compositions of underlying service operations, and show how functional-style service annotations can be easily realised using the OWL semantic Web language. Finally, we suggest techniques for automating the service annotations process, by analysing collections of workflows that use those services.

BACKGROUND: The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. RESULTS: Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. CONCLUSIONS: Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

UNLABELLED: Many data manipulation processes involve the use of programming libraries. These processes may beneficially be automated due to their repeated use. A convenient type of automation is in the form of workflows that also allow such processes to be shared amongst the community. The Taverna workflow system has been extended to enable it to use and invoke Java classes and methods as tasks within Taverna workflows. These classes and methods are selected for use during workflow construction by a Java Doclet application called the API Consumer. This selection is stored as an XML file which enables Taverna to present the subset of the API for use in the composition of workflows. The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model. AVAILABILITY: Taverna and the API Consumer application can be freely downloaded from http://taverna.sourceforge.net

BACKGROUND: There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. RESULTS: Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. CONCLUSION: Taverna can be used by data analysis experts as a generic tool for composing ad hoc analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.

Much has been written on the promise of Web service discovery and (semi-) automated composition. In this discussion, the value to practitioners of discovering and reusing existing service compositions, captured in workflows, is mostly ignored. This paper presents one solution to workflow discovery. Through a survey with 21 scientists and developers from the myGrid workflow environment, workflow discovery requirements are elicited. Through a user experiment with 13 scientists, an attempt is made to build a gold standard for workflow ranking. Through the design and implementation of a workflow discovery tool, a mechanism for ranking workflow fragments is provided based on graph sub-isomorphism matching. The tool evaluation, drawing on a corpus of 89 public workflows from bioinformatics and the results of the user experiment, finds that the average human ranking can largely be reproduced

Abstract Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co‐ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science. Copyright © 2005 John Wiley & Sons, Ltd.

MOTIVATION: In silico experiments in bioinformatics involve the co-ordinated use of computational tools and information repositories. A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses. RESULTS: The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community. The tool includes a workbench application which provides a graphical user interface for the composition of workflows. These workflows are written in a new language called the simple conceptual unified flow language (Scufl), where by each step within a workflow represents one atomic task. Two examples are used to illustrate the ease by which in silico experiments can be represented as Scufl workflows using the workbench application.

My Grid is an e-Science Grid project that aims to help biologists and bioinformaticians to perform workflow-based in silico experiments, and help them to automate the management of such workflows through personalisation, notification of change and publication of experiments. In this paper, we describe the architecture of my Grid and how it will be used by the scientist. We then show how my Grid can benefit from agents technologies. We have identified three key uses of agent technologies in my Grid: user agents, able to customize and personalise data, agent communication languages offering a generic and portable communication medium, and negotiation allowing multiple distributed entities to reach service level agreements.