Multiple Relations Classification using Imbalanced Predictions Adaptation

The relation classification task assigns the proper semantic relation to a pair of subject and object entities; the task plays a crucial role in various text mining applications, such as knowledge graph construction and entities interaction discovery in biomedical text. Current relation classification models employ additional procedures to identify multiple relations in a single sentence. Furthermore, they overlook the imbalanced predictions pattern. The pattern arises from the presence of a few valid relations that need positive labeling in a relatively large predefined relations set. We propose a multiple relations classification model that tackles these issues through a customized output architecture and by exploiting additional input features. Our findings suggest that handling the imbalanced predictions leads to significant improvements, even on a modest training design. The results demonstrate superiority performance on benchmark datasets commonly used in relation classification. To the best of our knowledge, this work is the first that recognizes the imbalanced predictions within the relation classification task.Comment:

An Error Handling Framework for the ORBWork Workflow Enactment Service of METEOR

Workflow Management Systems (WFMSs) can be used to re-engineer, streamline, automate, and track organizational processes involving humans and automated information systems. However, the state-of-the-art in workflow technology suffers from a number of limitations that prevent it from being widely used in large-scale mission critical applications. Error handling is one such issue. What makes the task of error handling challenging is the need to deal with errors that appear in various components of a complex distributed application execution environment, including various WFMS components, workflow application tasks of different types, and the heterogeneous computing infrastructure. In this paper, we discuss a top-down approach towards dealing with errors in the context of ORBWork, a CORBA-based fully distributed workflow enactment service for the METEOR2 WFMS. The paper discusses the types of errors that might occur including those involving the infrastructure of the enactment environment, system architecture of the workflow enactment service. In the context of the underlying workflow model for METEOR, we then present a three-level error model to provide a unified approach to specification, detection, and runtime recovery of errors in ORBWork. Implementation issues are also discussed. We expect the model and many of the techniques to be relevant and adaptable to other WFMS implementations

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies. We identify 32 functional domains enriched in cancer variants and PTMs and generate mechanistic hypotheses on overlapping variant and PTM sites by aggregating information at the residue, protein, pathway and species level from these resources. We experimentally test the hypothesis that S768 phosphorylation in the C-helix of EGFR is inhibitory by showing that oncogenic variants altering S768 phosphorylation increase basal EGFR activity. In contrast, oncogenic variants altering conserved phosphorylation sites in the \u27hydrophobic motif\u27 of PKCβII (S660F and S660C) are loss-of-function in that they reduce kinase activity and enhance membrane translocation. Our studies provide a framework for integrative, consistent, and reproducible annotation of the cancer kinomes. Sci Rep 2018 Apr 25; 8(1):6518

Workflow Applications to Research Agenda: Scalable and Dynamic Work Coordination and Collaboration Systems

A workflow is an activity involving the coordinated execution of multiple tasks performed by different processing entities [KS 95]. These tasks could be manual, or automated, either created specifically for the purpose of the workflow application being developed, or possibly already existing as legacy programs A workflow process is an automated organizational process involving both human (manual) and automated tasks

RDF Data Exploration and Visualization

We present Paged Graph Visualization (PGV), a new semiautonomous tool for RDF data exploration and visualization. PGV consists of two main components: a) the \u27PGV explorer\u27 and b) the \u27RDF pager\u27 module utilizing BRAHMS, our high performance main-memory RDF storage system. Unlike existing graph visualization techniques which attempt to display the entire graph and then filter out irrelevant data, PGV begins with a small graph and provides the tools to incrementally explore and visualize relevant data of very large RDF ontologies. We implemented several techniques to visualize and explore hot spots in the graph, i.e. nodes with large numbers of immediate neighbors. In response to the user-controlled, semantics-driven direction of the exploration, the PGV explorer obtains the necessary sub-graphs from the RDF pager and enables their incremental visualization leaving the previously laid out sub-graphs intact. We outline the problem of visualizing large RDF data sets, discuss our interface and its implementation, and through a controlled experiment we show the benefits of PGV

Perspectives in Modeling: Simulation, Database, and Workflow

Development of today\u27s advanced applications is increasingly being accomplished using multi-faceted modeling. For example, the areas of simulation and workflow modeling generally need data modeling as a foundational capability. In addition, simulation modeling and workflow modeling can be used together, synergistically. Based on the experience of the LSDIS group in developing systems and models, we have found that establishing rich linkages between disparate models works better than having one comprehensive unified model. In addition, we agree with the consensus that two dimensional models are generally considered to be easier to create and understand than one dimensional models. Furthermore, just as richly linked text is referred to as hyper-text, richly linked diagrams may be referred to as hyper-diagrams. Two modeling toolkits, METEOR Designer and the JSIM Modeling Toolkit, illustrate the advantages of using such approaches