Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

Abstract Background Despite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network has been explored to meet this challenge, employing existing biological knowledge for network prediction is difficult. The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven Bayesian network learning; and to further use the trained model to predict cellular responses. Results We applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition. The challenge results showed that our method accurately captured signal transduction of a network of protein kinases and phosphoproteins in that the predicted protein phosphorylation levels under all experimental conditions were highly correlated (R2 = 0.93) with the observed results. Based on the evaluation of the DREAM4 organizer, our team was ranked as one of the top five best performers in predicting network structure and protein phosphorylation activity under test conditions. Conclusions Bayesian network can be used to simulate the propagation of signals in cellular systems. Incorporating the Ontology Fingerprint as prior biological knowledge allows us to efficiently infer concise signaling network structure and to accurately predict cellular responses.http://deepblue.lib.umich.edu/bitstream/2027.42/109490/1/12918_2012_Article_989.pd

Modeling functional requirements using tacit knowledge: a design science research methodology informed approach

The research in this paper adds to the discussion linked to the challenge of capturing and modeling tacit knowledge throughout software development projects. The issue emerged when modeling functional requirements during a project for a client. However, using the design science research methodology at a particular point in the project helped to create an artifact, a functional requirements modeling technique, that resolved the issue with tacit knowledge. Accordingly, this paper includes research based upon the stages of the design science research methodology to design and test the artifact in an observable situation, empirically grounding the research undertaken. An integral component of the design science research methodology, the knowledge base, assimilated structuration and semiotic theories so that other researchers can test the validity of the artifact created. First, structuration theory helped to identify how tacit knowledge is communicated and can be understood when modeling functional requirements for new software. Second, structuration theory prescribed the application of semiotics which facilitated the development of the artifact. Additionally, following the stages of the design science research methodology and associated tasks allows the research to be reproduced in other software development contexts. As a positive outcome, using the functional requirements modeling technique created, specifically for obtaining tacit knowledge on the software development project, indicates that using such knowledge increases the likelihood of deploying software successfully

Staging Transformations for Multimodal Web Interaction Management

Multimodal interfaces are becoming increasingly ubiquitous with the advent of mobile devices, accessibility considerations, and novel software technologies that combine diverse interaction media. In addition to improving access and delivery capabilities, such interfaces enable flexible and personalized dialogs with websites, much like a conversation between humans. In this paper, we present a software framework for multimodal web interaction management that supports mixed-initiative dialogs between users and websites. A mixed-initiative dialog is one where the user and the website take turns changing the flow of interaction. The framework supports the functional specification and realization of such dialogs using staging transformations -- a theory for representing and reasoning about dialogs based on partial input. It supports multiple interaction interfaces, and offers sessioning, caching, and co-ordination functions through the use of an interaction manager. Two case studies are presented to illustrate the promise of this approach.Comment: Describes framework and software architecture for multimodal web interaction managemen

A Neural Network Approach to Context-Sensitive Generation of Conversational Responses

We present a novel response generation system that can be trained end to end on large quantities of unstructured Twitter conversations. A neural network architecture is used to address sparsity issues that arise when integrating contextual information into classic statistical models, allowing the system to take into account previous dialog utterances. Our dynamic-context generative models show consistent gains over both context-sensitive and non-context-sensitive Machine Translation and Information Retrieval baselines.Comment: A. Sordoni, M. Galley, M. Auli, C. Brockett, Y. Ji, M. Mitchell, J.-Y. Nie, J. Gao, B. Dolan. 2015. A Neural Network Approach to Context-Sensitive Generation of Conversational Responses. In Proc. of NAACL-HLT. Pages 196-20