BioCAD: an information fusion platform for bio-network inference and analysis

Background : As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far from practical applications due to too many false inferences and lack of comprehensible interpretation in the biological viewpoints. In order for applying to real problems, they should provide effective inference, reliable validation, rational elucidation, and sufficient extensibility to incorporate various relevant information sources. Results : We have been developing an information fusion software platform called BioCAD. It is utilizing both of local and global optimization for bio-network inference, text mining techniques for network validation and annotation, and Web services-based workflow techniques. In addition, it includes an effective technique to elucidate network edges by integrating various information sources. This paper presents the architecture of BioCAD and essential modules for bio-network inference and analysis. Conclusion : BioCAD provides a convenient infrastructure for network inference and network analysis. It automates series of users' processes by providing data preprocessing tools for various formats of data. It also helps inferring more accurate and reliable bio-networks by providing network inference tools which utilize information from distinct sources. And it can be used to analyze and validate the inferred bio-networks using information fusion tools.ope

Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

<p>Abstract</p> <p>Background</p> <p>The extraction of complex events from biomedical text is a challenging task and requires in-depth semantic analysis. Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge.</p> <p>Results</p> <p>We developed a system that deduces implicit events from explicitly expressed events by using inference rules that encode domain knowledge. We evaluated the system with the inference module on three tasks: First, when tested against a corpus with manually annotated events, the inference module of our system contributes 53.2% of correct extractions, but does not cause any incorrect results. Second, the system overall reproduces 33.1% of the transcription regulatory events contained in RegulonDB (up to 85.0% precision) and the inference module is required for 93.8% of the reproduced events. Third, we applied the system with minimum adaptations to the identification of cell activity regulation events, confirming that the inference improves the performance of the system also on this task.</p> <p>Conclusions</p> <p>Our research shows that the inference based on domain knowledge plays a significant role in extracting complex events from text. This approach has great potential in recognizing the complex concepts of such biomedical ontologies as Gene Ontology in the literature.</p

Graph theory enables drug repurposing - how a mathematical model can drive the discovery of hidden mechanisms of action.

We introduce a methodology to efficiently exploit natural-language expressed biomedical knowledge for repurposing existing drugs towards diseases for which they were not initially intended. Leveraging on developments in Computational Linguistics and Graph Theory, a methodology is defined to build a graph representation of knowledge, which is automatically analysed to discover hidden relations between any drug and any disease: these relations are specific paths among the biomedical entities of the graph, representing possible Modes of Action for any given pharmacological compound. We propose a measure for the likeliness of these paths based on a stochastic process on the graph. This measure depends on the abundance of indirect paths between a peptide and a disease, rather than solely on the strength of the shortest path connecting them. We provide real-world examples, showing how the method successfully retrieves known pathophysiological Mode of Action and finds new ones by meaningfully selecting and aggregating contributions from known bio-molecular interactions. Applications of this methodology are presented, and prove the efficacy of the method for selecting drugs as treatment options for rare diseases

Automated code compliance checking in the construction domain using semantic natural language processing and logic-based reasoning

Construction projects must comply with various regulations. The manual process of checking the compliance with regulations is costly, time consuming, and error prone. With the advancement in computing technology, there have been many research efforts in automating the compliance checking process, and many software development efforts led by industry bodies/associations, software companies, and/or government organizations to develop automated compliance checking (ACC) systems. However, two main gaps in the existing ACC efforts are: (1) manual effort is needed for extracting requirements from regulatory documents and encoding these requirements in a computer-processable rule format; and (2) there is a lack of a semantic representation for supporting automated compliance reasoning that is non-proprietary, non-hidden, and user-understandable and testable. To address these gaps, this thesis proposes a new ACC method that: (1) utilizes semantic natural language processing (NLP) techniques to automatically extract regulatory information from building codes and design information from building information models (BIMs); and (2) utilizes a semantic logic-based representation to represent and reason about the extracted regulatory information and design information for compliance checking. The proposed method is composed of four main methods/algorithms that are combined in one computational framework: (1) a semantic, rule-based method and algorithm that leverage NLP techniques to automatically extract regulatory information from building codes and represent the extracted information into semantic tuples, (2) a semantic, rule-based method and algorithm that leverage NLP techniques to automatically transform the extracted regulatory information into logic rules to prepare for automated reasoning, (3) a semantic, rule-based information extraction and information transformation method and algorithm to automatically extract design information from BIMs and transform the extracted information into logic facts to prepare for automated reasoning, and (4) a logic-based information representation and compliance reasoning schema to represent regulatory and design information for enabling the automated compliance reasoning process. To test the proposed method, a building information model test case was developed based on the Duplex Apartment Project from buildingSMARTalliance of the National Institute of Building Sciences. The test case was checked for compliance with a randomly selected chapter, Chapter 19, of the International Building Code 2009. Comparing to a manually developed gold standard, 87.6% precision and 98.7% recall in noncompliance detection were achieved, on the testing data