Achille B. Fokoue-Nkoutche

Structured data and inference in DeepQA

Although the majority of evidence analysis in DeepQA is focused on unstructured information (e.g., natural-language documents), several components in the DeepQA system use structured data (e.g., databases, knowledge bases, and ontologies) to generate potential candidate answers or find additional evidence. Structured data analytics are a natural complement to unstructured methods in that they typically cover a narrower range of questions but are more precise within that range. Moreover, structured data that has formal semantics is amenable to logical reasoning techniques that can be used to provide implicit evidence. The DeepQA system does not contain a single monolithic structured data module; instead, it allows for different components to use and integrate structured and semistructured data, with varying degrees of expressivity and formal specificity. This paper is a survey of DeepQA components that use structured data. Areas in which evidence from structured sources has the most impact include typing of answers, application of geospatial and temporal constraints, and the use of formally encoded a priori knowledge of commonly appearing entity types such as countries and U.S. presidents. We present details of appropriate components and demonstrate their end-to-end impact on the IBM Watsoni system.

Fusion: a system for business users to manage program variability

In order to make software components more flexible and reusable, it is desirable to provide business users with facilities to assemble and control them without their needing programming knowledge. This paper describes a fully functional prototype middleware system where variability is externalized so that core applications need not be altered for anticipated changes. In this system, application behavior modification is fast and easy, making this middleware suitable for frequently changing programs.

Molecular Docking for Prediction and Interpretation of Adverse Drug Reactions

AIM AND OBJECTIVE Adverse drug reactions (ADRs) present a major burden for patients and the healthcare industry. Various computational methods have been developed to predict ADRs for drug molecules. However, many of these methods require experimental or surveillance data and cannot be used when only structural information is available. MATERIALS AND METHODS We collected 1,231 small molecule drugs and 600 human proteins and utilized molecular docking to generate binding features among them. We developed machine learning models that use these docking features to make predictions for 1,533 ADRs. RESULTS These models obtain an overall area under the receiver operating characteristic curve (AUROC) of 0.843 and an overall area under the precision-recall curve (AUPR) of 0.395, outperforming seven structural fingerprint-based prediction models. Using the method, we predicted skin striae for fluticasone propionate, dermatitis acneiform for mometasone, and decreased libido for irinotecan, as demonstrations. Furthermore, we analyzed the top binding proteins associated with some of the ADRs, which can help to understand and/or generate hypotheses for underlying mechanisms of ADRs. CONCLUSION Machine learning combined with molecular docking can help to predict ADRs for drug molecules and provide possible explanations for the ADR mechanisms.