Building Data-Driven Pathways From Routinely Collected Hospital Data:A Case Study on Prostate Cancer

Background: Routinely collected data in hospitals is complex, typically heterogeneous, and scattered across multiple Hospital Information Systems (HIS). This big data, created as a byproduct of health care activities, has the potential to provide a better understanding of diseases, unearth hidden patterns, and improve services and cost. The extent and uses of such data rely on its quality, which is not consistently checked, nor fully understood. Nevertheless, using routine data for the construction of data-driven clinical pathways, describing processes and trends, is a key topic receiving increasing attention in the literature. Traditional algorithms do not cope well with unstructured processes or data, and do not produce clinically meaningful visualizations. Supporting systems that provide additional information, context, and quality assurance inspection are needed. Objective: The objective of the study is to explore how routine hospital data can be used to develop data-driven pathways that describe the journeys that patients take through care, and their potential uses in biomedical research; it proposes a framework for the construction, quality assessment, and visualization of patient pathways for clinical studies and decision support using a case study on prostate cancer. Methods: Data pertaining to prostate cancer patients were extracted from a large UK hospital from eight different HIS, validated, and complemented with information from the local cancer registry. Data-driven pathways were built for each of the 1904 patients and an expert knowledge base, containing rules on the prostate cancer biomarker, was used to assess the completeness and utility of the pathways for a specific clinical study. Software components were built to provide meaningful visualizations for the constructed pathways. Results: The proposed framework and pathway formalism enable the summarization, visualization, and querying of complex patient-centric clinical information, as well as the computation of quality indicators and dimensions. A novel graphical representation of the pathways allows the synthesis of such information. Conclusions: Clinical pathways built from routinely collected hospital data can unearth information about patients and diseases that may otherwise be unavailable or overlooked in hospitals. Data-driven clinical pathways allow for heterogeneous data (ie, semistructured and unstructured data) to be collated over a unified data model and for data quality dimensions to be assessed. This work has enabled further research on prostate cancer and its biomarkers, and on the development and application of methods to mine, compare, analyze, and visualize pathways constructed from routine data. This is an important development for the reuse of big data in hospitals

Data Cleaning for XML Electronic Dictionaries via Statistical Anomaly Detection

Many important forms of data are stored digitally in XML format. Errors can occur in the textual content of the data in the fields of the XML. Fixing these errors manually is time-consuming and expensive, especially for large amounts of data. There is increasing interest in the research, development, and use of automated techniques for assisting with data cleaning. Electronic dictionaries are an important form of data frequently stored in XML format that frequently have errors introduced through a mixture of manual typographical entry errors and optical character recognition errors. In this paper we describe methods for flagging statistical anomalies as likely errors in electronic dictionaries stored in XML format. We describe six systems based on different sources of information. The systems detect errors using various signals in the data including uncommon characters, text length, character-based language models, word-based language models, tied-field length ratios, and tied-field transliteration models. Four of the systems detect errors based on expectations automatically inferred from content within elements of a single field type. We call these single-field systems. Two of the systems detect errors based on correspondence expectations automatically inferred from content within elements of multiple related field types. We call these tied-field systems. For each system, we provide an intuitive analysis of the type of error that it is successful at detecting. Finally, we describe two larger-scale evaluations using crowdsourcing with Amazon's Mechanical Turk platform and using the annotations of a domain expert. The evaluations consistently show that the systems are useful for improving the efficiency with which errors in XML electronic dictionaries can be detected.Comment: 8 pages, 4 figures, 5 tables; published in Proceedings of the 2016 IEEE Tenth International Conference on Semantic Computing (ICSC), Laguna Hills, CA, USA, pages 79-86, February 201

Documentation and knowledge acquisition

Traditional approaches to knowledge acquisition have focused on interviews. An alternative focuses on the documentation associated with a domain. Adopting a documentation approach provides some advantages during familiarization. A knowledge management tool was constructed to gain these advantages

Statistical Inferences for Polarity Identification in Natural Language

Information forms the basis for all human behavior, including the ubiquitous decision-making that people constantly perform in their every day lives. It is thus the mission of researchers to understand how humans process information to reach decisions. In order to facilitate this task, this work proposes a novel method of studying the reception of granular expressions in natural language. The approach utilizes LASSO regularization as a statistical tool to extract decisive words from textual content and draw statistical inferences based on the correspondence between the occurrences of words and an exogenous response variable. Accordingly, the method immediately suggests significant implications for social sciences and Information Systems research: everyone can now identify text segments and word choices that are statistically relevant to authors or readers and, based on this knowledge, test hypotheses from behavioral research. We demonstrate the contribution of our method by examining how authors communicate subjective information through narrative materials. This allows us to answer the question of which words to choose when communicating negative information. On the other hand, we show that investors trade not only upon facts in financial disclosures but are distracted by filler words and non-informative language. Practitioners - for example those in the fields of investor communications or marketing - can exploit our insights to enhance their writings based on the true perception of word choice

Learning Dictionaries for Named Entity Recognition using Minimal Supervision

This paper describes an approach for automatic construction of dictionaries for Named Entity Recognition (NER) using large amounts of unlabeled data and a few seed examples. We use Canonical Correlation Analysis (CCA) to obtain lower dimensional embeddings (representations) for candidate phrases and classify these phrases using a small number of labeled examples. Our method achieves 16.5% and 11.3% F-1 score improvement over co-training on disease and virus NER respectively. We also show that by adding candidate phrase embeddings as features in a sequence tagger gives better performance compared to using word embeddings.Comment: In 14th Conference of the European Chapter of the Association for Computational Linguistic, 201

Creating information delivery specifications using linked data

The use of Building Information Management (BIM) has become mainstream in many countries. Exchanging data in open standards like the Industry Foundation Classes (IFC) is seen as the only workable solution for collaboration. To define information needs for collaboration, many organizations are now documenting what kind of data they need for their purposes. Currently practitioners define their requirements often a) in a format that cannot be read by a computer; b) by creating their own definitions that are not shared. This paper proposes a bottom up solution for the definition of new building concepts a property. The authors have created a prototype implementation and will elaborate on the capturing of information specifications in the future

Definitions in ontologies

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies