FHIR-DHP: A standardized clinical data harmonisation pipeline for scalable AI application deployment

Background Increasing digitalisation in the medical domain gives rise to large amounts of healthcare data which has the potential to expand clinical knowledge and transform patient care if leveraged through artificial intelligence (AI). Yet, big data and AI oftentimes cannot unlock their full potential at scale, owing to non-standardised data formats, lack of technical and semantic data interoperability, and limited cooperation between stakeholders in the healthcare system. Despite the existence of standardised data formats for the medical domain, such as Fast Healthcare Interoperability Resources (FHIR), their prevalence and usability for AI remains limited.Objective We developed a data harmonisation pipeline (DHP) for clinical data sets relying on the common FHIR data standard.Methods We validated the performance and usability of our FHIR-DHP with data from the MIMIC IV database including > 40,000 patients admitted to an intensive care unit.Results We present the FHIR-DHP workflow in respect of transformation of “raw” hospital records into a harmonised, AI-friendly data representation. The pipeline consists of five key preprocessing steps: querying of data from hospital database, FHIR mapping, syntactic validation, transfer of harmonised data into the patient-model database and export of data in an AI-friendly format for further medical applications. A detailed example of FHIR-DHP execution was presented for clinical diagnoses records.Conclusions Our approach enables scalable and needs-driven data modelling of large and heterogenous clinical data sets. The FHIR-DHP is a pivotal step towards increasing cooperation, interoperability and quality of patient care in the clinical routine and for medical research

Engineering Agile Big-Data Systems

To be effective, data-intensive systems require extensive ongoing customisation to reflect changing user requirements, organisational policies, and the structure and interpretation of the data they hold. Manual customisation is expensive, time-consuming, and error-prone. In large complex systems, the value of the data can be such that exhaustive testing is necessary before any new feature can be added to the existing design. In most cases, the precise details of requirements, policies and data will change during the lifetime of the system, forcing a choice between expensive modification and continued operation with an inefficient design.Engineering Agile Big-Data Systems outlines an approach to dealing with these problems in software and data engineering, describing a methodology for aligning these processes throughout product lifecycles. It discusses tools which can be used to achieve these goals, and, in a number of case studies, shows how the tools and methodology have been used to improve a variety of academic and business systems

Application of Common Sense Computing for the Development of a Novel Knowledge-Based Opinion Mining Engine

The ways people express their opinions and sentiments have radically changed in the past few years thanks to the advent of social networks, web communities, blogs, wikis and other online collaborative media. The distillation of knowledge from this huge amount of unstructured information can be a key factor for marketers who want to create an image or identity in the minds of their customers for their product, brand, or organisation. These online social data, however, remain hardly accessible to computers, as they are specifically meant for human consumption. The automatic analysis of online opinions, in fact, involves a deep understanding of natural language text by machines, from which we are still very far. Hitherto, online information retrieval has been mainly based on algorithms relying on the textual representation of web-pages. Such algorithms are very good at retrieving texts, splitting them into parts, checking the spelling and counting their words. But when it comes to interpreting sentences and extracting meaningful information, their capabilities are known to be very limited. Existing approaches to opinion mining and sentiment analysis, in particular, can be grouped into three main categories: keyword spotting, in which text is classified into categories based on the presence of fairly unambiguous affect words; lexical affinity, which assigns arbitrary words a probabilistic affinity for a particular emotion; statistical methods, which calculate the valence of affective keywords and word co-occurrence frequencies on the base of a large training corpus. Early works aimed to classify entire documents as containing overall positive or negative polarity, or rating scores of reviews. Such systems were mainly based on supervised approaches relying on manually labelled samples, such as movie or product reviews where the opinionist’s overall positive or negative attitude was explicitly indicated. However, opinions and sentiments do not occur only at document level, nor they are limited to a single valence or target. Contrary or complementary attitudes toward the same topic or multiple topics can be present across the span of a document. In more recent works, text analysis granularity has been taken down to segment and sentence level, e.g., by using presence of opinion-bearing lexical items (single words or n-grams) to detect subjective sentences, or by exploiting association rule mining for a feature-based analysis of product reviews. These approaches, however, are still far from being able to infer the cognitive and affective information associated with natural language as they mainly rely on knowledge bases that are still too limited to efficiently process text at sentence level. In this thesis, common sense computing techniques are further developed and applied to bridge the semantic gap between word-level natural language data and the concept-level opinions conveyed by these. In particular, the ensemble application of graph mining and multi-dimensionality reduction techniques on two common sense knowledge bases was exploited to develop a novel intelligent engine for open-domain opinion mining and sentiment analysis. The proposed approach, termed sentic computing, performs a clause-level semantic analysis of text, which allows the inference of both the conceptual and emotional information associated with natural language opinions and, hence, a more efficient passage from (unstructured) textual information to (structured) machine-processable data. The engine was tested on three different resources, namely a Twitter hashtag repository, a LiveJournal database and a PatientOpinion dataset, and its performance compared both with results obtained using standard sentiment analysis techniques and using different state-of-the-art knowledge bases such as Princeton’s WordNet, MIT’s ConceptNet and Microsoft’s Probase. Differently from most currently available opinion mining services, the developed engine does not base its analysis on a limited set of affect words and their co-occurrence frequencies, but rather on common sense concepts and the cognitive and affective valence conveyed by these. This allows the engine to be domain-independent and, hence, to be embedded in any opinion mining system for the development of intelligent applications in multiple fields such as Social Web, HCI and e-health. Looking ahead, the combined novel use of different knowledge bases and of common sense reasoning techniques for opinion mining proposed in this work, will, eventually, pave the way for development of more bio-inspired approaches to the design of natural language processing systems capable of handling knowledge, retrieving it when necessary, making analogies and learning from experience