Discovering medication patterns for high-complexity drug-using diseases through electronic medical records

An Electronic Medical Record (EMR) is a professional document that contains all data generated during the treatment process. The EMR can utilize various data formats, such as numerical data, text, and images. Mining the information and knowledge hidden in the huge amount of EMR data is an essential requirement for clinical decision support, such as clinical pathway formulation and evidence-based medical research. In this paper, we propose a machine-learning-based framework to mine the hidden medication patterns in EMR text. The framework systematically integrates the Jaccard similarity evaluation, spectral clustering, the modified Latent Dirichlet Allocation and cross-matching among multiple features to find the residuals that describe additional knowledge and clusters hidden in multiple perspectives of highly complex medication patterns. These methods work together, step by step to reveal the underlying medication pattern. We evaluated the method by using real data from EMR text (patients with cirrhotic ascites) from a large hospital in China. The proposed framework outperforms other approaches for medication pattern discovery, especially for this disease with subtle medication treatment variances. The results also revealed little overlap among the discovered patterns; thus, the distinct features of each pattern are well studied through the proposed framework

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

PaperRobot: Incremental Draft Generation of Scientific Ideas

We present a PaperRobot who performs as an automatic research assistant by (1) conducting deep understanding of a large collection of human-written papers in a target domain and constructing comprehensive background knowledge graphs (KGs); (2) creating new ideas by predicting links from the background KGs, by combining graph attention and contextual text attention; (3) incrementally writing some key elements of a new paper based on memory-attention networks: from the input title along with predicted related entities to generate a paper abstract, from the abstract to generate conclusion and future work, and finally from future work to generate a title for a follow-on paper. Turing Tests, where a biomedical domain expert is asked to compare a system output and a human-authored string, show PaperRobot generated abstracts, conclusion and future work sections, and new titles are chosen over human-written ones up to 30%, 24% and 12% of the time, respectively.Comment: 12 pages. Accepted by ACL 2019 Code and resource is available at https://github.com/EagleW/PaperRobo

Applying Process-Oriented Data Science to Dentistry

Background: Healthcare services now often follow evidence-based principles, so technologies such as process and data mining will help inform their drive towards optimal service delivery. Process mining (PM) can help the monitoring and reporting of this service delivery, measure compliance with guidelines, and assess effectiveness. In this research, PM extracts information about clinical activity recorded in dental electronic health records (EHRs) converts this into process-models providing stakeholders with unique insights to the dental treatment process. This thesis addresses a gap in prior research by demonstrating how process analytics can enhance our understanding of these processes and the effects of changes in strategy and policy over time. It also emphasises the importance of a rigorous and documented methodological approach often missing from the published literature. Aim: Apply the emerging technology of PM to an oral health dataset, illustrating the value of the data in the dental repository, and demonstrating how it can be presented in a useful and actionable manner to address public health questions. A subsidiary aim is to present the methodology used in this research in a way that provides useful guidance to future applications of dental PM. Objectives: Review dental and healthcare PM literature establishing state-of-the-art. Evaluate existing PM methods and their applicability to this research’s dataset. Extend existing PM methods achieving the aims of this research. Apply PM methods to the research dataset addressing public health questions. Document and present this research’s methodology. Apply data-mining, PM, and data-visualisation to provide insights into the variable pathways leading to different outcomes. Identify the data needed for PM of a dental EHR. Identify challenges to PM of dental EHR data. Methods: Extend existing PM methods to facilitate PM research in public health by detailing how data extracts from a dental EHR can be effectively managed, prepared, and used for PM. Use existing dental EHR and PM standards to generate a data reference model for effective PM. Develop a data-quality management framework. Results: Comparing the outputs of PM to established care-pathways showed that the dataset facilitated generation of high-level pathways but was less suitable for detailed guidelines. Used PM to identify the care pathway preceding a dental extraction under general anaesthetic and provided unique insights into this and the effects of policy decisions around school dental screenings. Conclusions: Research showed that PM and data-mining techniques can be applied to dental EHR data leading to fresh insights about dental treatment processes. This emerging technology along with established data mining techniques, should provide valuable insights to policy makers such as principal and chief dental officers to inform care pathways and policy decisions

Discovering Complex Relationships between Drugs and Diseases

Finding the complex semantic relations between existing drugs and new diseases will help in the drug development in a new way. Most of the drugs which have found new uses have been discovered due to serendipity. Hence, the prediction of the uses of drugs for more than one disease should be done in a systematic way by studying the semantic relations between the drugs and diseases and also the other entities involved in the relations. Hence, in order to study the complex semantic relations between drugs and diseases an application was developed that integrates the heterogeneous data in different formats from different public databases which are available online. A high level ontology was also developed to integrate the data and only the fields required for the current study were used. The data was collected from different data sources such as DrugBank, UniProt/SwissProt, GeneCards and OMIM. Most of these data sources are the standard data sources and have been used by National Committee of Biotechnology Information of Nation Institute of Health. The data was parsed and integrated and complex semantic relations were discovered. This is a simple and novel effort which may find uses in development of new drug targets and polypharmacology

Dynamic Risk Models for Characterising Chronic Diseases' Behaviour Using Process Mining Techniques

[ES] Los modelos de riesgo en el ámbito de la salud son métodos estadísticos que brindan advertencias tempranas sobre el riesgo de una persona de sufrir un episodio adverso en el futuro. Por lo general, utilizan la información almacenada de forma rutinaria en los sistemas de información hospitalaria para ofrecer una probabilidad individual de desarrollar un resultado negativo futuro en un período determinado. Concretamente, en el campo de las enfermedades crónicas que comparten factores de riesgo comunes, los modelos de riesgo se basan en el análisis de esos factores de riesgo -tensión arterial elevada, glucemia elevada, lípidos sanguíneos anormales, sobrepeso y obesidad- y sus medidas biométricas asociadas. Estas medidas se recopilan durante la práctica clínica de manera periódica y, se incorporan a los modelos de riesgo para apoyar a los médicos en la toma de decisiones. Para crear modelos de riesgo que incluyan la variable temporal, se podrían utilizar técnicas basadas en datos (Data-Driven), de forma que se tuviera en cuenta el historial de los pacientes almacenado en los registros médicos electrónicos, extrayendo conocimiento de los datos en bruto. Sin embargo, en el ámbito de la salud, los resultados de la minería de datos suelen ser percibidos por los expertos en salud como cajas negras y, en consecuencia, no confían en sus decisiones. El paradigma Interactivo permite a los expertos comprender los resultados, para que los profesionales puedan corregir esos modelos de acuerdo con su conocimiento y experiencia, proporcionando modelos perceptivos y cognitivos. En este contexto, la minería de procesos es una técnica de minería de datos que permite la implementación del paradigma Interactivo, ofreciendo una comprensión clara del proceso de atención y proporcionando modelos comprensibles para el ser humano. Las condiciones crónicas generalmente se describen mediante imágenes estáticas de variables, como factores genéticos, fisiológicos, ambientales y de comportamiento. Sin embargo, la perspectiva dinámica, temporal y de comportamiento no se consideran comúnmente en los modelos de riesgo. Eso significa que el último estado de riesgo se convierte en el estado real del paciente. No obstante, la condición de los pacientes podría verse influenciada por sus condiciones dinámicas pasadas. El objetivo de esta tesis es proporcionar una visión novedosa del riesgo asociado a un paciente, basada en tecnologías Data-Driven que ofrezcan una visión dinámica de su evolución con respecto a su condición crónica. Técnicamente, supone abordar los modelos de riesgo incorporando la perspectiva dinámica y comportamental de los pacientes gracias a la información incluida en la Historia Clínica Electrónica. Los resultados obtenidos a lo largo de esta tesis muestran cómo las tecnologías de minería de procesos pueden aportar una visión dinámica e interactiva de los modelos de riesgo de enfermedades crónicas. Estos resultados pueden ayudar a los profesionales de la salud en la práctica diaria para una mejor comprensión del estado de salud de los pacientes y una mejor clasificación de su estado de riesgo.[CA] Els models de risc en l'àmbit de la salut són mètodes estadístics que brinden advertències primerenques sobre el risc d'una persona de patir un episodi advers en el futur. Generalment, utilitzen la informació emmagatzemada de forma rutinària en els sistemes d'informació hospitalària per a oferir una probabilitat individual de desenrotllar un resultat negatiu futur en un període determinat. Concretament, en el camp de les malalties cròniques que compartixen factors de risc comú, els models de risc es basen en l'anàlisi d'eixos factors de risc -tensió arterial elevada, glucèmia elevada, lípids sanguinis anormals, sobrecàrrega i obesitat- i les seues mesures biomètriques associades. Estes mesures es recopilen durant la pràctica clínica ben sovint de manera periòdica i, en conseqüència, s'incorporen als models de risc i recolzen la presa de decisions dels metges. Per a crear estos models de risc que incloguen la variable temporal es podrien utilitzar tècniques basades en dades (Data-Driven) , de manera que es tinguera en compte l'historial dels pacients disponible en els registres mèdics electrònics, extraient coneixement de les dades en brut. No obstant això, en l'àmbit de la salut, els resultats de la mineria de dades solen ser percebuts pels experts en salut com a caixes negres i, en conseqüència, no confien en les decisions dels algoritmes. El paradigma Interactiu permet als experts comprendre els resultats, perquè els professionals puguen corregir eixos models d'acord amb el seu coneixement i experiència, proporcionant models perceptius i cognitius. En este context, la mineria de processos és una tècnica de mineria de dades que permet la implementació del paradigma Interactiu, oferint una comprensió clara del procés d'atenció i proporcionant models comprensibles per al ser humà. Les condicions cròniques generalment es descriuen per mitjà d'imatges estàtiques de variables, com a factors genètics, fisiològics, ambientals i de comportament. No obstant això, la perspectiva dinàmica, temporal i de comportament no es consideren comunament en els models de risc. Això significa que l'últim estat de risc es convertix en l'estat real del pacient. No obstant això, la condició dels pacients podria veure's influenciada per les seues condicions dinàmiques passades. L'objectiu d'esta tesi és proporcionar una visió nova del risc, associat a un pacient, basada en tecnologies Data-Driven que oferisquen una visió dinàmica de l'evo\-lució dels pacients respecte a la seua condició crònica. Tècnicament, suposa abordar els models de risc incorporant la perspectiva dinàmica i el comportament dels pacients als models de risc gràcies a la informació inclosa en la Història Clínica Electrònica. Els resultats obtinguts al llarg d'esta tesi mostren com les tecnologies de mineria de processos poden aportar una visió dinàmica i interactiva dels models de risc de malalties cròniques. Estos resultats poden ajudar els professionals de la salut en la pràctica diària per a una millor comprensió de l'estat de salut dels pacients i una millor classificació del seu estat de risc.[EN] Risk models in the healthcare domain are statistical methods that provide early warnings about a person's risk for an adverse episode in the future. They usually use the information routinely stored in Hospital Information Systems to offer an individual probability for developing a future negative outcome in a given period. Concretely, in the field of chronic diseases that share common risk factors, risk models are based on the analysis of those risk factors -raised blood pressure, raised glucose levels, abnormal blood lipids, and overweight and obesity- and their associated biometric measures. These measures are collected during clinical practice frequently in a periodic manner, and accordingly, they are incorporated into the risk models to support clinicians' decision-making. Data-Driven techniques could be used to create these temporal-aware risk models, considering the patients' history included in Electronic Health Records, and extracting knowledge from raw data. However, in the healthcare domain, Data Mining results are usually perceived by the health experts as black-boxes, and in consequence, they do not trust in the algorithms' decisions. The Interactive paradigm allows experts to understand the results, in that sense, professionals can correct those models according to their knowledge and experience, providing perceptual and cognitive models. In this context, Process Mining is a Data Mining technique that enables the implementation of the Interactive paradigm, offering a clear care process understanding and providing human-understandable models. Chronic conditions are usually described by static pictures of variables, such as genetic, physiological, environmental, and behavioural factors. Nevertheless, the dynamic, temporal, and behavioural perspectives are not commonly considered in the risk models. That means the last status of the risk becomes the actual status of the patient. However, the patients' condition could be influenced by their past dynamic circumstances. The objective of this thesis is to provide a novel risk vision based on Data-Driven technologies offering a dynamic view of the patients' evolution regarding their chro\-nic condition. Technically, it supposes to approach risk models incorporating the dynamic and behavioural perspective of patients to the risk models thanks to the information included in the Electronic Health Records. The results obtained throughout this thesis show how Process Mining technologies can bring a dynamic and interactive view of chronic disease risk models. These results can support health professionals in daily practice for a better understanding of the patients' health condition and a better classification of their risk status.Valero Ramón, Z. (2022). Dynamic Risk Models for Characterising Chronic Diseases' Behaviour Using Process Mining Techniques [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/181652TESI