Modeling Paradigms for Medical Diagnostic Decision Support: A Survey and Future Directions

XAI4EEG: spectral and spatio-temporal explanation of deep learning-based seizure detection in EEG time series

In clinical practice, algorithmic predictions may seriously jeopardise patients’ health and thus are required to be validated by medical experts before a final clinical decision is met. Towards that aim, there is need to incorporate explainable artificial intelligence techniques into medical research. In the specific field of epileptic seizure detection there are several machine learning algorithms but less methods on explaining them in an interpretable way. Therefore, we introduce XAI4EEG: an application-aware approach for an explainable and hybrid deep learning-based detection of seizures in multivariate EEG time series. In XAI4EEG, we combine deep learning models and domain knowledge on seizure detection, namely (a) frequency bands, (b) location of EEG leads and (c) temporal characteristics. XAI4EEG encompasses EEG data preparation, two deep learning models and our proposed explanation module visualizing feature contributions that are obtained by two SHAP explainers, each explaining the predictions of one of the two models. The resulting visual explanations provide an intuitive identification of decision-relevant regions in the spectral, spatial and temporal EEG dimensions. To evaluate XAI4EEG, we conducted a user study, where users were asked to assess the outputs of XAI4EEG, while working under time constraints, in order to emulate the fact that clinical diagnosis is done - more often than not - under time pressure. We found that the visualizations of our explanation module (1) lead to a substantially lower time for validating the predictions and (2) leverage an increase in interpretability, trust and confidence compared to selected SHAP feature contribution plots.

Extraction of Active Medications and Adherence Using Natural Language Processing for Glaucoma Patients

Accuracy of medication data in electronic health records (EHRs) is crucial for patient care and research, but many studies have shown that medication lists frequently contain errors. In contrast, physicians often pay more attention to the clinical notes and record medication information in them. The medication information in notes may be used for medication reconciliation to improve the medication lists' accuracy. However, accurately extracting patient's current medications from free-text narratives is challenging. In this study, we first explored the discrepancies between medication documentation in medication lists and progress notes for glaucoma patients by manually reviewing patients' charts. Next, we developed and validated a named entity recognition model to identify current medication and adherence from progress notes. Lastly, a prototype tool for medication reconciliation using the developed model was demonstrated. In the future, the model has the potential to be incorporated into the EHR system to help with realtime medication reconciliation.

Improving Emergency Department Patient-Physician Conversation Through an Artificial Intelligence Symptom-Taking Tool: Mixed Methods Pilot Observational Study

BACKGROUND

Establishing rapport and empathy between patients and their health care provider is important but challenging in the context of a busy and crowded emergency department (ED).

OBJECTIVE

We explore the hypotheses that rapport building, documentation, and time efficiency might be improved in the ED by providing patients a digital tool that uses Bayesian reasoning-based techniques to gather relevant symptoms and history for handover to clinicians.

METHODS

A 2-phase pilot evaluation was carried out in the ED of a German tertiary referral and major trauma hospital that treats an average of 120 patients daily. Phase 1 observations guided iterative improvement of the digital tool, which was then further evaluated in phase 2. All patients who were willing and able to provide consent were invited to participate, excluding those with severe injury or illness requiring immediate treatment, with traumatic injury, incapable of completing a health assessment, and aged <18 years. Over an 18-day period with 1699 patients presenting to the ED, 815 (47.96%) were eligible based on triage level. With available recruitment staff, 135 were approached, of whom 81 (60%) were included in the study. In a mixed methods evaluation, patients entered information into the tool, accessed by clinicians through a dashboard. All users completed evaluation Likert-scale questionnaires rating the tool's performance. The feasibility of a larger trial was evaluated through rates of recruitment and questionnaire completion.

RESULTS

Respondents strongly endorsed the tool for facilitating conversation (61/81, 75% of patients, 57/78, 73% of physician ratings, and 10/10, 100% of nurse ratings). Most nurses judged the tool as potentially time saving, whereas most physicians only agreed for a subset of medical specialties (eg, surgery). Patients reported high usability and understood the tool's questions. The tool was recommended by most patients (63/81, 78%), in 53% (41/77) of physician ratings, and in 76% (61/80) of nurse ratings. Questionnaire completion rates were 100% (81/81) by patients and 96% (78/81 enrolled patients) by physicians.

CONCLUSIONS

This pilot confirmed that a larger study in the setting would be feasible. The tool has clear potential to improve patient-health care provider interaction and could also contribute to ED efficiency savings. Future research and development will extend the range of patients for whom the history-taking tool has clinical utility.

TRIAL REGISTRATION

German Clinical Trials Register DRKS00024115; https://drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00024115.

Advancing the Regulation of Traditional and Complementary Medicine Products: A Comparison of Five Regulatory Systems on Traditional Medicines with a Long History of Use

Background

An appropriate regulatory system to ensure and promote the quality, safety, and efficacy of the products of traditional medicine (TM) and complementary medicine (CM) is critical to not only public health but also economic growth. The regulatory approach and evaluation standards for TM/CM products featured with a long history of use are yet to be developed. This study aims to investigate and compare the existing regulatory approaches for TM/CM products with a long history of use.

Method

A mixed approach of documentary analysis involving official and legal documents from official websites, as well as a scoping review of scholarly work in scientific databases about regulatory systems of TM/CM products in China, Hong Kong, Taiwan, Japan, and Korea, was employed in this study and used for comparison.

Results

For registration purposes, all five regulatory systems recognized the history of use as part of the totality of evidence when evaluating the safety and efficacy of TM/CM products with a long history of use. Generally, the list of classic formulas is predefined and bound to the formulas recommended in the prescribed list of ancient medical textbooks. Expedited pathways are usually in place and scientific data of nonclinical and clinical studies may be exempted. At the same time, additional restrictions with the scope of products constitute a comprehensive approach in the regulation. Quality assurance and postmarketing safety surveillance were found to be the major focus across the regulatory schemes investigated in this study.

Conclusion

The regulatory systems investigated in this study allow less stringent registration requirements for TM/CM products featured with a long history of use, assuming safety and efficacy to be plausible based on historic use. Considering the safety and efficacy of these products, regulatory standards should emphasize the technical requirements for quality control and postmarket surveillance.

Substituting clinical features using synthetic medical phrases: Medical text data augmentation techniques

Biomedical natural language processing (NLP) has an important role in extracting consequential information in medical discharge notes. Detecting meaningful features from unstructured notes is a challenging task in medical document classification. The domain specific phrases and different synonyms within the medical documents make it hard to analyze them. Analyzing clinical notes becomes more challenging for short documents like abstract texts. All of these can result in poor classification performance, especially when there is a shortage of the clinical data in real life. Two new approaches (an ontology-guided approach and a combined ontology-based with dictionary-based approach) are suggested for augmenting medical data to enrich training data. Three different deep learning approaches are used to evaluate the classification performance of the proposed methods. The obtained results show that the proposed methods improved the classification accuracy in clinical notes classification.

Digital Natives' Preferences on Mobile Artificial Intelligence Apps for Skin Cancer Diagnostics: Survey Study

Background

Artificial intelligence (AI) has shown potential to improve diagnostics of various diseases, especially for early detection of skin cancer. Studies have yet to investigate the clear application of AI technology in clinical practice or determine the added value for younger user groups. Translation of AI-based diagnostic tools can only be successful if they are accepted by potential users. Young adults as digital natives may offer the greatest potential for successful implementation of AI into clinical practice, while at the same time, representing the future generation of skin cancer screening participants.

Objective

We conducted an anonymous online survey to examine how and to what extent individuals are willing to accept AI-based mobile apps for skin cancer diagnostics. We evaluated preferences and relative influences of concerns, with a focus on younger age groups.

Methods

We recruited participants below 35 years of age using three social media channels—Facebook, LinkedIn, and Xing. Descriptive analysis and statistical tests were performed to evaluate participants’ attitudes toward mobile apps for skin examination. We integrated an adaptive choice-based conjoint to assess participants’ preferences. We evaluated potential concerns using maximum difference scaling.

Results

We included 728 participants in the analysis. The majority of participants (66.5%, 484/728; 95% CI 0.631-0.699) expressed a positive attitude toward the use of AI-based apps. In particular, participants residing in big cities or small towns (P=.02) and individuals that were familiar with the use of health or fitness apps (P=.02) were significantly more open to mobile diagnostic systems. Hierarchical Bayes estimation of the preferences of participants with a positive attitude (n=484) revealed that the use of mobile apps as an assistance system was preferred. Participants ruled out app versions with an accuracy of ≤65%, apps using data storage without encryption, and systems that did not provide background information about the decision-making process. However, participants did not mind their data being used anonymously for research purposes, nor did they object to the inclusion of clinical patient information in the decision-making process. Maximum difference scaling analysis for the negative-minded participant group (n=244) showed that data security, insufficient trust in the app, and lack of personal interaction represented the dominant concerns with respect to app use.

Conclusions

The majority of potential future users below 35 years of age were ready to accept AI-based diagnostic solutions for early detection of skin cancer. However, for translation into clinical practice, the participants’ demands for increased transparency and explainability of AI-based tools seem to be critical. Altogether, digital natives between 18 and 24 years and between 25 and 34 years of age expressed similar preferences and concerns when compared both to each other and to results obtained by previous studies that included other age groups.

Artificial intelligence methods for a Bayesian epistemology-powered evidence evaluation

RATIONALE, AIMS AND OBJECTIVES

The diversity of types of evidence (eg, case reports, animal studies and observational studies) makes the assessment of a drug's safety profile into a formidable challenge. While frequentist uncertain inference struggles in aggregating these signals, the more flexible Bayesian approaches seem better suited for this quest. Artificial Intelligence (AI) offers great promise to these approaches for information retrieval, decision support, and learning probabilities from data.

METHODS

E-Synthesis is a Bayesian framework for drug safety assessments built on philosophical principles and considerations. It aims to aggregate all the available information, in order to provide a Bayesian probability of a drug causing an adverse reaction. AI systems are being developed for evidence aggregation in medicine, which increasingly are automated.

RESULTS

We find that AI can help E-Synthesis with information retrieval, usability (graphical decision-making aids), learning Bayes factors from historical data, assessing quality of information and determining conditional probabilities for the so-called 'indicators' of causation for E-Synthesis. Vice versa, E-Synthesis offers a solid methodological basis for (semi-)automated evidence aggregation with AI systems.

CONCLUSIONS

Properly applied, AI can help the transition of philosophical principles and considerations concerning evidence aggregation for drug safety to a tool that can be used in practice.

Development of medical nomenclature and algorithms for diagnosis and treatment of gout in outpatient settings

Gout is a chronic systemic disease characterized by the deposition of monosodium urate crystals in various tissues and inflammation. In Russia, time to diagnosis may be as long as 8 years. This leads to serious complications, such as urate nephropathy, and disability. Effective strategies are needed to improve the quality of medical care for gout patients. One of such strategies is creation of an expert system to aid the clinician in establishing the diagnosis and selecting adequate therapy. The cornerstone of an expert system is a knowledge base. The aim of this paper was to develop a medical nomenclature and algorithms for the diagnosis and treatment of gout that will be used to create an expert system in the future. A total of 1,174 entities were selected that laid the basis for 40 diagnostic and 50 treatment algorithms for gout patients. All informational models were verified by the expert panel.

Applying regulatory science in traditional chinese medicines for improving public safety and facilitating innovation in China: a scoping review and regulatory implications

BACKGROUND

The National Medical Products Administration (NMPA) in China has set to advance the regulatory capacity of traditional Chinese medicines (TCMs) with the adoption of regulatory science (RS). However, the priority of actions at the interface of RS and TCMs were yet to be defined. This research aims to identify the priority areas and summarize core actions for advancing RS for traditional medicines in China.

METHODS

A mixed approach of documentary analysis of government policies, regulations and official information about TCMs regulation in China, and a scoping review of literature using 4 databases (PubMed, ScienceDirect, Scopus and CNKI) on major concerns in TCMs regulation was employed.

RESULTS

Ten priority areas in the development of TCM-related regulatory science in China have been identified, including: (1) modernizing the regulatory system with a holistic approach; (2) advancing the methodology for the quality control of TCMs; (3) fostering the control mechanism of TCMs manufacturing process; (4) improving clinical evaluation of TCMs and leveraging real world data; (5) re-evaluation of TCMs injection; (6) developing evaluation standards for classic TCMs formula; (7) harnessing diverse data to improve pharmacovigilance of TCMs; (8) evaluating the value of integrative medicine in clinical practice with scientific research; (9) advancing the regulatory capacity to encourage innovation in TCMs; and (10) advancing a vision of collaboration for RS development in TCMs.

CONCLUSIONS

RS for TCMs in China encompasses revolution of operational procedures, advancement in science and technology, and cross-disciplinary collaborations. Such experiences could be integrated in the communications among drug regulatory authorities to promote standardized and scientific regulation of traditional medicines.

"PhysIt" - A Diagnosis and Troubleshooting Tool for Physiotherapists in Training

Many physiotherapy treatments begin with a diagnosis process. The patient describes symptoms, upon which the physiotherapist decides which tests to perform until a final diagnosis is reached. The relationships between the anatomical components are too complex to keep in mind and the possible actions are abundant. A trainee physiotherapist with little experience naively applies multiple tests to reach the root cause of the symptoms, which is a highly inefficient process. This work proposes to assist students in this challenge by presenting three main contributions: (1) A compilation of the neuromuscular system as components of a system in a Model-Based Diagnosis problem; (2) The PhysIt is an AI-based tool that enables an interactive visualization and diagnosis to assist trainee physiotherapists; and (3) An empirical evaluation that comprehends performance analysis and a user study. The performance analysis is based on evaluation of simulated cases and common scenarios taken from anatomy exams. The user study evaluates the efficacy of the system to assist students in the beginning of the clinical studies. The results show that our system significantly decreases the number of candidate diagnoses, without discarding the correct diagnosis, and that students in their clinical studies find PhysIt helpful in the diagnosis process.

AI-Assisted Decision-making in Healthcare: The Application of an Ethics Framework for Big Data in Health and Research

Artificial intelligence (AI) is set to transform healthcare. Key ethical issues to emerge with this transformation encompass the accountability and transparency of the decisions made by AI-based systems, the potential for group harms arising from algorithmic bias and the professional roles and integrity of clinicians. These concerns must be balanced against the imperatives of generating public benefit with more efficient healthcare systems from the vastly higher and accurate computational power of AI. In weighing up these issues, this paper applies the deliberative balancing approach of the Ethics Framework for Big Data in Health and Research (Xafis et al. 2019). The analysis applies relevant values identified from the framework to demonstrate how decision-makers can draw on them to develop and implement AI-assisted support systems into healthcare and clinical practice ethically and responsibly. Please refer to Xafis et al. (2019) in this special issue of the Asian Bioethics Review for more information on how this framework is to be used, including a full explanation of the key values involved and the balancing approach used in the case study at the end of this paper.

An e-healthcare system for disease prediction using hybrid data mining technique

Purpose

The purpose of this study is to alleviate the specified issues to a great extent. To promote patients’ health via early prediction of diseases, knowledge extraction using data mining approaches shows an integral part of e-health system. However, medical databases are highly imbalanced, voluminous, conflicting and complex in nature, and these can lead to erroneous diagnosis of diseases (i.e. detecting class-values of diseases). In literature, numerous standard disease decision support system (DDSS) have been proposed, but most of them are disease specific. Also, they usually suffer from several drawbacks like lack of understandability, incapability of operating rare cases, inefficiency in making quick and correct decision, etc.

Design/methodology/approach

Addressing the limitations of the existing systems, the present research introduces a two-step framework for designing a DDSS, in which the first step (data-level optimization) deals in identifying an optimal data-partition (Popt) for each disease data set and then the best training set for Popt in parallel manner. On the other hand, the second step explores a generic predictive model (integrating C4.5 and PRISM learners) over the discovered information for effective diagnosis of disease. The designed model is a generic one (i.e. not disease specific).

Findings

The empirical results (in terms of top three measures, namely, accuracy, true positive rate and false positive rate) obtained over 14 benchmark medical data sets (collected from https://archive.ics.uci.edu/ml) demonstrate that the hybrid model outperforms the base learners in almost all cases for initial diagnosis of the diseases. After all, the proposed DDSS may work as an e-doctor to detect diseases.

Originality/value

The model designed in this study is original, and the necessary parallelized methods are implemented in C on Cluster HPC machine (FUJITSU) with total 256 cores (under one Master node).

Machine learning in critical care: state-of-the-art and a sepsis case study

BACKGROUND

Like other scientific fields, such as cosmology, high-energy physics, or even the life sciences, medicine and healthcare face the challenge of an extremely quick transformation into data-driven sciences. This challenge entails the daunting task of extracting usable knowledge from these data using algorithmic methods. In the medical context this may for instance realized through the design of medical decision support systems for diagnosis, prognosis and patient management. The intensive care unit (ICU), and by extension the whole area of critical care, is becoming one of the most data-driven clinical environments.

RESULTS

The increasing availability of complex and heterogeneous data at the point of patient attention in critical care environments makes the development of fresh approaches to data analysis almost compulsory. Computational Intelligence (CI) and Machine Learning (ML) methods can provide such approaches and have already shown their usefulness in addressing problems in this context. The current study has a dual goal: it is first a review of the state-of-the-art on the use and application of such methods in the field of critical care. Such review is presented from the viewpoint of the different subfields of critical care, but also from the viewpoint of the different available ML and CI techniques. The second goal is presenting a collection of results that illustrate the breath of possibilities opened by ML and CI methods using a single problem, the investigation of septic shock at the ICU.

CONCLUSION

We have presented a structured state-of-the-art that illustrates the broad-ranging ways in which ML and CI methods can make a difference in problems affecting the manifold areas of critical care. The potential of ML and CI has been illustrated in detail through an example concerning the sepsis pathology. The new definitions of sepsis and the relevance of using the systemic inflammatory response syndrome (SIRS) in its diagnosis have been considered. Conditional independence models have been used to address this problem, showing that SIRS depends on both organ dysfunction measured through the Sequential Organ Failure (SOFA) score and the ICU outcome, thus concluding that SIRS should still be considered in the study of the pathophysiology of Sepsis. Current assessment of the risk of dead at the ICU lacks specificity. ML and CI techniques are shown to improve the assessment using both indicators already in place and other clinical variables that are routinely measured. Kernel methods in particular are shown to provide the best performance balance while being amenable to representation through graphical models, which increases their interpretability and, with it, their likelihood to be accepted in medical practice.

From Big Data to Smart Data for Pharmacovigilance: The Role of Healthcare Databases and Other Emerging Sources

In the last decade 'big data' has become a buzzword used in several industrial sectors, including but not limited to telephony, finance and healthcare. Despite its popularity, it is not always clear what big data refers to exactly. Big data has become a very popular topic in healthcare, where the term primarily refers to the vast and growing volumes of computerized medical information available in the form of electronic health records, administrative or health claims data, disease and drug monitoring registries and so on. This kind of data is generally collected routinely during administrative processes and clinical practice by different healthcare professionals: from doctors recording their patients' medical history, drug prescriptions or medical claims to pharmacists registering dispensed prescriptions. For a long time, this data accumulated without its value being fully recognized and leveraged. Today big data has an important place in healthcare, including in pharmacovigilance. The expanding role of big data in pharmacovigilance includes signal detection, substantiation and validation of drug or vaccine safety signals, and increasingly new sources of information such as social media are also being considered. The aim of the present paper is to discuss the uses of big data for drug safety post-marketing assessment.

A Hybrid Predictive Model Integrating C4.5 and Decision Table Classifiers for Medical Data Sets

This article describes how, recently, data mining has been in great use for extracting meaningful patterns from medical domain data sets, and these patterns are then applied for clinical diagnosis. Truly, any accurate, precise and reliable classification models significantly assist the medical practitioners to improve diagnosis, prognosis and treatment processes of individual diseases. However, numerous intelligent models have been proposed in this respect but still they have several drawbacks like, disease specificity, class imbalance, conflicting and lack adequacy for dimensionality of patient's data. The present study has attempted to design a hybrid prediction model for medical domain data sets by combining the decision tree based classifier (mainly C4.5) and the decision table based classifier (DT). The experimental results validate in favour of the claims.

The Scope of Big Data in One Medicine: Unprecedented Opportunities and Challenges

Advances in high-throughput molecular biology and electronic health records (EHR), coupled with increasing computer capabilities have resulted in an increased interest in the use of big data in health care. Big data require collection and analysis of data at an unprecedented scale and represents a paradigm shift in health care, offering (1) the capacity to generate new knowledge more quickly than traditional scientific approaches; (2) unbiased collection and analysis of data; and (3) a holistic understanding of biology and pathophysiology. Big data promises more personalized and precision medicine for patients with improved accuracy and earlier diagnosis, and therapy tailored to an individual’s unique combination of genes, environmental risk, and precise disease phenotype. This promise comes from data collected from numerous sources, ranging from molecules to cells, to tissues, to individuals and populations—and the integration of these data into networks that improve understanding of heath and disease. Big data-driven science should play a role in propelling comparative medicine and “one medicine” (i.e., the shared physiology, pathophysiology, and disease risk factors across species) forward. Merging of data from EHR across institutions will give access to patient data on a scale previously unimaginable, allowing for precise phenotype definition and objective evaluation of risk factors and response to therapy. High-throughput molecular data will give insight into previously unexplored molecular pathophysiology and disease etiology. Investigation and integration of big data from a variety of sources will result in stronger parallels drawn at the molecular level between human and animal disease, allow for predictive modeling of infectious disease and identification of key areas of intervention, and facilitate step-changes in our understanding of disease that can make a substantial impact on animal and human health. However, the use of big data comes with significant challenges. Here we explore the scope of “big data,” including its opportunities, its limitations, and what is needed capitalize on big data in one medicine.

Multiclassifier Systems for Predicting Neurological Outcome of Patients with Severe Trauma and Polytrauma in Intensive Care Units

This paper presents an ensemble based classification proposal for predicting neurological outcome of severely traumatized patients. The study comprises both the whole group of patients and a subgroup containing those patients suffering traumatic brain injury (TBI). Data was gathered from patients hospitalized in the Intensive Care Unit (ICU) of the University Hospital in Salamanca. Predictive models were induced from both epidemiologic and clinical variables taken at the emergency room and along the stay in the ICU. The large number of variables leads to a low accuracy in the classifiers even when feature selection methods are used. In addition, the presence of a much larger number of instances of one of the classes in the subgroup of TBI patients produces a significantly lesser precision for the minority class. Usual ways of dealing with the last problem is to use undersampling and oversampling strategies, which can lead to the loss of valuable data and overfitting problems respectively. Our proposal for dealing with these problems is based in the use of ensemble multiclassifiers as well as in the use of an ensemble playing the role of base classifier in multiclassifiers. The proposed strategy gave the best values of the selected quality measures (accuracy, precision, sensitivity, specificity, F-measure and area under the Receiver Operator Characteristic curve) as well as the closest values of precision for the two classes under study in the case of the classification from imbalanced data.

A Method to Differentiate Mild Cognitive Impairment and Alzheimer in MR Images using Eigen Value Descriptors

Automated analysis and differentiation of mild cognitive impairment and Alzheimer's condition using MR images is clinically significant in dementic disorder. Alzheimer's Disease (AD) is a fatal and common form of dementia that progressively affects the patients. Shape descriptors could better differentiate the morphological alterations of brain structures and aid in the development of prospective disease modifying therapies. Ventricle enlargement is considered as a significant biomarker in the AD diagnosis. In this work, a method has been proposed to differentiate MCI from the healthy normal and AD subjects using Laplace-Beltrami (LB) eigen value shape descriptors. Prior to this, Reaction Diffusion (RD) level set is used to segment the ventricles in MR images and the results are validated against the Ground Truth (GT). LB eigen values are infinite series of spectrum that describes the intrinsic geometry of objects. Most significant LB shape descriptors are identified and their performance is analysed using linear Support Vector Machine (SVM) classifier. Results show that, the RD level set is able to segment the ventricles. The segmented ventricles are found to have high correlation with GT. The eigen values in the LB spectrum could show distinction in the feature space better than the geometric features. High accuracy is observed in the classification results of linear SVM. The proposed automated system is able to distinctly separate the MCI from normal and AD subjects. Thus this pipeline of work seems to be clinically significant in the automated analysis of dementic subjects.

Towards Automated Three-Dimensional Tracking of Nephrons through Stacked Histological Image Sets

An automated approach for tracking individual nephrons through three-dimensional histological image sets of mouse and rat kidneys is presented. In a previous study, the available images were tracked manually through the image sets in order to explore renal microarchitecture. The purpose of the current research is to reduce the time and effort required to manually trace nephrons by creating an automated, intelligent system as a standard tool for such datasets. The algorithm is robust enough to isolate closely packed nephrons and track their convoluted paths despite a number of nonideal, interfering conditions such as local image distortions, artefacts, and interstitial tissue interference. The system comprises image preprocessing, feature extraction, and a custom graph-based tracking algorithm, which is validated by a rule base and a machine learning algorithm. A study of a selection of automatically tracked nephrons, when compared with manual tracking, yields a 95% tracking accuracy for structures in the cortex, while those in the medulla have lower accuracy due to narrower diameter and higher density. Limited manual intervention is introduced to improve tracking, enabling full nephron paths to be obtained with an average of 17 manual corrections per mouse nephron and 58 manual corrections per rat nephron.

Electronic health records: current and future use

This paper provides an overview of the current state of the electronic medical record, including benefits and shortcomings, and presents key factors likely to drive development in the next decade and beyond. The current electronic medical record to a large extent represents a digital version of the traditional paper legal record, owned and maintained by the practitioner. The future electronic health record is expected to be a shared tool, engaging patients in decision making, wellness and disease management and providing data for individual decision support, population management and analytics. Many drivers will determine this path, including payment model reform, proliferation of mobile platforms, telemedicine, genomics and individualized medicine and advances in 'big data' technologies.

A systematic approach for using DICOM structured reports in clinical processes: focus on breast cancer

This paper describes a methodology for redesigning the clinical processes to manage diagnosis, follow-up, and response to treatment episodes of breast cancer. This methodology includes three fundamental elements: (1) identification of similar and contrasting cases that may be of clinical relevance based upon a target study, (2) codification of reports with standard medical terminologies, and (3) linking and indexing the structured reports obtained with different techniques in a common system. The combination of these elements should lead to improvements in the clinical management of breast cancer patients. The motivation for this work is the adaptation of the clinical processes for breast cancer created by the Valencian Community health authorities to the new techniques available for data processing. To achieve this adaptation, it was necessary to design nine Digital Imaging and Communications in Medicine (DICOM) structured report templates: six diagnosis templates and three summary templates that combine reports from clinical episodes. A prototype system is also described that links the lesion to the reports. Preliminary tests of the prototype have shown that the interoperability among the report templates allows correlating parameters from different reports. Further work is in progress to improve the methodology in order that it can be applied to clinical practice.

Clinical implementation of a neonatal seizure detection algorithm

Technologies for automated detection of neonatal seizures are gradually moving towards cot-side implementation. The aim of this paper is to present different ways to visualize the output of a neonatal seizure detection system and analyse their influence on performance in a clinical environment. Three different ways to visualize the detector output are considered: a binary output, a probabilistic trace, and a spatio-temporal colormap of seizure observability. As an alternative to visual aids, audified neonatal EEG is also considered. Additionally, a survey on the usefulness and accuracy of the presented methods has been performed among clinical personnel. The main advantages and disadvantages of the presented methods are discussed. The connection between information visualization and different methods to compute conventional metrics is established. The results of the visualization methods along with the system validation results indicate that the developed neonatal seizure detector with its current level of performance would unambiguously be of benefit to clinicians as a decision support system. The results of the survey suggest that a suitable way to visualize the output of neonatal seizure detection systems in a clinical environment is a combination of a binary output and a probabilistic trace. The main healthcare benefits of the tool are outlined. The decision support system with the chosen visualization interface is currently undergoing pre-market European multi-centre clinical investigation to support its regulatory approval and clinical adoption.

Cardiovascular risk analysis by means of pulse morphology and clustering methodologies

The purpose of this study was the development of a clustering methodology to deal with arterial pressure waveform (APW) parameters to be used in the cardiovascular risk assessment. One hundred sixteen subjects were monitored and divided into two groups. The first one (23 hypertensive subjects) was analyzed using APW and biochemical parameters, while the remaining 93 healthy subjects were only evaluated through APW parameters. The expectation maximization (EM) and k-means algorithms were used in the cluster analysis, and the risk scores (the Framingham Risk Score (FRS), the Systematic COronary Risk Evaluation (SCORE) project, the Assessing cardiovascular risk using Scottish Intercollegiate Guidelines Network (ASSIGN) and the PROspective Cardiovascular Münster (PROCAM)), commonly used in clinical practice were selected to the cluster risk validation. The result from the clustering risk analysis showed a very significant correlation with ASSIGN (r=0.582, p<0.01) and a significant correlation with FRS (r=0.458, p<0.05). The results from the comparison of both groups also allowed to identify the cluster with higher cardiovascular risk in the healthy group. These results give new insights to explore this methodology in future scoring trials.

A survey on computer aided diagnosis for ocular diseases

Background

Computer Aided Diagnosis (CAD), which can automate the detection process for ocular diseases, has attracted extensive attention from clinicians and researchers alike. It not only alleviates the burden on the clinicians by providing objective opinion with valuable insights, but also offers early detection and easy access for patients.

Method

We review ocular CAD methodologies for various data types. For each data type, we investigate the databases and the algorithms to detect different ocular diseases. Their advantages and shortcomings are analyzed and discussed.

Result

We have studied three types of data (i.e., clinical, genetic and imaging) that have been commonly used in existing methods for CAD. The recent developments in methods used in CAD of ocular diseases (such as Diabetic Retinopathy, Glaucoma, Age-related Macular Degeneration and Pathological Myopia) are investigated and summarized comprehensively.

Conclusion

While CAD for ocular diseases has shown considerable progress over the past years, the clinical importance of fully automatic CAD systems which are able to embed clinical knowledge and integrate heterogeneous data sources still show great potential for future breakthrough.

"Big data" and the electronic health record

OBJECTIVES

Implementation of Electronic Health Record (EHR) systems continues to expand. The massive number of patient encounters results in high amounts of stored data. Transforming clinical data into knowledge to improve patient care has been the goal of biomedical informatics professionals for many decades, and this work is now increasingly recognized outside our field. In reviewing the literature for the past three years, we focus on "big data" in the context of EHR systems and we report on some examples of how secondary use of data has been put into practice.

METHODS

We searched PubMed database for articles from January 1, 2011 to November 1, 2013. We initiated the search with keywords related to "big data" and EHR. We identified relevant articles and additional keywords from the retrieved articles were added. Based on the new keywords, more articles were retrieved and we manually narrowed down the set utilizing predefined inclusion and exclusion criteria.

RESULTS

Our final review includes articles categorized into the themes of data mining (pharmacovigilance, phenotyping, natural language processing), data application and integration (clinical decision support, personal monitoring, social media), and privacy and security.

CONCLUSION

The increasing adoption of EHR systems worldwide makes it possible to capture large amounts of clinical data. There is an increasing number of articles addressing the theme of "big data", and the concepts associated with these articles vary. The next step is to transform healthcare big data into actionable knowledge.

Formative evaluation of the accuracy of a clinical decision support system for cervical cancer screening

Objectives

We previously developed and reported on a prototype clinical decision support system (CDSS) for cervical cancer screening. However, the system is complex as it is based on multiple guidelines and free-text processing. Therefore, the system is susceptible to failures. This report describes a formative evaluation of the system, which is a necessary step to ensure deployment readiness of the system.

Materials and methods

Care providers who are potential end-users of the CDSS were invited to provide their recommendations for a random set of patients that represented diverse decision scenarios. The recommendations of the care providers and those generated by the CDSS were compared. Mismatched recommendations were reviewed by two independent experts.

Results

A total of 25 users participated in this study and provided recommendations for 175 cases. The CDSS had an accuracy of 87% and 12 types of CDSS errors were identified, which were mainly due to deficiencies in the system's guideline rules. When the deficiencies were rectified, the CDSS generated optimal recommendations for all failure cases, except one with incomplete documentation.

Discussion and conclusions

The crowd-sourcing approach for construction of the reference set, coupled with the expert review of mismatched recommendations, facilitated an effective evaluation and enhancement of the system, by identifying decision scenarios that were missed by the system's developers. The described methodology will be useful for other researchers who seek rapidly to evaluate and enhance the deployment readiness of complex decision support systems.

Clinical decision support with automated text processing for cervical cancer screening

OBJECTIVE

To develop a computerized clinical decision support system (CDSS) for cervical cancer screening that can interpret free-text Papanicolaou (Pap) reports.

MATERIALS AND METHODS

The CDSS was constituted by two rulebases: the free-text rulebase for interpreting Pap reports and a guideline rulebase. The free-text rulebase was developed by analyzing a corpus of 49 293 Pap reports. The guideline rulebase was constructed using national cervical cancer screening guidelines. The CDSS accesses the electronic medical record (EMR) system to generate patient-specific recommendations. For evaluation, the screening recommendations made by the CDSS for 74 patients were reviewed by a physician.

RESULTS AND DISCUSSION

Evaluation revealed that the CDSS outputs the optimal screening recommendations for 73 out of 74 test patients and it identified two cases for gynecology referral that were missed by the physician. The CDSS aided the physician to amend recommendations in six cases. The failure case was because human papillomavirus (HPV) testing was sometimes performed separately from the Pap test and these results were reported by a laboratory system that was not queried by the CDSS. Subsequently, the CDSS was upgraded to look up the HPV results missed earlier and it generated the optimal recommendations for all 74 test cases.

LIMITATIONS

Single institution and single expert study.

CONCLUSION

An accurate CDSS system could be constructed for cervical cancer screening given the standardized reporting of Pap tests and the availability of explicit guidelines. Overall, the study demonstrates that free text in the EMR can be effectively utilized through natural language processing to develop clinical decision support tools.

Bayesian ontology querying for accurate and noise-tolerant semantic searches

MOTIVATION

Ontologies provide a structured representation of the concepts of a domain of knowledge as well as the relations between them. Attribute ontologies are used to describe the characteristics of the items of a domain, such as the functions of proteins or the signs and symptoms of disease, which opens the possibility of searching a database of items for the best match to a list of observed or desired attributes. However, naive search methods do not perform well on realistic data because of noise in the data, imprecision in typical queries and because individual items may not display all attributes of the category they belong to.

RESULTS

We present a method for combining ontological analysis with Bayesian networks to deal with noise, imprecision and attribute frequencies and demonstrate an application of our method as a differential diagnostic support system for human genetics.

AVAILABILITY

We provide an implementation for the algorithm and the benchmark at http://compbio.charite.de/boqa/.

CONTACT

Sebastian.Bauer@charite.de or Peter.Robinson@charite.de

SUPPLEMENTARY INFORMATION

Supplementary Material for this article is available at Bioinformatics online.