Biomedical informatics for computer-aided decision support systems: a survey

Synthesis, characterization, antiproliferative activity, docking, and molecular dynamics simulation of new 1,3-dihydro-2H-benzimidazol-2-one derivatives

Cancer is a global public health problem that affects millions each year. Novel anticancer drug candidates are in need to treat various cancers and to overcome the resistance that exists against drugs in use. Benzimidazole derivatives have been reported as anticancer agents. These lead us to synthesize similar benzimidazole derivatives and investigate their anticancer activity. In this study, six new 1,3-dihydro-2H-benzimidazol-2-one-based molecules (2a-f) were synthesized. The structures of these molecules were verified by spectroscopic methods. The antiproliferative activities of molecules 2a-f were screened against a panel of human cancer cell lines, including the liver, colon, lung, and breast. The molecules were also tested towards normal human lung cell line to determine their selectivity. The results demonstrated that compound 2d had the highest cytotoxic effect compared to compounds 2a-c, 2e, and 2f against DLD-1 and MDA-MB-231 cell lines. The binding potential of the relatively active compound, 2d, with three targets was investigated through molecular docking. The stability of target-compound complexes procured from the docking was explored through molecular dynamics (MD) simulation. The docking and MD simulation studies revealed that compound 2d had the highest potential to bind to GALR3 among the targets. Furthermore, the computational pharmacokinetic study demonstrated that the synthesized compounds had drug-like properties.Communicated by Ramaswamy H. Sarma.

Prediction of the occurrence of leprosy reactions based on Bayesian networks

Introduction

Leprosy reactions (LR) are severe episodes of intense activation of the host inflammatory response of uncertain etiology, today the leading cause of permanent nerve damage in leprosy patients. Several genetic and non-genetic risk factors for LR have been described; however, there are limited attempts to combine this information to estimate the risk of a leprosy patient developing LR. Here we present an artificial intelligence (AI)-based system that can assess LR risk using clinical, demographic, and genetic data.

Methods

The study includes four datasets from different regions of Brazil, totalizing 1,450 leprosy patients followed prospectively for at least 2 years to assess the occurrence of LR. Data mining using WEKA software was performed following a two-step protocol to select the variables included in the AI system, based on Bayesian Networks, and developed using the NETICA software.

Results

Analysis of the complete database resulted in a system able to estimate LR risk with 82.7% accuracy, 79.3% sensitivity, and 86.2% specificity. When using only databases for which host genetic information associated with LR was included, the performance increased to 87.7% accuracy, 85.7% sensitivity, and 89.4% specificity.

Conclusion

We produced an easy-to-use, online, free-access system that identifies leprosy patients at risk of developing LR. Risk assessment of LR for individual patients may detect candidates for close monitoring, with a potentially positive impact on the prevention of permanent disabilities, the quality of life of the patients, and upon leprosy control programs.

A Computer-Assisted Approach to Assess the Precision of the Reciprocating Angles and the Rotation Speeds of Endodontic Motors

Endodontic reciprocating motors are largely used to support a series of procedures in dentistry treatments, useful for those different circular movement patterns. In the last years, different motors have been available on the market, with varying costs and promised performance for the users; however, since their reciprocating angles and rotation speeds may have significant outcomes on the employed endodontic files, there should be an affordable and practical way to assess the actual performance of such motors concerning their expected operation. Actually, endodontic files attached to reciprocating motors will move too fast to be easily accounted, which has fostered the development of computational methods to allow the proper validation of their movements according to their official datasheets. In this scenario, this paper describes a feasible method to detect the movement patterns of different reciprocating endodontic motors by the processing of a set of consecutive images taken by a high-speed camera. The performed experiments for three different off-the-shelf reciprocating endodontic motors showed that their actual movement characteristics are slightly different from their specifications, and that each considered motor has a particular movement pattern.

Utilization of Artificial Intelligence in Disease Prevention: Diagnosis, Treatment, and Implications for the Healthcare Workforce

Artificial intelligence (AI) has been described as one of the extremely effective and promising scientific tools available to mankind. AI and its associated innovations are becoming more popular in industry and culture, and they are starting to show up in healthcare. Numerous facets of healthcare, as well as regulatory procedures within providers, payers, and pharmaceutical companies, may be transformed by these innovations. As a result, the purpose of this review is to identify the potential machine learning applications in the field of infectious diseases and the general healthcare system. The literature on this topic was extracted from various databases, such as Google, Google Scholar, Pubmed, Scopus, and Web of Science. The articles having important information were selected for this review. The most challenging task for AI in such healthcare sectors is to sustain its adoption in daily clinical practice, regardless of whether the programs are scalable enough to be useful. Based on the summarized data, it has been concluded that AI can assist healthcare staff in expanding their knowledge, allowing them to spend more time providing direct patient care and reducing weariness. Overall, we might conclude that the future of "conventional medicine" is closer than we realize, with patients seeing a computer first and subsequently a doctor.

A machine-learning algorithm for neonatal seizure recognition: a multicentre, randomised, controlled trial

BACKGROUND

Despite the availability of continuous conventional electroencephalography (cEEG), accurate diagnosis of neonatal seizures is challenging in clinical practice. Algorithms for decision support in the recognition of neonatal seizures could improve detection. We aimed to assess the diagnostic accuracy of an automated seizure detection algorithm called Algorithm for Neonatal Seizure Recognition (ANSeR).

METHODS

This multicentre, randomised, two-arm, parallel, controlled trial was done in eight neonatal centres across Ireland, the Netherlands, Sweden, and the UK. Neonates with a corrected gestational age between 36 and 44 weeks with, or at significant risk of, seizures requiring EEG monitoring, received cEEG plus ANSeR linked to the EEG monitor displaying a seizure probability trend in real time (algorithm group) or cEEG monitoring alone (non-algorithm group). The primary outcome was diagnostic accuracy (sensitivity, specificity, and false detection rate) of health-care professionals to identify neonates with electrographic seizures and seizure hours with and without the support of the ANSeR algorithm. Neonates with data on the outcome of interest were included in the analysis. This study is registered with ClinicalTrials.gov, NCT02431780.

FINDINGS

Between Feb 13, 2015, and Feb 7, 2017, 132 neonates were randomly assigned to the algorithm group and 132 to the non-algorithm group. Six neonates were excluded (four from the algorithm group and two from the non-algorithm group). Electrographic seizures were present in 32 (25·0%) of 128 neonates in the algorithm group and 38 (29·2%) of 130 neonates in the non-algorithm group. For recognition of neonates with electrographic seizures, sensitivity was 81·3% (95% CI 66·7-93·3) in the algorithm group and 89·5% (78·4-97·5) in the non-algorithm group; specificity was 84·4% (95% CI 76·9-91·0) in the algorithm group and 89·1% (82·5-94·7) in the non-algorithm group; and the false detection rate was 36·6% (95% CI 22·7-52·1) in the algorithm group and 22·7% (11·6-35·9) in the non-algorithm group. We identified 659 h in which seizures occurred (seizure hours): 268 h in the algorithm versus 391 h in the non-algorithm group. The percentage of seizure hours correctly identified was higher in the algorithm group than in the non-algorithm group (177 [66·0%; 95% CI 53·8-77·3] of 268 h vs 177 [45·3%; 34·5-58·3] of 391 h; difference 20·8% [3·6-37·1]). No significant differences were seen in the percentage of neonates with seizures given at least one inappropriate antiseizure medication (37·5% [95% CI 25·0 to 56·3] vs 31·6% [21·1 to 47·4]; difference 5·9% [-14·0 to 26·3]).

INTERPRETATION

ANSeR, a machine-learning algorithm, is safe and able to accurately detect neonatal seizures. Although the algorithm did not enhance identification of individual neonates with seizures beyond conventional EEG, recognition of seizure hours was improved with use of ANSeR. The benefit might be greater in less experienced centres, but further study is required.

FUNDING

Wellcome Trust, Science Foundation Ireland, and Nihon Kohden.

Use of artificial intelligence in infectious diseases

Infectious diseases are caused by microorganisms belonging to the class of bacteria, viruses, fungi, or parasites. These pathogens are transmitted, directly or indirectly, and can lead to epidemics or even pandemics. The resulting infection may lead to mild-to-severe symptoms such as life-threatening fever or diarrhea. Infectious diseases may be asymptomatic in some individuals but may lead to disastrous effects in others. Despite the advances in medicine, infectious diseases are a leading cause of death worldwide, especially in low-income countries. With the advent of mathematical tools, scientists are now able to better predict epidemics, understand the specificity of each pathogen, and identify potential targets for drug development. Artificial intelligence and its components have been widely publicized for their ability to better diagnose certain types of cancer from imaging data. This chapter aims at identifying potential applications of machine learning in the field of infectious diseases. We are deliberately focusing on key aspects of infection: diagnosis, transmission, response to treatment, and resistance. We are proposing the use of extreme values as an avenue of interest for future developments in the field of infectious diseases. This chapter covers a series of applications selectively chosen to showcase how artificial intelligence is moving the field of infectious disease further and how it helps institutions to better tackles them, especially in low-income countries.

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.

Opportunities and obstacles for deep learning in biology and medicine

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

Personalization and Patient Involvement in Decision Support Systems: Current Trends

OBJECTIVES

This survey aims at highlighting the latest trends (2012-2014) on the development, use, and evaluation of Information and Communication Technologies (ICT) based decision support systems (DSSs) in medicine, with a particular focus on patient-centered and personalized care.

METHODS

We considered papers published on scientific journals, by querying PubMed and Web of ScienceTM. Included studies focused on the implementation or evaluation of ICT-based tools used in clinical practice. A separate search was performed on computerized physician order entry systems (CPOEs), since they are increasingly embedding patient-tailored decision support.

RESULTS

We found 73 papers on DSSs (53 on specific ICT tools) and 72 papers on CPOEs. Although decision support through the delivery of recommendations is frequent (28/53 papers), our review highlighted also DSSs only based on efficient information presentation (25/53). Patient participation in making decisions is still limited (9/53), and mostly focused on risk communication. The most represented medical area is cancer (12%). Policy makers are beginning to be included among stakeholders (6/73), but integration with hospital information systems is still low. Concerning knowledge representation/management issues, we identified a trend towards building inference engines on top of standard data models. Most of the tools (57%) underwent a formal assessment study, even if half of them aimed at evaluating usability and not effectiveness.

CONCLUSIONS

Overall, we have noticed interesting evolutions of medical DSSs to improve communication with the patient, consider the economic and organizational impact, and use standard models for knowledge representation. However, systems focusing on patient-centered care still do not seem to be available at large.

Semantic interpretation of robust imaging features for Fuhrman grading of renal carcinoma

Pattern recognition in tissue biopsy images can assist in clinical diagnosis and identify relevant image characteristics linked with various biological characteristics. Although previous work suggests several informative imaging features for pattern recognition, there exists a semantic gap between characteristics of these features and pathologists' interpretation of histopathological images. To address this challenge, we develop a clinical decision support system for automated Fuhrman grading of renal carcinoma biopsy images. We extract 1316 color, shape, texture and topology features and develop one vs. all models for four Fuhrman grades. Our models are highly accurate with 90.4% accuracy in a four-class prediction. Predictivity analysis suggests good generalization of the model development methodology through robustness to dataset sampling in cross-validation. We provide a semantic interpretation for the imaging features used in these models by linking features to pathologists' grading criteria. Our study identifies novel imaging features that are semantically linked to Fuhrman grading criteria.

Big Data Analytics in Healthcare

The rapidly expanding field of big data analytics has started to play a pivotal role in the evolution of healthcare practices and research. It has provided tools to accumulate, manage, analyze, and assimilate large volumes of disparate, structured, and unstructured data produced by current healthcare systems. Big data analytics has been recently applied towards aiding the process of care delivery and disease exploration. However, the adoption rate and research development in this space is still hindered by some fundamental problems inherent within the big data paradigm. In this paper, we discuss some of these major challenges with a focus on three upcoming and promising areas of medical research: image, signal, and genomics based analytics. Recent research which targets utilization of large volumes of medical data while combining multimodal data from disparate sources is discussed. Potential areas of research within this field which have the ability to provide meaningful impact on healthcare delivery are also examined.

Random Forest ensembles for detection and prediction of Alzheimer's disease with a good between-cohort robustness

Computer-aided diagnosis of Alzheimer's disease (AD) is a rapidly developing field of neuroimaging with strong potential to be used in practice. In this context, assessment of models' robustness to noise and imaging protocol differences together with post-processing and tuning strategies are key tasks to be addressed in order to move towards successful clinical applications. In this study, we investigated the efficacy of Random Forest classifiers trained using different structural MRI measures, with and without neuroanatomical constraints in the detection and prediction of AD in terms of accuracy and between-cohort robustness. From The ADNI database, 185 AD, and 225 healthy controls (HC) were randomly split into training and testing datasets. 165 subjects with mild cognitive impairment (MCI) were distributed according to the month of conversion to dementia (4-year follow-up). Structural 1.5-T MRI-scans were processed using Freesurfer segmentation and cortical reconstruction. Using the resulting output, AD/HC classifiers were trained. Training included model tuning and performance assessment using out-of-bag estimation. Subsequently the classifiers were validated on the AD/HC test set and for the ability to predict MCI-to-AD conversion. Models' between-cohort robustness was additionally assessed using the AddNeuroMed dataset acquired with harmonized clinical and imaging protocols. In the ADNI set, the best AD/HC sensitivity/specificity (88.6%/92.0% - test set) was achieved by combining cortical thickness and volumetric measures. The Random Forest model resulted in significantly higher accuracy compared to the reference classifier (linear Support Vector Machine). The models trained using parcelled and high-dimensional (HD) input demonstrated equivalent performance, but the former was more effective in terms of computation/memory and time costs. The sensitivity/specificity for detecting MCI-to-AD conversion (but not AD/HC classification performance) was further improved from 79.5%/75%-83.3%/81.3% by a combination of morphometric measurements with ApoE-genotype and demographics (age, sex, education). When applied to the independent AddNeuroMed cohort, the best ADNI models produced equivalent performance without substantial accuracy drop, suggesting good robustness sufficient for future clinical implementation.

Ratsnake: a versatile image annotation tool with application to computer-aided diagnosis

Image segmentation and annotation are key components of image-based medical computer-aided diagnosis (CAD) systems. In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system. In order to demonstrate this unique capability, we present its novel application for the evaluation and quantification of salient objects and structures of interest in kidney biopsy images. Accurate annotation identifying and quantifying such structures in microscopy images can provide an estimation of pathogenesis in obstructive nephropathy, which is a rather common disease with severe implication in children and infants. However a tool for detecting and quantifying the disease is not yet available. A machine learning-based approach, which utilizes prior domain knowledge and textural image features, is considered for the generation of an image force field customizing the presented tool for automatic evaluation of kidney biopsy images. The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.