Patient empowerment for cancer patients through a novel ICT infrastructure.

As a result of recent advances in cancer research and "precision medicine" approaches, i.e. the idea of treating each patient with the right drug at the right time, more and more cancer patients are being cured, or might have to cope with a life with cancer. For many people, cancer survival today means living with a complex and chronic condition. Surviving and living with or beyond cancer requires the long-term management of the disease, leading to a significant need for active rehabilitation of the patients. In this paper, we present a novel methodology employed in the iManageCancer project for cancer patient empowerment in which personal health systems, serious games, psychoemotional monitoring and other novel decision-support tools are combined into an integrated patient empowerment platform. We present in detail the ICT infrastructure developed and our evaluation with the involvement of cancer patients on two sites, a large-scale pilot for adults and a small-scale test for children. The evaluation showed mixed evidences on the improvement of patient empowerment, while ability to cope with cancer, including improvement in mood and resilience to cancer, increased for the participants of the adults' pilot.

minepath.org: a free interactive pathway analysis web server.

Minepath: ( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer.

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.

Pathway analysis methodologies couple traditional gene expression analysis with knowledge encoded in established molecular pathway networks, offering a promising approach towards the biological interpretation of phenotype differentiating genes. Early pathway analysis methodologies, named as gene set analysis (GSA), view pathways just as plain lists of genes without taking into account either the underlying pathway network topology or the involved gene regulatory relations. These approaches, even if they achieve computational efficiency and simplicity, consider pathways that involve the same genes as equivalent in terms of their gene enrichment characteristics. Most recent pathway analysis approaches take into account the underlying gene regulatory relations by examining their consistency with gene expression profiles and computing a score for each profile. Even with this approach, assessing and scoring single-relations limits the ability to reveal key gene regulation mechanisms hidden in longer pathway sub-paths. We introduce MinePath, a pathway analysis methodology that addresses and overcomes the aforementioned problems. MinePath facilitates the decomposition of pathways into their constituent sub-paths. Decomposition leads to the transformation of single-relations to complex regulation sub-paths. Regulation sub-paths are then matched with gene expression sample profiles in order to evaluate their functional status and to assess phenotype differential power. Assessment of differential power supports the identification of the most discriminant profiles. In addition, MinePath assess the significance of the pathways as a whole, ranking them by their p-values. Comparison results with state-of-the-art pathway analysis systems are indicative for the soundness and reliability of the MinePath approach. In contrast with many pathway analysis tools, MinePath is a web-based system (www.minepath.org) offering dynamic and rich pathway visualization functionality, with the unique characteristic to color regulatory relations between genes and reveal their phenotype inclination. This unique characteristic makes MinePath a valuable tool for in silico molecular biology experimentation as it serves the biomedical researchers' exploratory needs to reveal and interpret the regulatory mechanisms that underlie and putatively govern the expression of target phenotypes.

The INTEGRATE project: Delivering solutions for efficient multi-centric clinical research and trials.

The objective of the INTEGRATE project (http://www.fp7-integrate.eu/) that has recently concluded successfully was the development of innovative biomedical applications focused on streamlining the execution of clinical research, on enabling multidisciplinary collaboration, on management and large-scale sharing of multi-level heterogeneous datasets, and on the development of new methodologies and of predictive multi-scale models in cancer. In this paper, we present the way the INTEGRATE consortium has approached important challenges such as the integration of multi-scale biomedical data in the context of post-genomic clinical trials, the development of predictive models and the implementation of tools to facilitate the efficient execution of postgenomic multi-centric clinical trials in breast cancer. Furthermore, we provide a number of key "lessons learned" during the process and give directions for further future research and development.

Workflow-driven clinical decision support for personalized oncology.

BACKGROUND: The adoption in oncology of Clinical Decision Support (CDS) may help clinical users to efficiently deal with the high complexity of the domain, lead to improved patient outcomes, and reduce the current knowledge gap between clinical research and practice. While significant effort has been invested in the implementation of CDS, the uptake in the clinic has been limited. The barriers to adoption have been extensively discussed in the literature. In oncology, current CDS solutions are not able to support the complex decisions required for stratification and personalized treatment of patients and to keep up with the high rate of change in therapeutic options and knowledge. RESULTS: To address these challenges, we propose a framework enabling efficient implementation of meaningful CDS that incorporates a large variety of clinical knowledge models to bring to the clinic comprehensive solutions leveraging the latest domain knowledge. We use both literature-based models and models built within the p-medicine project using the rich datasets from clinical trials and care provided by the clinical partners. The framework is open to the biomedical community, enabling reuse of deployed models by third-party CDS implementations and supporting collaboration among modelers, CDS implementers, biomedical researchers and clinicians. To increase adoption and cope with the complexity of patient management in oncology, we also support and leverage the clinical processes adhered to by healthcare organizations. We design an architecture that extends the CDS framework with workflow functionality. The clinical models are embedded in the workflow models and executed at the right time, when and where the recommendations are needed in the clinical process. CONCLUSIONS: In this paper we present our CDS framework developed in p-medicine and the CDS implementation leveraging the framework. To support complex decisions, the framework relies on clinical models that encapsulate relevant clinical knowledge. Next to assisting the decisions, this solution supports by default (through modeling and implementation of workflows) the decision processes as well and exploits the knowledge embedded in those processes.

Semantic biomedical resource discovery: a Natural Language Processing framework.

BACKGROUND: A plethora of publicly available biomedical resources do currently exist and are constantly increasing at a fast rate. In parallel, specialized repositories are been developed, indexing numerous clinical and biomedical tools. The main drawback of such repositories is the difficulty in locating appropriate resources for a clinical or biomedical decision task, especially for non-Information Technology expert users. In parallel, although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications has been slow and lags behind progress in the general NLP domain. The aim of the present study is to investigate the use of semantics for biomedical resources annotation with domain specific ontologies and exploit Natural Language Processing methods in empowering the non-Information Technology expert users to efficiently search for biomedical resources using natural language. METHODS: A Natural Language Processing engine which can "translate" free text into targeted queries, automatically transforming a clinical research question into a request description that contains only terms of ontologies, has been implemented. The implementation is based on information extraction techniques for text in natural language, guided by integrated ontologies. Furthermore, knowledge from robust text mining methods has been incorporated to map descriptions into suitable domain ontologies in order to ensure that the biomedical resources descriptions are domain oriented and enhance the accuracy of services discovery. The framework is freely available as a web application at ( http://calchas.ics.forth.gr/ ). RESULTS: For our experiments, a range of clinical questions were established based on descriptions of clinical trials from the ClinicalTrials.gov registry as well as recommendations from clinicians. Domain experts manually identified the available tools in a tools repository which are suitable for addressing the clinical questions at hand, either individually or as a set of tools forming a computational pipeline. The results were compared with those obtained from an automated discovery of candidate biomedical tools. For the evaluation of the results, precision and recall measurements were used. Our results indicate that the proposed framework has a high precision and low recall, implying that the system returns essentially more relevant results than irrelevant. CONCLUSIONS: There are adequate biomedical ontologies already available, sufficiency of existing NLP tools and quality of biomedical annotation systems for the implementation of a biomedical resources discovery framework, based on the semantic annotation of resources and the use on NLP techniques. The results of the present study demonstrate the clinical utility of the application of the proposed framework which aims to bridge the gap between clinical question in natural language and efficient dynamic biomedical resources discovery.

LETHE: A Digital Intervention for Cognitive Decline.

Dementia is the main cause of disability in elderly populations. It has been shown that the risk factors of dementia are a mixture of pathological, lifestyle and heritable factors, with some of those being provably modifiable. Early diagnosis of dementia and approaches to slow down its evolution are currently the most prominent management methodologies due to lack of a cure. For that reason, a plethora of home-based assistive technologies for dementia management do exist, with most of them focusing on the improvement of memory and thinking. The main objective of LETHE is prevention in the whole spectrum of cognitive decline in the elderly population at risk reaching from asymptomatic to subjective or mild cognitive impairment to prodromal Dementia. LETHE will provide a Big Data collection platform and analysis system, that will allow prevention, personalized risk detection and intervention on cognitive decline. Through the subsequent 2-year clinical trial, the LETHE system, as well as the respective knowledge gained will be evaluated and validated. The scope of the current paper is to introduce the LETHE study and its respective novel platform as a holistic approach to multidomain lifestyle intervention trial studies. The present work depicts the architectural perspective and extends beyond state-of-the-art guidelines and approaches to health management systems and cloud platform development.Clinical Relevance - Patient Management Systems as well as lifestyle management platforms have significant clinical relevance as they allow for remote and continuous monitoring of patients' health status. LETHE aims to improve patient outcomes by providing predictive models for cognitive decline and patient adherence to the multimodal lifestyle intervention, enabling prompt and appropriate medical decisions.

Type 1 Diabetes Hypoglycemia Prediction Algorithms: Systematic Review.

BACKGROUND: Diabetes is a chronic condition that necessitates regular monitoring and self-management of the patient's blood glucose levels. People with type 1 diabetes (T1D) can live a productive life if they receive proper diabetes care. Nonetheless, a loose glycemic control might increase the risk of developing hypoglycemia. This incident can occur because of a variety of causes, such as taking additional doses of insulin, skipping meals, or overexercising. Mainly, the symptoms of hypoglycemia range from mild dysphoria to more severe conditions, if not detected in a timely manner. OBJECTIVE: In this review, we aimed to report on innovative detection techniques and tactics for identifying and preventing hypoglycemic episodes, focusing on T1D. METHODS: A systematic literature search following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines was performed focusing on the PubMed, GoogleScholar, IEEEXplore, and ACM Digital Library to find articles on technologies related to hypoglycemia detection in patients with T1D. RESULTS: The presented approaches have been used or devised to enhance blood glucose monitoring and boost its efficacy in forecasting future glucose levels, which could aid the prediction of future episodes of hypoglycemia. We detected 19 predictive models for hypoglycemia, specifically on T1D, using a wide range of algorithmic methodologies, spanning from statistics (1.9/19, 10%) to machine learning (9.88/19, 52%) and deep learning (7.22/19, 38%). The algorithms used most were the Kalman filtering and classification models (support vector machine, k-nearest neighbors, and random forests). The performance of the predictive models was found to be satisfactory overall, reaching accuracies between 70% and 99%, which proves that such technologies are capable of facilitating the prediction of T1D hypoglycemia. CONCLUSIONS: It is evident that continuous glucose monitoring can improve glucose control in diabetes; however, predictive models for hypo- and hyperglycemia using only mainstream noninvasive sensors such as wristbands and smartwatches are foreseen to be the next step for mobile health in T1D. Prospective studies are required to demonstrate the value of such models in real-life mobile health interventions.

Deep Learning in mHealth for Cardiovascular Disease, Diabetes, and Cancer: Systematic Review.

BACKGROUND: Major chronic diseases such as cardiovascular disease (CVD), diabetes, and cancer impose a significant burden on people and health care systems around the globe. Recently, deep learning (DL) has shown great potential for the development of intelligent mobile health (mHealth) interventions for chronic diseases that could revolutionize the delivery of health care anytime, anywhere. OBJECTIVE: The aim of this study is to present a systematic review of studies that have used DL based on mHealth data for the diagnosis, prognosis, management, and treatment of major chronic diseases and advance our understanding of the progress made in this rapidly developing field. METHODS: A search was conducted on the bibliographic databases Scopus and PubMed to identify papers with a focus on the deployment of DL algorithms that used data captured from mobile devices (eg, smartphones, smartwatches, and other wearable devices) targeting CVD, diabetes, or cancer. The identified studies were synthesized according to the target disease, the number of enrolled participants and their age, and the study period as well as the DL algorithm used, the main DL outcome, the data set used, the features selected, and the achieved performance. RESULTS: In total, 20 studies were included in the review. A total of 35% (7/20) of DL studies targeted CVD, 45% (9/20) of studies targeted diabetes, and 20% (4/20) of studies targeted cancer. The most common DL outcome was the diagnosis of the patient's condition for the CVD studies, prediction of blood glucose levels for the studies in diabetes, and early detection of cancer. Most of the DL algorithms used were convolutional neural networks in studies on CVD and cancer and recurrent neural networks in studies on diabetes. The performance of DL was found overall to be satisfactory, reaching >84% accuracy in most studies. In comparison with classic machine learning approaches, DL was found to achieve better performance in almost all studies that reported such comparison outcomes. Most of the studies did not provide details on the explainability of DL outcomes. CONCLUSIONS: The use of DL can facilitate the diagnosis, management, and treatment of major chronic diseases by harnessing mHealth data. Prospective studies are now required to demonstrate the value of applied DL in real-life mHealth tools and interventions.

Randomization of Clinical Trial Participants via an Integrated Web Service.

Randomization is an inherent part of Randomized Clinical Trials (RCTs), typically requiring the split of participants in intervention and control groups. We present a web service supporting randomized patient distribution, developed in the context of the MyPal project RCT. The randomization process is based on a block permutation approach to mitigate the risk of various kind of biases. The presented service can be used via its web user interface to produce randomized lists of patients distributed in the various study groups, with a variant block size. Alternatively, the presented service can be integrated as part of wider IT systems supporting clinical trials via a REST interface following a micro-service architectural pattern.

Fostering Palliative Care Through Digital Intervention: A Platform for Adult Patients With Hematologic Malignancies.

Patient-reported outcomes (PROs) are an emerging paradigm in clinical research and healthcare, aiming to capture the patient's self-assessed health status in order to gauge efficacy of treatment from their perspective. As these patient-generated health data provide insights into the effects of healthcare processes in real-life settings beyond the clinical setting, they can also be viewed as a resolution beyond what can be gleaned directly by the clinician. To this end, patients are identified as a key stakeholder of the healthcare decision making process, instead of passively following their doctor's guidance. As this joint decision-making process requires constant and high-quality communication between the patient and his/her healthcare providers, novel methodologies and tools have been proposed to promote richer and preemptive communication to facilitate earlier recognition of potential complications. To this end, as PROs can be used to quantify the patient impact (especially important for chronic conditions such as cancer), they can play a prominent role in providing patient-centric care. In this paper, we introduce the MyPal platform that aims to support adults suffering from hematologic malignancies, focusing on the technical design and highlighting the respective challenges. MyPal is a Horizon 2020 European project aiming to support palliative care for cancer patients via the electronic PROs (ePROs) paradigm, building upon modern eHealth technologies. To this end, MyPal project evaluate the proposed eHealth intervention via clinical studies and assess its potential impact on the provided palliative care. More specifically, MyPal platform provides specialized applications supporting the regular answering of well-defined and standardized questionnaires, spontaneous symptoms reporting, educational material provision, notifications etc. The presented platform has been validated by end-users and is currently in the phase of pilot testing in a clinical study to evaluate its feasibility and its potential impact on the quality of life of palliative care patients with hematologic malignancies.

Scientific discovery workflows in bioinformatics: a scenario for the coupling of molecular regulatory pathways and gene-expression profiles.

Scientific workflow technologies and tools have become an important weapon in the arsenal of the bioinformaticians and computational biologists. To support this view we present a typical exploratory data analysis scenario involving the combination of information from Gene Regulatory Networks and gene expression data. We further describe the implementation of this scenario using the Workflow Environment implemented in the context of a large EU funded project. In this process desirable features that similar environments should offer are identified and analyzed. The ICT platform presented is evaluated using the chosen scenario as a benchmark. Finally we conclude with an outlook to future work.

Deep learning models in genomics; are we there yet?

With the evolution of biotechnology and the introduction of the high throughput sequencing, researchers have the ability to produce and analyze vast amounts of genomics data. Since genomics produce big data, most of the bioinformatics algorithms are based on machine learning methodologies, and lately deep learning, to identify patterns, make predictions and model the progression or treatment of a disease. Advances in deep learning created an unprecedented momentum in biomedical informatics and have given rise to new bioinformatics and computational biology research areas. It is evident that deep learning models can provide higher accuracies in specific tasks of genomics than the state of the art methodologies. Given the growing trend on the application of deep learning architectures in genomics research, in this mini review we outline the most prominent models, we highlight possible pitfalls and discuss future directions. We foresee deep learning accelerating changes in the area of genomics, especially for multi-scale and multimodal data analysis for precision medicine.

Artificial intelligence radiogenomics for advancing precision and effectiveness in oncologic care (Review).

The new era of artificial intelligence (AI) has introduced revolutionary data­driven analysis paradigms that have led to significant advancements in information processing techniques in the context of clinical decision­support systems. These advances have created unprecedented momentum in computational medical imaging applications and have given rise to new precision medicine research areas. Radiogenomics is a novel research field focusing on establishing associations between radiological features and genomic or molecular expression in order to shed light on the underlying disease mechanisms and enhance diagnostic procedures towards personalized medicine. The aim of the current review was to elucidate recent advances in radiogenomics research, focusing on deep learning with emphasis on radiology and oncology applications. The main deep learning radiogenomics architectures, together with the clinical questions addressed, and the achieved genetic or molecular correlations are presented, while a performance comparison of the proposed methodologies is conducted. Finally, current limitations, potentially understudied topics and future research directions are discussed.

Electronic Patient-Reported Outcome-Based Interventions for Palliative Cancer Care: A Systematic and Mapping Review.

PURPOSE: Capitalizing on the promise of patient-reported outcomes (PROs), electronic implementations of PROs (ePROs) are expected to play an important role in the development of novel digital health interventions targeting palliative cancer care. We performed a systematic and mapping review of the scientific literature on the current ePRO-based approaches used for palliative cancer care. METHODS: Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement guidelines, the conducted review answered the research questions: "What are the current ePRO-based approaches for palliative cancer care; what is their contribution/value in the domain of palliative cancer care; and what are the potential gaps, challenges, and opportunities for further research?" After a screening step, the corpus of included articles indexed in PubMed or the Web of Science underwent full text review, which mapped the articles across 15 predefined axes. RESULTS: The corpus of 24 mapped studies includes 9 study protocols, 7 technical tools/solutions, 7 pilot/feasibility/acceptability studies, and 1 evaluation study. The review of the corpus revealed (1) an archetype of ePRO-enabled interventions for palliative cancer care, which most commonly use ePROs as study end point assessment instruments rather than integral intervention components; (2) the fact that the literature has not fully embraced the modern definitions that expand the scope of palliative care; (3) the striking shortage of promising ubiquitous computing devices (eg, smart activity trackers); and (4) emerging evidence about the benefits of narrowing down the target cancer population, especially when combined with modern patient-centered intervention design methodologies. CONCLUSION: Although research on exploiting ePROs for the development of digital palliative cancer care interventions is considerably active and demonstrates several successful cases, there is considerable room for improvement along the directions of the aforementioned findings.

Dementia Care Frameworks and Assistive Technologies for Their Implementation: A Review.

In this review, we focus on the various integrated care models that have been applied for the management of dementia patients. We explore the different types of assistive technologies (mobile, wearable, and home-based systems) for dementia care, with a special emphasis on technologies that involve or target the informal caregiver as end user. In an attempt to reveal the needs for information sharing, communication, and collaboration between people with dementia and caregivers involved in the effective and integrated management of the disease, we analyze the trends in research and development to date, we seek to understand and reflect upon the state of the art in assistive technologies for dementia, and we highlight domains that appear underexplored, in order to guide future research. We also explore the cost effectiveness of such technologies and integrated care models for the management of dementia patients and comment on current limitations and future trends and directions. Findings indicate the urgent need and the current lack of a comprehensive and cost-effective solution that will incorporate information system technologies for the provision of integrated care services to dementia patients and their informal caregivers.

iSupport: Building a Resilience Support Tool for Improving the Health Condition of the Patient During the Care Path.

Anxiety and stress are very common symptoms of patients facing a forthcoming surgery. However, limited time and resources within healthcare systems make the provision of stress relief interventions difficult to provide. Research has shown that provision of preoperative stress relief and educational resources can improve health outcomes and speed recovery. Information and Communication Technology (ICT) can be a valuable tool in providing stress relief and educational support to patients and family before but also after an operation, enabling better self-management and self-empowerment. To this direction, this paper reports on the design of a novel technical infrastructure for a resilience support tool for improving the health condition of patients, during the care path, using Virtual Reality (VR). The designed platform targets, among others, at improving the knowledge on the patient data, effectiveness and adherence to treatment, as well as providing for effective communication channels between patients and clinicians.

Development of an eHealth tool for cancer patients: monitoring psycho-emotional aspects with the Family Resilience (FaRe) Questionnaire.

In the last decade, clinicians have started to shift from an individualistic perspective of the patient towards family-centred models of care, due to the increasing evidence from research and clinical practice of the crucial role of significant others in determining the patient's adjustment to cancer disease and management. eHealth tools can be considered a means to compensate the services gap and support outpatient care flows. Within the works of the European H2020 iManageCancer project, a review of the literature in the field of family resilience was conducted, in order to determine how to monitor the patient and his/her family's resilience through an eHealth platform. An analysis of existing family resilience questionnaires suggested that no measure was appropriate for cancer patients and their families. For this reason, a new family resilience questionnaire (named FaRe) was developed to screen the patient's and caregiver's psycho-emotional resources. Composed of 24 items, it is divided into four subscales: Communication and Cohesion, Perceived Family Coping, Religiousness and Spirituality, and Perceived Social Support. Embedded in the iManageCancer eHealth platform, it allows users and clinicians to monitor the patient's and the caregivers' resilience throughout the cancer trajectory.

Personal Health Information Recommender: implementing a tool for the empowerment of cancer patients.

Nowadays, patients have a wealth of information available on the Internet. Despite the potential benefits of Internet health information seeking, several concerns have been raised about the quality of information and about the patient's capability to evaluate medical information and to relate it to their own disease and treatment. As such, novel tools are required to effectively guide patients and provide high-quality medical information in an intelligent and personalised manner. With this aim, this paper presents the Personal Health Information Recommender (PHIR), a system to empower patients by enabling them to search in a high-quality document repository selected by experts, avoiding the information overload of the Internet. In addition, the information provided to the patients is personalised, based on individual preferences, medical conditions and other profiling information. Despite the generality of our approach, we apply the PHIR to a personal health record system constructed for cancer patients and we report on the design, the implementation and a preliminary validation of the platform. To the best of our knowledge, our platform is the only one combining natural language processing, ontologies and personal information to offer a unique user experience.