The interactome data are available though the PIP (Potential Interactions of Proteins) web server at http://bmm.cancerresearchuk.org/servers/pip. Further additional material is available at http://bmm.cancerresearchuk.org/servers/pip/bioinformatics/

Machine learning (ML), artificial intelligence (AI) and other modern statistical methods are providing new opportunities to operationalize previously untapped and rapidly growing sources of data for patient benefit. Whilst there is a lot of promising research currently being undertaken, the literature as a whole lacks: transparency; clear reporting to facilitate replicability; exploration for potential ethical concerns; and, clear demonstrations of effectiveness. There are many reasons for why these issues exist, but one of the most important that we provide a preliminary solution for here is the current lack of ML/AIspecific best practice guidance. Although there is no consensus on what best practice looks in this field, we believe that interdisciplinary groups pursuing research and impact projects in the ML/AI for health domain would benefit from answering a series of questions based on the important issues that exist when undertaking work of this nature. Here we present 20 questions that span the entire project life cycle, from inception, data analysis, and model evaluation, to implementation, as a means to facilitate project planning and post-hoc (structured) independent evaluation. By beginning to answer these questions in different settings, we can start to understand what constitutes a good answer, and we expect that the resulting discussion will be central to developing an international consensus framework for transparent, replicable, ethical and effective research in artificial intelligence (AI-TREE) for health.

BackgroundReimbursement decisions are conventionally based on evidence from randomised controlled trials (RCTs), which often have high internal validity but low external validity. Real-world data (RWD) may provide complimentary evidence for relative effectiveness assessments (REAs) and cost-effectiveness assessments (CEAs). This study examines whether RWD is incorporated in health technology assessment (HTA) of melanoma drugs by European HTA agencies, as well as differences in RWD use between agencies and across time.MethodsHTA reports published between 1 January 2011 and 31 December 2016 were retrieved from websites of agencies representing five jurisdictions: England [National Institute for Health and Care Excellence (NICE)], Scotland [Scottish Medicines Consortium (SMC)], France [Haute Autorité de santé (HAS)], Germany [Institute for Quality and Efficacy in Healthcare (IQWiG)] and The Netherlands [Zorginstituut Nederland (ZIN)]. A standardized data extraction form was used to extract information on RWD inclusion for both REAs and CEAs.ResultsOverall, 52 reports were retrieved, all of which contained REAs; CEAs were present in 25 of the reports. RWD was included in 28 of the 52 REAs (54%), mainly to estimate melanoma prevalence, and in 22 of the 25 (88%) CEAs, mainly to extrapolate long-term effectiveness and/or identify drug-related costs. Differences emerged between agencies regarding RWD use in REAs; the ZIN and IQWiG cited RWD for evidence on prevalence, whereas the NICE, SMC and HAS additionally cited RWD use for drug effectiveness. No visible trend for RWD use in REAs and CEAs over time was observed.ConclusionIn general, RWD inclusion was higher in CEAs than REAs, and was mostly used to estimate melanoma prevalence in REAs or to predict long-term effectiveness in CEAs. Differences emerged between agencies’ use of RWD; however, no visible trends for RWD use over time were observed.Electronic supplementary materialThe online version of this article (10.1007/s40273-017-0596-z) contains supplementary material, which is available to authorized users.

Background: Protein-protein interactions have traditionally been studied on a small scale, using classical biochemical methods to investigate the proteins of interest. More recently large-scale methods, such as two-hybrid screens, have been utilised to survey extensive portions of genomes. Current high-throughput approaches have a relatively high rate of errors, whereas in-depth biochemical studies are too expensive and time-consuming to be practical for extensive studies. As a result, there are gaps in our knowledge of many key biological networks, for which computational approaches are particularly suitable.

Real-world data (RWD) and the derivations of these data into real-world evidence (RWE) are rapidly expanding from informing healthcare decisions at the patient and health system level to influencing major health policy decisions, including regulatory approvals and coverage. Recent examples include the approval of palbociclib in combination with endocrine therapy for male breast cancer and the inclusion of RWE in the label of paliperidone palmitate for schizophrenia. This interest has created an urgency to develop processes that promote trust in the evidence-generation process. Key stakeholders and decision-makers include patients and their healthcare providers; learning health systems; health technology assessment bodies and payers; pharmacoepidemiologists and other clinical reseachers, and policy makers interested in bioethical and regulatory issues. A key to optimal uptake of RWE is transparency of the research process to enable decision-makers to evaluate the quality of the methods used and the applicability of the evidence that results from the RWE studies. Registration of RWE studies-particularly for hypothesis evaluating treatment effectiveness (HETE) studies-has been proposed to improve transparency, trust, and research replicability. Although registration would not guarantee better RWE studies would be conducted, it would encourage the prospective disclosure of study plans, timing, and rationale for modifications. A joint task force of the International Society for Pharmacoeconomics and Outcomes Research (ISPOR) and the International Society for Pharmacoepidemiology (ISPE) recommended that investigators preregister their RWE studies and post their study protocols in a publicly available forum before starting studies to reduce publication bias and improve the transparency of research methods.Recognizing that published recommendations alone are insufficient, especially without accessible registration options and with no incentives, a group of experts gathered on February 25 and 26, 2019, in National Harbor, Maryland, to explore the structural and practical challenges to the successful implementation of the recommendations of the ISPOR/ISPE task force for preregistration. This positioning article describes a plan for making registration of HETE RWE studies routine. The plan includes specifying the rationale for registering HETE RWE studies, the studies that should be registered, where and when these studies should be registered, how and when analytic deviations from protocols should be reported, how and when to publish results, and incentives to encourage registration. Table 1 summarizes the rationale, goals, and potential solutions that increase transparency, in addition to unique concerns about secondary data studies.Definitions of terms used throughout this report are provided in Table 2.

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Decision-makers have become increasingly interested in incorporating real-world evidence (RWE) into their decision-making process. Due to concerns regarding the reliability and quality of RWE, stakeholders have issued numerous recommendation documents to assist in setting RWE standards. The fragmented nature of these documents poses a challenge to researchers and decision-makers looking for guidance on what is ‘high-quality’ RWE and how it can be used in decision-making. We offer researchers and decision-makers a structure to organize the landscape of RWE recommendations and identify consensus and gaps in the current recommendations. To provide researchers with a much needed pathway for generating RWE, we discuss how decision-makers can move from fragmented recommendations to comprehensive guidance.

Health technology assessment (HTA) is increasingly informed by nonrandomized studies, but there is limited guidance from HTA bodies on expectations around evidence quality and study conduct. We developed recommendations to support the appropriate use of such evidence based on a pragmatic literature review and a workshop involving 16 experts from eight countries as part of the EU’s Horizon-2020 IMPACT-HTA program (work package six). To ensure HTA processes remain rigorous and robust, HTA bodies should demand clear, extensive and structured reporting of nonrandomized studies, including an in-depth assessment of the risk of bias. In recognition of the additional uncertainty imparted by nonrandomized designs in estimates of treatment effects, HTA bodies should strengthen early scientific advice and engage in collaborative efforts to improve use of real-world data.