Illuminating protein space with a programmable generative model.

Three billion years of evolution has produced a tremendous diversity of protein molecules1, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.

Regional differences in utilization of 17α-hydroxyprogesterone caproate (17-OHP).

OBJECTIVES: To describe regional differences in utilization of 17α-hydroxyprogesterone caproate (17-OHP). METHODS: Retrospective cohort study of a large, US commercial managed care plan claims database with pharmacy coverage from 2008 to 2018. Singleton pregnancies with at least one prior spontaneous preterm birth (sPTB) were included. Regional and state-based differences in 17-OHP use were compared. Data were analyzed using t-tests and Fisher's exact tests. RESULTS: Of the 4,514 individuals with an indication for 17-OHP, 580 (12.8%) were prescribed 17-OHP. Regional and state-based differences in 17-OHP utilization were identified; Northeast 15.7%, Midwest 13.7%, South 12.0%, and West 10.4% (p=0.003). CONCLUSIONS: While significant regional differences in 17-OHP utilization were demonstrated, 17-OHP utilization remained low despite this cohort having insurance through a US commercial managed care plan. Suboptimal utilization demonstrates a disconnect between research and uptake in clinical practice. This underscores a need for implementation science in obstetrics to translate updated recommendations more effectively and efficiently into clinical practice.

Cost Savings Without Increased Risk of Respiratory Hospitalization for Preterm Children after the 2014 Palivizumab Policy Update.

OBJECTIVE: Our objective was to compare rates of hospitalizations for respiratory illnesses in preterm and full-term (FT) children for 4 years before and after the 2014 update to the American Academy of Pediatrics (AAP) respiratory syncytial virus (RSV) immunoprophylaxis guidance, which restricted eligibility among infants born at 29 to 34 weeks in the first winter and all preterm infants in the second winter after neonatal discharge. STUDY DESIGN: We conducted pre-post and interrupted time series analyses on claims data from a commercial national managed care plan. We compared the number of RSV and all respiratory hospital admissions in the first and second RSV seasons after neonatal discharge among a cohort of preterm children, regardless of palivizumab status, in the 4 years before and after the implementation of the 2014 palivizumab eligibility change. A FT group was included for reference. RESULTS: The cohort included 821 early preterm (EP, <29 weeks), 4,790 moderate preterm (MP, 29-34 weeks), and 130,782 FT children. Palivizumab use after the policy update decreased among MP children in the first and second RSV seasons after neonatal discharge, without any change in the odds of hospitalization with RSV or respiratory illness. For the EP group, there was no change in the rate of palivizumab or the odds of hospitalization with RSV or respiratory illness after the policy update. For the FT group, there was a slight decrease in odds of hospitalization post-2014 after the policy update. The interrupted time series did not reveal any secular trends over time in hospitalization rates among preterm children. Following the policy change, there were cost savings for MP children in the first and second RSV seasons, when accounting for the cost of hospitalizations and the cost of palivizumab. CONCLUSION: Hospitalizations for RSV or respiratory illness did not increase, and cost savings were obtained after the implementation of the 2014 AAP palivizumab prophylaxis policy. KEY POINTS: · Palivizumab use decreased among children born moderate preterm (29 to34 weeks) after the 2014 palivizuamb policy update.. · There was no change in odds of hospitalization with respiratory syncitial virus or respiratory illness among preterm infants after the policy update when compared to before.. · There were cost savings, when accounting for the cost of hospitalizations and the cost of palivizumab, after the policy update among children born moderate preterm..

Effectiveness of 17-OHP for Prevention of Recurrent Preterm Birth: A Retrospective Cohort Study.

OBJECTIVE: 17-α-hydroxyprogesterone caproate (17-OHP) has been recommended by professional societies for the prevention of recurrent preterm birth, but subsequent clinical studies have reported conflicting efficacy results. This study aimed to contribute to the evidence base regarding the effectiveness of 17-OHP in clinical practice using real-world data. STUDY DESIGN: A total of 4,422 individuals meeting inclusion criteria representing recurrent spontaneous preterm birth (sPTB) were identified in a database of insurance claims, and 568 (12.8%) received 17-OHP. Crude and propensity score-matched recurrence rates and risk ratios (RRs) for the association of receiving 17-OHP on recurrent sPTB were calculated. RESULTS: Raw sPTB recurrence rates were higher among those treated versus not treated; after propensity score matching, no association was detected (26.3 vs. 23.8%, RR = 1.1, 95% CI: 0.9-1.4). CONCLUSION: We failed to identify a beneficial effect of 17-OHP for the prevention of spontaneous recurrent preterm birth in our observational, U.S. based cohort. KEY POINTS: · •We observed higher risk for sPTB in the group receiving 17-OHP in the unmatched analysis. · •After propensity-score matching, we still failed to identify a beneficial effect of 17-OHP on sPTB. · •Sensitivity analyses demonstrated robustness to the inclusion criteria and modeling assumptions..

Empirical Frequentist Coverage of Deep Learning Uncertainty Quantification Procedures.

Uncertainty quantification for complex deep learning models is increasingly important as these techniques see growing use in high-stakes, real-world settings. Currently, the quality of a model's uncertainty is evaluated using point-prediction metrics, such as the negative log-likelihood (NLL), expected calibration error (ECE) or the Brier score on held-out data. Marginal coverage of prediction intervals or sets, a well-known concept in the statistical literature, is an intuitive alternative to these metrics but has yet to be systematically studied for many popular uncertainty quantification techniques for deep learning models. With marginal coverage and the complementary notion of the width of a prediction interval, downstream users of deployed machine learning models can better understand uncertainty quantification both on a global dataset level and on a per-sample basis. In this study, we provide the first large-scale evaluation of the empirical frequentist coverage properties of well-known uncertainty quantification techniques on a suite of regression and classification tasks. We find that, in general, some methods do achieve desirable coverage properties on in distribution samples, but that coverage is not maintained on out-of-distribution data. Our results demonstrate the failings of current uncertainty quantification techniques as dataset shift increases and reinforce coverage as an important metric in developing models for real-world applications.

Bayesian neural networks for detecting epistasis in genetic association studies.

BACKGROUND: Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS: A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing genetic association studies. Demonstrations on synthetic and real data reveal they are able to efficiently and accurately determine which variants are involved in determining case-control status. By using graphics processing units (GPUs) the time needed to build these models is decreased by several orders of magnitude. In comparison with commonly used approaches for detecting interactions, Bayesian neural networks perform very well across a broad spectrum of possible genetic relationships. CONCLUSIONS: The proposed framework is shown to be a powerful method for detecting causal SNPs while being computationally efficient enough to handle large datasets.

Artificial intelligence in the neonatal intensive care unit: the time is now.

Artificial intelligence (AI) has the potential to revolutionize the neonatal intensive care unit (NICU) care by leveraging the large-scale, high-dimensional data that are generated by NICU patients. There is an emerging recognition that the confluence of technological progress, commercialization pathways, and rich data sets provides a unique opportunity for AI to make a lasting impact on the NICU. In this perspective article, we discuss four broad categories of AI applications in the NICU: imaging interpretation, prediction modeling of electronic health record data, integration of real-time monitoring data, and documentation and billing. By enhancing decision-making, streamlining processes, and improving patient outcomes, AI holds the potential to transform the quality of care for vulnerable newborns, making the excitement surrounding AI advancements well-founded and the potential for significant positive change stronger than ever before.

Statin Twitter: Human and Automated Bot Contributions, 2010 to 2022.

BACKGROUND: Many individuals eligible for statin therapy decline treatment, often due to fear of adverse effects. Misinformation about statins is common and drives statin reluctance, but its prevalence on social media platforms, such as Twitter (now X) remains unclear. Social media bots are known to proliferate medical misinformation, but their involvement in statin-related discourse is unknown. This study examined temporal trends in volume, author type (bot or human), and sentiment of statin-related Twitter posts (tweets). METHODS AND RESULTS: We analyzed original tweets with statin-related terms from 2010 to 2022 using a machine learning-derived classifier to determine the author's bot probability, natural language processing to assign each tweet a negative or positive sentiment, and manual qualitative analysis to identify statin skepticism in a random sample of all tweets and in highly influential tweets. We identified 1 155 735 original statin-related tweets. Bots produced 333 689 (28.9%), humans produced 699 876 (60.6%), and intermediate probability accounts produced 104 966 (9.1%). Over time, the proportion of bot tweets decreased from 47.8% to 11.3%, and human tweets increased from 43.6% to 79.8%. The proportion of negative-sentiment tweets increased from 27.8% to 43.4% for bots and 30.9% to 38.4% for humans. Manually coded statin skepticism increased from 8.0% to 19.0% for bots and from 26.0% to 40.0% for humans. CONCLUSIONS: Over the past decade, humans have overtaken bots as generators of statin-related content on Twitter. Negative sentiment and statin skepticism have increased across all user types. Twitter may be an important forum to combat statin-related misinformation.

Concordance of randomised controlled trials for artificial intelligence interventions with the CONSORT-AI reporting guidelines.

The Consolidated Standards of Reporting Trials extension for Artificial Intelligence interventions (CONSORT-AI) was published in September 2020. Since its publication, several randomised controlled trials (RCTs) of AI interventions have been published but their completeness and transparency of reporting is unknown. This systematic review assesses the completeness of reporting of AI RCTs following publication of CONSORT-AI and provides a comprehensive summary of RCTs published in recent years. 65 RCTs were identified, mostly conducted in China (37%) and USA (18%). Median concordance with CONSORT-AI reporting was 90% (IQR 77-94%), although only 10 RCTs explicitly reported its use. Several items were consistently under-reported, including algorithm version, accessibility of the AI intervention or code, and references to a study protocol. Only 3 of 52 included journals explicitly endorsed or mandated CONSORT-AI. Despite a generally high concordance amongst recent AI RCTs, some AI-specific considerations remain systematically poorly reported. Further encouragement of CONSORT-AI adoption by journals and funders may enable more complete adoption of the full CONSORT-AI guidelines.

Prediction of extubation failure among low birthweight neonates using machine learning.

OBJECTIVE: To develop machine learning models predicting extubation failure in low birthweight neonates using large amounts of clinical data. STUDY DESIGN: Retrospective cohort study using MIMIC-III, a large single-center, open-source clinical dataset. Logistic regression and boosted-tree (XGBoost) models using demographics, medications, and vital sign and ventilatory data were developed to predict extubation failure, defined as reintubation within 7 days. RESULTS: 1348 low birthweight (≤2500 g) neonates who received mechanical ventilation within the first 7 days were included, of which 350 (26%) failed a trial of extubation. The best-performing model was a boosted-tree model incorporating demographics, vital signs, ventilator parameters, and medications (AUROC 0.82). The most important features were birthweight, last FiO2, average mean airway pressure, caffeine use, and gestational age. CONCLUSIONS: Machine learning models identified low birthweight ventilated neonates at risk for extubation failure. These models will need to be validated across multiple centers to determine generalizability of this tool.

Artificial Intelligence Based on Machine Learning in Pharmacovigilance: A Scoping Review.

INTRODUCTION: Artificial intelligence based on machine learning has made large advancements in many fields of science and medicine but its impact on pharmacovigilance is yet unclear. OBJECTIVE: The present study conducted a scoping review of the use of artificial intelligence based on machine learning to understand how it is used for pharmacovigilance tasks, characterize differences with other fields, and identify opportunities to improve pharmacovigilance through the use of machine learning. DESIGN: The PubMed, Embase, Web of Science, and IEEE Xplore databases were searched to identify articles pertaining to the use of machine learning in pharmacovigilance published from the year 2000 to September 2021. After manual screening of 7744 abstracts, a total of 393 papers met the inclusion criteria for further analysis. Extraction of key data on study design, data sources, sample size, and machine learning methodology was performed. Studies with the characteristics of good machine learning practice were defined and manual review focused on identifying studies that fulfilled these criteria and results that showed promise. RESULTS: The majority of studies (53%) were focused on detecting safety signals using traditional statistical methods. Of the studies that used more recent machine learning methods, 61% used off-the-shelf techniques with minor modifications. Temporal analysis revealed that newer methods such as deep learning have shown increased use in recent years. We found only 42 studies (10%) that reflect current best practices and trends in machine learning. In the subset of 154 papers that focused on data intake and ingestion, 30 (19%) were found to incorporate the same best practices. CONCLUSION: Advances from artificial intelligence have yet to fully penetrate pharmacovigilance, although recent studies show signs that this may be changing.

The false hope of current approaches to explainable artificial intelligence in health care.

The black-box nature of current artificial intelligence (AI) has caused some to question whether AI must be explainable to be used in high-stakes scenarios such as medicine. It has been argued that explainable AI will engender trust with the health-care workforce, provide transparency into the AI decision making process, and potentially mitigate various kinds of bias. In this Viewpoint, we argue that this argument represents a false hope for explainable AI and that current explainability methods are unlikely to achieve these goals for patient-level decision support. We provide an overview of current explainability techniques and highlight how various failure cases can cause problems for decision making for individual patients. In the absence of suitable explainability methods, we advocate for rigorous internal and external validation of AI models as a more direct means of achieving the goals often associated with explainability, and we caution against having explainability be a requirement for clinically deployed models.

Second opinion needed: communicating uncertainty in medical machine learning.

There is great excitement that medical artificial intelligence (AI) based on machine learning (ML) can be used to improve decision making at the patient level in a variety of healthcare settings. However, the quantification and communication of uncertainty for individual predictions is often neglected even though uncertainty estimates could lead to more principled decision-making and enable machine learning models to automatically or semi-automatically abstain on samples for which there is high uncertainty. In this article, we provide an overview of different approaches to uncertainty quantification and abstention for machine learning and highlight how these techniques could improve the safety and reliability of current ML systems being used in healthcare settings. Effective quantification and communication of uncertainty could help to engender trust with healthcare workers, while providing safeguards against known failure modes of current machine learning approaches. As machine learning becomes further integrated into healthcare environments, the ability to say "I'm not sure" or "I don't know" when uncertain is a necessary capability to enable safe clinical deployment.

Medication utilization in children born preterm in the first two years of life.

OBJECTIVE: To compare medications dispensed during the first 2 years in children born preterm and full-term. STUDY DESIGN: Retrospective analysis of claims data from a commercial national managed care plan 2008-2019. 329,855 beneficiaries were enrolled from birth through 2 years, of which 25,408 (7.7%) were preterm (<37 weeks). Filled prescription claims and paid amount over 2 years were identified. RESULTS: In preterm children, the number of filled prescriptions was 1.4 times and cost was 3.8 times that of full-term children. Number and cost of medications were inversely related to gestational age. Differences peak at 4-9 months and resolve by 19 months after discharge. Palivizumab, ranitidine, albuterol, lansoprazole, budesonide, and prednisolone had the greatest differences in utilization. CONCLUSION: Prescription medication utilization among preterm children under 2 years is driven by palivizumab, anti-reflux, and respiratory medications, despite little evidence regarding efficacy for many medications and concern for harm with certain classes.

Machine learning for patient risk stratification: standing on, or looking over, the shoulders of clinicians?

Machine learning can help clinicians to make individualized patient predictions only if researchers demonstrate models that contribute novel insights, rather than learning the most likely next step in a set of actions a clinician will take. We trained deep learning models using only clinician-initiated, administrative data for 42.9 million admissions using three subsets of data: demographic data only, demographic data and information available at admission, and the previous data plus charges recorded during the first day of admission. Models trained on charges during the first day of admission achieve performance close to published full EMR-based benchmarks for inpatient outcomes: inhospital mortality (0.89 AUC), prolonged length of stay (0.82 AUC), and 30-day readmission rate (0.71 AUC). Similar performance between models trained with only clinician-initiated data and those trained with full EMR data purporting to include information about patient state and physiology should raise concern in the deployment of these models. Furthermore, these models exhibited significant declines in performance when evaluated over only myocardial infarction (MI) patients relative to models trained over MI patients alone, highlighting the importance of physician diagnosis in the prognostic performance of these models. These results provide a benchmark for predictive accuracy trained only on prior clinical actions and indicate that models with similar performance may derive their signal by looking over clinician's shoulders-using clinical behavior as the expression of preexisting intuition and suspicion to generate a prediction. For models to guide clinicians in individual decisions, performance exceeding these benchmarks is necessary.

Protocol for development of a reporting guideline (TRIPOD-AI) and risk of bias tool (PROBAST-AI) for diagnostic and prognostic prediction model studies based on artificial intelligence.

INTRODUCTION: The Transparent Reporting of a multivariable prediction model of Individual Prognosis Or Diagnosis (TRIPOD) statement and the Prediction model Risk Of Bias ASsessment Tool (PROBAST) were both published to improve the reporting and critical appraisal of prediction model studies for diagnosis and prognosis. This paper describes the processes and methods that will be used to develop an extension to the TRIPOD statement (TRIPOD-artificial intelligence, AI) and the PROBAST (PROBAST-AI) tool for prediction model studies that applied machine learning techniques. METHODS AND ANALYSIS: TRIPOD-AI and PROBAST-AI will be developed following published guidance from the EQUATOR Network, and will comprise five stages. Stage 1 will comprise two systematic reviews (across all medical fields and specifically in oncology) to examine the quality of reporting in published machine-learning-based prediction model studies. In stage 2, we will consult a diverse group of key stakeholders using a Delphi process to identify items to be considered for inclusion in TRIPOD-AI and PROBAST-AI. Stage 3 will be virtual consensus meetings to consolidate and prioritise key items to be included in TRIPOD-AI and PROBAST-AI. Stage 4 will involve developing the TRIPOD-AI checklist and the PROBAST-AI tool, and writing the accompanying explanation and elaboration papers. In the final stage, stage 5, we will disseminate TRIPOD-AI and PROBAST-AI via journals, conferences, blogs, websites (including TRIPOD, PROBAST and EQUATOR Network) and social media. TRIPOD-AI will provide researchers working on prediction model studies based on machine learning with a reporting guideline that can help them report key details that readers need to evaluate the study quality and interpret its findings, potentially reducing research waste. We anticipate PROBAST-AI will help researchers, clinicians, systematic reviewers and policymakers critically appraise the design, conduct and analysis of machine learning based prediction model studies, with a robust standardised tool for bias evaluation. ETHICS AND DISSEMINATION: Ethical approval has been granted by the Central University Research Ethics Committee, University of Oxford on 10-December-2020 (R73034/RE001). Findings from this study will be disseminated through peer-review publications. PROSPERO REGISTRATION NUMBER: CRD42019140361 and CRD42019161764.