Data Science Opportunities To Improve Radiotherapy Planning and Clinical Decision Making.

Radiotherapy aims to achieve a high tumor control probability while minimizing damage to normal tissues. Personalizing radiotherapy treatments for individual patients, therefore, depends on integrating physical treatment planning with predictive models of tumor control and normal tissue complications. Predictive models could be improved using a wide range of rich data sources, including tumor and normal tissue genomics, radiomics, and dosiomics. Deep learning will drive improvements in classifying normal tissue tolerance, predicting intra-treatment tumor changes, tracking accumulated dose distributions, and quantifying the tumor response to radiotherapy based on imaging. Mechanistic patient-specific computer simulations ('digital twins') could also be used to guide adaptive radiotherapy. Overall, we are entering an era where improved modeling methods will allow the use of newly available data sources to better guide radiotherapy treatments.

[Synthetic data in medicine: Generation, evaluation and limits]. / Données synthétiques en médecine : génération, évaluation et limites.

Recent technological advances in data science hold great promise in medicine. Large-sized high-quality datasets are essential but often difficult to obtain due to privacy, cost, and practical challenges. Here, we discuss synthetic data's generation, evaluation, and regulation, highlighting its current applications and limits.

A Perspective on Neuroscience Data Standardization with Neurodata Without Borders.

Neuroscience research has evolved to generate increasingly large and complex experimental data sets, and advanced data science tools are taking on central roles in neuroscience research. Neurodata Without Borders (NWB), a standard language for neurophysiology data, has recently emerged as a powerful solution for data management, analysis, and sharing. We here discuss our labs' efforts to implement NWB data science pipelines. We describe general principles and specific use cases that illustrate successes, challenges, and non-trivial decisions in software engineering. We hope that our experience can provide guidance for the neuroscience community and help bridge the gap between experimental neuroscience and data science. Key takeaways from this article are that (1) standardization with NWB requires non-trivial design choices; (2) the general practice of standardization in the lab promotes data awareness and literacy, and improves transparency, rigor, and reproducibility in our science; (3) we offer several feature suggestions to ease the extensibility, publishing/sharing, and usability for NWB standard and users of NWB data.

Data Analytics in Physical Activity Studies With Accelerometers: Scoping Review.

BACKGROUND: Monitoring free-living physical activity (PA) through wearable devices enables the real-time assessment of activity features associated with health outcomes and provision of treatment recommendations and adjustments. The conclusions of studies on PA and health depend crucially on reliable statistical analyses of digital data. Data analytics, however, are challenging due to the various metrics adopted for measuring PA, different aims of studies, and complex temporal variations within variables. The application, interpretation, and appropriateness of these analytical tools have yet to be summarized. OBJECTIVE: This research aimed to review studies that used analytical methods for analyzing PA monitored by accelerometers. Specifically, this review addressed three questions: (1) What metrics are used to describe an individual's free-living daily PA? (2) What are the current analytical tools for analyzing PA data, particularly under the aims of classification, association with health outcomes, and prediction of health events? and (3) What challenges exist in the analyses, and what recommendations for future research are suggested regarding the use of statistical methods in various research tasks? METHODS: This scoping review was conducted following an existing framework to map research studies by exploring the information about PA. Three databases, PubMed, IEEE Xplore, and the ACM Digital Library, were searched in February 2024 to identify related publications. Eligible articles were classification, association, or prediction studies involving human PA monitored through wearable accelerometers. RESULTS: After screening 1312 articles, 428 (32.62%) eligible studies were identified and categorized into at least 1 of the following 3 thematic categories: classification (75/428, 17.5%), association (342/428, 79.9%), and prediction (32/428, 7.5%). Most articles (414/428, 96.7%) derived PA variables from 3D acceleration, rather than 1D acceleration. All eligible articles (428/428, 100%) considered PA metrics represented in the time domain, while a small fraction (16/428, 3.7%) also considered PA metrics in the frequency domain. The number of studies evaluating the influence of PA on health conditions has increased greatly. Among the studies in our review, regression-type models were the most prevalent (373/428, 87.1%). The machine learning approach for classification research is also gaining popularity (32/75, 43%). In addition to summary statistics of PA, several recent studies used tools to incorporate PA trajectories and account for temporal patterns, including longitudinal data analysis with repeated PA measurements and functional data analysis with PA as a continuum for time-varying association (68/428, 15.9%). CONCLUSIONS: Summary metrics can quickly provide descriptions of the strength, frequency, and duration of individuals' overall PA. When the distribution and profile of PA need to be evaluated or detected, considering PA metrics as longitudinal or functional data can provide detailed information and improve the understanding of the role PA plays in health. Depending on the research goal, appropriate analytical tools can ensure the reliability of the scientific findings.

Privacy-Enhancing Technologies in Biomedical Data Science.

The rapidly growing scale and variety of biomedical data repositories raise important privacy concerns. Conventional frameworks for collecting and sharing human subject data offer limited privacy protection, often necessitating the creation of data silos. Privacy-enhancing technologies (PETs) promise to safeguard these data and broaden their usage by providing means to share and analyze sensitive data while protecting privacy. Here, we review prominent PETs and illustrate their role in advancing biomedicine. We describe key use cases of PETs and their latest technical advances and highlight recent applications of PETs in a range of biomedical domains. We conclude by discussing outstanding challenges and social considerations that need to be addressed to facilitate a broader adoption of PETs in biomedical data science.

Human-AI Teaming in Critical Care: A Comparative Analysis of Data Scientists' and Clinicians' Perspectives on AI Augmentation and Automation.

BACKGROUND: Artificial intelligence (AI) holds immense potential for enhancing clinical and administrative health care tasks. However, slow adoption and implementation challenges highlight the need to consider how humans can effectively collaborate with AI within broader socio-technical systems in health care. OBJECTIVE: In the example of intensive care units (ICUs), we compare data scientists' and clinicians' assessments of the optimal utilization of human and AI capabilities by determining suitable levels of human-AI teaming for safely and meaningfully augmenting or automating 6 core tasks. The goal is to provide actionable recommendations for policy makers and health care practitioners regarding AI design and implementation. METHODS: In this multimethod study, we combine a systematic task analysis across 6 ICUs with an international Delphi survey involving 19 health data scientists from the industry and academia and 61 ICU clinicians (25 physicians and 36 nurses) to define and assess optimal levels of human-AI teaming (level 1=no performance benefits; level 2=AI augments human performance; level 3=humans augment AI performance; level 4=AI performs without human input). Stakeholder groups also considered ethical and social implications. RESULTS: Both stakeholder groups chose level 2 and 3 human-AI teaming for 4 out of 6 core tasks in the ICU. For one task (monitoring), level 4 was the preferred design choice. For the task of patient interactions, both data scientists and clinicians agreed that AI should not be used regardless of technological feasibility due to the importance of the physician-patient and nurse-patient relationship and ethical concerns. Human-AI design choices rely on interpretability, predictability, and control over AI systems. If these conditions are not met and AI performs below human-level reliability, a reduction to level 1 or shifting accountability away from human end users is advised. If AI performs at or beyond human-level reliability and these conditions are not met, shifting to level 4 automation should be considered to ensure safe and efficient human-AI teaming. CONCLUSIONS: By considering the sociotechnical system and determining appropriate levels of human-AI teaming, our study showcases the potential for improving the safety and effectiveness of AI usage in ICUs and broader health care settings. Regulatory measures should prioritize interpretability, predictability, and control if clinicians hold full accountability. Ethical and social implications must be carefully evaluated to ensure effective collaboration between humans and AI, particularly considering the most recent advancements in generative AI.

Community-Engaged Data Science (CEDS): A Case Study of Working with Communities to Use Data to Inform Change.

Data-informed decision making is a critical goal for many community-based public health research initiatives. However, community partners often encounter challenges when interacting with data. The Community-Engaged Data Science (CEDS) model offers a goal-oriented, iterative guide for communities to collaborate with research data scientists through data ambassadors. This study presents a case study of CEDS applied to research on the opioid epidemic in 18 counties in Ohio as part of the HEALing Communities Study (HCS). Data ambassadors provided a pivotal role in empowering community coalitions to translate data into action using key steps of CEDS which included: data landscapes identifying available data in the community; data action plans from logic models based on community data needs and gaps of data; data collection/sharing agreements; and data systems including portals and dashboards. Throughout the CEDS process, data ambassadors emphasized sustainable data workflows, supporting continued data engagement beyond the HCS. The implementation of CEDS in Ohio underscored the importance of relationship building, timing of implementation, understanding communities' data preferences, and flexibility when working with communities. Researchers should consider implementing CEDS and integrating a data ambassador in community-based research to enhance community data engagement and drive data-informed interventions to improve public health outcomes.

A data science roadmap for open science organizations engaged in early-stage drug discovery.

The Structural Genomics Consortium is an international open science research organization with a focus on accelerating early-stage drug discovery, namely hit discovery and optimization. We, as many others, believe that artificial intelligence (AI) is poised to be a main accelerator in the field. The question is then how to best benefit from recent advances in AI and how to generate, format and disseminate data to enable future breakthroughs in AI-guided drug discovery. We present here the recommendations of a working group composed of experts from both the public and private sectors. Robust data management requires precise ontologies and standardized vocabulary while a centralized database architecture across laboratories facilitates data integration into high-value datasets. Lab automation and opening electronic lab notebooks to data mining push the boundaries of data sharing and data modeling. Important considerations for building robust machine-learning models include transparent and reproducible data processing, choosing the most relevant data representation, defining the right training and test sets, and estimating prediction uncertainty. Beyond data-sharing, cloud-based computing can be harnessed to build and disseminate machine-learning models. Important vectors of acceleration for hit and chemical probe discovery will be (1) the real-time integration of experimental data generation and modeling workflows within design-make-test-analyze (DMTA) cycles openly, and at scale and (2) the adoption of a mindset where data scientists and experimentalists work as a unified team, and where data science is incorporated into the experimental design.

TREADS: Target Research for Anti-epileptic Drugs Using Data Science.

CONTEXT: Epilepsy is a common neurological disease and is classified into different types based on features such as the kind of seizure, age of onset, part of brain effected, etc. There are nearly 30 approved anti-epileptic drugs (AEDs) for treating different epilepsies and each drug targets proteins exhibiting a specific molecular mechanism of action. There are many genes, proteins, and microRNAs known to be associated with different epileptic disorders. This rich information on epilepsy-associated data is not available at one single location and is scattered across multiple publicly available repositories. There is a need to have a single platform integrated with the data, as well as tools required for epilepsy research. METHODS AND MATERIAL: Text mining approaches are used to extract data from multiple biological sources. The data is curated and populated within an in-house developed epilepsy database. Machine-learning based models are built in-house to know the probability of a protein being druggable based on the significant protein features. A web interface is provided for the access of the epilepsy database as well as the ML-based tool developed in-house. RESULTS: The epilepsy-associated data is made accessible through a web browser. For a protein of interest, the platform provides all the feature values, and the results generated using different machine learning models are displayed as visualization plots. CONCLUSIONS: To meet these objectives, we present TREADS, a platform for epilepsy research community, having both database and an ML-based tool for the study of AED targets. TO ACCESS TREADS: https://treads-aer.cdacb.in.

Using a digital data analytic tool to capture dynamic change in coordination patterns: An exploratory study of the Apollo 13 mission.

The operational environment of complex sociotechnical systems is inherently uncertain, demanding constant coordination restructuring to adapt to dynamic situational demands. However, coordination changes in the Human Factors and Ergonomics Field have primarily been studied using static methods, overlooking moment-by-moment adjustments. In the current study, we address coordination restructuring by using THEME, a digital analytical tool capable of visualising and exploring coordination restructuring from a multi-layered perspective. We examine restructuring in coordination patterns during NASA's Apollo 13 Mission, revealing significant shifts from stable, long-duration 'coordination hubs' in routine operations to shorter-duration patterns during a crisis situation. Additionally, the results highlight the importance of flexible switching between reciprocal and one-directed coordination, along with enhanced role distribution. This study underscores how exploring temporality-sensitive phenomena like coordination through digital technologies such as THEME, advances our understanding of incident analysis and resilient performance within complex systems.

Interfacing data science with cell therapy manufacturing: where we are and where we need to be.

Although several cell-based therapies have received FDA approval, and others are showing promising results, scalable, and quality-driven reproducible manufacturing of therapeutic cells at a lower cost remains challenging. Challenges include starting material and patient variability, limited understanding of manufacturing process parameter effects on quality, complex supply chain logistics, and lack of predictive, well-understood product quality attributes. These issues can manifest as increased production costs, longer production times, greater batch-to-batch variability, and lower overall yield of viable, high-quality cells. The lack of data-driven insights and decision-making in cell manufacturing and delivery is an underlying commonality behind all these problems. Data collection and analytics from discovery, preclinical and clinical research, process development, and product manufacturing have not been sufficiently utilized to develop a "systems" understanding and identify actionable controls. Experience from other industries shows that data science and analytics can drive technological innovations and manufacturing optimization, leading to improved consistency, reduced risk, and lower cost. The cell therapy manufacturing industry will benefit from implementing data science tools, such as data-driven modeling, data management and mining, AI, and machine learning. The integration of data-driven predictive capabilities into cell therapy manufacturing, such as predicting product quality and clinical outcomes based on manufacturing data, or ensuring robustness and reliability using data-driven supply-chain modeling could enable more precise and efficient production processes and lead to better patient access and outcomes. In this review, we introduce some of the relevant computational and data science tools and how they are being or can be implemented in the cell therapy manufacturing workflow. We also identify areas where innovative approaches are required to address challenges and opportunities specific to the cell therapy industry. We conclude that interfacing data science throughout a cell therapy product lifecycle, developing data-driven manufacturing workflow, designing better data collection tools and algorithms, using data analytics and AI-based methods to better understand critical quality attributes and critical-process parameters, and training the appropriate workforce will be critical for overcoming current industry and regulatory barriers and accelerating clinical translation.

Unveiling the Future of Oncology and Precision Medicine through Data Science.

Information generated via next-generation sequencing (NGS) technologies is often termed multi-omics data [...].

The role of artificial intelligence and data science in nanoparticles development: a review.

Artificial intelligence has revolutionized many sectors with unparalleled predictive capabilities supported by machine learning (ML). So far, this tool has not been able to provide the same level of development in pharmaceutical nanotechnology. This review discusses the current data science methodologies related to polymeric drug-loaded nanoparticle production from an innovative multidisciplinary perspective while considering the strictest data science practices. Several methodological and data interpretation flaws were identified by analyzing the few qualified ML studies. Most issues lie in following appropriate analysis steps, such as cross-validation, balancing data, or testing alternative models. Thus, better-planned studies following the recommended data science analysis steps along with adequate numbers of experiments would change the current landscape, allowing the exploration of the full potential of ML.

[Box: see text].

Data Science Methods for Real-World Evidence Generation in Real-World Data.

In the healthcare landscape, data science (DS) methods have emerged as indispensable tools to harness real-world data (RWD) from various data sources such as electronic health records, claim and registry data, and data gathered from digital health technologies. Real-world evidence (RWE) generated from RWD empowers researchers, clinicians, and policymakers with a more comprehensive understanding of real-world patient outcomes. Nevertheless, persistent challenges in RWD (e.g., messiness, voluminousness, heterogeneity, multimodality) and a growing awareness of the need for trustworthy and reliable RWE demand innovative, robust, and valid DS methods for analyzing RWD. In this article, I review some common current DS methods for extracting RWE and valuable insights from complex and diverse RWD. This article encompasses the entire RWE-generation pipeline, from study design with RWD to data preprocessing, exploratory analysis, methods for analyzing RWD, and trustworthiness and reliability guarantees, along with data ethics considerations and open-source tools. This review, tailored for an audience that may not be experts in DS, aspires to offer a systematic review of DS methods and assists readers in selecting suitable DS methods and enhancing the process of RWE generation for addressing their specific challenges.

The Arcus Experience: Bridging the Data Science Gap for Nurse Researchers.

BACKGROUND: For years, nurse researchers have been called upon to engage with "big data" in the electronic health record (EHR) by leading studies focusing on nurse-centric patient outcomes and providing clinical analysis of potential outcome indicators. However, the current gap in nurses' data science education and training poses a significant barrier. OBJECTIVES: We aimed to evaluate the viability of conducting nurse-led, big-data research projects within a custom-designed computational laboratory and examine the support required by a team of researchers with little to no big-data experience. METHODS: Four nurse-led research teams developed a research question reliant on existing EHR data. Each team was given its own virtual computational laboratory populated with raw data. A data science education team provided instruction in coding languages-primarily structured query language and R-and data science techniques to organize and analyze the data. RESULTS: Three research teams have completed studies, resulting in one manuscript currently undergoing peer review and two manuscripts in progress. The final team is performing data analysis. Five barriers and five facilitators to big-data projects were identified. DISCUSSION: As the data science learning curve is steep, organizations need to help bridge the gap between what is currently taught in doctoral nursing programs and what is required of clinical nurse researchers to successfully engage in big-data methods. In addition, clinical nurse researchers require protected research time and a data science infrastructure that supports novice efforts with education, mentorship, and computational laboratory resources.

Biomedical Data Science, Artificial Intelligence, and Ethics: Navigating Challenges in the Face of Explosive Growth.

Advances in biomedical data science and artificial intelligence (AI) are profoundly changing the landscape of healthcare. This article reviews the ethical issues that arise with the development of AI technologies, including threats to privacy, data security, consent, and justice, as they relate to donors of tissue and data. It also considers broader societal obligations, including the importance of assessing the unintended consequences of AI research in biomedicine. In addition, this article highlights the challenge of rapid AI development against the backdrop of disparate regulatory frameworks, calling for a global approach to address concerns around data misuse, unintended surveillance, and the equitable distribution of AI's benefits and burdens. Finally, a number of potential solutions to these ethical quandaries are offered. Namely, the merits of advocating for a collaborative, informed, and flexible regulatory approach that balances innovation with individual rights and public welfare, fostering a trustworthy AI-driven healthcare ecosystem, are discussed.