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Register a new userTargeting Learning: Robust Statistics for Reproducible Research
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Added by
Alan Hubbard
Publication date
2020
fields
Mathematical Statistics
and research's language is
English
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Targeted Learning is a subfield of statistics that unifies advances in causal inference, machine learning and statistical theory to help answer scientifically impactful questions with statistical confidence. Targeted Learning is driven by complex problems in data science and has been implemented in a diversity of real-world scenarios: observational studies with missing treatments and outcomes, personalized interventions, longitudinal settings with time-varying treatment regimes, survival analysis, adaptive randomized trials, mediation analysis, and networks of connected subjects. In contrast to the (mis)application of restrictive modeling strategies that dominate the current practice of statistics, Targeted Learning establishes a principled standard for statistical estimation and inference (i.e., confidence intervals and p-values). This multiply robust approach is accompanied by a guiding roadmap and a burgeoning software ecosystem, both of which provide guidance on the construction of estimators optimized to best answer the motivating question. The roadmap of Targeted Learning emphasizes tailoring statistical procedures so as to minimize their assumptions, carefully grounding them only in the scientific knowledge available. The end result is a framework that honestly reflects the uncertainty in both the background knowledge and the available data in order to draw reliable conclusions from statistical analyses - ultimately enhancing the reproducibility and rigor of scientific findings.
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Q-learning is a regression-based approach that is widely used to formalize the development of an optimal dynamic treatment strategy. Finite dimensional working models are typically used to estimate certain nuisance parameters, and misspecification of these working models can result in residual confounding and/or efficiency loss. We propose a robust Q-learning approach which allows estimating such nuisance parameters using data-adaptive techniques. We study the asymptotic behavior of our estimators and provide simulation studies that highlight the need for and usefulness of the proposed method in practice. We use the data from the Extending Treatment Effectiveness of Naltrexone multi-stage randomized trial to illustrate our proposed methods.
The field of deep learning is experiencing a trend towards producing reproducible research. Nevertheless, it is still often a frustrating experience to reproduce scientific results. This is especially true in the machine learning community, where it is considered acceptable to have black boxes in your experiments. We present DeepDIVA, a framework designed to facilitate easy experimentation and their reproduction. This framework allows researchers to share their experiments with others, while providing functionality that allows for easy experimentation, such as: boilerplate code, experiment management, hyper-parameter optimization, verification of data integrity and visualization of data and results. Additionally, the code of DeepDIVA is well-documented and supported by several tutorials that allow a new user to quickly familiarize themselves with the framework.
We describe the current state and future plans for a set of tools for scientific data management (SDM) designed to support scientific transparency and reproducible research. SDM has been in active use at our MRI Center for more than two years. We designed the system to be used from the beginning of a research project, which contrasts with conventional end-state databases that accept data as a project concludes. A number of benefits accrue from using scientific data management tools early and throughout the project, including data integrity as well as reuse of the data and of computational methods.
This paper introduces reproducible research, and explains its importance, benefits and challenges. Some important tools for conducting reproducible research in Transportation Research are also introduced. Moreover, the source code for generating this paper has been designed in a way so that it can be used as a template for researchers to write their future journal papers as dynamic and reproducible documents.
Reproducibility of computational studies is a hallmark of scientific methodology. It enables researchers to build with confidence on the methods and findings of others, reuse and extend computational pipelines, and thereby drive scientific progress. Since many experimental studies rely on computational analyses, biologists need guidance on how to set up and document reproducible data analyses or simulations. In this paper, we address several questions about reproducibility. For example, what are the technical and non-technical barriers to reproducible computational studies? What opportunities and challenges do computational notebooks offer to overcome some of these barriers? What tools are available and how can they be used effectively? We have developed a set of rules to serve as a guide to scientists with a specific focus on computational notebook systems, such as Jupyter Notebooks, which have become a tool of choice for many applications. Notebooks combine detailed workflows with narrative text and visualization of results. Combined with software repositories and open source licensing, notebooks are powerful tools for transparent, collaborative, reproducible, and reusable data analyses.
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