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A mapping between interactions and interference: implications for vaccine trials.

ABSTRACT: In this paper, we discuss relationships between causal interactions within the counterfactual framework and interference in which the exposure of one person may affect the outcomes of another. We show that the empirical tests for causal interactions can, in fact, all be adapted to empirical tests for particular forms of interference. In the context of interference, by recoding the response as some function of the outcomes of the various persons within a cluster, a wide range of different forms of interference can potentially be detected. The correspondence between causal interactions and forms of interference extends to encompass n-way causal interactions, interference between n persons within a cluster, and multivalued exposures. The theory for causal interactions provides a complete conceptual apparatus for assessing interference as well. The results are illustrated using data from a hypothetical vaccine trial to reason about specific forms of interference and spillover effects that may be present in this vaccine setting. We discuss the implications of this correspondence for our conceptualizations of interaction and for application to vaccine trials and many other settings in which spillover effects may be present.

SUBMITTER: VanderWeele TJ

PROVIDER: S-EPMC4580340 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature

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A mapping between interactions and interference: implications for vaccine trials.

VanderWeele Tyler J TJ Vandenbroucke Jan P JP Tchetgen Eric J Tchetgen EJ Robins James M JM

Epidemiology (Cambridge, Mass.) 20120301 2

In this paper, we discuss relationships between causal interactions within the counterfactual framework and interference in which the exposure of one person may affect the outcomes of another. We show that the empirical tests for causal interactions can, in fact, all be adapted to empirical tests for particular forms of interference. In the context of interference, by recoding the response as some function of the outcomes of the various persons within a cluster, a wide range of different forms o ...[more]

PMID: 22317812

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Project description:BackgroundVaccines have revolutionized public health by providing protection against infectious diseases. They stimulate the immune system and generate memory cells to defend against targeted diseases. Clinical trials evaluate vaccine performance, including dosage, administration routes, and potential side effects.Clinicaltrialsgov is a valuable repository of clinical trial information, but the vaccine data in them lacks standardization, leading to challenges in automatic concept mapping, vaccine-related knowledge development, evidence-based decision-making, and vaccine surveillance.ResultsIn this study, we developed a cascaded framework that capitalized on multiple domain knowledge sources, including clinical trials, the Unified Medical Language System (UMLS), and the Vaccine Ontology (VO), to enhance the performance of domain-specific language models for automated mapping of VO from clinical trials. The Vaccine Ontology (VO) is a community-based ontology that was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Our methodology involved extracting and annotating data from various sources. We then performed pre-training on the PubMedBERT model, leading to the development of CTPubMedBERT. Subsequently, we enhanced CTPubMedBERT by incorporating SAPBERT, which was pretrained using the UMLS, resulting in CTPubMedBERT + SAPBERT. Further refinement was accomplished through fine-tuning using the Vaccine Ontology corpus and vaccine data from clinical trials, yielding the CTPubMedBERT + SAPBERT + VO model. Finally, we utilized a collection of pre-trained models, along with the weighted rule-based ensemble approach, to normalize the vaccine corpus and improve the accuracy of the process. The ranking process in concept normalization involves prioritizing and ordering potential concepts to identify the most suitable match for a given context. We conducted a ranking of the Top 10 concepts, and our experimental results demonstrate that our proposed cascaded framework consistently outperformed existing effective baselines on vaccine mapping, achieving 71.8% on top 1 candidate's accuracy and 90.0% on top 10 candidate's accuracy.ConclusionThis study provides a detailed insight into a cascaded framework of fine-tuned domain-specific language models improving mapping of VO from clinical trials. By effectively leveraging domain-specific information and applying weighted rule-based ensembles of different pre-trained BERT models, our framework can significantly enhance the mapping of VO from clinical trials.

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A mapping between interactions and interference: implications for vaccine trials.

Publications

A mapping between interactions and interference: implications for vaccine trials.

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