Recent studies suggest that the microbiome can be an important mediator in the effect of a treatment on an outcome. Microbiome data generated from sequencing experiments contain the relative abundance of a large number of microbial taxa with their ev
olutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator invalidates standard mediation analyses. We propose a phylogeny-based mediation analysis method (PhyloMed) for the microbiome mediator. PhyloMed models the microbiome mediation effect through a cascade of independent local mediation models on the internal nodes of the phylogenetic tree. Each local model captures the mediation effect of a subcomposition at a given taxonomic resolution. The method improves the power of the mediation test by enriching weak and sparse signals across mediating taxa that tend to cluster on the tree. In each local model, we further empower PhyloMed by using a mixture distribution to obtain the subcomposition mediation test p-value, which takes into account the composite nature of the null hypothesis. PhyloMed enables us to test the overall mediation effect of the entire microbial community and pinpoint internal nodes with significant subcomposition mediation effects. Our extensive simulations demonstrate the validity of PhyloMed and its substantial power gain over existing methods. An application to a real study further showcases the advantages of our method.
Scientists frequently generalize population level causal quantities such as average treatment effect from a source population to a target population. When the causal effects are heterogeneous, differences in subject characteristics between the source
and target populations may make such a generalization difficult and unreliable. Reweighting or regression can be used to adjust for such differences when generalizing. However, these methods typically suffer from large variance if there is limited covariate distribution overlap between the two populations. We propose a generalizability score to address this issue. The score can be used as a yardstick to select target subpopulations for generalization. A simplified version of the score avoids using any outcome information and thus can prevent deliberate biases associated with inadvertent access to such information. Both simulation studies and real data analysis demonstrate convincing results for such selection.
Previous works mainly focus on improving cross-lingual transfer for NLU tasks with multilingual pretrained encoder (MPE), or improving the translation performance on NMT task with BERT. However, how to improve the cross-lingual transfer of NMT model
with multilingual pretrained encoder is under-explored. In this paper, we focus on a zero-shot cross-lingual transfer task in NMT. In this task, the NMT model is trained with one parallel dataset and an off-the-shelf MPE, then is directly tested on zero-shot language pairs. We propose SixT, a simple yet effective model for this task. The SixT model leverages the MPE with a two-stage training schedule and gets further improvement with a position disentangled encoder and a capacity-enhanced decoder. The extensive experiments prove that SixT significantly improves the translation quality of the unseen languages. With much less computation cost and training data, our model achieves better performance on many-to-English testsets than CRISS and m2m-100, two strong multilingual NMT baselines.
With increasing data availability, causal treatment effects can be evaluated across different datasets, both randomized controlled trials (RCTs) and observational studies. RCTs isolate the effect of the treatment from that of unwanted (confounding) c
o-occurring effects. But they may struggle with inclusion biases, and thus lack external validity. On the other hand, large observational samples are often more representative of the target population but can conflate confounding effects with the treatment of interest. In this paper, we review the growing literature on methods for causal inference on combined RCTs and observational studies, striving for the best of both worlds. We first discuss identification and estimation methods that improve generalizability of RCTs using the representativeness of observational data. Classical estimators include weighting, difference between conditional outcome models, and doubly robust estimators. We then discuss methods that combine RCTs and observational data to improve (conditional) average treatment effect estimation, handling possible unmeasured confounding in the observational data. We also connect and contrast works developed in both the potential outcomes framework and the structural causal model framework. Finally, we compare the main methods using a simulation study and real world data to analyze the effect of tranexamic acid on the mortality rate in major trauma patients. Code to implement many of the methods is provided.
