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Abstract Microbiome data from sequencing experiments contain the relative abundance of a large number of microbial taxa with their evolutionary relationships represented by a phylogenetic tree. The compositional and high-dimensional nature of the microbiome mediator challenges the validity of standard mediation analyses. We propose a phylogeny-based mediation analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, PhyloMed discovers mediation signals by analyzing subcompositions defined on the phylogenic tree. PhyloMed produces well-calibrated mediation test p -values and yields substantially higher discovery power than existing methods. 

Abstract We propose an explainable approach for relation extraction that mitigates the tension between generalization and explainability by jointly training for the two goals. Our approach uses a multi-task learning architecture, which jointly trains a classifier for relation extraction, and a sequence model that labels words in the context of the relations that explain the decisions of the relation classifier. We also convert the model outputs to rules to bring global explanations to this approach. This sequence model is trained using a hybrid strategy: supervised, when supervision from pre-existing patterns is available, and semi-supervised otherwise. In the latter situation, we treat the sequence model’s labels as latent variables, and learn the best assignment that maximizes the performance of the relation classifier. We evaluate the proposed approach on the two datasets and show that the sequence model provides labels that serve as accurate explanations for the relation classifier’s decisions, and, importantly, that the joint training generally improves the performance of the relation classifier. We also evaluate the performance of the generated rules and show that the new rules are a great add-on to the manual rules and bring the rule-based system much closer to the neural models. 

We propose an explainable approach for relation extraction that mitigates the tension between generalization and explainability by jointly training for the two goals. Our approach uses a multi-task learning architecture, which jointly trains a classifier for relation extraction, and a sequence model that labels words in the context of the relation that explain the decisions of the relation classifier. We also convert the model outputs to rules to bring global explanations to this approach. This sequence model is trained using a hybrid strategy: supervised, when supervision from pre-existing patterns is available, and semi-supervised otherwise. In the latter situation, we treat the sequence model’s labels as latent variables, and learn the best assignment that maximizes the performance of the relation classifier. We evaluate the proposed approach on the two datasets and show that the sequence model provides labels that serve as accurate explanations for the relation classifier’s decisions, and, importantly, that the joint training generally improves the performance of the relation classifier. We also evaluate the performance of the generated rules and show that the new rules are great add-on to the manual rules and bring the rule-based system much closer to the neural models. 

Three fused-ring electron acceptors ( SIDIC , DIDIC and TIDIC ) were designed and synthesized using single bond, vinylene and acetylene units linked indaceno[3,2- b ]dithiophene dimers as electron-rich cores and 3-(1,1-dicyanomethylene)-5,6-difluoro-1-indanone as electron-deficient termini. These molecules exhibit strong absorption from 550 to 900 nm with large attenuation coefficients of 1.8–2.0 × 10 5 M −1 cm −1 and high electron mobilities of 2.2–4.9 × 10 −3 cm 2 V −1 s −1 . In combination with wide-bandgap polymer FTAZ as a donor, organic solar cells exhibit efficiencies of 9.3–13.1%. Effects of the linking units on optical, electronic, morphologic, and photovoltaic properties were revealed. Relative to SIDIC , vinylene-bridged DIDIC shows red-shifted absorption, while acetylene-bridged TIDIC shows blue-shifted absorption. Compared with SIDIC and DIDIC , TIDIC has a lower HOMO, higher electron mobility, and higher device efficiency.