Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples

Combining relational and attributional similarity for semantic relation classification

International Conference Recent Advances in Natural Language Processing, RANLP323-33

SemEval-2013 task 4: Free paraphrases of noun compounds

Contains fulltext : 122615.pdf (publisher's version ) (Open Access

Towards Pragmatic Production Strategies for Natural Language Generation

This position paper proposes a conceptual framework for the design of Natural Language Generation (NLG) systems that follow efficient and effective production strategies in order to achieve complex communicative goals. In this general framework, efficiency is characterised as the parsimonious regulation of production and comprehension costs while effectiveness is measured with respect to task-oriented and contextually grounded communicative goals. We provide concrete suggestions for the estimation of goals, costs, and utility via modern statistical methods, demonstrating applications of our framework to the classic pragmatic task of visually grounded referential games and to abstractive text summarisation, two popular generation tasks with real-world applications. In sum, we advocate for the development of NLG systems that learn to make pragmatic production decisions from experience, by reasoning about goals, costs, and utility in a human-like way

Towards Pragmatic Production Strategies for Natural Language Generation

This position paper proposes a conceptual framework for the design of Natural Language Generation (NLG) systems that follow efficient and effective production strategies in order to achieve complex communicative goals. In this general framework, efficiency is characterised as the parsimonious regulation of production and comprehension costs while effectiveness is measured with respect to task-oriented and contextually grounded communicative goals. We provide concrete suggestions for the estimation of goals, costs, and utility via modern statistical methods, demonstrating applications of our framework to the classic pragmatic task of visually grounded referential games and to abstractive text summarisation, two popular generation tasks with real-world applications. In sum, we advocate for the development of NLG systems that learn to make pragmatic production decisions from experience, by reasoning about goals, costs, and utility in a human-like way

Sampling-Based Approximations to Minimum Bayes Risk Decoding for Neural Machine Translation

In NMT we search for the mode of the model distribution to form predictions. The mode and other high-probability translations found by beam search have been shown to often be inadequate in a number of ways. This prevents improving translation quality through better search, as these idiosyncratic translations end up selected by the decoding algorithm, a problem known as the beam search curse. Recently, an approximation to minimum Bayes risk (MBR) decoding has been proposed as an alternative decision rule that would likely not suffer from the same problems. We analyse this approximation and establish that it has no equivalent to the beam search curse. We then design approximations that decouple the cost of exploration from the cost of robust estimation of expected utility. This allows for much larger hypothesis spaces, which we show to be beneficial. We also show that mode-seeking strategies can aid in constructing compact sets of promising hypotheses and that MBR is effective in identifying good translations in them. We conduct experiments on three language pairs varying in amounts of resources available: English into and from German, Romanian, and Nepali