Searching for Smallest Grammars on Large Sequences and Application to DNA

International audienceMotivated by the inference of the structure of genomic sequences, we address here the smallest grammar problem. In previous work, we introduced a new perspective on this problem, splitting the task into two different optimization problems: choosing which words will be considered constituents of the final grammar and finding a minimal parsing with these constituents. Here we focus on making these ideas applicable on large sequences. First, we improve the complexity of existing algorithms by using the concept of maximal repeats when choosing which substrings will be the constituents of the grammar. Then, we improve the size of the grammars by cautiously adding a minimal parsing optimization step. Together, these approaches enable us to propose new practical algorithms that return smaller grammars (up to 10\%) in approximately the same amount of time than their competitors on a classical set of genomic sequences and on whole genomes of model organisms

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

M.: A Note on the Expressive Power of Probabilistic Context Free Grammars

Abstract. We examine the expressive power of probabilistic context free grammars (PCFGs), with a special focus on the use of probabilities as a mechanism for reducing ambiguity by filtering out unwanted parses. Probabilities in PCFGs induce an ordering relation among the set of trees that yield a given input sentence. PCFG parsers return the trees bearing the maximum probability for a given sentence, discarding all other possible trees. This mechanism is naturally viewed as a way of defining a new class of tree languages. We formalize the tree language thus defined, study its expressive power, and show that the latter is beyond context freeness. While the increased expressive power offered by PCFGs helps to reduce ambiguity, we show that, in general, it cannot be decided whether a PCFG removes all ambiguities. 1

Rijke. Comparing the ambiguity reduction abilities of probabilistic context-free grammars

We present a measure for evaluating Probabilistic Context Free Grammars (PCFG) based on their ambiguity resolution capabilities. Probabilities in a PCFG can be seen as a filtering mechanism: For an ambiguous sentence, the trees bearing maximum probability are single out, while all others are discarded. The level of ambiguity is related to the size of the singled out set of trees. Under our measure, a grammar is better than other if the first one has reduced the level of ambiguity in a higher degree. The measure we present is computed over a finite sample set of sentence because, as we show, it can not be computed over the set of sentences accepted by the grammar. 1

A Note on the Expressive Power of Probabilistic Context Free Grammars

We examine the expressive power of probabilistic context free grammars (PCFGs), with a special focus on the use of probabilities as a mechanism for reducing ambiguity by filtering out unwanted parses. Probabilities in PCFGs induce an ordering relation among the set of trees that yield a given input sentence. PCFG parsers return the trees bearing the maximum probability for a given sentence, discarding all other possible trees. This mechanism is naturally viewed as a way of defining a new class of tree languages. We formalize the tree language thus defined, study its expressive power, and show that the latter is beyond context freeness. While the increased expressive power offered by PCFGs helps to reduce ambiguity, we show that, in general, it cannot be decided whether a PCFG removes all ambiguities