Search

Automated machine-reading biocuration systems typically use sentence-by-sentence information extraction to construct meaning representations for use by curators. This does not directly reflect the typical discourse structure used by scientists to construct an argument from the experimental data available within a article, and is therefore less likely to correspond to representations typically used in biomedical informatics systems (let alone to the mental models that scientists have). In this study, we develop Natural Language Processing methods to locate, extract, and classify the individual passages of text from articles' Results sections that refer to experimental data. In our domain of interest (molecular biology studies of cancer signal transduction pathways), individual articles may contain as many as 30 small-scale individual experiments describing a variety of findings, upon which authors base their overall research conclusions. Our system automatically classifies discourse segments in these texts into seven categories (fact, hypothesis, problem, goal, method, result, implication) with an F-score of 0.68. These segments describe the essential building blocks of scientific discourse to (i) provide context for each experiment, (ii) report experimental details and (iii) explain the data's meaning in context. We evaluate our system on text passages from articles that were curated in molecular biology databases (the Pathway Logic Datum repository, the Molecular Interaction MINT and INTACT databases) linking individual experiments in articles to the type of assay used (coprecipitation, phosphorylation, translocation etc.). We use supervised machine learning techniques on text passages containing unambiguous references to experiments to obtain baseline F1 scores of 0.59 for MINT, 0.71 for INTACT and 0.63 for Pathway Logic. Although preliminary, these results support the notion that targeting information extraction methods to experimental results could provide accurate, automated methods for biocuration. We also suggest the need for finer-grained curation of experimental methods used when constructing molecular biology databases. [ABSTRACT FROM AUTHOR]

Abstract Background We address the goal of curating observations from published experiments in a generalizable form; reasoning over these observations to generate interpretations and then querying this interpreted knowledge to supply the supporting evidence. We present web-application software as part of the 'BioScholar' project (R01-GM083871) that fully instantiates this process for a well-defined domain: using tract-tracing experiments to study the neural connectivity of the rat brain. Results The main contribution of this work is to provide the first instantiation of a knowledge representation for experimental observations called 'Knowledge Engineering from Experimental Design' (KEfED) based on experimental variables and their interdependencies. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a 'neural connection matrix' interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. BioScholar is built in Flex 3.5. It uses Persevere (a noSQL database) as a flexible data store and PowerLoom® (a mature First Order Logic reasoning system) to execute queries using spatial reasoning over the BAMS neuroanatomical ontology. Conclusions We first introduce the KEfED approach as a general approach and describe its possible role as a way of introducing structured reasoning into models of argumentation within new models of scientific publication. We then describe the design and implementation of our example application: the BioScholar software. This is presented as a possible biocuration interface and supplementary reasoning toolkit for a larger, more specialized bioinformatics system: the Brain Architecture Management System (BAMS).

The task of aspect-based sentiment analysis aims to identify sentiment polarities of given aspects in a sentence. Recent advances have demonstrated the advantage of incorporating the syntactic dependency structure with graph convolutional networks (GCNs). However, their performance of these GCN-based methods largely depends on the dependency parsers, which would produce diverse parsing results for a sentence. In this article, we propose a dual GCN (DualGCN) that jointly considers the syntax structures and semantic correlations. Our DualGCN model mainly comprises four modules: 1) SynGCN: instead of explicitly encoding syntactic structure, the SynGCN module uses the dependency probability matrix as a graph structure to implicitly integrate the syntactic information; 2) SemGCN: we design the SemGCN module with multihead attention to enhance the performance of the syntactic structure with the semantic information; 3) Regularizers: we propose orthogonal and differential regularizers to precisely capture semantic correlations between words by constraining attention scores in the SemGCN module; and 4) Mutual BiAffine: we use the BiAffine module to bridge relevant information between the SynGCN and SemGCN modules. Extensive experiments are conducted compared with up-to-date pretrained language encoders on two groups of datasets, one including Restaurant14, Laptop14, and Twitter and the other including Restaurant15 and Restaurant16. The experimental results demonstrate that the parsing results of various dependency parsers affect their performance of the GCN-based models. Our DualGCN model achieves superior performance compared with the state-of-the-art approaches. The source code and preprocessed datasets are provided and publicly available on GitHub (see https://github.com/CCChenhao997/DualGCN-ABSA).

ChatGPT is a high-performance large language model that has the potential to significantly improve human-computer interactions. It can provide advice on a range of topics, but it is unclear how good this advice is relative to that provided by competent humans, especially in situations where empathy is required. Here, we report the first investigation of whether ChatGPT's responses are perceived as better than those of humans in a task where humans were attempting to be empathetic. Fifty social dilemma questions were randomly selected from 10 well-known advice columns. In a pre-registered survey, participants ( N  = 404) were each shown one question, along with the corresponding response by an advice columnist and by ChatGPT. ChatGPT's advice was perceived as more balanced, complete, empathetic, helpful, and better than the advice provided by professional advice columnists (all values of p  < 0.001). Although participants could not determine which response was written by ChatGPT (54%, p  = 0.29), most participants preferred that their own social dilemma questions be answered by a human than by a computer (77%, p  < 0.001). ChatGPT's responses were longer than those produced by the advice columnists (mean 280.9 words vs. 142.2 words, p  < 0.001). In a second pre-registered survey, each ChatGPT answer was constrained to be approximately the same length as that of the advice columnist (mean 143.2 vs. 142.2 words, p  = 0.95). This survey ( N  = 401) replicated the above findings, showing that the benefit of ChatGPT was not solely due to it writing longer answers., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Howe, Fay, Saletta and Hovy.)

The definitions of two coreference scoring metrics- B 3 and CEAF-are underspecified with respect to predicted , as opposed to key (or gold ) mentions. Several variations have been proposed that manipulate either, or both, the key and predicted mentions in order to get a one-to-one mapping. On the other hand, the metric BLANC was, until recently, limited to scoring partitions of key mentions. In this paper, we (i) argue that mention manipulation for scoring predicted mentions is unnecessary, and potentially harmful as it could produce unintuitive results; (ii) illustrate the application of all these measures to scoring predicted mentions; (iii) make available an open-source, thoroughly-tested reference implementation of the main coreference evaluation measures; and (iv) rescore the results of the CoNLL-2011/2012 shared task systems with this implementation. This will help the community accurately measure and compare new end-to-end coreference resolution algorithms.

BLANC is a link-based coreference evaluation metric for measuring the quality of coreference systems on gold mentions. This paper extends the original BLANC ("BLANC-gold" henceforth) to system mentions, removing the gold mention assumption. The proposed BLANC falls back seamlessly to the original one if system mentions are identical to gold mentions, and it is shown to strongly correlate with existing metrics on the 2011 and 2012 CoNLL data.

This report documents the program and the outcomes of Dagstuhl Perspectives Workshop 11331 "The Future of Research Communication". The purpose of the workshop was to bring together researchers from these different disciplines, whose core research goal is changing the formats, standards, and means by which we communicate science.