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PyPlutchik: Visualising and comparing emotion-annotated corpora.

ABSTRACT: The increasing availability of textual corpora and data fetched from social networks is fuelling a huge production of works based on the model proposed by psychologist Robert Plutchik, often referred simply as the "Plutchik Wheel". Related researches range from annotation tasks description to emotions detection tools. Visualisation of such emotions is traditionally carried out using the most popular layouts, as bar plots or tables, which are however sub-optimal. The classic representation of the Plutchik's wheel follows the principles of proximity and opposition between pairs of emotions: spatial proximity in this model is also a semantic proximity, as adjacent emotions elicit a complex emotion (a primary dyad) when triggered together; spatial opposition is a semantic opposition as well, as positive emotions are opposite to negative emotions. The most common layouts fail to preserve both features, not to mention the need of visually allowing comparisons between different corpora in a blink of an eye, that is hard with basic design solutions. We introduce PyPlutchik the Pyplutchik package is available as a Github repository (http://github.com/alfonsosemeraro/pyplutchik) or through the installation commands pip or conda. For any enquiry about usage or installation feel free to contact the corresponding author, a Python module specifically designed for the visualisation of Plutchik's emotions in texts or in corpora. PyPlutchik draws the Plutchik's flower with each emotion petal sized after how much that emotion is detected or annotated in the corpus, also representing three degrees of intensity for each of them. Notably, PyPlutchik allows users to display also primary, secondary, tertiary and opposite dyads in a compact, intuitive way. We substantiate our claim that PyPlutchik outperforms other classic visualisations when displaying Plutchik emotions and we showcase a few examples that display our module's most compelling features.

SUBMITTER: Semeraro A

PROVIDER: S-EPMC8409663 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The availability of annotated corpora has facilitated the application of machine learning algorithms to concept extraction from clinical notes. However, high expenditure and labor are required for creating the annotations. A potential alternative is to reuse existing corpora from other institutions by pooling with local corpora, for training machine taggers. In this paper we have investigated the latter approach by pooling corpora from 2010 i2b2/VA NLP challenge and Mayo Clinic Rochester, to evaluate taggers for recognition of medical problems. The corpora were annotated for medical problems, but with different guidelines. The taggers were constructed using an existing tagging system MedTagger that consisted of dictionary lookup, part of speech (POS) tagging and machine learning for named entity prediction and concept extraction. We hope that our current work will be a useful case study for facilitating reuse of annotated corpora across institutions.We found that pooling was effective when the size of the local corpus was small and after some of the guideline differences were reconciled. The benefits of pooling, however, diminished as more locally annotated documents were included in the training data. We examined the annotation guidelines to identify factors that determine the effect of pooling.The effectiveness of pooling corpora, is dependent on several factors, which include compatibility of annotation guidelines, distribution of report types and size of local and foreign corpora. Simple methods to rectify some of the guideline differences can facilitate pooling. Our findings need to be confirmed with further studies on different corpora. To facilitate the pooling and reuse of annotated corpora, we suggest that - i) the NLP community should develop a standard annotation guideline that addresses the potential areas of guideline differences that are partly identified in this paper; ii) corpora should be annotated with a two-pass method that focuses first on concept recognition, followed by normalization to existing ontologies; and iii) metadata such as type of the report should be created during the annotation process.

Project description:BACKGROUND:The location and modular structure of eukaryotic protein-coding genes in genomic sequences can be automatically predicted by gene annotation algorithms. These predictions are often used for comparative studies on gene structure, gene repertoires, and genome evolution. However, automatic annotation algorithms do not yet correctly identify all genes within a genome, and manual annotation is often necessary to obtain accurate gene models and gene sets. As manual annotation is time-consuming, only a fraction of the gene models in a genome is typically manually annotated, and this fraction often differs between species. To assess the impact of manual annotation efforts on genome-wide analyses of gene structural properties, we compared the structural properties of protein-coding genes in seven diverse insect species sequenced by the i5k initiative. RESULTS:Our results show that the subset of genes chosen for manual annotation by a research community (3.5-7% of gene models) may have structural properties (e.g., lengths and exon counts) that are not necessarily representative for a species' gene set as a whole. Nonetheless, the structural properties of automatically generated gene models are only altered marginally (if at all) through manual annotation. Major correlative trends, for example a negative correlation between genome size and exonic proportion, can be inferred from either the automatically predicted or manually annotated gene models alike. Vice versa, some previously reported trends did not appear in either the automatic or manually annotated gene sets, pointing towards insect-specific gene structural peculiarities. CONCLUSIONS:In our analysis of gene structural properties, automatically predicted gene models proved to be sufficiently reliable to recover the same gene-repertoire-wide correlative trends that we found when focusing on manually annotated gene models only. We acknowledge that analyses on the individual gene level clearly benefit from manual curation. However, as genome sequencing and annotation projects often differ in the extent of their manual annotation and curation efforts, our results indicate that comparative studies analyzing gene structural properties in these genomes can nonetheless be justifiable and informative.

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PyPlutchik: Visualising and comparing emotion-annotated corpora.

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