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Pia Droop

dblp:371/0869 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2024
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
1 paper
Information extraction and text analysis · 67% Knowledge representation and reasoning · 33%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Natural language and speech › Information extraction and text analysis › named entity recognition
biomedical named entity recognition
0.812024
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools · Bioinform. 2024
Natural language and speech › Information extraction and text analysis
entity normalization
0.812024
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools · Bioinform. 2024
Knowledge, reasoning and agents › Knowledge representation and reasoning › knowledge base
knowledge base grounding
0.812024
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools · Bioinform. 2024
YearPublicationVenuePosition
2024 HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools
abstract
MOTIVATION: With the exponential growth of the life sciences literature, biomedical text mining (BTM) has become an essential technology for accelerating the extraction of insights from publications. The identification of entities in texts, such as diseases or genes, and their normalization, i.e. grounding them in knowledge base, are crucial steps in any BTM pipeline to enable information aggregation from multiple documents. However, tools for these two steps are rarely applied in the same context in which they were developed. Instead, they are applied "in the wild," i.e. on application-dependent text collections from moderately to extremely different from those used for training, varying, e.g. in focus, genre or text type. This raises the question whether the reported performance, usually obtained by training and evaluating on different partitions of the same corpus, can be trusted for downstream applications. RESULTS: Here, we report on the results of a carefully designed cross-corpus benchmark for entity recognition and normalization, where tools were applied systematically to corpora not used during their training. Based on a survey of 28 published systems, we selected five, based on predefined criteria like feature richness and availability, for an in-depth analysis on three publicly available corpora covering four entity types. Our results present a mixed picture and show that cross-corpus performance is significantly lower than the in-corpus performance. HunFlair2, the redesigned and extended successor of the HunFlair tool, showed the best performance on average, being closely followed by PubTator Central. Our results indicate that users of BTM tools should expect a lower performance than the original published one when applying tools in "the wild" and show that further research is necessary for more robust BTM tools. AVAILABILITY AND IMPLEMENTATION: All our models are integrated into the Natural Language Processing (NLP) framework flair: https://github.com/flairNLP/flair. Code to reproduce our results is available at: https://github.com/hu-ner/hunflair2-experiments.
Mario Sänger, Samuele Garda, Xing David Wang, Leon Weber-Genzel, Pia Droop, Benedikt Fuchs, Alan Akbik, Ulf Leser
Bioinform.5