Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integration scheme to augment structural resources and generate a large biomedical NED dataset for pretraining. Our pretrained model with injected structural knowledge achieves state-of-the-art performance on two benchmark medical NED datasets: MedMentions and BC5CDR. Furthermore, we improve disambiguation of rare entities by up to 57 accuracy points.

Cross-Domain Data Integration for Named Entity Disambiguation in Biomedical Text

Findings Papers - NLP Applications

technical paper

EMNLP 2021 is planned to be a hybrid event in Punta Cana, Dominican Republic, with both on-site and fully virtual participation possible. The experience for on-site participants would closely approximate a normal pre-COVID *ACL conference, with 5-6 thematically organized parallel sessions and live Q/A and interactive discussion immediately after the talks. Presentations by virtual participants will be equitably interleaved with those of on-site participants, projected on the auditorium screens as if on-site, and also followed immediately by live Q/A and interactive discussion at a time during reasonable waking hours for the virtual presenter. For all participants, on-site and virtual, who are unable to attend a session due to either time-zone issues or because they are participating in another session live, talk recordings and slides will be available online at a minimum after the live presentation (and in many cases before as well), and questions may be submitted in advance on session-specific discussion boards and answered live in session with the usual visual aids if desired.

<iframe style="width:700px;height:400px" src="https://online.fliphtml5.com/ebtyf/ceby/"  seamless="seamless" scrolling="no" frameborder="0" allowtransparency="true" allowfullscreen="true" ></iframe>

Please Note: The EMNLP registration system is not currently connected to the underline site as we are still in the process of building out EMNLP 2021. You will receive access instructions from underline the week of November 1st. 

Access is given only to EMNLP upon registration, if you have not registered please do so [here](https://2021.emnlp.org/registration).

Registered attendees will receive access the week of November 1st.

EMNLP 2021

EMNLP 2021 is planned to be a hybrid event in Punta Cana, Dominican Republic, with both on-site and fully virtual participation possible.

Christopher Ré

1

SHORT BIO

Presentations

Cross-Domain Data Integration for Named Entity Disambiguation in Biomedical Text

Stay up to date with the latest Underline news!

PRESENTATIONS

CONFERENCES

COMPANY

RESOURCES