BioRED: a rich biomedical relation extraction dataset

L Luo, PT Lai, CH Wei, CN Arighi… - Briefings in …, 2022 - academic.oup.com
Automated relation extraction (RE) from biomedical literature is critical for many downstream
text mining applications in both research and real-world settings. However, most existing …

A review of large language models and autonomous agents in chemistry

MC Ramos, CJ Collison, AD White - Chemical Science, 2025 - pubs.rsc.org
Large language models (LLMs) have emerged as powerful tools in chemistry, significantly
impacting molecule design, property prediction, and synthesis optimization. This review …

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions

R Oughtred, J Rust, C Chang, BJ Breitkreutz… - Protein …, 2021 - Wiley Online Library
Abstract The BioGRID (Biological General Repository for Interaction Datasets, thebiogrid.
org) is an open‐access database resource that houses manually curated protein and …

Text2mol: Cross-modal molecule retrieval with natural language queries

C Edwards, CX Zhai, H Ji - … of the 2021 Conference on Empirical …, 2021 - aclanthology.org
We propose a new task, Text2Mol, to retrieve molecules using natural language descriptions
as queries. Natural language and molecules encode information in very different ways …

Scifive: a text-to-text transformer model for biomedical literature

LN Phan, JT Anibal, H Tran, S Chanana… - arxiv preprint arxiv …, 2021 - arxiv.org
In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on
large biomedical corpora. Our model outperforms the current SOTA methods (ie BERT …

A review on utilizing machine learning technology in the fields of electronic emergency triage and patient priority systems in telemedicine: Coherent taxonomy …

OH Salman, Z Taha, MQ Alsabah, YS Hussein… - Computer Methods and …, 2021 - Elsevier
Background With the remarkable increasing in the numbers of patients, the triaging and
prioritizing patients into multi-emergency level is required to accommodate all the patients …

In-boxbart: Get instructions into biomedical multi-task learning

M Parmar, S Mishra, M Purohit, M Luo… - arxiv preprint arxiv …, 2022 - arxiv.org
Single-task models have proven pivotal in solving specific tasks; however, they have
limitations in real-world applications where multi-tasking is necessary and domain shifts are …

BIAS: Transparent reporting of biomedical image analysis challenges

L Maier-Hein, A Reinke, M Kozubek, AL Martel… - Medical image …, 2020 - Elsevier
The number of biomedical image analysis challenges organized per year is steadily
increasing. These international competitions have the purpose of benchmarking algorithms …

Automated assembly of molecular mechanisms at scale from text mining and curated databases

JA Bachman, BM Gyori, PK Sorger - Molecular Systems Biology, 2023 - embopress.org
The analysis of omic data depends on machine‐readable information about protein
interactions, modifications, and activities as found in protein interaction networks, databases …

NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature

R Islamaj, R Leaman, S Kim, D Kwon, CH Wei… - Scientific data, 2021 - nature.com
Automatically identifying chemical and drug names in scientific publications advances
information access for this important class of entities in a variety of biomedical disciplines by …