[HTML][HTML] AI-based language models powering drug discovery and development

Z Liu, RA Roberts, M Lal-Nag, X Chen, R Huang… - Drug Discovery …, 2021 - Elsevier
The discovery and development of new medicines is expensive, time-consuming, and often
inefficient, with many failures along the way. Powered by artificial intelligence (AI), language …

Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison

B Song, F Li, Y Liu, X Zeng - Briefings in Bioinformatics, 2021 - academic.oup.com
The biomedical literature is growing rapidly, and the extraction of meaningful information
from the large amount of literature is increasingly important. Biomedical named entity …

LitCovid: an open database of COVID-19 literature

Q Chen, A Allot, Z Lu - Nucleic acids research, 2021 - academic.oup.com
Since the outbreak of the current pandemic in 2020, there has been a rapid growth of
published articles on COVID-19 and SARS-CoV-2, with about 10 000 new articles added …

Large language models in biomedical natural language processing: benchmarks, baselines, and recommendations

Q Chen, J Du, Y Hu, VK Keloth, X Peng, K Raja… - arXiv preprint arXiv …, 2023 - arxiv.org
Biomedical literature is growing rapidly, making it challenging to curate and extract
knowledge manually. Biomedical natural language processing (BioNLP) techniques that …

[HTML][HTML] Zinc against COVID-19? Symptom surveillance and deficiency risk groups

MP Joachimiak - PLoS neglected tropical diseases, 2021 - journals.plos.org
A wide variety of symptoms is associated with Severe Acute Respiratory Syndrome
Coronavirus 2 (SARS-CoV-2) infection, and these symptoms can overlap with other …

A survey on event extraction for natural language understanding: Riding the biomedical literature wave

G Frisoni, G Moro, A Carbonaro - IEEE Access, 2021 - ieeexplore.ieee.org
Motivation: The scientific literature embeds an enormous amount of relational knowledge,
encompassing interactions between biomedical entities, like proteins, drugs, and symptoms …

[HTML][HTML] GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT

Y Chen, J Zou - bioRxiv, 2023 - ncbi.nlm.nih.gov
There has been significant recent progress in leveraging large-scale gene expression data
to develop foundation models for single-cell biology. Models such as Geneformer and …

EntityBERT: Entity-centric masking strategy for model pretraining for the clinical domain

C Lin, T Miller, D Dligach, S Bethard, G Savova - 2021 - repository.arizona.edu
Transformer-based neural language models have led to breakthroughs for a variety of
natural language processing (NLP) tasks. However, most models are pretrained on general …

[HTML][HTML] Bioformer: an efficient transformer language model for biomedical text mining

L Fang, Q Chen, CH Wei, Z Lu, K Wang - ArXiv, 2023 - ncbi.nlm.nih.gov
Pretrained language models such as Bidirectional Encoder Representations from
Transformers (BERT) have achieved state-of-the-art performance in natural language …

A literature embedding model for cardiovascular disease prediction using risk factors, symptoms, and genotype information

J Moon, HF Posada-Quintero, KH Chon - Expert Systems with Applications, 2023 - Elsevier
Accurate prediction of cardiovascular disease (CVD) requires multifaceted information
consisting of not only a patient's medical history, but genomic data, symptoms, lifestyle, and …