Alignment-free k-mer-based algorithms in whole genome sequence comparisons remainan ongoing challenge. Here, we explore the possibility to use Topic Modeling for organismwhole-genome comparisons. We analyzed 30 complete genomes from three bacterial families bytopic modeling. For this, each genome was considered as a document and 13-mer nucleotiderepresentations as words. Latent Dirichlet allocation was used as the probabilistic modeling of thecorpus. We where able to identify the topic distribution among analyzed genomes, which is highlyconsistent with traditional hierarchical classification. It is possible that topic modeling may be appliedto establish relationships between genome's composition and biological phenomena.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7074292 | PMC |
| http://dx.doi.org/10.3390/genes11020197 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Development and validation of a radiomics-visual evoked potential nomogram for preoperative prediction of visual outcome after endoscopic craniopharyngioma resection.
J Neurosurg
January 2025
Departments of1Neurosurgery.
Objective: Craniopharyngiomas are rare, benign brain tumors that are primarily treated with surgery. Although the extended endoscopic endonasal approach (EEEA) has evolved as a more reliable surgical alternative and yields better visual outcomes than traditional craniotomy, postoperative visual deterioration remains one of the most common complications, and relevant risk factors are still poorly defined. Hence, identifying risk factors and developing a predictive model for postoperative visual deterioration is indeed necessary.
View Article and Find Full Text PDFVirtual patients using large language models: Scalable, contextualized simulation of clinician-patient dialog with feedback.
J Med Internet Res
January 2025
Division of General Internal Medicine, Mayo Clinic College of Medicine and Science, 200 First St SW, Rochester, US.
Background: Virtual patients (VPs) are computer screen-based simulations of patient-clinician encounters. VP use is limited by cost and low scalability.
Objective: Show proof-of-concept that VPs powered by large language models (LLMs) generate authentic dialogs, accurate representations of patient preferences, and personalized feedback on clinical performance; and explore LLMs for rating dialog and feedback quality.
Efficacy of different routes of triamcinolone acetonide administration on macular edema: A systematic review and network meta-analysis.
PLoS One
January 2025
Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China.
There is different administration routes of triamcinolone acetonide (TA) administration for macular edema, but the efficacy ranking remains unclear. The purpose of this study is to assess the efficacy of different administration routes of TA employed in macular edema. PubMed, Medline, Embase, and Cochrane Central Register of Controlled Trials were systematically searched for published articles comparing macular edema in patients with triamcinolone acetonide in different administration.
View Article and Find Full Text PDFThe etiology of attention deficit disorder with hyperactivity: A protocol for an umbrella review.
PLoS One
January 2025
School of Nursing, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
Introduction: Attention deficit hyperactivity disorder (ADHD) is one of the common neurodevelopmental disorders and is widely prevalent worldwide. The primary symptoms of ADHD include inattention, impulsivity, and hyperactivity, which significantly impact the cognitive, behavioral, and emotional dimensions of individuals. These disorders often continue throughout adulthood and, along with associated complications, affect various domains such as personal health, academic achievement, and social interactions.
View Article and Find Full Text PDFExamining hurricane-related social media topics longitudinally and at scale: A transformer-based approach.
PLoS One
January 2025
Computational Media Lab, University of Texas at Austin, Austin, Texas, United States of America.
Instead of turning to emergency phone systems, social media platforms, such as Twitter, have emerged as alternative and sometimes preferred venues for members of the public in the US to communicate during hurricanes and other natural disasters. However, relevant posts are likely to be missed by responders given the volume of content on platforms. Previous work successfully identified relevant posts through machine-learned methods, but depended on human annotators.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!