相关论文: A Silver Standard Corpus of Human Phenotype-Gene R…
Identifying phenotype-associated genes is a common first step in polygenic risk score construction, enrichment testing, target prioritisation and variant interpretation, but relevant evidence is distributed across heterogeneous databases…
Identifying causative genes from patient phenotypes remains a significant challenge in precision medicine, with important implications for the diagnosis and treatment of genetic disorders. We propose a novel graph-based approach for…
Many rare genetic diseases exhibit recognizable facial phenotypes, which are often used as diagnostic clues. However, current facial phenotype diagnostic models, which are trained on image datasets, have high accuracy but often suffer from…
Background: The learning of genotype-phenotype associations and history of human disease by doing detailed and precise analysis of phenotypic abnormalities can be defined as deep phenotyping. To understand and detect this interaction…
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…
Phenotyping is fundamental to rare disease diagnosis, but manual curation of structured phenotypes from clinical notes is labor-intensive and difficult to scale. Existing artificial intelligence approaches typically optimize individual…
Understanding disease similarity is critical for advancing diagnostics, drug discovery, and personalized treatment strategies. We present PhenoGnet, a novel graph-based contrastive learning framework designed to predict disease similarity…
The use of Project Gutenberg (PG) as a text corpus has been extremely popular in statistical analysis of language for more than 25 years. However, in contrast to other major linguistic datasets of similar importance, no consensual full…
Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to…
The RareDis corpus contains more than 5,000 rare diseases and almost 6,000 clinical manifestations are annotated. Moreover, the Inter Annotator Agreement evaluation shows a relatively high agreement (F1-measure equal to 83.5% under exact…
Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…
In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can straightforwardly expand into full-length, DNA-level genomes. The synthetic genotypes mimic…
Identifying phenotypes plays an important role in furthering our understanding of disease biology through practical applications within healthcare and the life sciences. The challenge of dealing with the complexities and noise within…
Semantic relation extraction is one of the frontiers of biomedical natural language processing research. Gold standards are key tools for advancing this research. It is challenging to generate these standards because of the high cost of…
Identifying a patient's key problems over time is a common task for providers at the point care, yet a complex and time-consuming activity given current electric health records. To enable a problem-oriented summarizer to identify a…
We present a novel corpus of 445 human- and computer-generated documents, comprising about 27,000 clauses, annotated for semantic clause types and coherence relations that allow for nuanced comparison of artificial and natural discourse…
A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may…
The linking genotype to phenotype is the fundamental aim of modern genetics. We focus on study of links between gene expression data and phenotype data through integrative analysis. We propose three approaches. 1) The inherent complexity of…
The paper presents a systematic review of state-of-the-art approaches to identify patient cohorts using electronic health records. It gives a comprehensive overview of the most commonly de-tected phenotypes and its underlying data sets.…