相关论文: DomainScope: A disease network based on protein do…
Disease-symptom datasets are significant and in demand for medical research, disease diagnosis, clinical decision-making, and AI-driven health management applications. These datasets help identify symptom patterns associated with specific…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
Dot-science was launched in 2015 as a new academic top-level domain (TLD) aimed to provide 'a dedicated, easily accessible location for global Internet users with an interest in science'. The main objective of this work is to find out the…
The generalization of deep neural networks to unknown domains is a major challenge despite their tremendous progress in recent years. For this reason, the dynamic area of domain generalization (DG) has emerged. In contrast to unsupervised…
Genetic interaction measures how different genes collectively contribute to a phenotype, and can reveal functional compensation and buffering between pathways under genetic perturbations. Recently, genome-wide screening for genetic…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
Identifying disease genes from human genome is an important and fundamental problem in biomedical research. Despite many publications of machine learning methods applied to discover new disease genes, it still remains a challenge because of…
In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the…
The structure and function of a protein are determined by its amino acid sequence. While random mutations change a protein's sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral…
Foundation models have transformed computational pathology by providing generalizable representations from large-scale histology datasets. However, existing models are predominantly trained on surgical pathology data, which is enriched for…
Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…
Dietary flavonoids associate with disease prevention in epidemiological studies, yet their polypharmacological mechanisms remain unclear. We establish network pharmacology as a systematic framework to characterize flavonoid therapeutic…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
Domain adaptation aims to leverage knowledge from a well-labeled source domain to a poorly-labeled target domain. A majority of existing works transfer the knowledge at either feature level or sample level. Recent researches reveal that…
Motivation Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a tar get protein based on the…
Network pharmacology (NP) explores pharmacological mechanisms through biological networks. Multi-omics data enable multi-layer network construction under diverse conditions, requiring integration into NP analyses. We developed POINT, a…
We consider the following problem: Given an undirected (mixed) network and a set of ordered source-target, or cause-effect pairs, direct all edges so as to maximize the number of pairs that admit a directed source-target path. This is…
With more than 294 million registered domain names as of late 2015, the domain name ecosystem has evolved to become a cornerstone for the operation of the Internet. Domain names today serve everyone, from individuals for their online…
Hand-crafted features based on linguistic and domain-knowledge play crucial role in determining the performance of disease name recognition systems. Such methods are further limited by the scope of these features or in other words, their…
Investigating how different ingredients are combined in popular dishes is crucial to uncover the principles behind food preferences. Here, we use data from public food repositories and network analysis to characterize and compare worldwide…