Related papers: Extracting Protein-Protein Interactions (PPIs) fro…
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
Protein-protein interactions (PPIs) are critical for various biological processes, and understanding their dynamics is essential for decoding molecular mechanisms and advancing fields such as cancer research and drug discovery. Mutations in…
Many real world systems need to operate on heterogeneous information networks that consist of numerous interacting components of different types. Examples include systems that perform data analysis on biological information networks; social…
Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types:…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…
Objective: To develop a high-throughput biomedical relation extraction system that takes advantage of the large language models'(LLMs) reading comprehension ability and biomedical world knowledge in a scalable and evidential manner.…
Identification of disease genes, which are a set of genes associated with a disease, plays an important role in understanding and curing diseases. In this paper, we present a biomedical knowledge graph designed specifically for this…
miRNA mRNA relations are closely linked to several biological processes and disease mechanisms In a recent study we tested the performance of large language models LLMs on extracting miRNA mRNA relations from PubMed PubMedBERT achieved the…
Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential…
Constructing large-scaled medical knowledge graphs can significantly boost healthcare applications for medical surveillance, bring much attention from recent research. An essential step in constructing large-scale MKG is extracting…
Many protein-protein interaction (PPI) networks take place in the fluid yet structured plasma membrane. Lipid domains, sometimes termed rafts, have been implicated in the functioning of various membrane-bound signaling processes. Here, we…
Mitochondrial diseases are largely caused by dysfunction in mitochondrial proteins. However, annotations of human mitochondrial proteins are scattered across various public databases and individual studies. To facilitate research aimed at…
While attention mechanisms have been proven to be effective in many NLP tasks, majority of them are data-driven. We propose a novel knowledge-attention encoder which incorporates prior knowledge from external lexical resources into deep…
Nanomaterial-protein interactions (NPI) are pivotal to realizing the therapeutic and diagnostic potential of nanomaterials. Although AI promises to accelerate mechanistic understanding and enable rational nanomaterial design, robust…
We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with…
Relation Extraction is an important task in Information Extraction which deals with identifying semantic relations between entity mentions. Traditionally, relation extraction is carried out after entity extraction in a "pipeline" fashion,…
The Clinical E-Science Framework (CLEF) project was used to extract important information from medical texts by building a system for the purpose of clinical research, evidence-based healthcare and genotype-meets-phenotype informatics. The…
The ongoing opioid crisis highlights the urgent need for novel therapeutic strategies that can be rapidly deployed. This study presents a novel approach to identify potential repurposable drugs for the treatment of opioid addiction, aiming…
Protein complexes conserved across species indicate processes that are core to cellular machinery (e.g. cell-cycle or DNA damage-repair complexes conserved across human and yeast). While numerous computational methods have been devised to…
With the advent of high-throughput wet lab technologies the amount of protein interaction data available publicly has increased substantially, in turn spurring a plethora of computational methods for in silico knowledge discovery from this…