Related papers: Leveraging Prior Knowledge for Protein-Protein Int…

Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…

The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both…

The identification of essential proteins in protein-protein interaction networks (PINs) can help to discover drug targets and prevent disease. In order to improve the accuracy of the identification of essential proteins, researchers…

Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods…

Recurrent Neural Networks (RNNs) have achieved remarkable performance on a range of tasks. A key step to further empowering RNN-based approaches is improving their explainability and interpretability. In this work we present MEME: a model…

Currently, we are overwhelmed by a deluge of experimental data, and network physics has the potential to become an invaluable method to increase our understanding of large interacting datasets. However, this potential is often unrealized…

PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…

Automatic relationship extraction (RE) from biomedical literature is critical for managing the vast amount of scientific knowledge produced each year. In recent years, utilizing pre-trained language models (PLMs) has become the prevalent…

Complexes of physically interacting proteins constitute fundamental functional units responsible for driving biological processes within cells. A faithful reconstruction of the entire set of complexes is therefore essential to understand…

Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps…

Pruning has emerged as the primary approach used to limit the resource requirements of large neural networks (NNs). Since the proposal of the lottery ticket hypothesis, researchers have focused either on pruning at initialization or after…

Natural Language Inference (NLI) is a fundamental and challenging task in Natural Language Processing (NLP). Most existing methods only apply one-pass inference process on a mixed matching feature, which is a concatenation of different…

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through…

Predictive Process Monitoring (PPM) aims at leveraging historic process execution data to predict how ongoing executions will continue up to their completion. In recent years, PPM techniques for the prediction of the next activities have…

Accurately predicting complex protein-protein interactions (PPIs) is crucial for decoding biological processes, from cellular functioning to disease mechanisms. However, experimental methods for determining PPIs are computationally…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

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…

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on…

Existing RNN-based approaches for action recognition from depth sequences require either skeleton joints or hand-crafted depth features as inputs. An end-to-end manner, mapping from raw depth maps to action classes, is non-trivial to design…

The identification of essential proteins can help in understanding the minimum requirements for cell survival and development. Network-based centrality approaches are commonly used to identify essential proteins from protein-protein…