q-bio.MN

arXiv:2501.12309v1 Announce Type: new Abstract: This paper presents a novel graph-based deep learning model for tasks involving relations between two nodes (edge-centric tasks), where the focus lies on predicting relationships and interactions between pairs of nodes rather than node properties themselves. This model combines supervised and self-supervised learning, taking into account for the loss function the embeddings learned and patterns with and without ground truth. Additionally it incorporates an attention mechanism that leverages both node and edge features. The architecture, trained end-to-end, comprises two primary components: embedding generation and prediction. First, a graph neural network (GNN) transform raw node features into dense, low-dimensional embeddings, incorporating edge attributes. Then, a feedforward neural model processes the node embeddings to produce the final output. Experiments demonstrate that our model matches or exceeds existing methods for protein-protein interactions prediction and Gene Ontology (GO) terms prediction. The model also performs effectively with one-hot encoding for node features, providing a solution for the previously unsolved problem of predicting similarity between compounds with unknown structures.

arXiv:2501.03235v1 Announce Type: cross Abstract: Neural networks based on soft and biological matter constitute an interesting potential alternative to traditional implementations based on electric circuits. DNA is a particularly promising system in this context due its natural ability to store information. In recent years, researchers have started to construct neural networks that are based on DNA. In this chapter, I provide a very basic introduction to the concept of DNA neural networks, aiming at an audience that is not familiar with biochemistry.

arXiv:2309.10629v3 Announce Type: replace-cross Abstract: The exploration of pathways and alternative pathways that have a specific function is of interest in numerous chemical contexts. A framework for specifying and searching for pathways has previously been developed, but a focus on which of the many pathway solutions are realisable, or can be made realisable, is missing. Realisable here means that there actually exists some sequencing of the reactions of the pathway that will execute the pathway. We present a method for analysing the realisability of pathways based on the reachability question in Petri nets. For realisable pathways, our method also provides a certificate encoding an order of the reactions which realises the pathway. We present two extended notions of realisability of pathways, one of which is related to the concept of network catalysts. We exemplify our findings on the pentose phosphate pathway. Furthermore, we discuss the relevance of our concepts for elucidating the choices often implicitly made when depicting pathways. Lastly, we lay the foundation for the mathematical theory of realisability.