13 papers · ranked by Valyu relevance
Fabio Cumbo, Kabir Dhillon, Jayadev Joshi, Davide Chicco + 2 more
Viral species classification is crucial for understanding viral evolution, epidemiology, and developing effective diagnostics and treatments. Traditional methods often rely on sequence similarity, which can be challenging for rapidly evolving viruses. Pangenomes, offering a comprehensive representation of species’…
Zhiyuan Ding, Alex Baras
Recent advances in computation pathology have seen the development of various forms of foundational models that have enabled high-quality, generalpurpose feature extraction from tissue patches. However, most of these models are somewhat limited in their ability to capture cell-to-cell spatial relationships essential…
Haiteng Zhao, Shengchao Liu, Chang Ma, Hannan Xu + 4 more
Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for tasks, this study investigates the feasibility of employing natural language…
Md Toki Tahmid, Tanjeem Azwad Zaman, Mohammad Saifur Rahman
Understanding complex graph-structured data is a cornerstone of modern research in fields like cheminformatics and bioinformatics, where molecules and biological systems are naturally represented as graphs. However, traditional graph neural networks (GNNs) often fall short by focusing mainly on node features while…
Jordan M. Eizenga, Adam M. Novak, Emily Kobayashi, Flavia Villani + 6 more
Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic data sets can be challenging to work at. These challenges have impeded…
Peter Heringer, Daniel Doerr
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly…
Yunsheng Chen, Vanessa Giuliano, Ian Dacillo, Wenjun Lin + 2 more
Accurate prioritization of T-cell receptor (TCR)-epitope interactions and identification of tumor-reactive T cells are important but difficult steps in immunotherapy-oriented bioinformatics workflows. Existing methods typically address these tasks separately and either model TCR-epitope pairs as independent…
Ian T. Hoffecker, Yunshi Yang, Giulio Bernardinelli, Pekka Orponen + 1 more
Barcoded DNA polony amplification techniques provide a means to impart a unique sequence identity onto specific locations of a surface wafer or chip. We describe a method whereby micro-scale spatial information such as the relative positions of biomolecules on a surface can be transferred to a sequence-based format and…
Fawaz Dabbaghie
The representation of genomes and genomic sequences through graph structures has undergone a period of rapid development in recent years, particularly to accommodate the growing size of genome sequences that are being produced. Genome graphs have been employed extensively for a variety of purposes, including assembly…
Xiaoxiao Li, Yuan Zhou, Siyuan Gao, Nicha Dvornek + 7 more
Understanding how certain brain regions relate to a specific neurological disorder or cognitive stimuli has been an important area of neuroimaging research. We propose BrainGNN, a graph neural network (GNN) framework to analyze functional magnetic resonance images (fMRI) and discover neurological biomarkers. In…
Jianshu Zhao, Jean Pierre Both, Rob Knight
Graph/network representation learning (or graph/network embedding) is a widely used machine learning technique in industry recommending systems and has recently been applied in computational biology. Popular network representation learning algorithms include random walk and matrix factorization methods, but they do not…
Srijani Bagchi, Anasua Sarkar, Ujjwal Maulik
In times like this, it is imperative to be cautious about the effects of drugs or vaccination doses on patients who are already suffering from other serious diseases. It’s not only the virus which can affect the body metabolisms, drugs to encounter the virus may also end up having unwanted negative effects. Therapeutic…
Benedict Paten, Adam M Novak, Erik Garrison, Glenn Hickey
A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can be considered to represent the set of possible sequences at a location in a genome. Bidirected and biedged graphs are a generalization of…