Related papers: ProLiVis: Protein-Protein Interaction Literature V…
Proteins are inherently multiscale physical systems whose functional properties emerge from coordinated structural organization across multiple spatial resolutions, ranging from atomic interactions to global fold topology. However, existing…
Many complex natural and cultural phenomena are well modelled by systems of simple interactions between particles. A number of architectures have been developed to articulate this kind of structure, both implicitly and explicitly. We…
We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules…
We consider representation learning for proteins with 3D structures. We build 3D graphs based on protein structures and develop graph networks to learn their representations. Depending on the levels of details that we wish to capture,…
Protein structure representation is an important tool in structural biology. There exists different methods of representing the protein 3D structures and different biologists favor different methods based on the information they require.…
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains…
Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug…
This paper presents a Progressively-connected Light Field network (ProLiF), for the novel view synthesis of complex forward-facing scenes. ProLiF encodes a 4D light field, which allows rendering a large batch of rays in one training step…
Visualisation facilitates the understanding of scientific data both through exploration and explanation of visualised data. Provenance contributes to the understanding of data by containing the contributing factors behind a result. With the…
Current visual foundation models (VFMs) face a fundamental limitation in transferring knowledge from vision language models (VLMs), while VLMs excel at modeling cross-modal interactions through unified representation spaces, existing VFMs…
Summary: The development of automated servers to predict the three-dimensional structure of proteins has seen much progress over the years. These servers make modeling simpler, but largely exclude users from the process. We present an…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…
When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very…
Background and Objective: Prototype-based methods improve interpretability by learning fine-grained part-prototypes; however, their visualization in the input pixel space is not always consistent with human-understandable biomarkers. In…
Protein representation learning methods have shown great potential to yield useful representation for many downstream tasks, especially on protein classification. Moreover, a few recent studies have shown great promise in addressing…
Pyvis is a Python module that enables visualizing and interactively manipulating network graphs in the Jupyter notebook, or as a standalone web application. Pyvis is built on top of the powerful and mature VisJS JavaScript library, which…
Discovering disease pathways, which can be defined as sets of proteins associated with a given disease, is an important problem that has the potential to provide clinically actionable insights for disease diagnosis, prognosis, and…
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…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
This paper proposes a web-based visual graph analytics platform for interactive graph mining, visualization, and real-time exploration of networks. GraphVis is fast, intuitive, and flexible, combining interactive visualizations with…