Related papers: ProLiVis: Protein-Protein Interaction Literature V…

Accurately predicting the likelihood of interaction between two objects (compound-protein sequence, user-item, author-paper, etc.) is a fundamental problem in Computer Science. Current deep-learning models rely on learning accurate…

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…

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…

Protein can be represented by amino acid interaction network. This network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. This interaction network is the first step of proteins…

Training neural networks is difficult to interpret, particularly for newcomers. We introduce NeuroViz, an interactive visualization tool that supports real-time exploration of fully connected neural network training. Users can configure…

Proteins encode diverse functions within complex three-dimensional structures, yet most deep learning representations remain highly entangled, obscuring the biophysical signals that underlie function. Here we introduce ProtDiS, a…

Utilizing Visualization-oriented Natural Language Interfaces (V-NLI) as a complementary input modality to direct manipulation for visual analytics can provide an engaging user experience. It enables users to focus on their tasks rather than…

Multilayer relationships among entities and information about entities must be accompanied by the means to analyze, visualize, and obtain insights from such data. We present open-source software (muxViz) that contains a collection of…

Deep neural networks excel at comprehending complex visual signals, delivering on par or even superior performance to that of human experts. However, ad-hoc visual explanations of model decisions often reveal an alarming level of reliance…

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and…

Prototypical networks aim to build intrinsically explainable models based on the linear summation of concepts. Concepts are coherent entities that we, as humans, can recognize and associate with a certain object or entity. However,…

Motivation: Drug discovery demands rapid quantification of compound-protein interaction (CPI). However, there is a lack of methods that can predict compound-protein affinity from sequences alone with high applicability, accuracy, and…

Learning long-term dynamics models is the key to understanding physical common sense. Most existing approaches on learning dynamics from visual input sidestep long-term predictions by resorting to rapid re-planning with short-term models.…

Cellular function is widely believed to be organized in a modular fashion. On all scales and at all levels of complexity, relatively independent sub-units perform relatively independent sub-tasks of biological function. This functional…

Information Visualization techniques are built on a context with many factors related to both vision and cognition, making it difficult to draw a clear picture of how data visually turns into comprehension. In the intent of promoting a…

Prompt learning has been designed as an alternative to fine-tuning for adapting Vision-language (V-L) models to the downstream tasks. Previous works mainly focus on text prompt while visual prompt works are limited for V-L models. The…

Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…

How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…

Motivation: Network visualizations of complex biological datasets usually result in 'hairball' images, which do not discriminate network modules. Results: We present the EntOptLayout Cytoscape plug-in based on a recently developed network…