Axes of Biology

Axes of Biology employs a novel axes-based network embedding paradigm to decipher the functional mechanisms of cells by shifting functional exploration from gene embedding vectors to the axes of the embedding space.

Key Features:

• Axes-based functional exploration: Shifts analysis from gene embedding vectors to the axes of the embedding space itself to better disentangle biological information.
• Data-driven functional interaction discovery: Uncovers new functional interactions that are unregistered in functional ontologies but biologically coherent.
• Axes-Specific Functional Annotations: Defines new higher-level annotations derived from discovered interactions, validated through literature curation.
• Evolutionary connection analysis: Leverages the methodology to discover evolutionary connections between cellular functions and the evolution of species.

Scientific Applications:

• Functional mechanism deciphering: Identifies currently unknown cell functioning mechanisms that are hindered by limitations of functional annotation resources and gene cluster interpretation difficulties.
• Novel functional annotation generation: Creates new higher-level functional annotations beyond existing ontologies through data-driven discovery and literature validation.
• Comparative evolutionary biology: Reveals evolutionary connections between cellular functions and species evolution.

Methodology:

The methodology uses network embedding algorithms and shifts functional exploration from the embedding vectors of genes in space to the axes of the space itself.