Integration of relational and hierarchical network information for protein function prediction

BACKGROUND:In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.RESULTS:We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.CONCLUSION:A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.

Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? A 3D FORMOTION model specifies how 3D boundary representations, which separate figures from backgrounds within cortical area V2, capture motion signals at the appropriate depths in MT; how motion signals in MT disambiguate boundaries in V2 via MT-to-Vl-to-V2 feedback; how sparse feature tracking signals are amplified; and how a spatially anisotropic motion grouping process propagates across perceptual space via MT-MST feedback to integrate feature-tracking and ambiguous motion signals to determine a global object motion percept. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.

Form Perception

National Science Foundation (SBE-0354378); Office of Naval Research (N00014-01-1-0624)

Laminar Cortical Dynamics of Visual Form and Motion Interactions During Coherent Object Motion Perception

How do visual form and motion processes cooperate to compute object motion when each process separately is insufficient? Consider, for example, a deer moving behind a bush. Here the partially occluded fragments of motion signals available to an observer must be coherently grouped into the motion of a single object. A 3D FORMOTION model comprises five important functional interactions involving the brain’s form and motion systems that address such situations. Because the model’s stages are analogous to areas of the primate visual system, we refer to the stages by corresponding anatomical names. In one of these functional interactions, 3D boundary representations, in which figures are separated from their backgrounds, are formed in cortical area V2. These depth-selective V2 boundaries select motion signals at the appropriate depths in MT via V2-to-MT signals. In another, motion signals in MT disambiguate locally incomplete or ambiguous boundary signals in V2 via MT-to-V1-to-V2 feedback. The third functional property concerns resolution of the aperture problem along straight moving contours by propagating the influence of unambiguous motion signals generated at contour terminators or corners. Here, sparse “feature tracking signals” from, e.g., line ends, are amplified to overwhelm numerically superior ambiguous motion signals along line segment interiors. In the fourth, a spatially anisotropic motion grouping process takes place across perceptual space via MT-MST feedback to integrate veridical feature-tracking and ambiguous motion signals to determine a global object motion percept. The fifth property uses the MT-MST feedback loop to convey an attentional priming signal from higher brain areas back to V1 and V2. The model's use of mechanisms such as divisive normalization, endstopping, cross-orientation inhibition, and longrange cooperation is described. Simulated data include: the degree of motion coherence of rotating shapes observed through apertures, the coherent vs. element motion percepts separated in depth during the chopsticks illusion, and the rigid vs. non-rigid appearance of rotating ellipses.