ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster

Multi-scale Deep Learning Architectures for Person Re-identification

Person Re-identification (re-id) aims to match people across non-overlapping camera views in a public space. It is a challenging problem because many people captured in surveillance videos wear similar clothes. Consequently, the differences in their appearance are often subtle and only detectable at the right location and scales. Existing re-id models, particularly the recently proposed deep learning based ones match people at a single scale. In contrast, in this paper, a novel multi-scale deep learning model is proposed. Our model is able to learn deep discriminative feature representations at different scales and automatically determine the most suitable scales for matching. The importance of different spatial locations for extracting discriminative features is also learned explicitly. Experiments are carried out to demonstrate that the proposed model outperforms the state-of-the art on a number of benchmarksComment: 9 pages, 3 figures, accepted by ICCV 201

Transport-Based Neural Style Transfer for Smoke Simulations

Artistically controlling fluids has always been a challenging task. Optimization techniques rely on approximating simulation states towards target velocity or density field configurations, which are often handcrafted by artists to indirectly control smoke dynamics. Patch synthesis techniques transfer image textures or simulation features to a target flow field. However, these are either limited to adding structural patterns or augmenting coarse flows with turbulent structures, and hence cannot capture the full spectrum of different styles and semantically complex structures. In this paper, we propose the first Transport-based Neural Style Transfer (TNST) algorithm for volumetric smoke data. Our method is able to transfer features from natural images to smoke simulations, enabling general content-aware manipulations ranging from simple patterns to intricate motifs. The proposed algorithm is physically inspired, since it computes the density transport from a source input smoke to a desired target configuration. Our transport-based approach allows direct control over the divergence of the stylization velocity field by optimizing incompressible and irrotational potentials that transport smoke towards stylization. Temporal consistency is ensured by transporting and aligning subsequent stylized velocities, and 3D reconstructions are computed by seamlessly merging stylizations from different camera viewpoints.Comment: ACM Transaction on Graphics (SIGGRAPH ASIA 2019), additional materials: http://www.byungsoo.me/project/neural-flow-styl