Deep Video Color Propagation

Traditional approaches for color propagation in videos rely on some form of matching between consecutive video frames. Using appearance descriptors, colors are then propagated both spatially and temporally. These methods, however, are computationally expensive and do not take advantage of semantic information of the scene. In this work we propose a deep learning framework for color propagation that combines a local strategy, to propagate colors frame-by-frame ensuring temporal stability, and a global strategy, using semantics for color propagation within a longer range. Our evaluation shows the superiority of our strategy over existing video and image color propagation methods as well as neural photo-realistic style transfer approaches.Comment: BMVC 201

Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact?

<p>Abstract</p> <p>Background</p> <p>Gene clusters are of interest for the understanding of genome evolution since they provide insight in large-scale duplications events as well as patterns of individual gene losses. Vertebrates tend to have multiple copies of gene clusters that typically are only single clusters or are not present at all in genomes of invertebrates. We investigated the genomic architecture and conserved non-coding sequences of vertebrate <it>KCNA </it>gene clusters. <it>KCNA </it>genes encode shaker-related voltage-gated potassium channels and are arranged in two three-gene clusters in tetrapods. Teleost fish are found to possess four clusters. The two tetrapod <it>KNCA </it>clusters are of approximately the same age as the <it>Hox </it>gene clusters that arose through duplications early in vertebrate evolution. For some genes, their conserved retention and arrangement in clusters are thought to be related to regulatory elements in the intergenic regions, which might prevent rearrangements and gene loss. Interestingly, this hypothesis does not appear to apply to the <it>KCNA </it>clusters, as too few conserved putative regulatory elements are retained.</p> <p>Results</p> <p>We obtained <it>KCNA </it>coding sequences from basal ray-finned fishes (sturgeon, gar, bowfin) and confirmed that the duplication of these genes is specific to teleosts and therefore consistent with the fish-specific genome duplication (FSGD). Phylogenetic analyses of the genes suggest a basal position of the only intron containing <it>KCNA </it>gene in vertebrates (<it>KCNA7</it>). Sistergroup relationships of <it>KCNA1/2 </it>and <it>KCNA3/6 </it>support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of <it>KCNA </it>clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. The orthologous teleost clusters, however, show sequence conservation in these regions.</p> <p>Conclusion</p> <p>The lack of overall conserved sequences in intergenic regions suggests that there are either other processes than regulatory evolution leading to cluster conservation or that the ancestral regulatory relationships among genes in <it>KCNA </it>clusters have been changed together with their regulatory sites.</p

Efficient Feature Extraction for High-resolution Video Frame Interpolation

Most deep learning methods for video frame interpolation consist of three main components: feature extraction, motion estimation, and image synthesis. Existing approaches are mainly distinguishable in terms of how these modules are designed. However, when interpolating high-resolution images, e.g. at 4K, the design choices for achieving high accuracy within reasonable memory requirements are limited. The feature extraction layers help to compress the input and extract relevant information for the latter stages, such as motion estimation. However, these layers are often costly in parameters, computation time, and memory. We show how ideas from dimensionality reduction combined with a lightweight optimization can be used to compress the input representation while keeping the extracted information suitable for frame interpolation. Further, we require neither a pretrained flow network nor a synthesis network, additionally reducing the number of trainable parameters and required memory. When evaluating on three 4K benchmarks, we achieve state-of-the-art image quality among the methods without pretrained flow while having the lowest network complexity and memory requirements overall.Comment: Accepted to BMVC 2022. Code: https://github.com/visinf/fldr-vf

An information-theoretic approach to unsupervised keypoint representation learning

Extracting informative representations from videos is fundamental for the effective learning of various downstream tasks. Inspired by classical works on saliency, we present a novel information-theoretic approach to discover meaningful representations from videos in an unsupervised fashion. We argue that local entropy of pixel neighborhoods and its evolution in a video stream is a valuable intrinsic supervisory signal for learning to attend to salient features. We, thus, abstract visual features into a concise representation of keypoints that serve as dynamic information transporters. We discover in an unsupervised fashion spatio-temporally consistent keypoint representations that carry the prominent information across video frames, thanks to two original information-theoretic losses. First, a loss that maximizes the information covered by the keypoints in a frame. Second, a loss that encourages optimized keypoint transportation over time, thus, imposing consistency of the information flow. We evaluate our keypoint-based representation compared to state-of-the-art baselines in different downstream tasks such as learning object dynamics. To evaluate the expressivity and consistency of the keypoints, we propose a new set of metrics. Our empirical results showcase the superior performance of our information-driven keypoints that resolve challenges like attendance to both static and dynamic objects, and to objects abruptly entering and leaving the scene

Species-Specific Differences in the Susceptibility of Fungi to the Antifungal Protein AFP Depend on C-3 Saturation of Glycosylceramides

AFP is an antimicrobial peptide (AMP) produced by the filamentous fungus Aspergillus giganteus and is a very potent inhibitor of fungal growth that does not affect the viability of bacteria, plant, or mammalian cells. It targets chitin synthesis and causes plasma membrane permeabilization in many human- and plant-pathogenic fungi, but its exact mode of action is not known. After adoption of the “damage-response framework of microbial pathogenesis” regarding the analysis of interactions between AMPs and microorganisms, we have recently proposed that the cytotoxic capacity of a given AMP depends not only on the presence/absence of its target(s) in the host and the AMP concentration applied but also on other variables, such as microbial survival strategies. We show here using the examples of three filamentous fungi (Aspergillus niger, Aspergillus fumigatus, and Fusarium graminearum) and two yeasts (Saccharomyces cerevisiae and Pichia pastoris) that the important parameters defining the AFP susceptibilities of these fungi are (i) the presence/absence of glycosylceramides, (ii) the presence/absence of Δ3(E) desaturation of the fatty acid chain therein, and (iii) the (dis)ability of these fungi to respond to AFP inhibitory effects with the fortification of their cell walls via increased chitin and β-(1,3)-glucan synthesis. These observations support the idea of the adoption of the damage-response framework to holistically understand the outcome of AFP inhibitory effects.TU Berlin, Open-Access-Mittel - 201

S2S^2-Flow: Joint Semantic and Style Editing of Facial Images

The high-quality images yielded by generative adversarial networks (GANs) have motivated investigations into their application for image editing. However, GANs are often limited in the control they provide for performing specific edits. One of the principal challenges is the entangled latent space of GANs, which is not directly suitable for performing independent and detailed edits. Recent editing methods allow for either controlled style edits or controlled semantic edits. In addition, methods that use semantic masks to edit images have difficulty preserving the identity and are unable to perform controlled style edits. We propose a method to disentangle a GAN$\text{'}$s latent space into semantic and style spaces, enabling controlled semantic and style edits for face images independently within the same framework. To achieve this, we design an encoder-decoder based network architecture ($S^2$-Flow), which incorporates two proposed inductive biases. We show the suitability of $S^2$-Flow quantitatively and qualitatively by performing various semantic and style edits.Comment: Accepted to BMVC 202

Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates

BACKGROUND: Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution. RESULTS: We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found. CONCLUSION: The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function

Interaction between two invasive organisms on the European chestnut: does the chestnut blight fungus benefit from the presence of the gall wasp?

The impact of invasive fungal pathogens and pests on trees is often studied individually, thereby omitting possible interactions. In this study the ecological interaction between the chestnut blight fungus Cryphonectria parasitica and the chestnut gall wasp Dryocosmus kuriphilus was investigated. We determined if abandoned galls could be colonized by C. parasitica and thereby act as an entry point and a source of pathogen inoculum. Moreover we assessed the identity and diversity of other gall-colonizing fungal species. A total of 1973 galls were randomly sampled from 200 chestnut trees in eight Swiss stands. In a stand C. parasitica was isolated from 0.4-19.2% of the galls. The incidence of C. parasitica on the galls and the fungal diversity significantly increased with the residence time of D. kuriphilus in a stand. All but one C. parasitica cultures were virulent. The predominant fungus isolated from galls was Gnomoniopsis castanea whose abundance influenced negatively that of C. parasitica. This study shows that D. kuriphilus galls can be colonized by virulent strains of the chestnut blight fungus C. parasitica. This can have effects on the chestnut blight incidence even in chestnut stands where the disease is successfully controlled by hypovirulence. The gall wasp presence influences also the fungal species composition on chestnut tree