The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis

Simultaneous Codeword Optimization (SimCO) for Dictionary Update and Learning

We consider the data-driven dictionary learning problem. The goal is to seek an over-complete dictionary from which every training signal can be best approximated by a linear combination of only a few codewords. This task is often achieved by iteratively executing two operations: sparse coding and dictionary update. In the literature, there are two benchmark mechanisms to update a dictionary. The first approach, such as the MOD algorithm, is characterized by searching for the optimal codewords while fixing the sparse coefficients. In the second approach, represented by the K-SVD method, one codeword and the related sparse coefficients are simultaneously updated while all other codewords and coefficients remain unchanged. We propose a novel framework that generalizes the aforementioned two methods. The unique feature of our approach is that one can update an arbitrary set of codewords and the corresponding sparse coefficients simultaneously: when sparse coefficients are fixed, the underlying optimization problem is similar to that in the MOD algorithm; when only one codeword is selected for update, it can be proved that the proposed algorithm is equivalent to the K-SVD method; and more importantly, our method allows us to update all codewords and all sparse coefficients simultaneously, hence the term simultaneous codeword optimization (SimCO). Under the proposed framework, we design two algorithms, namely, primitive and regularized SimCO. We implement these two algorithms based on a simple gradient descent mechanism. Simulations are provided to demonstrate the performance of the proposed algorithms, as compared with two baseline algorithms MOD and K-SVD. Results show that regularized SimCO is particularly appealing in terms of both learning performance and running speed.Comment: 13 page

Predictive Encoding of Contextual Relationships for Perceptual Inference, Interpolation and Prediction

We propose a new neurally-inspired model that can learn to encode the global relationship context of visual events across time and space and to use the contextual information to modulate the analysis by synthesis process in a predictive coding framework. The model learns latent contextual representations by maximizing the predictability of visual events based on local and global contextual information through both top-down and bottom-up processes. In contrast to standard predictive coding models, the prediction error in this model is used to update the contextual representation but does not alter the feedforward input for the next layer, and is thus more consistent with neurophysiological observations. We establish the computational feasibility of this model by demonstrating its ability in several aspects. We show that our model can outperform state-of-art performances of gated Boltzmann machines (GBM) in estimation of contextual information. Our model can also interpolate missing events or predict future events in image sequences while simultaneously estimating contextual information. We show it achieves state-of-art performances in terms of prediction accuracy in a variety of tasks and possesses the ability to interpolate missing frames, a function that is lacking in GBM