Post-Transcriptional Mechanisms of Neuronal Translational Control in Synaptic Plasticity

The dynamic complexity of synaptic function is matched by extensive multidimensional regulation of neuronal mRNA translation which is achieved by a number of post‐transcriptional mechanisms. The first key aspect of this regulatory capacity is mRNA distal trafficking through RNA‐binding proteins, which governs the transcriptomic composition of post‐synaptic compartments. Small non‐coding microRNA and associated machinery have the capacity to precisely coordinate neural gene networks in space and time by providing a flexible specificity dimension to translational regulation. This RNA‐guided subcellular fine‐tuning of protein synthesis is an exquisite mechanism used in neurons to exert control of synaptic properties. Emerging evidence also implicates brain‐enriched long non‐coding RNA and novel circular RNA in posttranscriptional regulation of gene expression through the modulation of both mRNA and miRNA functions, thereby exemplifying the complex nature of neuronal translation. Herein, we review current knowledge of these regulatory systems and analyse how these mechanisms of transcriptomic regulation may be linked together to achieve high‐order spatiotemporal control of post‐synaptic translation

Learning Compositional Visual Concepts with Mutual Consistency

Compositionality of semantic concepts in image synthesis and analysis is appealing as it can help in decomposing known and generatively recomposing unknown data. For instance, we may learn concepts of changing illumination, geometry or albedo of a scene, and try to recombine them to generate physically meaningful, but unseen data for training and testing. In practice however we often do not have samples from the joint concept space available: We may have data on illumination change in one data set and on geometric change in another one without complete overlap. We pose the following question: How can we learn two or more concepts jointly from different data sets with mutual consistency where we do not have samples from the full joint space? We present a novel answer in this paper based on cyclic consistency over multiple concepts, represented individually by generative adversarial networks (GANs). Our method, ConceptGAN, can be understood as a drop in for data augmentation to improve resilience for real world applications. Qualitative and quantitative evaluations demonstrate its efficacy in generating semantically meaningful images, as well as one shot face verification as an example application.Comment: 10 pages, 8 figures, 4 tables, CVPR 201

Multi-channel Encoder for Neural Machine Translation

Attention-based Encoder-Decoder has the effective architecture for neural machine translation (NMT), which typically relies on recurrent neural networks (RNN) to build the blocks that will be lately called by attentive reader during the decoding process. This design of encoder yields relatively uniform composition on source sentence, despite the gating mechanism employed in encoding RNN. On the other hand, we often hope the decoder to take pieces of source sentence at varying levels suiting its own linguistic structure: for example, we may want to take the entity name in its raw form while taking an idiom as a perfectly composed unit. Motivated by this demand, we propose Multi-channel Encoder (MCE), which enhances encoding components with different levels of composition. More specifically, in addition to the hidden state of encoding RNN, MCE takes 1) the original word embedding for raw encoding with no composition, and 2) a particular design of external memory in Neural Turing Machine (NTM) for more complex composition, while all three encoding strategies are properly blended during decoding. Empirical study on Chinese-English translation shows that our model can improve by 6.52 BLEU points upon a strong open source NMT system: DL4MT1. On the WMT14 English- French task, our single shallow system achieves BLEU=38.8, comparable with the state-of-the-art deep models.Comment: Accepted by AAAI-201

BattRAE: Bidimensional Attention-Based Recursive Autoencoders for Learning Bilingual Phrase Embeddings

In this paper, we propose a bidimensional attention based recursive autoencoder (BattRAE) to integrate clues and sourcetarget interactions at multiple levels of granularity into bilingual phrase representations. We employ recursive autoencoders to generate tree structures of phrases with embeddings at different levels of granularity (e.g., words, sub-phrases and phrases). Over these embeddings on the source and target side, we introduce a bidimensional attention network to learn their interactions encoded in a bidimensional attention matrix, from which we extract two soft attention weight distributions simultaneously. These weight distributions enable BattRAE to generate compositive phrase representations via convolution. Based on the learned phrase representations, we further use a bilinear neural model, trained via a max-margin method, to measure bilingual semantic similarity. To evaluate the effectiveness of BattRAE, we incorporate this semantic similarity as an additional feature into a state-of-the-art SMT system. Extensive experiments on NIST Chinese-English test sets show that our model achieves a substantial improvement of up to 1.63 BLEU points on average over the baseline.Comment: 7 pages, accepted by AAAI 201

TITER: predicting translation initiation sites by deep learning.

MotivationTranslation initiation is a key step in the regulation of gene expression. In addition to the annotated translation initiation sites (TISs), the translation process may also start at multiple alternative TISs (including both AUG and non-AUG codons), which makes it challenging to predict TISs and study the underlying regulatory mechanisms. Meanwhile, the advent of several high-throughput sequencing techniques for profiling initiating ribosomes at single-nucleotide resolution, e.g. GTI-seq and QTI-seq, provides abundant data for systematically studying the general principles of translation initiation and the development of computational method for TIS identification.MethodsWe have developed a deep learning-based framework, named TITER, for accurately predicting TISs on a genome-wide scale based on QTI-seq data. TITER extracts the sequence features of translation initiation from the surrounding sequence contexts of TISs using a hybrid neural network and further integrates the prior preference of TIS codon composition into a unified prediction framework.ResultsExtensive tests demonstrated that TITER can greatly outperform the state-of-the-art prediction methods in identifying TISs. In addition, TITER was able to identify important sequence signatures for individual types of TIS codons, including a Kozak-sequence-like motif for AUG start codon. Furthermore, the TITER prediction score can be related to the strength of translation initiation in various biological scenarios, including the repressive effect of the upstream open reading frames on gene expression and the mutational effects influencing translation initiation efficiency.Availability and implementationTITER is available as an open-source software and can be downloaded from https://github.com/zhangsaithu/titer [email protected] or [email protected] informationSupplementary data are available at Bioinformatics online