Exposing the Functionalities of Neurons for Gated Recurrent Unit Based Sequence-to-Sequence Model

The goal of this paper is to report certain scientific discoveries about a Seq2Seq model. It is known that analyzing the behavior of RNN-based models at the neuron level is considered a more challenging task than analyzing a DNN or CNN models due to their recursive mechanism in nature. This paper aims to provide neuron-level analysis to explain why a vanilla GRU-based Seq2Seq model without attention can achieve token-positioning. We found four different types of neurons: storing, counting, triggering, and outputting and further uncover the mechanism for these neurons to work together in order to produce the right token in the right position.Comment: 9 pages (excluding reference), 10 figure

ProKware: integrated software for presenting protein structural properties in protein tertiary structures

Protein tertiary structure plays an essential role in deciphering protein functions, especially protein structural properties, including domains, active sites and post-translational modifications. These properties typically yield useful clues for understanding protein functions. This work presents an integrated software, named ProKware, that presents protein structural properties in protein tertiary structures, such as domains, functional sites, families, active sites, binding sites, post-translational modifications and domain–domain interaction. Using this web-based and Windows-based interface, users can manipulate and visualize three-dimensional protein structures, as well as the supported structural properties that are curated in the protein knowledge database. ProKware is an effective and convenient solution for investigating protein functions and structural relationships. This software can be accessed on the internet at

KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites

KinasePhos is a novel web server for computationally identifying catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the profile hidden Markov model, computational models are learned from the kinase-specific groups of the phosphorylation sites. After evaluating the learned models, the model with highest accuracy was selected from each kinase-specific group, for use in a web-based prediction tool for identifying protein phosphorylation sites. Therefore, this work developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. The prediction tool is freely available at

Star Formation History and Chemical Evolution of the Sextans Dwarf Spheroidal Galaxy

We present the star formation history and chemical evolution of the Sextans dSph dwarf galaxy as a function of galactocentric distance. We derive these from the $VI$ photometry of stars in the $42' \times 28'$ field using the SMART model developed by Yuk & Lee (2007, ApJ, 668, 876) and adopting a closed-box model for chemical evolution. For the adopted age of Sextans 15 Gyr, we find that $>$84% of the stars formed prior to 11 Gyr ago, significant star formation extends from 15 to 11 Gyr ago ($\sim$ 65% of the stars formed 13 to 15 Gyr ago while $\sim$ 25% formed 11 to 13 Gyr ago), detectable star formation continued to at least 8 Gyr ago, the star formation history is more extended in the central regions than the outskirts, and the difference in star formation rates between the central and outer regions is most marked 11 to 13 Gyr ago. Whether blue straggler stars are interpreted as intermediate age main sequence stars affects conclusions regarding the star formation history for times 4 to 8 Gyr ago, but this is at most only a trace population. We find that the metallicity of the stars increased rapidly up to [Fe/H]=--1.6 in the central region and to [Fe/H]=--1.8 in the outer region within the first Gyr, and has varied slowly since then. The abundance ratios of several elements derived in this study are in good agreement with the observational data based on the high resolution spectroscopy in the literature. We conclude that the primary driver for the radial gradient of the stellar population in this galaxy is the star formation history, which self-consistently drives the chemical enrichment history.Comment: 36 pages, 14 figures, To appear in the ApJ, 200

PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

<p>Abstract</p> <p>Background</p> <p>The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as <it>A. thaliana</it>, <it>O. sativa </it>and <it>Z. mays</it>. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands) in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs) is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required.</p> <p>Results</p> <p>This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator), for recognizing combinatorial <it>cis</it>-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0), AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs) within a defined distance (20 bp to 200 bp) to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented.</p> <p>Conclusion</p> <p>In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at <url>http://PlantPAN.mbc.nctu.edu.tw</url>.</p