Comments on social media are very diverse, in terms of content, style and vocabulary, which make generating comments much more challenging than other existing natural language generation (NLG) tasks. Besides, since different user has different expression habits, it is necessary to take the user's profile into consideration when generating comments. In this paper, we introduce the task of automatic generation of personalized comment (AGPC) for social media. Based on tens of thousands of users' real comments and corresponding user profiles on weibo, we propose Personalized Comment Generation Network (PCGN) for AGPC. The model utilizes user feature embedding with a gated memory and attends to user description to model personality of users. In addition, external user representation is taken into consideration during the decoding to enhance the comments generation. Experimental results show that our model can generate natural, human-like and personalized comments. 1 * Equal Contribution. 1 Source codes of this paper are available at
Transformer-based language models are successfully used to address massive text-related tasks. DNA methylation is an important epigenetic mechanism and its analysis provides valuable insights into gene regulation and biomarker identification. Several deep learning-based methods have been proposed to identify DNA methylation and each seeks to strike a balance between computational effort and accuracy. Here, we introduce a MuLan-Methyl, a deep learning framework for predicting DNA methylation sites, which is based on multiple (five) popular transformer-based language models. The framework identifies methylation sites for three different types of DNA methylation, namely N6-adenine (6mA), N4-cytosine (4mC), and 5-hydroxymethylcytosine (5hmC). Each of the five employed language models is adapted to the task using the "pre-train and fine-tune" paradigm. Pre-training is performed on a custom corpus consisting of DNA fragments and taxonomy lineages using self-supervised learning. Fine-tuning then aims at predicting the DNA-methylation status of each type. The five models are used to collectively predict the DNA methylation status. We report excellent performance of MuLan-Methyl on a benchmark dataset. Moreover, we show that the model captures characteristic differences between different species that are relevant for methylation. This work demonstrates that language models can be successfully adapted to this domain of application and that joint utilization of different language models improves model performance.
The current COVID-19 pandemic, caused by the rapid worldwide spread of the SARS-CoV-2 virus, is having severe consequences for human health and the world economy. The virus affects different individuals differently, with many infected patients showing only mild symptoms, and others showing critical illness. To lessen the impact of the epidemic, one problem is to determine which factors play an important role in a patient’s progression of the disease. Here, we construct an enhanced COVID-19 structured dataset from more than one source, using natural language processing to add local weather conditions and country-specific research sentiment. The enhanced structured dataset contains 301,363 samples and 43 features, and we applied both machine learning algorithms and deep learning algorithms on it so as to forecast patient’s survival probability. In addition, we import alignment sequence data to improve the performance of the model. Application of Extreme Gradient Boosting (XGBoost) on the enhanced structured dataset achieves 97% accuracy in predicting patient’s survival; with climatic factors, and then age, showing the most importance. Similarly, the application of a Multi-Layer Perceptron (MLP) achieves 98% accuracy. This work suggests that enhancing the available data, mostly basic information on patients, so as to include additional, potentially important features, such as weather conditions, is useful. The explored models suggest that textual weather descriptions can improve outcome forecast.
Motivation Metagenomic projects often involve large numbers of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases have required that the user first download the computed data from the server, an increasingly time-consuming process. Here we present MeganServer, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis in MEGAN, without requiring prior download of the data. We describe a number of different application scenarios. Availability MeganServer is provided as a standalone program tools/megan-server in the MEGAN software suite, available at https://software-ab.cs.uni-tuebingen.de/download/megan6. Source available at: https://github.com/husonlab/megan-ce/tree/master/src/megan/ms. Supplementary information A description of how to get started is available at Bioinformatics online.
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