As a newly-identified protein post-translational modification, malonylation is involved in a variety of biological functions. Recognizing malonylation sites in substrates represents an initial but crucial step in elucidating the molecular mechanisms underlying protein malonylation. In this study, we constructed a deep learning (DL) network classifier based on long short-term memory (LSTM) with word embedding (LSTMWE) for the prediction of mammalian malonylation sites. LSTMWE performs better than traditional classifiers developed with common pre-defined feature encodings or a DL classifier based on LSTM with a one-hot vector. The performance of LSTMWE is sensitive to the size of the training set, but this limitation can be overcome by integration with a traditional machine learning (ML) classifier. Accordingly, an integrated approach called LEMP was developed, which includes LSTMWE and the random forest classifier with a novel encoding of enhanced amino acid content. LEMP performs not only better than the individual classifiers but also superior to the currently-available malonylation predictors. Additionally, it demonstrates a promising performance with a low false positive rate, which is highly useful in the prediction application. Overall, LEMP is a useful tool for easily identifying malonylation sites with high confidence. LEMP is available at http://www.bioinfogo.org/lemp.

Late gadolinium enhancement magnetic resonance imaging (LGE MRI) appears to be a promising alternative for scar assessment in patients with atrial fibrillation (AF). Automating the quantification and analysis of atrial scars can be challenging due to the low image quality. In this work, we propose a fully automated method based on the graph-cuts framework, where the potentials of the graph are learned on a surface mesh of the left atrium (LA) using a multi-scale convolutional neural network (MS-CNN). For validation, we have employed fifty-eight images with manual delineations. MS-CNN, which can efficiently incorporate both the local and global texture information of the images, has been shown to evidently improve the segmentation accuracy of the proposed graph-cuts based method. The segmentation could be further improved when the contribution between the t-link and n-link weights of the graph is balanced. The proposed method achieves a mean accuracy of 0.856 ± 0.033 and mean Dice score of 0.702 ± 0.071 for LA scar quantification. Compared with the conventional methods, which are based on the manual delineation of LA for initialization, our method is fully automatic and has demonstrated significantly better Dice score and accuracy (p < 0.01). The method is promising and can be useful in diagnosis and prognosis of AF.

N6-methyladenosine (m6A) is a prevalent RNA methylation modification involved in several biological processes. Hundreds or thousands of m6A sites identified from different species using high-throughput experiments provides a rich resource to construct in-silico approaches for identifying m6A sites. The existing m6A predictors are developed using conventional machine-learning (ML) algorithms and most are species-centric. In this paper, we develop a novel cross-species deep-learning classifier based on bidirectional Gated Recurrent Unit (BGRU) for the prediction of m6A sites. In comparison with conventional ML approaches, BGRU achieves outstanding performance for the Mammalia dataset that contains over fifty thousand m6A sites but inferior for the Saccharomyces cerevisiae dataset that covers around a thousand positives. The accuracy of BGRU is sensitive to the data size and the sensitivity is compensated by the integration of a random forest classifier with a novel encoding of enhanced nucleic acid content. The integrated approach dubbed as BGRU-based Ensemble RNA Methylation site Predictor (BERMP) has competitive performance in both cross-validation test and independent test. BERMP also outperforms existing m6A predictors for different species. Therefore, BERMP is a novel multi-species tool for identifying m6A sites with high confidence. This classifier is freely available at http://www.bioinfogo.org/bermp.

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We present a new, embarrassingly simple approach to instance segmentation in images. Compared to many other dense prediction tasks, e.g., semantic segmentation, it is the arbitrary number of instances that have made instance segmentation much more challenging. In order to predict a mask for each instance, mainstream approaches either follow the "detect-thensegment" strategy, as used by, e.g., Mask R-CNN, or predict embedding vectors first then use clustering techniques to group pixels into individual instances. We view the task of instance segmentation from a completely new perspective by introducing the notion of "instance categories", which assigns categories to each pixel within an instance according to the instance's location and size, thus nicely converting instance mask segmentation into a classification-solvable problem. Now instance segmentation is decomposed into two classification tasks. We demonstrate a much simpler and flexible instance segmentation framework with strong performance, achieving on par accuracy with Mask R-CNN and outperforming recent singleshot instance segmenters in accuracy. We hope that this very simple and strong framework can serve as a baseline for many instance-level recognition tasks besides instance segmentation.

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Text attribute transfer is modifying certain linguistic attributes (e.g. sentiment, style, authorship, etc.) of a sentence and transforming them from one type to another. In this paper, we aim to analyze and interpret what is changed during the transfer process. We start from the observation that in many existing models and datasets, certain words within a sentence play important roles in determining the sentence attribute class. These words are referred to as the Pivot Words. Based on these pivot words, we propose a lexical analysis framework, the Pivot Analysis, to quantitatively analyze the effects of these words in text attribute classification and transfer. We apply this framework to existing datasets and models, and show that: (1) the pivot words are strong features for the classification of sentence attributes; (2) to change the attribute of a sentence, many datasets only requires to change certain pivot words; (3) consequently, many transfer models only perform the lexical-level modification, while leaving higher-level sentence structures unchanged. Our work provides an in-depth understanding of linguistic attribute transfer and further identifies the future requirements and challenges of this task 1 .

Recent years see an increasing concern over the trustworthiness of Internet-based software. By analyzing the trustworthiness of Internet-based software and the nature of the Internet applications, we point out that, on the one hand, due to the openness and dynamic nature of the Internet, the identity trustworthiness and the capability trustworthiness of the software are facing serious challenges; on the other hand, in order to ensure the trustworthiness of the whole system, emerging computing paradigms based on the collaboration of autonomous software need some impacts on the behavior of the software. Here we put forward a conceptual model for the trustworthiness of Internet-based software, and propose a trustworthy assurance framework for Internet-based virtual computing environment (iVCE). This framework deals with the trustworthy properties of software on identity, capability and behavior in a combinated way. The authorization management in inter-domain computing environment, assurance on high availability of service and incentive mechanism for autonomic collaboration are taken as three core mechanisms of iVCE trustworthy assurance.