Motivation Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. Results We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug–drug interaction (DDI) prediction, protein–protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks. Availability and implementation As part of our contributions in the paper, we develop an easy-to-use Python package with detailed instructions, BioNEV, available at: https://github.com/xiangyue9607/BioNEV, including all source code and datasets, to facilitate studying various graph embedding methods on biomedical tasks. Supplementary information Supplementary data are available at Bioinformatics online.

Text-based Captchas have been widely deployed across the Internet to defend against undesirable or malicious bot programs. Many attacks have been proposed; these fine prior art advanced the scientific understanding of Captcha robustness, but most of them have a limited applicability. In this paper, we report a simple, low-cost but powerful attack that effectively breaks a wide range of text Captchas with distinct design features, including those deployed by Google, Microsoft, Yahoo!, Amazon and other Internet giants. For all the schemes, our attack achieved a success rate ranging from 5% to 77%, and achieved an average speed of solving a puzzle in less than 15 seconds on a standard desktop computer (with a 3.3GHz Intel Core i3 CPU and 2 GB RAM). This is to date the simplest generic attack on text Captchas. Our attack is based on Log-Gabor filters; a famed application of Gabor filters in computer security is John Daugman's iris recognition algorithm. Our work is the first to apply Gabor filters for breaking Captchas.

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