BACKGROUND: The number of applications of deep learning algorithms in bioinformatics is increasing as they usually achieve superior performance over classical approaches, especially, when bigger training datasets are available. In deep learning applications, discrete data, e.g. words or n-grams in language, or amino acids or nucleotides in bioinformatics, are generally represented as a continuous vector through an embedding matrix. Recently, learning this embedding matrix directly from the data as part of the continuous iteration of the model to optimize the target prediction - a process called 'end-to-end learning' - has led to state-of-the-art results in many fields. Although usage of embeddings is well described in the bioinformatics literature, the potential of end-to-end learning for single amino acids, as compared to more classical manually-curated encoding strategies, has not been systematically addressed. To this end, we compared classical encoding matrices, namely one-hot, VHSE8 and BLOSUM62, to end-to-end learning of amino acid embeddings for two different prediction tasks using three widely used architectures, namely recurrent neural networks (RNN), convolutional neural networks (CNN), and the hybrid CNN-RNN. RESULTS: By using different deep learning architectures, we show that end-to-end learning is on par with classical encodings for embeddings of the same dimension even when limited training data is available, and might allow for a reduction in the embedding dimension without performance loss, which is critical when deploying the models to devices with limited computational capacities. We found that the embedding dimension is a major factor in controlling the model performance. Surprisingly, we observed that deep learning models are capable of learning from random vectors of appropriate dimension. CONCLUSION: Our study shows that end-to-end learning is a flexible and powerful method for amino acid encoding. Further, due to the flexibility of deep learning systems, amino acid encoding schemes should be benchmarked against random vectors of the same dimension to disentangle the information content provided by the encoding scheme from the distinguishability effect provided by the scheme.

This paper presents recent improvements on a previous published practical approach to object segmentation from still images called SIOX: simple interactive object extraction. The basic method has been improved further and applied to a variety of applications. In the case of videos, this technique allows scale and rotation invariant real-time tracking of foreground objects including the classification of newly introduced objects. In the case of still-images, the method has been extended to cope with highly detailed textures with sub-pixel accuracy. The approach is robust in the presence of noise and can be applied to a variety of problems where objects have to be extracted, tracked and/or identified. The approach has been released as an open source framework. We discuss various applications of the algorithm and incorporated experiences and user feedback from several projects that have begun to integrate the algorithm

The presented alg rithm rec nstructs collections of arbitrary curves (open, closed, smooth, with corners, with or without intersections). The algorithm is very simple and short and follows a novel and simple greedy strategy. The corner and intersection points are not required to but allowed to be in the sample. The described method works for curves in any dimension d asymptotically in O (n2-1/d) time with involved data structures. Experiments show already a good performance with a very simple kd-tree structure.