The current and the attainable coverage by X-ray structures of proteins and their functions on the scale of the ‘protein universe’ are estimated. A detailed analysis of the coverage across nearly 2000 proteomes from all superkingdoms of life and functional annotations is performed, with particular focus on the human proteome and the family of GPCR proteins.

This paper presents the development of several models of a deep convolutional auto-encoder in the Caffe deep learning framework and their experimental evaluation on the example of MNIST dataset. We have created five models of a convolutional auto-encoder which differ architecturally by the presence or absence of pooling and unpooling layers in the auto-encoder’s encoder and decoder parts. Our results show that the developed models provide very good results in dimensionality reduction and unsupervised clustering tasks, and small classification errors when we used the learned internal code as an input of a supervised linear classifier and multi-layer perceptron. The best results were provided by a model where the encoder part contains convolutional and pooling layers, followed by an analogous decoder part with deconvolution and unpooling layers without the use of switch variables in the decoder part. The paper also discusses practical details of the creation of a deep convolutional auto-encoder in the very popular Caffe deep learning framework. We believe that our approach and results presented in this paper could help other researchers to build efficient deep neural network architectures in the future.

Adolescent idiopathic scoliosis (AIS) is a three-dimensional spinal deformity. Brace treatment is a common non-surgical treatment, intended to prevent progression (worsening) of the condition during adolescence. Estimating a braced patient's risk of progression is an essential part of planning treatment, so method for predicting this risk would be a useful decision support tool for practitioners. This work attempts to discover whether failure of brace treatment (progression) can be predicted at the start of treatment. Records were obtained for 62 AIS patients who had completed brace treatment. Subjects were labeled as "progressive" if their condition had progressed despite brace treatment and "non-progressive" otherwise. Wrapper-based feature selection selected two useful predictor variables from a list of 14 clinical measurements taken from the records. A logistic regression model was trained to classify patients as "progressive" or "non-progressive" using these two variables. The logistic regression model's simplicity and interpretability should facilitate its clinical acceptance. The model was tested on data from an additional 28 patients and found to be 75 % accurate. This accuracy is sufficient to make the predictions clinically useful. It can be used online: http://www.ece.ualberta.ca/~dchalmer/SimpleBracePredictor.html .

The reinforcement learning (RL) paradigm allows agents to solve tasks through trial-and-error learning. To be capable of efficient, long-term learning, RL agents should be able to apply knowledge gained in the past to new tasks they may encounter in the future. The ability to predict actions' consequences may facilitate such knowledge transfer. We consider here domains where an RL agent has access to two kinds of information: agent-centric information with constant semantics across tasks, and environment-centric information, which is necessary to solve the task, but with semantics that differ between tasks. For example, in robot navigation, environment-centric information may include the robot's geographic location, while agent-centric information may include sensor readings of various nearby obstacles. We propose that these situations provide an opportunity for a very natural style of knowledge transfer, in which the agent learns to predict actions' environmental consequences using agent-centric information. These predictions contain important information about the affordances and dangers present in a novel environment, and can effectively transfer knowledge from agent-centric to environment-centric learning systems. Using several example problems including spatial navigation and network routing, we show that our knowledge transfer approach can allow faster and lower cost learning than existing alternatives.

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