Predicting the biological function of molecules, be it proteins or drug-like compounds, from their atomic structure is an important and long-standing problem. Function is dictated by structure, since it is by spatial interactions that molecules interact with each other, both in terms of steric complementarity, as well as intermolecular forces. Thus, the electron density field and electrostatic potential field of a molecule contain the "raw fingerprint" of how this molecule can fit to binding partners. In this paper, we show that deep learning can predict biological function of molecules directly from their raw 3D approximated electron density and electrostatic potential fields. Protein function based on EC numbers is predicted from the approximated electron density field. In another experiment, the activity of small molecules is predicted with quality comparable to state-of-the-art descriptor-based methods. We propose several alternative computational models for the GPU with different memory and runtime requirements for different sizes of molecules and of databases. We also propose application-specific multi-channel data representations. With future improvements of training datasets and neural network settings in combination with complementary information sources (sequence, genomic context, expression level), deep learning can be expected to show its generalization power and revolutionize the field of molecular function prediction.
This paper presents a new method named AQueReBET, which automatically refines a query set by an information seeker searching on the web. A revelation of the intention of an information seeker who is running a search can bring a significant improvement to the search process and to browsing as well. It is practically impossible to acquire such intention by the explicit indication (feedback) due to the fact that web browsing takes place in real time. Therefore the intention must be determined in some other way. We hypothesize that it can be approximated by means of the implicit feedback preferably in the form of data from an eye tracker and mouse. We propose a method which automatically refines a seeker's search query, and thus we can offer documents with higher relevance, decrease the number of query reformulations and increase the seeker's satisfaction. The query refinement is based on an analysis of gaze data from an eye tracker and on groupization. In the proposed method, we calculate word-level importance based on term frequency, term uniqueness (tf-idf) and total fixation duration within the subdocument (word's snippet in search results).
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