BackgroundThe subcellular localization of a protein is an important aspect of its function. However, the experimental annotation of locations is not even complete for well-studied model organisms. Text mining might aid database curators to add experimental annotations from the scientific literature. Existing extraction methods have difficulties to distinguish relationships between proteins and cellular locations co-mentioned in the same sentence.ResultsLocText was created as a new method to extract protein locations from abstracts and full texts. LocText learned patterns from syntax parse trees and was trained and evaluated on a newly improved LocTextCorpus. Combined with an automatic named-entity recognizer, LocText achieved high precision (P = 86%±4). After completing development, we mined the latest research publications for three organisms: human (Homo sapiens), budding yeast (Saccharomyces cerevisiae), and thale cress (Arabidopsis thaliana). Examining 60 novel, text-mined annotations, we found that 65% (human), 85% (yeast), and 80% (cress) were correct. Of all validated annotations, 40% were completely novel, i.e. did neither appear in the annotations nor the text descriptions of Swiss-Prot.ConclusionsLocText provides a cost-effective, semi-automated workflow to assist database curators in identifying novel protein localization annotations. The annotations suggested through text-mining would be verified by experts to guarantee high-quality standards of manually-curated databases such as Swiss-Prot.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-018-2021-9) contains supplementary material, which is available to authorized users.

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We present PredProp, a method for bidirectional, parallel and local optimisation of weights, activities and precision in neural networks. PredProp jointly addresses inference and learning, scales learning rates dynamically and weights gradients by the curvature of the loss function by optimizing prediction error precision. PredProp optimizes network parameters with Stochastic Gradient Descent and error forward propagation based strictly on prediction errors and variables locally available to each layer. Neighboring layers optimise shared activity variables so that prediction errors can propagate forward in the network, while predictions propagate backwards. This process minimises the negative Free Energy, or evidence lower bound of the entire network. We show that networks trained with PredProp resemble gradient based predictive coding when the number of weights between neighboring activity variables is one. In contrast to related work, PredProp generalizes towards backward connections of arbitrary depth and optimizes precision for any deep network architecture. Due to the analogy between prediction error precision and the Fisher information for each layer, PredProp implements a form of Natural Gradient Descent. When optimizing DNN models, layer-wise PredProp renders the model a bidirectional predictive coding network. Alternatively DNNs can parameterize the weights between two activity variables. We evaluate Pred-Prop for dense DNNs on simple inference, learning and combined tasks. We show that, without an explicit sampling step in the network, PredProp implements a form of variational inference that allows to learn disentangled embeddings from low amounts of data and leave evaluation on more complex tasks and datasets to future work.

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