Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret.REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based Critical Assessment of protein Function Annotation (CAFA) experiment. Fifty-four methods representing the state-of-the-art for protein function prediction were evaluated on a target set of 866 proteins from eleven organisms. Two findings stand out: (i) today’s best protein function prediction algorithms significantly outperformed widely-used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is significant need for improvement of currently available tools.

Many current natural language processing applications for social media rely on representation learning and utilize pre-trained word embeddings. There currently exist several publicly-available, pre-trained sets of word embeddings, but they contain few or no emoji representations even as emoji usage in social media has increased. In this paper we release emoji2vec, pre-trained embeddings for all Unicode emojis which are learned from their description in the Unicode emoji standard. 1 The resulting emoji embeddings can be readily used in downstream social natural language processing applications alongside word2vec. We demonstrate, for the downstream task of sentiment analysis, that emoji embeddings learned from short descriptions outperforms a skip-gram model trained on a large collection of tweets, while avoiding the need for contexts in which emojis need to appear frequently in order to estimate a representation.

Reasoning with knowledge expressed in natural language and Knowledge Bases (KBs) is a major challenge for Artificial Intelligence, with applications in machine reading, dialogue, and question answering. General neural architectures that jointly learn representations and transformations of text are very data-inefficient, and it is hard to analyse their reasoning process. These issues are addressed by end-to-end differentiable reasoning systems such as Neural Theorem Provers (NTPs), although they can only be used with small-scale symbolic KBs. In this paper we first propose Greedy NTPs (GNTPs), an extension to NTPs addressing their complexity and scalability limitations, thus making them applicable to real-world datasets. This result is achieved by dynamically constructing the computation graph of NTPs and including only the most promising proof paths during inference, thus obtaining orders of magnitude more efficient models 1. Then, we propose a novel approach for jointly reasoning over KBs and textual mentions, by embedding logic facts and natural language sentences in a shared embedding space. We show that GNTPs perform on par with NTPs at a fraction of their cost while achieving competitive link prediction results on large datasets, providing explanations for predictions, and inducing interpretable models.

Many machine reading approaches, from shallow information extraction to deep semantic parsing, map natural language to symbolic representations of meaning. Representations such as first-order logic capture the richness of natural language and support complex reasoning, but often fail in practice due to their reliance on logical background knowledge and the difficulty of scaling up inference. In contrast, low-dimensional embeddings (i.e. distributional representations) are efficient and enable generalization, but it is unclear how reasoning with embeddings could support the full power of symbolic representations such as first-order logic. In this proof-ofconcept paper we address this by learning embeddings that simulate the behavior of first-order logic.