Deep learning for extracting protein-protein interactions from biomedical literature

State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN compares favorably to the state-of-the-art rich-feature and single-kernel based methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on "difficult" instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.Comment: Accepted for publication in Proceedings of the 2017 Workshop on Biomedical Natural Language Processing, 10 pages, 2 figures, 6 table

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Introduction to the special issue on cross-language algorithms and applications

With the increasingly global nature of our everyday interactions, the need for multilingual technologies to support efficient and efective information access and communication cannot be overemphasized. Computational modeling of language has been the focus of Natural Language Processing, a subdiscipline of Artificial Intelligence. One of the current challenges for this discipline is to design methodologies and algorithms that are cross-language in order to create multilingual technologies rapidly. The goal of this JAIR special issue on Cross-Language Algorithms and Applications (CLAA) is to present leading research in this area, with emphasis on developing unifying themes that could lead to the development of the science of multi- and cross-lingualism. In this introduction, we provide the reader with the motivation for this special issue and summarize the contributions of the papers that have been included. The selected papers cover a broad range of cross-lingual technologies including machine translation, domain and language adaptation for sentiment analysis, cross-language lexical resources, dependency parsing, information retrieval and knowledge representation. We anticipate that this special issue will serve as an invaluable resource for researchers interested in topics of cross-lingual natural language processing.Postprint (published version

Knowledge will Propel Machine Understanding of Content: Extrapolating from Current Examples

Machine Learning has been a big success story during the AI resurgence. One particular stand out success relates to learning from a massive amount of data. In spite of early assertions of the unreasonable effectiveness of data, there is increasing recognition for utilizing knowledge whenever it is available or can be created purposefully. In this paper, we discuss the indispensable role of knowledge for deeper understanding of content where (i) large amounts of training data are unavailable, (ii) the objects to be recognized are complex, (e.g., implicit entities and highly subjective content), and (iii) applications need to use complementary or related data in multiple modalities/media. What brings us to the cusp of rapid progress is our ability to (a) create relevant and reliable knowledge and (b) carefully exploit knowledge to enhance ML/NLP techniques. Using diverse examples, we seek to foretell unprecedented progress in our ability for deeper understanding and exploitation of multimodal data and continued incorporation of knowledge in learning techniques.Comment: Pre-print of the paper accepted at 2017 IEEE/WIC/ACM International Conference on Web Intelligence (WI). arXiv admin note: substantial text overlap with arXiv:1610.0770

Entity Recognition at First Sight: Improving NER with Eye Movement Information

Previous research shows that eye-tracking data contains information about the lexical and syntactic properties of text, which can be used to improve natural language processing models. In this work, we leverage eye movement features from three corpora with recorded gaze information to augment a state-of-the-art neural model for named entity recognition (NER) with gaze embeddings. These corpora were manually annotated with named entity labels. Moreover, we show how gaze features, generalized on word type level, eliminate the need for recorded eye-tracking data at test time. The gaze-augmented models for NER using token-level and type-level features outperform the baselines. We present the benefits of eye-tracking features by evaluating the NER models on both individual datasets as well as in cross-domain settings.Comment: Accepted at NAACL-HLT 201

A matter of words: NLP for quality evaluation of Wikipedia medical articles

Automatic quality evaluation of Web information is a task with many fields of applications and of great relevance, especially in critical domains like the medical one. We move from the intuition that the quality of content of medical Web documents is affected by features related with the specific domain. First, the usage of a specific vocabulary (Domain Informativeness); then, the adoption of specific codes (like those used in the infoboxes of Wikipedia articles) and the type of document (e.g., historical and technical ones). In this paper, we propose to leverage specific domain features to improve the results of the evaluation of Wikipedia medical articles. In particular, we evaluate the articles adopting an "actionable" model, whose features are related to the content of the articles, so that the model can also directly suggest strategies for improving a given article quality. We rely on Natural Language Processing (NLP) and dictionaries-based techniques in order to extract the bio-medical concepts in a text. We prove the effectiveness of our approach by classifying the medical articles of the Wikipedia Medicine Portal, which have been previously manually labeled by the Wiki Project team. The results of our experiments confirm that, by considering domain-oriented features, it is possible to obtain sensible improvements with respect to existing solutions, mainly for those articles that other approaches have less correctly classified. Other than being interesting by their own, the results call for further research in the area of domain specific features suitable for Web data quality assessment

ExTaSem! Extending, Taxonomizing and Semantifying Domain Terminologies

We introduce EXTASEM!, a novel approach for the automatic learning of lexical taxonomies from domain terminologies. First, we exploit a very large semantic network to collect thousands of in-domain textual definitions. Second, we extract (hyponym, hypernym) pairs from each definition with a CRF-based algorithm trained on manuallyvalidated data. Finally, we introduce a graph induction procedure which constructs a full-fledged taxonomy where each edge is weighted according to its domain pertinence. EXTASEM! achieves state-of-the-art results in the following taxonomy evaluation experiments: (1) Hypernym discovery, (2) Reconstructing gold standard taxonomies, and (3) Taxonomy quality according to structural measures. We release weighted taxonomies for six domains for the use and scrutiny of the communit