Sense classification of shallow discourse relations with focused RNNs.

Understanding the sense of discourse relations between segments of text is essential to truly comprehend any natural language text. Several automated approaches have been suggested, but all rely on external resources, linguistic feature engineering, and their processing pipelines are built from substantially different models. In this paper, we introduce a novel system for sense classification of shallow discourse relations (FR system) based on focused recurrent neural networks (RNNs). In contrast to existing systems, FR system consists of a single end-to-end trainable model for handling all types and senses of discourse relations, requires no feature engineering or external resources, is language-independent, and can be applied at the word and even character levels. At its core, we present our novel generalization of the focused RNNs layer, the first multi-dimensional RNN-attention mechanism for constructing text/argument embeddings. The filtering/gating RNN enables downstream RNNs to focus on different aspects of the input sequence and project it into several embedding subspaces. These argument embeddings are then used to perform sense classification. FR system has been evaluated using the official datasets and methodology of CoNLL 2016 Shared Task. It does not fall a lot behind state-of-the-art performance on English, the most researched and supported language, but it outperforms existing best systems by 2.5% overall results on the Chinese blind dataset.

Process models of interrelated speech intentions from online health-related conversations.

Being related to the adoption of new beliefs, attitudes and, ultimately, behaviors, analyzing online communication is of utmost importance for medicine. Multiple health care, academic communities, such as information seeking and dissemination and persuasive technologies, acknowledge this need. However, in order to obtain understanding, a relevant way to model online communication for the study of behavior is required. In this paper, we propose an automatic method to reveal process models of interrelated speech intentions from conversations. Specifically, a domain-independent taxonomy of speech intentions is adopted, an annotated corpus of Reddit conversations is released, supervised classifiers for speech intention prediction from utterances are trained and assessed using 10-fold cross validation (multi-class, one-versus-all and multi-label setups) and an approach to transform conversations into well-defined, representative logs of verbal behavior, needed by process mining techniques, is designed. The experimental results show that: (1) the automatic classification of intentions is feasible (with Kappa scores varying between 0.52 and 1); (2) predicting pairs of intentions, also known as adjacency pairs, or including more utterances from even other heterogeneous corpora can improve the predictions of some classes; and (3) the classifiers in the current state are robust to be used on other corpora, although the results are poorer and suggest that the input corpus may not sufficiently capture varied ways of expressing certain speech intentions. The extracted process models of interrelated speech intentions open new views on grasping the formation of beliefs and behavioral intentions in and from speech, but in-depth evaluation of these conversational models is further required.

Sieve-based relation extraction of gene regulatory networks from biological literature.

BACKGROUND: Relation extraction is an essential procedure in literature mining. It focuses on extracting semantic relations between parts of text, called mentions. Biomedical literature includes an enormous amount of textual descriptions of biological entities, their interactions and results of related experiments. To extract them in an explicit, computer readable format, these relations were at first extracted manually from databases. Manual curation was later replaced with automatic or semi-automatic tools with natural language processing capabilities. The current challenge is the development of information extraction procedures that can directly infer more complex relational structures, such as gene regulatory networks. RESULTS: We develop a computational approach for extraction of gene regulatory networks from textual data. Our method is designed as a sieve-based system and uses linear-chain conditional random fields and rules for relation extraction. With this method we successfully extracted the sporulation gene regulation network in the bacterium Bacillus subtilis for the information extraction challenge at the BioNLP 2013 conference. To enable extraction of distant relations using first-order models, we transform the data into skip-mention sequences. We infer multiple models, each of which is able to extract different relationship types. Following the shared task, we conducted additional analysis using different system settings that resulted in reducing the reconstruction error of bacterial sporulation network from 0.73 to 0.68, measured as the slot error rate between the predicted and the reference network. We observe that all relation extraction sieves contribute to the predictive performance of the proposed approach. Also, features constructed by considering mention words and their prefixes and suffixes are the most important features for higher accuracy of extraction. Analysis of distances between different mention types in the text shows that our choice of transforming data into skip-mention sequences is appropriate for detecting relations between distant mentions. CONCLUSIONS: Linear-chain conditional random fields, along with appropriate data transformations, can be efficiently used to extract relations. The sieve-based architecture simplifies the system as new sieves can be easily added or removed and each sieve can utilize the results of previous ones. Furthermore, sieves with conditional random fields can be trained on arbitrary text data and hence are applicable to broad range of relation extraction tasks and data domains.

Quantifying the consistency of scientific databases.

Science is a social process with far-reaching impact on our modern society. In recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific publications that is increasingly becoming available. The data is contained in several databases such as Web of Science or PubMed, maintained by various public and private entities. Unfortunately, these databases are not always consistent, which considerably hinders this study. Relying on the powerful framework of complex networks, we conduct a systematic analysis of the consistency among six major scientific databases. We found that identifying a single "best" database is far from easy. Nevertheless, our results indicate appreciable differences in mutual consistency of different databases, which we interpret as recipes for future bibliometric studies.

The CHEMDNER corpus of chemicals and drugs and its annotation principles.

The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/.

Network-based statistical comparison of citation topology of bibliographic databases.

Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies.

SkipCor: skip-mention coreference resolution using linear-chain conditional random fields.

Coreference resolution tries to identify all expressions (called mentions) in observed text that refer to the same entity. Beside entity extraction and relation extraction, it represents one of the three complementary tasks in Information Extraction. In this paper we describe a novel coreference resolution system SkipCor that reformulates the problem as a sequence labeling task. None of the existing supervised, unsupervised, pairwise or sequence-based models are similar to our approach, which only uses linear-chain conditional random fields and supports high scalability with fast model training and inference, and a straightforward parallelization. We evaluate the proposed system against the ACE 2004, CoNLL 2012 and SemEval 2010 benchmark datasets. SkipCor clearly outperforms two baseline systems that detect coreferentiality using the same features as SkipCor. The obtained results are at least comparable to the current state-of-the-art in coreference resolution.

Unfolding communities in large complex networks: combining defensive and offensive label propagation for core extraction.

Label propagation has proven to be a fast method for detecting communities in large complex networks. Recent developments have also improved the accuracy of the approach; however, a general algorithm is still an open issue. We present an advanced label propagation algorithm that combines two unique strategies of community formation, namely, defensive preservation and offensive expansion of communities. The two strategies are combined in a hierarchical manner to recursively extract the core of the network and to identify whisker communities. The algorithm was evaluated on two classes of benchmark networks with planted partition and on 23 real-world networks ranging from networks with tens of nodes to networks with several tens of millions of edges. It is shown to be comparable to the current state-of-the-art community detection algorithms and superior to all previous label propagation algorithms, with comparable time complexity. In particular, analysis on real-world networks has proven that the algorithm has almost linear complexity, O(m¹·¹9), and scales even better than the basic label propagation algorithm (m is the number of edges in the network).