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

Transfer Learning for Speech and Language Processing

Transfer learning is a vital technique that generalizes models trained for one setting or task to other settings or tasks. For example in speech recognition, an acoustic model trained for one language can be used to recognize speech in another language, with little or no re-training data. Transfer learning is closely related to multi-task learning (cross-lingual vs. multilingual), and is traditionally studied in the name of `model adaptation'. Recent advance in deep learning shows that transfer learning becomes much easier and more effective with high-level abstract features learned by deep models, and the `transfer' can be conducted not only between data distributions and data types, but also between model structures (e.g., shallow nets and deep nets) or even model types (e.g., Bayesian models and neural models). This review paper summarizes some recent prominent research towards this direction, particularly for speech and language processing. We also report some results from our group and highlight the potential of this very interesting research field.Comment: 13 pages, APSIPA 201

Hybridity in MT: experiments on the Europarl corpus

(Way & Gough, 2005) demonstrate that their Marker-based EBMT system is capable of outperforming a word-based SMT system trained on reasonably large data sets. (Groves & Way, 2005) take this a stage further and demonstrate that while the EBMT system also outperforms a phrase-based SMT (PBSMT) system, a hybrid 'example-based SMT' system incorporating marker chunks and SMT sub-sentential alignments is capable of outperforming both baseline translation models for French{English translation. In this paper, we show that similar gains are to be had from constructing a hybrid 'statistical EBMT' system capable of outperforming the baseline system of (Way & Gough, 2005). Using the Europarl (Koehn, 2005) training and test sets we show that this time around, although all 'hybrid' variants of the EBMT system fall short of the quality achieved by the baseline PBSMT system, merging elements of the marker-based and SMT data, as in (Groves & Way, 2005), to create a hybrid 'example-based SMT' system, outperforms the baseline SMT and EBMT systems from which it is derived. Furthermore, we provide further evidence in favour of hybrid systems by adding an SMT target language model to all EBMT system variants and demonstrate that this too has a positive e®ect on translation quality

Acquiring Legal Ontologies from Domain-specific Texts

The paper reports on methodology and preliminary results of a case study in automatically extracting ontological knowledge from Italian legislative texts in the environmental domain. We use a fully-implemented ontology learning system (T2K) that includes a battery of tools for Natural Language Processing (NLP), statistical text analysis and machine language learning. Tools are dynamically integrated to provide an incremental representation of the content of vast repositories of unstructured documents. Evaluated results, however preliminary, are very encouraging, showing the great potential of NLP-powered incremental systems like T2K for accurate large-scale semi?automatic extraction of legal ontologies

Message-Passing Protocols for Real-World Parsing -- An Object-Oriented Model and its Preliminary Evaluation

We argue for a performance-based design of natural language grammars and their associated parsers in order to meet the constraints imposed by real-world NLP. Our approach incorporates declarative and procedural knowledge about language and language use within an object-oriented specification framework. We discuss several message-passing protocols for parsing and provide reasons for sacrificing completeness of the parse in favor of efficiency based on a preliminary empirical evaluation.Comment: 12 pages, uses epsfig.st

A hybrid formalism to parse sign languages

International audienceSign Language (SL) linguistic is dependent on the expensive task of annotating. Some automation is already available for low-level information (eg. body part tracking) and the lexical level has shown significant progresses. The syntactic level lacks annotated corpora as well as complete and consistent models. This article presents a solution for the automatic annotation of SL syntactic elements. It exposes a formalism able to represent both constituency-based and dependency-based models. The first enable the representation the structures one may want to annotate, the second aims at fulfilling the holes of the first. A parser is presented and used to conduct two experiments on the solution. One experiment is on a real corpus, the other is on a synthetic corpus

Ontology learning from Italian legal texts

The paper reports on the methodology and preliminary results of a case study in automatically extracting ontological knowledge from Italian legislative texts. We use a fully-implemented ontology learning system (T2K) that includes a battery of tools for Natural Language Processing (NLP), statistical text analysis and machine language learning. Tools are dynamically integrated to provide an incremental representation of the content of vast repositories of unstructured documents. Evaluated results, however preliminary, show the great potential of NLP-powered incremental systems like T2K for accurate large-scale semi-automatic extraction of legal ontologies

Semantic Role Labeling for Knowledge Graph Extraction from Text

This paper introduces TakeFive, a new semantic role labeling method that transforms a text into a frame-oriented knowledge graph. It performs dependency parsing, identifies the words that evoke lexical frames, locates the roles and fillers for each frame, runs coercion techniques, and formalizes the results as a knowledge graph. This formal representation complies with the frame semantics used in Framester, a factual-linguistic linked data resource. We tested our method on the WSJ section of the Peen Treebank annotated with VerbNet and PropBank labels and on the Brown corpus. The evaluation has been performed according to the CoNLL Shared Task on Joint Parsing of Syntactic and Semantic Dependencies. The obtained precision, recall, and F1 values indicate that TakeFive is competitive with other existing methods such as SEMAFOR, Pikes, PathLSTM, and FRED. We finally discuss how to combine TakeFive and FRED, obtaining higher values of precision, recall, and F1 measure