Spanish named entity recognition in the biomedical domain

Named Entity Recognition in the clinical domain and in languages different from English has the difficulty of the absence of complete dictionaries, the informality of texts, the polysemy of terms, the lack of accordance in the boundaries of an entity, the scarcity of corpora and of other resources available. We present a Named Entity Recognition method for poorly resourced languages. The method was tested with Spanish radiology reports and compared with a conditional random fields system.Peer ReviewedPostprint (author's final draft

Synapse at CAp 2017 NER challenge: Fasttext CRF

We present our system for the CAp 2017 NER challenge which is about named entity recognition on French tweets. Our system leverages unsupervised learning on a larger dataset of French tweets to learn features feeding a CRF model. It was ranked first without using any gazetteer or structured external data, with an F-measure of 58.89\%. To the best of our knowledge, it is the first system to use fasttext embeddings (which include subword representations) and an embedding-based sentence representation for NER

Efficient Multi-Template Learning for Structured Prediction

Conditional random field (CRF) and Structural Support Vector Machine (Structural SVM) are two state-of-the-art methods for structured prediction which captures the interdependencies among output variables. The success of these methods is attributed to the fact that their discriminative models are able to account for overlapping features on the whole input observations. These features are usually generated by applying a given set of templates on labeled data, but improper templates may lead to degraded performance. To alleviate this issue, in this paper, we propose a novel multiple template learning paradigm to learn structured prediction and the importance of each template simultaneously, so that hundreds of arbitrary templates could be added into the learning model without caution. This paradigm can be formulated as a special multiple kernel learning problem with exponential number of constraints. Then we introduce an efficient cutting plane algorithm to solve this problem in the primal, and its convergence is presented. We also evaluate the proposed learning paradigm on two widely-studied structured prediction tasks, \emph{i.e.} sequence labeling and dependency parsing. Extensive experimental results show that the proposed method outperforms CRFs and Structural SVMs due to exploiting the importance of each template. Our complexity analysis and empirical results also show that our proposed method is more efficient than OnlineMKL on very sparse and high-dimensional data. We further extend this paradigm for structured prediction using generalized $p$-block norm regularization with $p>1$, and experiments show competitive performances when $p \in [1,2)$

Information Extraction in Illicit Domains

Extracting useful entities and attribute values from illicit domains such as human trafficking is a challenging problem with the potential for widespread social impact. Such domains employ atypical language models, have `long tails' and suffer from the problem of concept drift. In this paper, we propose a lightweight, feature-agnostic Information Extraction (IE) paradigm specifically designed for such domains. Our approach uses raw, unlabeled text from an initial corpus, and a few (12-120) seed annotations per domain-specific attribute, to learn robust IE models for unobserved pages and websites. Empirically, we demonstrate that our approach can outperform feature-centric Conditional Random Field baselines by over 18\% F-Measure on five annotated sets of real-world human trafficking datasets in both low-supervision and high-supervision settings. We also show that our approach is demonstrably robust to concept drift, and can be efficiently bootstrapped even in a serial computing environment.Comment: 10 pages, ACM WWW 201

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Motivation: The recognition and normalization of cell line names in text is an important task in biomedical text mining research, facilitating for instance the identification of synthetically lethal genes from the literature. While several tools have previously been developed to address cell line recognition, it is unclear whether available systems can perform sufficiently well in realistic and broad-coverage applications such as extracting synthetically lethal genes from the cancer literature. In this study, we revisit the cell line name recognition task, evaluating both available systems and newly introduced methods on various resources to obtain a reliable tagger not tied to any specific subdomain. In support of this task, we introduce two text collections manually annotated for cell line names: the broad-coverage corpus Gellus and CLL, a focused target domain corpus. Results: We find that the best performance is achieved using NERsuite, a machine learning system based on Conditional Random Fields, trained on the Gellus corpus and supported with a dictionary of cell line names. The system achieves an F-score of 88.46% on the test set of Gellus and 85.98% on the independently annotated CLL corpus. It was further applied at large scale to 24 302 102 unannotated articles, resulting in the identification of 5 181 342 cell line mentions, normalized to 11 755 unique cell line database identifiers

Challenges and solutions for Latin named entity recognition

Although spanning thousands of years and genres as diverse as liturgy, historiography, lyric and other forms of prose and poetry, the body of Latin texts is still relatively sparse compared to English. Data sparsity in Latin presents a number of challenges for traditional Named Entity Recognition techniques. Solving such challenges and enabling reliable Named Entity Recognition in Latin texts can facilitate many down-stream applications, from machine translation to digital historiography, enabling Classicists, historians, and archaeologists for instance, to track the relationships of historical persons, places, and groups on a large scale. This paper presents the first annotated corpus for evaluating Named Entity Recognition in Latin, as well as a fully supervised model that achieves over 90% F-score on a held-out test set, significantly outperforming a competitive baseline. We also present a novel active learning strategy that predicts how many and which sentences need to be annotated for named entities in order to attain a specified degree of accuracy when recognizing named entities automatically in a given text. This maximizes the productivity of annotators while simultaneously controlling quality

Efficient Learning of Sparse Conditional Random Fields for Supervised Sequence Labelling

Conditional Random Fields (CRFs) constitute a popular and efficient approach for supervised sequence labelling. CRFs can cope with large description spaces and can integrate some form of structural dependency between labels. In this contribution, we address the issue of efficient feature selection for CRFs based on imposing sparsity through an L1 penalty. We first show how sparsity of the parameter set can be exploited to significantly speed up training and labelling. We then introduce coordinate descent parameter update schemes for CRFs with L1 regularization. We finally provide some empirical comparisons of the proposed approach with state-of-the-art CRF training strategies. In particular, it is shown that the proposed approach is able to take profit of the sparsity to speed up processing and hence potentially handle larger dimensional models