2,330 research outputs found
TriviaQA: A Large Scale Distantly Supervised Challenge Dataset for Reading Comprehension
We present TriviaQA, a challenging reading comprehension dataset containing
over 650K question-answer-evidence triples. TriviaQA includes 95K
question-answer pairs authored by trivia enthusiasts and independently gathered
evidence documents, six per question on average, that provide high quality
distant supervision for answering the questions. We show that, in comparison to
other recently introduced large-scale datasets, TriviaQA (1) has relatively
complex, compositional questions, (2) has considerable syntactic and lexical
variability between questions and corresponding answer-evidence sentences, and
(3) requires more cross sentence reasoning to find answers. We also present two
baseline algorithms: a feature-based classifier and a state-of-the-art neural
network, that performs well on SQuAD reading comprehension. Neither approach
comes close to human performance (23% and 40% vs. 80%), suggesting that
TriviaQA is a challenging testbed that is worth significant future study. Data
and code available at -- http://nlp.cs.washington.edu/triviaqa/Comment: Added references, fixed typos, minor baseline updat
Unsupervised Domain Adaptation on Reading Comprehension
Reading comprehension (RC) has been studied in a variety of datasets with the
boosted performance brought by deep neural networks. However, the
generalization capability of these models across different domains remains
unclear. To alleviate this issue, we are going to investigate unsupervised
domain adaptation on RC, wherein a model is trained on labeled source domain
and to be applied to the target domain with only unlabeled samples. We first
show that even with the powerful BERT contextual representation, the
performance is still unsatisfactory when the model trained on one dataset is
directly applied to another target dataset. To solve this, we provide a novel
conditional adversarial self-training method (CASe). Specifically, our approach
leverages a BERT model fine-tuned on the source dataset along with the
confidence filtering to generate reliable pseudo-labeled samples in the target
domain for self-training. On the other hand, it further reduces domain
distribution discrepancy through conditional adversarial learning across
domains. Extensive experiments show our approach achieves comparable accuracy
to supervised models on multiple large-scale benchmark datasets.Comment: 8 pages, 6 figures, 5 tables, Accepted by AAAI 202
Overview of BioCreative II gene mention recognition.
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions
BioRED: A Comprehensive Biomedical Relation Extraction Dataset
Automated relation extraction (RE) from biomedical literature is critical for
many downstream text mining applications in both research and real-world
settings. However, most existing benchmarking datasets for bio-medical RE only
focus on relations of a single type (e.g., protein-protein interactions) at the
sentence level, greatly limiting the development of RE systems in biomedicine.
In this work, we first review commonly used named entity recognition (NER) and
RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus
with multiple entity types (e.g., gene/protein, disease, chemical) and relation
pairs (e.g., gene-disease; chemical-chemical), on a set of 600 PubMed articles.
Further, we label each relation as describing either a novel finding or
previously known background knowledge, enabling automated algorithms to
differentiate between novel and background information. We assess the utility
of BioRED by benchmarking several existing state-of-the-art methods, including
BERT-based models, on the NER and RE tasks. Our results show that while
existing approaches can reach high performance on the NER task (F-score of
89.3%), there is much room for improvement for the RE task, especially when
extracting novel relations (F-score of 47.7%). Our experiments also demonstrate
that such a comprehensive dataset can successfully facilitate the development
of more accurate, efficient, and robust RE systems for biomedicine
Information Extraction from Text for Improving Research on Small Molecules and Histone Modifications
The cumulative number of publications, in particular in the life sciences, requires efficient methods for the automated extraction of information and semantic information retrieval. The recognition and identification of information-carrying units in text – concept denominations and named entities – relevant to a certain domain is a fundamental step. The focus of this thesis lies on the recognition of chemical entities and the new biological named entity type histone modifications, which are both important in the field of drug discovery. As the emergence of new research fields as well as the discovery and generation of novel entities goes along with the coinage of new terms, the perpetual adaptation of respective named entity recognition approaches to new domains is an important step for information extraction. Two methodologies have been investigated in this concern: the state-of-the-art machine learning method, Conditional Random Fields (CRF), and an approximate string search method based on dictionaries. Recognition methods that rely on dictionaries are strongly dependent on the availability of entity terminology collections as well as on its quality. In the case of chemical entities the terminology is distributed over more than 7 publicly available data sources. The join of entries and accompanied terminology from selected resources enables the generation of a new dictionary comprising chemical named entities. Combined with the automatic processing of respective terminology – the dictionary curation – the recognition performance reached an F1 measure of 0.54. That is an improvement by 29 % in comparison to the raw dictionary. The highest recall was achieved for the class of TRIVIAL-names with 0.79. The recognition and identification of chemical named entities provides a prerequisite for the extraction of related pharmacological relevant information from literature data. Therefore, lexico-syntactic patterns were defined that support the automated extraction of hypernymic phrases comprising pharmacological function terminology related to chemical compounds. It was shown that 29-50 % of the automatically extracted terms can be proposed for novel functional annotation of chemical entities provided by the reference database DrugBank. Furthermore, they are a basis for building up concept hierarchies and ontologies or for extending existing ones. Successively, the pharmacological function and biological activity concepts obtained from text were included into a novel descriptor for chemical compounds. Its successful application for the prediction of pharmacological function of molecules and the extension of chemical classification schemes, such as the the Anatomical Therapeutic Chemical (ATC), is demonstrated. In contrast to chemical entities, no comprehensive terminology resource has been available for histone modifications. Thus, histone modification concept terminology was primary recognized in text via CRFs with a F1 measure of 0.86. Subsequent, linguistic variants of extracted histone modification terms were mapped to standard representations that were organized into a newly assembled histone modification hierarchy. The mapping was accomplished by a novel developed term mapping approach described in the thesis. The combination of term recognition and term variant resolution builds up a new procedure for the assembly of novel terminology collections. It supports the generation of a term list that is applicable in dictionary-based methods. For the recognition of histone modification in text it could be shown that the named entity recognition method based on dictionaries is superior to the used machine learning approach. In conclusion, the present thesis provides techniques which enable an enhanced utilization of textual data, hence, supporting research in epigenomics and drug discovery
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