Single Model for Organic and Inorganic Chemical Named Entity Recognition in ChemDataExtractor.
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SUBMITTER: Isazawa T
PROVIDER: S-EPMC9049593 | biostudies-literature | 2022 Mar
REPOSITORIES: biostudies-literature
Publications
Single Model for Organic and Inorganic Chemical Named Entity Recognition in ChemDataExtractor.
Isazawa Taketomo T Cole Jacqueline M JM
Journal of chemical information and modeling 20220224 5
Chemical Named Entity Recognition (NER) forms the basis of information extraction tasks in the chemical domain. However, while such tasks can involve multiple domains of chemistry at the same time, currently available named entity recognizers are specialized in one part of chemistry, resulting in such workflows failing for a biased subset of mentions. This paper presents a single model that performs at close to the state-of-the-art for <i>both</i> organic (CHEMDNER, 89.7 F1 score) and inorganic ...[more]
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Project description:MotivationChemical named entity recognition is used to automatically identify mentions to chemical compounds in text and is the basis for more elaborate information extraction. However, only a small number of applications are freely available to identify such mentions. Particularly challenging and useful is the identification of International Union of Pure and Applied Chemistry (IUPAC) chemical compounds, which due to the complex morphology of IUPAC names requires more advanced techniques than that of brand names.ResultsWe present CheNER, a tool for automated identification of systematic IUPAC chemical mentions. We evaluated different systems using an established literature corpus to show that CheNER has a superior performance in identifying IUPAC names specifically, and that it makes better use of computational resources.Availability and implementationhttp://metres.udl.cat/index.php/9-download/4-chener, http://chener.bioinfo.cnio.es/
| S-EPMC3967102 | biostudies-literature
Project description:SummaryBiomedical named entity recognition (NER) plays a crucial role in extracting information from documents in biomedical applications. However, many of these applications require NER models to operate at a document level, rather than just a sentence level. This presents a challenge, as the extension from a sentence model to a document model is not always straightforward. Despite the existence of document NER models that are able to make consistent predictions, they still fall short of meeting the expectations of researchers and practitioners in the field. To address this issue, we have undertaken an investigation into the underlying causes of inconsistent predictions. Our research has led us to believe that the use of adjectives and prepositions within entities may be contributing to low label consistency. In this article, we present our method, ConNER, to enhance a label consistency of modifiers such as adjectives and prepositions. By refining the labels of these modifiers, ConNER is able to improve representations of biomedical entities. The effectiveness of our method is demonstrated on four popular biomedical NER datasets. On three datasets, we achieve a higher F1 score than the previous state-of-the-art model. Our method shows its efficacy on two datasets, resulting in 7.5%-8.6% absolute improvements in the F1 score. Our findings suggest that our ConNER method is effective on datasets with intrinsically low label consistency. Through qualitative analysis, we demonstrate how our approach helps the NER model generate more consistent predictions.Availability and implementationOur code and resources are available at https://github.com/dmis-lab/ConNER/.
| S-EPMC10272703 | biostudies-literature
Project description:The dataset is constructed from the drone flight log messages extracted from publicly available drone image datasets provided by VTO Labs under the Drone Forensic Program. The entire process of building this dataset includes extraction, decryption, parsing, cleansing, unique filtering, annotation, splitting, and analysis. The resulting dataset is in CoNLL format, annotated using the IOB2 scheme with six entity types. The total number of log messages acquired from 12 DJI drone models is 1850. The data are split based on the drone models, resulting in 1412 messages for training and 438 messages for testing. The average length of log messages is 6.5 globally, 6.6 and 8.8 for the train and the test sets, respectively.
| S-EPMC10293979 | biostudies-literature
Project description:BackgroundThe development of robust methods for chemical named entity recognition, a challenging natural language processing task, was previously hindered by the lack of publicly available, large-scale, gold standard corpora. The recent public release of a large chemical entity-annotated corpus as a resource for the CHEMDNER track of the Fourth BioCreative Challenge Evaluation (BioCreative IV) workshop greatly alleviated this problem and allowed us to develop a conditional random fields-based chemical entity recogniser. In order to optimise its performance, we introduced customisations in various aspects of our solution. These include the selection of specialised pre-processing analytics, the incorporation of chemistry knowledge-rich features in the training and application of the statistical model, and the addition of post-processing rules.ResultsOur evaluation shows that optimal performance is obtained when our customisations are integrated into the chemical entity recogniser. When its performance is compared with that of state-of-the-art methods, under comparable experimental settings, our solution achieves competitive advantage. We also show that our recogniser that uses a model trained on the CHEMDNER corpus is suitable for recognising names in a wide range of corpora, consistently outperforming two popular chemical NER tools.ConclusionThe contributions resulting from this work are two-fold. Firstly, we present the details of a chemical entity recognition methodology that has demonstrated performance at a competitive, if not superior, level as that of state-of-the-art methods. Secondly, the developed suite of solutions has been made publicly available as a configurable workflow in the interoperable text mining workbench Argo. This allows interested users to conveniently apply and evaluate our solutions in the context of other chemical text mining tasks.
| S-EPMC4331696 | biostudies-literature
Project description:BackgroundDue to various factors such as the increasing aging of the population and the upgrading of people's health consumption needs, the demand group for rehabilitation medical care is expanding. Currently, China's rehabilitation medical care encounters several challenges, such as inadequate awareness and a scarcity of skilled professionals. Enhancing public awareness about rehabilitation and improving the quality of rehabilitation services are particularly crucial. Named entity recognition is an essential first step in information processing as it enables the automated extraction of rehabilitation medical entities. These entities play a crucial role in subsequent tasks, including information decision systems and the construction of medical knowledge graphs.MethodsIn order to accomplish this objective, we construct the BERT-Span model to complete the Chinese rehabilitation medicine named entity recognition task. First, we collect rehabilitation information from multiple sources to build a corpus in the field of rehabilitation medicine, and fine-tune Bidirectional Encoder Representation from Transformers (BERT) with the rehabilitation medicine corpus. For the rehabilitation medicine corpus, we use BERT to extract the feature vectors of rehabilitation medicine entities in the text, and use the span model to complete the annotation of rehabilitation medicine entities.ResultCompared to existing baseline models, our model achieved the highest F1 value for the named entity recognition task in the rehabilitation medicine corpus. The experimental results demonstrate that our method outperforms in recognizing both long medical entities and nested medical entities in rehabilitation medical texts.ConclusionThe BERT-Span model can effectively identify and extract entity knowledge in the field of rehabilitation medicine in China, which supports the construction of the knowledge graph of rehabilitation medicine and the development of the decision-making system of rehabilitation medicine.
| S-EPMC10495977 | biostudies-literature
Project description:BACKGROUND:Biomedical named-entity recognition (BioNER) is widely modeled with conditional random fields (CRF) by regarding it as a sequence labeling problem. The CRF-based methods yield structured outputs of labels by imposing connectivity between the labels. Recent studies for BioNER have reported state-of-the-art performance by combining deep learning-based models (e.g., bidirectional Long Short-Term Memory) and CRF. The deep learning-based models in the CRF-based methods are dedicated to estimating individual labels, whereas the relationships between connected labels are described as static numbers; thereby, it is not allowed to timely reflect the context in generating the most plausible label-label transitions for a given input sentence. Regardless, correctly segmenting entity mentions in biomedical texts is challenging because the biomedical terms are often descriptive and long compared with general terms. Therefore, limiting the label-label transitions as static numbers is a bottleneck in the performance improvement of BioNER. RESULTS:We introduce DTranNER, a novel CRF-based framework incorporating a deep learning-based label-label transition model into BioNER. DTranNER uses two separate deep learning-based networks: Unary-Network and Pairwise-Network. The former is to model the input for determining individual labels, and the latter is to explore the context of the input for describing the label-label transitions. We performed experiments on five benchmark BioNER corpora. Compared with current state-of-the-art methods, DTranNER achieves the best F1-score of 84.56% beyond 84.40% on the BioCreative II gene mention (BC2GM) corpus, the best F1-score of 91.99% beyond 91.41% on the BioCreative IV chemical and drug (BC4CHEMD) corpus, the best F1-score of 94.16% beyond 93.44% on the chemical NER, the best F1-score of 87.22% beyond 86.56% on the disease NER of the BioCreative V chemical disease relation (BC5CDR) corpus, and a near-best F1-score of 88.62% on the NCBI-Disease corpus. CONCLUSIONS:Our results indicate that the incorporation of the deep learning-based label-label transition model provides distinctive contextual clues to enhance BioNER over the static transition model. We demonstrate that the proposed framework enables the dynamic transition model to adaptively explore the contextual relations between adjacent labels in a fine-grained way. We expect that our study can be a stepping stone for further prosperity of biomedical literature mining.
| S-EPMC7014657 | biostudies-literature
Project description:MotivationApplication of chemical named entity recognition (CNER) algorithms allows retrieval of information from texts about chemical compound identifiers and creates associations with physical-chemical properties and biological activities. Scientific texts represent low-formalized sources of information. Most methods aimed at CNER are based on machine learning approaches, including conditional random fields and deep neural networks. In general, most machine learning approaches require either vector or sparse word representation of texts. Chemical named entities (CNEs) constitute only a small fraction of the whole text, and the datasets used for training are highly imbalanced.Methods and resultsWe propose a new method for extracting CNEs from texts based on the naïve Bayes classifier combined with specially developed filters. In contrast to the earlier developed CNER methods, our approach uses the representation of the data as a set of fragments of text (FoTs) with the subsequent preparati`on of a set of multi-n-grams (sequences from one to n symbols) for each FoT. Our approach may provide the recognition of novel CNEs. For CHEMDNER corpus, the values of the sensitivity (recall) was 0.95, precision was 0.74, specificity was 0.88, and balanced accuracy was 0.92 based on five-fold cross validation. We applied the developed algorithm to the extracted CNEs of potential Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) inhibitors. A set of CNEs corresponding to the chemical substances evaluated in the biochemical assays used for the discovery of Mpro inhibitors was retrieved. Manual analysis of the appropriate texts showed that CNEs of potential SARS-CoV-2 Mpro inhibitors were successfully identified by our method.ConclusionThe obtained results show that the proposed method can be used for filtering out words that are not related to CNEs; therefore, it can be successfully applied to the extraction of CNEs for the purposes of cheminformatics and medicinal chemistry.
| S-EPMC9375066 | biostudies-literature
Project description:MotivationAutomatic biomedical named entity recognition (BioNER) is a key task in biomedical information extraction. For some time, state-of-the-art BioNER has been dominated by machine learning methods, particularly conditional random fields (CRFs), with a recent focus on deep learning. However, recent work has suggested that the high performance of CRFs for BioNER may not generalize to corpora other than the one it was trained on. In our analysis, we find that a popular deep learning-based approach to BioNER, known as bidirectional long short-term memory network-conditional random field (BiLSTM-CRF), is correspondingly poor at generalizing. To address this, we evaluate three modifications of BiLSTM-CRF for BioNER to improve generalization: improved regularization via variational dropout, transfer learning and multi-task learning.ResultsWe measure the effect that each strategy has when training/testing on the same corpus ('in-corpus' performance) and when training on one corpus and evaluating on another ('out-of-corpus' performance), our measure of the model's ability to generalize. We found that variational dropout improves out-of-corpus performance by an average of 4.62%, transfer learning by 6.48% and multi-task learning by 8.42%. The maximal increase we identified combines multi-task learning and variational dropout, which boosts out-of-corpus performance by 10.75%. Furthermore, we make available a new open-source tool, called Saber that implements our best BioNER models.Availability and implementationSource code for our biomedical IE tool is available at https://github.com/BaderLab/saber. Corpora and other resources used in this study are available at https://github.com/BaderLab/Towards-reliable-BioNER.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6956779 | biostudies-literature
Project description:MotivationDictionary-based named entity recognition (NER) allows terms to be detected in a corpus and normalized to biomedical databases and ontologies. However, adaptation to different entity types requires new high-quality dictionaries and associated lists of blocked names for each type. The latter are so far created by identifying cases that cause many false positives through manual inspection of individual names, a process that scales poorly.ResultsIn this work, we aim to improve block list s by automatically identifying names to block, based on the context in which they appear. By comparing results of three well-established biomedical NER methods, we generated a dataset of over 12.5 million text spans where the methods agree on the boundaries and type of entity tagged. These were used to generate positive and negative examples of contexts for four entity types (genes, diseases, species, and chemicals), which were used to train a Transformer-based model (BioBERT) to perform entity type classification. Application of the best model (F1-score = 96.7%) allowed us to generate a list of problematic names that should be blocked. Introducing this into our system doubled the size of the previous list of corpus-wide blocked names. In addition, we generated a document-specific list that allows ambiguous names to be blocked in specific documents. These changes boosted text mining precision by ∼5.5% on average, and over 8.5% for chemical and 7.5% for gene names, positively affecting several biological databases utilizing this NER system, like the STRING database, with only a minor drop in recall (0.6%).Availability and implementationAll resources are available through Zenodo https://doi.org/10.5281/zenodo.11243139 and GitHub https://doi.org/10.5281/zenodo.10289360.
| S-EPMC11373323 | biostudies-literature
Project description:Research on specialized biological systems is often hampered by a lack of consistent terminology, especially across species. In bacterial Type IV secretion systems genes within one set of orthologs may have over a dozen different names. Classifying research publications based on biological processes, cellular components, molecular functions, and microorganism species should improve the precision and recall of literature searches allowing researchers to keep up with the exponentially growing literature, through resources such as the Pathosystems Resource Integration Center (PATRIC, patricbrc.org). We developed named entity recognition (NER) tools for four entities related to Type IV secretion systems: 1) bacteria names, 2) biological processes, 3) molecular functions, and 4) cellular components. These four entities are important to pathogenesis and virulence research but have received less attention than other entities, e.g., genes and proteins. Based on an annotated corpus, large domain terminological resources, and machine learning techniques, we developed recognizers for these entities. High accuracy rates (>80%) are achieved for bacteria, biological processes, and molecular function. Contrastive experiments highlighted the effectiveness of alternate recognition strategies; results of term extraction on contrasting document sets demonstrated the utility of these classes for identifying T4SS-related documents.
| S-EPMC3066171 | biostudies-literature