yuz9yuz/NLPImpact huggingface dataset:
Title: VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: This paper presents the participation of the VSP team for the PharmaCoNER Tracks from the BioNLP Open Shared Task 2019. The system consists of a neural model for the Named Entity Recognition of drugs, medications and chemical entities in Spanish and the use of the Spanish Edition of SNOMED CT term search engine for the concept normalization of the recognized mentions. The neural network is implemented with two bidirectional Recurrent Neural Networks with LSTM cells that creates a feature vector for each word of the sentences in order to classify the entities. The first layer uses the characters of each word and the resulting vector is aggregated to the second layer together with its word embedding in order to create the feature vector of the word. Besides, a Conditional Random Field layer classifies the vector representation of each word in one of the mention types. The system obtains a performance of 76.29%, and 60.34% in F1 for the classification of the Named Entity Recognition task and the Concept indexing task, respectively. This method presents good results with a basic approach without using pretrained word embeddings or any hand-crafted features.
Title: IxaMed at PharmacoNER Challenge 2019
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: The aim of this paper is to present our approach (IxaMed) in the PharmacoNER 2019 task. The task consists of identifying chemical, drug, and gene/protein mentions from clinical case studies written in Spanish. The evaluation of the task is divided in two scenarios: one corresponding to the detection of named entities and one corresponding to the indexation of named entities that have been previously identified. In order to identify named entities we have made use of a Bi-LSTM with a CRF on top in combination with different types of word embeddings. We have achieved our best result (86.81 F-Score) combining pretrained word embeddings of Wikipedia and Electronic Health Records (50M words) with contextual string embeddings of Wikipedia and Electronic Health Records. On the other hand, for the indexation of the named entities we have used the Levenshtein distance obtaining a 85.34 F-Score as our best result.
Title: NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection
Venue: EMNLP (2019)
Topic: information extraction
Abstract: Named entity recognition has been extensively studied on English news texts. However, the transfer to other domains and languages is still a challenging problem. In this paper, we describe the system with which we participated in the first subtrack of the PharmaCoNER competition of the BioNLP Open Shared Tasks 2019. Aiming at pharmacological entity detection in Spanish texts, the task provides a non-standard domain and language setting. However, we propose an architecture that requires neither language nor domain expertise. We treat the task as a sequence labeling task and experiment with attention-based embedding selection and the training on automatically annotated data to further improve our system’s performance. Our system achieves promising results, especially by combining the different techniques, and reaches up to 88.6% F1 in the competition.
Title: A Deep Learning-Based System for PharmaCoNER
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: The Biological Text Mining Unit at BSC and CNIO organized the first shared task on chemical & drug mention recognition from Spanish medical texts called PharmaCoNER (Pharmacological Substances, Compounds and proteins and Named Entity Recognition track) in 2019, which includes two tracks: one for NER offset and entity classification (track 1) and the other one for concept indexing (track 2). We developed a pipeline system based on deep learning methods for this shared task, specifically, a subsystem based on BERT (Bidirectional Encoder Representations from Transformers) for NER offset and entity classification and a subsystem based on Bpool (Bi-LSTM with max/mean pooling) for concept indexing. Evaluation conducted on the shared task data showed that our system achieves a micro-average F1-score of 0.9105 on track 1 and a micro-average F1-score of 0.8391 on track 2.
Title: Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text
Venue: EMNLP (2019)
Topic: information extraction
Abstract: In this work, we introduce a Deep Learning architecture for pharmaceutical and chemical Named Entity Recognition in Spanish clinical cases texts. We propose a hybrid model approach based on two Bidirectional Long Short-Term Memory (Bi-LSTM) network and Conditional Random Field (CRF) network using character, word, concept and sense embeddings to deal with the extraction of semantic, syntactic and morphological features. The approach was evaluated on the PharmaCoNER Corpus obtaining an F-measure of 85.24% for subtask 1 and 49.36% for subtask2. These results prove that deep learning methods with specific domain embedding representations can outperform the state-of-the-art approaches.
Title: A Neural Pipeline Approach for the PharmaCoNER Shared Task using Contextual Exhaustive Models
Venue: EMNLP (2019)
Topic: information extraction
Abstract: We present a neural pipeline approach that performs named entity recognition (NER) and concept indexing (CI), which links them to concept unique identifiers (CUIs) in a knowledge base, for the PharmaCoNER shared task on pharmaceutical drugs and chemical entities. We proposed a neural NER model that captures the surrounding semantic information of a given sequence by capturing the forward- and backward-context of bidirectional LSTM (Bi-LSTM) output of a target span using contextual span representation-based exhaustive approach. The NER model enumerates all possible spans as potential entity mentions and classify them into entity types or no entity with deep neural networks. For representing span, we compare several different neural network architectures and their ensembling for the NER model. We then perform dictionary matching for CI and, if there is no matching, we further compute similarity scores between a mention and CUIs using entity embeddings to assign the CUI with the highest score to the mention. We evaluate our approach on the two sub-tasks in the shared task. Among the five submitted runs, the best run for each sub-task achieved the F-score of 86.76% on Sub-task 1 (NER) and the F-score of 79.97% (strict) on Sub-task 2 (CI).
Title: Biomedical Named Entity Recognition with Multilingual BERT
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: We present the approach of the Turku NLP group to the PharmaCoNER task on Spanish biomedical named entity recognition. We apply a CRF-based baseline approach and multilingual BERT to the task, achieving an F-score of 88% on the development data and 87% on the test set with BERT. Our approach reflects a straightforward application of a state-of-the-art multilingual model that is not specifically tailored to either the language nor the application domain. The source code is available at: https://github.com/chaanim/pharmaconer
Title: An Overview of the Active Gene Annotation Corpus and the BioNLP OST 2019 AGAC Track Tasks
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: The active gene annotation corpus (AGAC) was developed to support knowledge discovery for drug repurposing. Based on the corpus, the AGAC track of the BioNLP Open Shared Tasks 2019 was organized, to facilitate cross-disciplinary collaboration across BioNLP and Pharmacoinformatics communities, for drug repurposing. The AGAC track consists of three subtasks: 1) named entity recognition, 2) thematic relation extraction, and 3) loss of function (LOF) / gain of function (GOF) topic classification. The AGAC track was participated by five teams, of which the performance are compared and analyzed. The the results revealed a substantial room for improvement in the design of the task, which we analyzed in terms of “imbalanced data”, “selective annotation” and “latent topic annotation”.
Title: Trigger Word Detection and Thematic Role Identification via BERT and Multitask Learning
Venue: EMNLP (2019)
Topic: information extraction
Abstract: The prediction of the relationship between the disease with genes and its mutations is a very important knowledge extraction task that can potentially help drug discovery. In this paper, we present our approaches for trigger word detection (task 1) and the identification of its thematic role (task 2) in AGAC track of BioNLP Open Shared Task 2019. Task 1 can be regarded as the traditional name entity recognition (NER), which cultivates molecular phenomena related to gene mutation. Task 2 can be regarded as relation extraction which captures the thematic roles between entities. For two tasks, we exploit the pre-trained biomedical language representation model (i.e., BERT) in the pipe of information extraction for the collection of mutation-disease knowledge from PubMed. And also, we design a fine-tuning technique and extra features by using multi-task learning. The experiment results show that our proposed approaches achieve 0.60 (ranks 1) and 0.25 (ranks 2) on task 1 and task 2 respectively in terms of F_1 metric.
Title: DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: Understanding the pathogenesis of genetic diseases through different gene activities and their relations to relevant diseases is important for new drug discovery and drug repositioning. In this paper, we present a joint deep learning model in a multi-task learning paradigm for gene mutation-disease knowledge extraction, DeepGeneMD, which adapts the state-of-the-art hierarchical multi-task learning framework for joint inference on named entity recognition (NER) and relation extraction (RE) in the context of the AGAC (Active Gene Annotation Corpus) track at 2019 BioNLP Open Shared Tasks (BioNLP-OST). It simultaneously extracts gene mutation related activities, diseases, and their relations from the published scientific literature. In DeepGeneMD, we explore the task decomposition to create auxiliary subtasks so that more interactions between different learning subtasks can be leveraged in model training. Our model achieves the average F1 score of 0.45 on recognizing gene activities and disease entities, ranking 2nd in the AGAC NER task; and the average F1 score of 0.35 on extracting relations, ranking 1st in the AGAC RE task.
Title: Biomedical relation extraction with pre-trained language representations and minimal task-specific architecture
Venue: EMNLP (2019)
Topic: information extraction
Abstract: This paper presents our participation in the AGAC Track from the 2019 BioNLP Open Shared Tasks. We provide a solution for Task 3, which aims to extract “gene - function change - disease” triples, where “gene” and “disease” are mentions of particular genes and diseases respectively and “function change” is one of four pre-defined relationship types. Our system extends BERT (Devlin et al., 2018), a state-of-the-art language model, which learns contextual language representations from a large unlabelled corpus and whose parameters can be fine-tuned to solve specific tasks with minimal additional architecture. We encode the pair of mentions and their textual context as two consecutive sequences in BERT, separated by a special symbol. We then use a single linear layer to classify their relationship into five classes (four pre-defined, as well as ‘no relation’). Despite considerable class imbalance, our system significantly outperforms a random baseline while relying on an extremely simple setup with no specially engineered features.
Title: RACAI’s System at PharmaCoNER 2019
Venue: EMNLP (2019)
Topic: information extraction
Abstract: This paper describes the Named Entity Recognition system of the Institute for Artificial Intelligence “Mihai Drăgănescu” of the Romanian Academy (RACAI for short). Our best F1 score of 0.84984 was achieved using an ensemble of two systems: a gazetteer-based baseline and a RNN-based NER system, developed specially for PharmaCoNER 2019. We will describe the individual systems and the ensemble algorithm, compare the final system to the current state of the art, as well as discuss our results with respect to the quality of the training data and its annotation strategy. The resulting NER system is language independent, provided that language-dependent resources and preprocessing tools exist, such as tokenizers and POS taggers.
Title: Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: To date, a large amount of biomedical content has been published in non-English texts, especially for clinical documents. Therefore, it is of considerable significance to conduct Natural Language Processing (NLP) research in non-English literature. PharmaCoNER is the first Named Entity Recognition (NER) task to recognize chemical and protein entities from Spanish biomedical texts. Since there have been abundant resources in the NLP field, how to exploit these existing resources to a new task to obtain competitive performance is a meaningful study. Inspired by the success of transfer learning with language models, we introduce the BERT benchmark to facilitate the research of PharmaCoNER task. In this paper, we evaluate two baselines based on Multilingual BERT and BioBERT on the PharmaCoNER corpus. Experimental results show that transferring the knowledge learned from source large-scale datasets to the target domain offers an effective solution for the PharmaCoNER task.
Title: A Multi-Task Learning Framework for Extracting Bacteria Biotope Information
Venue: EMNLP (2019)
Topic: information extraction
Abstract: This paper presents a novel transfer multi-task learning method for Bacteria Biotope rel+ner task at BioNLP-OST 2019. To alleviate the data deficiency problem in domain-specific information extraction, we use BERT(Bidirectional Encoder Representations from Transformers) and pre-train it using mask language models and next sentence prediction on both general corpus and medical corpus like PubMed. In fine-tuning stage, we fine-tune the relation extraction layer and mention recognition layer designed by us on the top of BERT to extract mentions and relations simultaneously. The evaluation results show that our method achieves the best performance on all metrics (including slot error rate, precision and recall) in the Bacteria Biotope rel+ner subtask.
Title: YNU-junyi in BioNLP-OST 2019: Using CNN-LSTM Model with Embeddings for SeeDev Binary Event Extraction
Venue: EMNLP (2019)
Topic: information extraction
Abstract: We participated in the BioNLP 2019 Open Shared Tasks: binary relation extraction of SeeDev task. The model was constructed us- ing convolutional neural networks (CNN) and long short term memory networks (LSTM). The full text information and context information were collected using the advantages of CNN and LSTM. The model consisted of two main modules: distributed semantic representation construction, such as word embedding, distance embedding and entity type embed- ding; and CNN-LSTM model. The F1 value of our participated task on the test data set of all types was 0.342. We achieved the second highest in the task. The results showed that our proposed method performed effectively in the binary relation extraction.
Title: Using Snomed to recognize and index chemical and drug mentions.
Venue: EMNLP (2019)
Topic: syntax: tagging, chunking and parsing
Abstract: In this paper we describe a new named entity extraction system. Our work proposes a system for the identification and annotation of drug names in Spanish biomedical texts based on machine learning and deep learning models. Subsequently, a standardized code using Snomed is assigned to these drugs, for this purpose, Natural Language Processing tools and techniques have been used, and a dictionary of different sources of information has been built. The results are promising, we obtain 78% in F1 score on the first sub-track and in the second task we map with Snomed correctly 72% of the found entities.
Title: Bacteria Biotope at BioNLP Open Shared Tasks 2019
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: This paper presents the fourth edition of the Bacteria Biotope task at BioNLP Open Shared Tasks 2019. The task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts, and the characterization of these entities with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on biodiversity for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, and the challenge organization. We also provide an analysis of the results obtained by participants, and inspect the evolution of the results since the last edition in 2016.
Title: Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019
Venue: EMNLP (2019)
Topic: information extraction
Abstract: Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity Recognition including nested entities extraction, Entity Normalization and Relation Extraction. Our proposed approach of Named Entities can be generalized to different languages and we have shown it’s effectiveness for English and Spanish text. We investigated linguistic features, hybrid loss including ranking and Conditional Random Fields (CRF), multi-task objective and token level ensembling strategy to improve NER. We employed dictionary based fuzzy and semantic search to perform Entity Normalization. Finally, our RE system employed Support Vector Machine (SVM) with linguistic features. Our NER submission (team:MIC-CIS) ranked first in BB-2019 norm+NER task with standard error rate (SER) of 0.7159 and showed competitive performance on PharmaCo NER task with F1-score of 0.8662. Our RE system ranked first in the SeeDev-binary Relation Extraction Task with F1-score of 0.3738.
Title: An ensemble CNN method for biomedical entity normalization
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: Different representations of the same concept could often be seen in scientific reports and publications. Entity normalization (or entity linking) is the task to match the different representations to their standard concepts. In this paper, we present a two-step ensemble CNN method that normalizes microbiology-related entities in free text to concepts in standard dictionaries. The method is capable of linking entities when only a small microbiology-related biomedical corpus is available for training, and achieved reasonable performance in the online test of the BioNLP-OST19 shared task Bacteria Biotope.
Title: BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes
Venue: EMNLP (2019)
Topic: nlp applications
Abstract: This paper presents our participation to the Bacteria Biotope Task of the BioNLP Shared Task 2019. Our participation includes two systems for the two subtasks of the Bacteria Biotope Task: the normalization of entities (BB-norm) and the identification of the relations between the entities given a biomedical text (BB-rel). For the normalization of entities, we utilized word embeddings and syntactic re-ranking. For the relation extraction task, pre-defined rules are used. Although both approaches are unsupervised, in the sense that they do not need any labeled data, they achieved promising results. Especially, for the BB-norm task, the results have shown that the proposed method performs as good as deep learning based methods, which require labeled data.
Title: Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs
Venue: EMNLP (2019)
Topic: information extraction
Abstract: abstract In this article, we describe our approach for the Bacteria Biotopes relation extraction (BB-rel) subtask in the BioNLP Shared Task 2019. This task aims to promote the development of text mining systems that extract relationships between Microorganism, Habitat and Phenotype entities. In this paper, we propose a novel approach for dependency graph construction based on lexical chains, so one dependency graph can represent one or multiple sentences. After that, we propose a neural network model which consists of the bidirectional long short-term memories and an attention graph convolution neural network to learn relation extraction features from the graph. Our approach is able to extract both intra- and inter-sentence relations, and meanwhile utilize syntax information. The results show that our approach achieved the best F1 (66.3%) in the official evaluation participated by 7 teams.
Title: Integration of Deep Learning and Traditional Machine Learning for Knowledge Extraction from Biomedical Literature
Venue: EMNLP (2019)
Topic: information extraction
Abstract: In this paper, we present our participation in the Bacteria Biotope (BB) task at BioNLP-OST 2019. Our system utilizes fine-tuned language representation models and machine learning approaches based on word embedding and lexical features for entities recognition, normalization and relation extraction. It achieves the state-of-the-art performance and is among the top two systems in five of all six subtasks.
Title: CRAFT Shared Tasks 2019 Overview — Integrated Structure, Semantics, and Coreference
Venue: EMNLP (2019)
Topic: discourse and pragmatics
Abstract: As part of the BioNLP Open Shared Tasks 2019, the CRAFT Shared Tasks 2019 provides a platform to gauge the state of the art for three fundamental language processing tasks — dependency parse construction, coreference resolution, and ontology concept identification — over full-text biomedical articles. The structural annotation task requires the automatic generation of dependency parses for each sentence of an article given only the article text. The coreference resolution task focuses on linking coreferring base noun phrase mentions into chains using the symmetrical and transitive identity relation. The ontology concept annotation task involves the identification of concept mentions within text using the classes of ten distinct ontologies in the biomedical domain, both unmodified and augmented with extension classes. This paper provides an overview of each task, including descriptions of the data provided to participants and the evaluation metrics used, and discusses participant results relative to baseline performances for each of the three tasks.
Title: UZH@CRAFT-ST: a Sequence-labeling Approach to Concept Recognition
Venue: EMNLP (2019)
Topic: information extraction
Abstract: As our submission to the CRAFT shared task 2019, we present two neural approaches to concept recognition. We propose two different systems for joint named entity recognition (NER) and normalization (NEN), both of which model the task as a sequence labeling problem. Our first system is a BiLSTM network with two separate outputs for NER and NEN trained from scratch, whereas the second system is an instance of BioBERT fine-tuned on the concept-recognition task. We exploit two strategies for extending concept coverage, ontology pretraining and backoff with a dictionary lookup. Our results show that the backoff strategy effectively tackles the problem of unseen concepts, addressing a major limitation of the chosen design. In the cross-system comparison, BioBERT proves to be a strong basis for creating a concept-recognition system, although some entity types are predicted more accurately by the BiLSTM-based system.