ymoslem/acl-abstracts huggingface dataset:
SYSTRAN @ WNGT 2019: DGT Task (2019)

This paper describes SYSTRAN participation to the Document-level Generation and Trans- lation (DGT) Shared Task of the 3rd Workshop on Neural Generation and Translation (WNGT 2019). We participate for the first time using a Transformer network enhanced with modified input embeddings and optimising an additional objective function that considers content selection. The network takes in structured data of basketball games and outputs a summary of the game in natural language.
University of Edinburgh`s submission to the Document-level Generation and Translation Shared Task (2019)

The University of Edinburgh participated in all six tracks: NLG, MT, and MT+NLG with both English and German as targeted languages. For the NLG track, we submitted a multilingual system based on the Content Selection and Planning model of Puduppully et al (2019). For the MT track, we submitted Transformer-based Neural Machine Translation models, where out-of-domain parallel data was augmented with in-domain data extracted from monolingual corpora. Our MT+NLG systems disregard the structured input data and instead rely exclusively on the source summaries.
Naver Labs Europe`s Systems for the Document-Level Generation and Translation Task at WNGT 2019 (2019)

Recently, neural models led to significant improvements in both machine translation (MT) and natural language generation tasks (NLG). However, generation of long descriptive summaries conditioned on structured data remains an open challenge. Likewise, MT that goes beyond sentence-level context is still an open issue (e.g., document-level MT or MT with metadata). To address these challenges, we propose to leverage data from both tasks and do transfer learning between MT, NLG, and MT with source-side metadata (MT+NLG). First, we train document-based MT systems with large amounts of parallel data. Then, we adapt these models to pure NLG and MT+NLG tasks by fine-tuning with smaller amounts of domain-specific data. This end-to-end NLG approach, without data selection and planning, outperforms the previous state of the art on the Rotowire NLG task. We participated to the {\textquotedblleft}Document Generation and Translation{\textquotedblright} task at WNGT 2019, and ranked first in all tracks.
From Research to Production and Back: Ludicrously Fast Neural Machine Translation (2019)

This paper describes the submissions of the {\textquotedblleft}Marian{\textquotedblright} team to the WNGT 2019 efficiency shared task. Taking our dominating submissions to the previous edition of the shared task as a starting point, we develop improved teacher-student training via multi-agent dual-learning and noisy backward-forward translation for Transformer-based student models. For efficient CPU-based decoding, we propose pre-packed 8-bit matrix products, improved batched decoding, cache-friendly student architectures with parameter sharing and light-weight RNN-based decoder architectures. GPU-based decoding benefits from the same architecture changes, from pervasive 16-bit inference and concurrent streams. These modifications together with profiler-based C++ code optimization allow us to push the Pareto frontier established during the 2018 edition towards 24x (CPU) and 14x (GPU) faster models at comparable or higher BLEU values. Our fastest CPU model is more than 4x faster than last year`s fastest submission at more than 3 points higher BLEU. Our fastest GPU model at 1.5 seconds translation time is slightly faster than last year`s fastest RNN-based submissions, but outperforms them by more than 4 BLEU and 10 BLEU points respectively.
Selecting, Planning, and Rewriting: A Modular Approach for Data-to-Document Generation and Translation (2019)

In this paper, we report our system submissions to all 6 tracks of the WNGT 2019 shared task on Document-Level Generation and Translation. The objective is to generate a textual document from either structured data: generation task, or a document in a different language: translation task. For the translation task, we focused on adapting a large scale system trained on WMT data by fine tuning it on the RotoWire data. For the generation task, we participated with two systems based on a selection and planning model followed by (a) a simple language model generation, and (b) a GPT-2 pre-trained language model approach. The selection and planning module chooses a subset of table records in order, and the language models produce text given such a subset.
Efficiency through Auto-Sizing: Notre Dame NLP`s Submission to the WNGT 2019 Efficiency Task (2019)

This paper describes the Notre Dame Natural Language Processing Group`s (NDNLP) submission to the WNGT 2019 shared task (Hayashi et al., 2019). We investigated the impact of auto-sizing (Murray and Chiang, 2015; Murray et al., 2019) to the Transformer network (Vaswani et al., 2017) with the goal of substantially reducing the number of parameters in the model. Our method was able to eliminate more than 25{\%} of the model`s parameters while suffering a decrease of only 1.1 BLEU.
PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track (2019)

One of the biomedical entity types of relevance for medicine or biosciences are chemical compounds and drugs. The correct detection these entities is critical for other text mining applications building on them, such as adverse drug-reaction detection, medication-related fake news or drug-target extraction. Although a significant effort was made to detect mentions of drugs/chemicals in English texts, so far only very limited attempts were made to recognize them in medical documents in other languages. Taking into account the growing amount of medical publications and clinical records written in Spanish, we have organized the first shared task on detecting drug and chemical entities in Spanish medical documents. Additionally, we included a clinical concept-indexing sub-track asking teams to return SNOMED-CT identifiers related to drugs/chemicals for a collection of documents. For this task, named PharmaCoNER, we generated annotation guidelines together with a corpus of 1,000 manually annotated clinical case studies. A total of 22 teams participated in the sub-track 1, (77 system runs), and 7 teams in the sub-track 2 (19 system runs). Top scoring teams used sophisticated deep learning approaches yielding very competitive results with F-measures above 0.91. These results indicate that there is a real interest in promoting biomedical text mining efforts beyond English. We foresee that the PharmaCoNER annotation guidelines, corpus and participant systems will foster the development of new resources for clinical and biomedical text mining systems of Spanish medical data.
When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in Spanish (2019)

The recognition of pharmacological substances, compounds and proteins is an essential preliminary work for the recognition of relations between chemicals and other biomedically relevant units. In this paper, we describe an approach to Task 1 of the PharmaCoNER Challenge, which involves the recognition of mentions of chemicals and drugs in Spanish medical texts. We train a state-of-the-art BiLSTM-CRF sequence tagger with stacked Pooled Contextualized Embeddings, word and sub-word embeddings using the open-source framework FLAIR. We present a new corpus composed of articles and papers from Spanish health science journals, termed the Spanish Health Corpus, and use it to train domain-specific embeddings which we incorporate in our model training. We achieve a result of 89.76{\%} F1-score using pre-trained embeddings and are able to improve these results to 90.52{\%} F1-score using specialized embeddings.
VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases (2019)

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.
IxaMed at PharmacoNER Challenge 2019 (2019)

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.
NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection (2019)

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.
A Deep Learning-Based System for PharmaCoNER (2019)

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.
Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text (2019)

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.
A Neural Pipeline Approach for the PharmaCoNER Shared Task using Contextual Exhaustive Models (2019)

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).
Biomedical Named Entity Recognition with Multilingual BERT (2019)

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: \url{https://github.com/chaanim/pharmaconer}
An Overview of the Active Gene Annotation Corpus and the BioNLP OST 2019 AGAC Track Tasks (2019)

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 {\textquotedblleft}imbalanced data{\textquotedblright}, {\textquotedblleft}selective annotation{\textquotedblright} and {\textquotedblleft}latent topic annotation{\textquotedblright}.
Trigger Word Detection and Thematic Role Identification via BERT and Multitask Learning (2019)

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.
DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature (2019)

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.
Biomedical relation extraction with pre-trained language representations and minimal task-specific architecture (2019)

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 {\textquotedblleft}gene - function change - disease{\textquotedblright} triples, where {\textquotedblleft}gene{\textquotedblright} and {\textquotedblleft}disease{\textquotedblright} are mentions of particular genes and diseases respectively and {\textquotedblleft}function change{\textquotedblright} 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 {\textquoteleft}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.
RACAI`s System at PharmaCoNER 2019 (2019)

This paper describes the Named Entity Recognition system of the Institute for Artificial Intelligence {\textquotedblleft}Mihai Dr{\u{a}}g{\u{a}}nescu{\textquotedblright} 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.
Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task (2019)

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.
A Multi-Task Learning Framework for Extracting Bacteria Biotope Information (2019)

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.
YNU-junyi in BioNLP-OST 2019: Using CNN-LSTM Model with Embeddings for SeeDev Binary Event Extraction (2019)

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.
Using Snomed to recognize and index chemical and drug mentions. (2019)

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.