Objective: Today's neural machine translation (NMT) can achieve near human-level translation quality and greatly facilitates international communications, but the lack of parallel corpora poses a key problem to the development of translation systems for highly specialized domains, such as biomedicine. This work presents an unsupervised algorithm for deriving parallel corpora from document-level translations by using sentence alignment and explores how training materials affect the performance of biomedical NMT systems. Materials and Methods: Document-level translations are mixed to train bilingual word embeddings (BWEs) for the evaluation of cross-lingual word similarity, and sentence distance is defined by combining semantic and positional similarities of the sentences. The alignment of sentences is formulated as an extended earth mover's distance problem. A Chinese-English biomedical parallel corpus is derived with the proposed algorithm using bilingual articles from UpToDate and translations of PubMed abstracts, which is then used for the training and evaluation of NMT. Results: On two manually aligned translation datasets, the proposed algorithm achieved accurate sentence alignment in the 1-to-1 cases and outperformed competing algorithms in the many-to-many cases. The NMT model fine-tuned on biomedical data significantly improved the in-domain translation quality (zh-en: +17.72 BLEU; en-zh: +17.02 BLEU). Both the size of the training data and the combination of different corpora can significantly affect the model's performance. Conclusion: The proposed algorithm relaxes the assumption for sentence alignment and effectively generates accurate translation pairs that facilitate training high quality biomedical NMT models.
Neural machine translation (NMT) has arguably achieved human level parity when trained and evaluated at the sentence-level. Document-level neural machine translation has received less attention and lags behind its sentence-level counterpart. The majority of the proposed document-level approaches investigate ways of conditioning the model on several source or target sentences to capture document context. These approaches require training a specialized NMT model from scratch on parallel document-level corpora. We propose an approach that doesn't require training a specialized model on parallel d…
Document-level machine translation incorporates inter-sentential dependencies into the translation of a source sentence. In this paper, we propose a new framework to model cross-sentence dependencies by training neural machine translation (NMT) to predict both the target translation and surrounding sentences of a source sentence. By enforcing the NMT model to predict source context, we want the model to learn "contextualized" source sentence representations that capture document-level dependencies on the source side. We further propose two different methods to learn and integrate such contextu…
Enhancing Document-level Translation of Large Language Model via Translation Mixed-instructions
The Key Laboratory of Linguistic and Cultural Computing of Ministry of Education（教育部语言与文化计算重点实验室）；Institute of Artificial Intelligence（人工智能研究所）；Northwest Minzu University（西北民族大学）；Soochow University（苏州大学）
National Laboratory of Pattern Recognition, Institute of Automation, CAS（中国科学院自动化研究所模式识别国家重点实验室）；School of Artificial Intelligence, University of Chinese Academy of Sciences（中国科学院大学人工智能学院）；Beijing Academy of Artificial Intelligence（北京人工智能研究院）；CAS Center for Excellence in Brain Science and Intelligence Technology（中国科学院脑科学与智能技术卓越创新中心）
Document-level neural machine translation has yielded attractive improvements. However, majority of existing methods roughly use all context sentences in a fixed scope. They neglect the fact that different source sentences need different sizes of context. To address this problem, we propose an effective approach to select dynamic context so that the document-level translation model can utilize the more useful selected context sentences to produce better translations. Specifically, we introduce a selection module that is independent of the translation module to score each candidate context sent…
Recovering document annotations for sentence-level bitext
Johns Hopkins University（约翰斯·霍普金斯大学）；Human Language Technology Center of Excellence（卓越人类语言技术中心）；Center of Language and Speech Processing（语言与言语处理中心）；Microsoft（微软公司）
Charles University（查理大学）；Faculty of Mathematics and Physics（数学与物理学院）；Institute of Formal and Applied Linguistics（形式与应用语言学研究所）
We describe our NMT systems submitted to the WMT19 shared task in English-Czech news translation. Our systems are based on the Transformer model implemented in either Tensor2Tensor (T2T) or Marian framework. We aimed at improving the adequacy and coherence of translated documents by enlarging the context of the source and target. Instead of translating each sentence independently, we split the document into possibly overlapping multi-sentence segments. In case of the T2T implementation, this "document-level"-trained system achieves a $+0.6$ BLEU improvement ($p<0.05$) relative to the same syst…
Universidade Federal do Rio Grande do Sul（南里奥格兰德联邦大学）；Barcelona Supercomputing Center（巴塞罗那超级计算中心）
The BVS database (Health Virtual Library) is a centralized source of biomedical information for Latin America and Carib, created in 1998 and coordinated by BIREME (Biblioteca Regional de Medicina) in agreement with the Pan American Health Organization (OPAS). Abstracts are available in English, Spanish, and Portuguese, with a subset in more than one language, thus being a possible source of parallel corpora. In this article, we present the development of parallel corpora from BVS in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algor…
Multilingual Contextualization of Large Language Models for Document-Level Machine Translation
Instituto Superior Técnico, Universidade de Lisboa (ELLIS Unit Lisbon)（里斯本大学理工学院（ELLIS单位里斯本））；Instituto de Telecomunicações（电信研究所）；Carnegie Mellon University（卡内基梅隆大学）；Unbabel
University of Zurich（苏黎世大学）；University of Edinburgh（爱丁堡大学）
Recent research suggests that neural machine translation achieves parity with professional human translation on the WMT Chinese--English news translation task. We empirically test this claim with alternative evaluation protocols, contrasting the evaluation of single sentences and entire documents. In a pairwise ranking experiment, human raters assessing adequacy and fluency show a stronger preference for human over machine translation when evaluating documents as compared to isolated sentences. Our findings emphasise the need to shift towards document-level evaluation as machine translation im…
Although many context-aware neural machine translation models have been proposed to incorporate contexts in translation, most of those models are trained end-to-end on parallel documents aligned in sentence-level. Because only a few domains (and language pairs) have such document-level parallel data, we cannot perform accurate context-aware translation in most domains. We therefore present a simple method to turn a sentence-level translation model into a context-aware model by incorporating a document-level language model into the decoder. Our context-aware decoder is built upon only a sentenc…
University of Edinburgh（爱丁堡大学）；Google Research（谷歌研究院）
Document-level neural machine translation (DocNMT) achieves coherent translations by incorporating cross-sentence context. However, for most language pairs there's a shortage of parallel documents, although parallel sentences are readily available. In this paper, we study whether and how contextual modeling in DocNMT is transferable via multilingual modeling. We focus on the scenario of zero-shot transfer from teacher languages with document level data to student languages with no documents but sentence level data, and for the first time treat document-level translation as a transfer learning …
National Key Laboratory for Novel Software Technology, Nanjing University（南京大学计算机软件新技术全国重点实验室）；University of Edinburgh（爱丁堡大学）
Document-level machine translation manages to outperform sentence level models by a small margin, but have failed to be widely adopted. We argue that previous research did not make a clear use of the global context, and propose a new document-level NMT framework that deliberately models the local context of each sentence with the awareness of the global context of the document in both source and target languages. We specifically design the model to be able to deal with documents containing any number of sentences, including single sentences. This unified approach allows our model to be trained…
We show that Bayes' rule provides an effective mechanism for creating document translation models that can be learned from only parallel sentences and monolingual documents---a compelling benefit as parallel documents are not always available. In our formulation, the posterior probability of a candidate translation is the product of the unconditional (prior) probability of the candidate output document and the "reverse translation probability" of translating the candidate output back into the source language. Our proposed model uses a powerful autoregressive language model as the prior on targ…
Document alignment aims to identify pairs of documents in two distinct languages that are of comparable content or translations of each other. Such aligned data can be used for a variety of NLP tasks from training cross-lingual representations to mining parallel data for machine translation. In this paper we develop an unsupervised scoring function that leverages cross-lingual sentence embeddings to compute the semantic distance between documents in different languages. These semantic distances are then used to guide a document alignment algorithm to properly pair cross-lingual web documents a…
The complexity of sentences characteristic to biomedical articles poses a challenge to natural language parsers, which are typically trained on large-scale corpora of non-technical text. We propose a text simplification process, bioSimplify, that seeks to reduce the complexity of sentences in biomedical abstracts in order to improve the performance of syntactic parsers on the processed sentences. Syntactic parsing is typically one of the first steps in a text mining pipeline. Thus, any improvement in performance would have a ripple effect over all processing steps. We evaluated our method usin…
BACKGROUND: In this study, we investigated the efficacy of current state-of-the-art neural sentence embedding models for semantic similarity estimation of sentences from biomedical literature. We trained different neural embedding models on 1.7 million articles from the PubMed Open Access dataset, and evaluated them based on a biomedical benchmark set containing 100 sentence pairs annotated by human experts and a smaller contradiction subset derived from the original benchmark set. RESULTS: With a Pearson correlation of 0.819, our best unsupervised model based on the Paragraph Vector Distribut…
Department of Biomedical Informatics, Arizona State University（亚利桑那州立大学生物医学信息学系）
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task …
Accurate systems for extracting Protein-Protein Interactions (PPIs) automatically from biomedical articles can help accelerate biomedical research. Biomedical Informatics researchers are collaborating to provide metaservices and advance the state-of-art in PPI extraction. One problem often neglected by current Natural Language Processing systems is the characteristic complexity of the sentences in biomedical literature. In this paper, we report on the impact that automatic simplification of sentences has on the performance of a state-of-art PPI extraction system, showing a substantial improvem…
Empowering Language Model with Guided Knowledge Fusion for Biomedical Document Re-ranking
Lister Hill National Center for Biomedical Communications（利斯特·希尔国家生物医学交流中心）；National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）
The University of Melbourne（墨尔本大学）；MBZUAI（穆罕默德·本·扎耶德人工智能大学）；RMIT University（皇家墨尔本理工大学）
In this paper we report on our submission to the Multidocument Summarisation for Literature Review (MSLR) shared task. Specifically, we adapt PRIMERA (Xiao et al., 2022) to the biomedical domain by placing global attention on important biomedical entities in several ways. We analyse the outputs of the 23 resulting models, and report patterns in the results related to the presence of additional global attention, number of training steps, and the input configuration.
Macquarie University（麦考瑞大学）；Australian National University（澳大利亚国立大学）
This paper presents the participation of Macquarie University and the Australian National University for Task B Phase B of the 2020 BioASQ Challenge (BioASQ8b). Our overall framework implements Query focused multi-document extractive summarisation by applying either a classification or a regression layer to the candidate sentence embeddings and to the comparison between the question and sentence embeddings. We experiment with variants using BERT and BioBERT, Siamese architectures, and reinforcement learning. We observe the best results when BERT is used to obtain the word embeddings, followed …
Kangwon National University（江原大学）；Konkuk University（建国大学）
Previous researchers have considered sentiment analysis as a document classification task, in which input documents are classified into predefined sentiment classes. Although there are sentences in a document that support important evidences for sentiment analysis and sentences that do not, they have treated the document as a bag of sentences. In other words, they have not considered the importance of each sentence in the document. To effectively determine polarity of a document, each sentence in the document should be dealt with different degrees of importance. To address this problem, we pro…
Automated entity relation extraction (RE) from literature provides an important source for constructing biomedical database, which is more efficient and extensible than manual curation. However, existing RE models usually ignore the information contained in sentence structures and target entities. In this paper, we propose BERE, a deep learning based model which uses Gumbel Tree-GRU to learn sentence structures and joint embedding to incorporate entity information. It also employs word-level attention for improved relation extraction and sentence-level attention to suit the distantly supervise…
This paper presents Macquarie University's participation to the two most recent BioASQ Synergy Tasks (as per June 2022), and to the BioASQ10 Task~B (BioASQ10b), Phase~B. In these tasks, participating systems are expected to generate complex answers to biomedical questions, where the answers may contain more than one sentence. We apply query-focused extractive summarisation techniques. In particular, we follow a sentence classification-based approach that scores each candidate sentence associated to a question, and the $n$ highest-scoring sentences are returned as the answer. The Synergy Task c…
Objective: This work aimed to demonstrate the effectiveness of a hybrid approach based on Sentence BERT model and retrofitting algorithm to compute relatedness between any two biomedical concepts. Materials and Methods: We generated concept vectors by encoding concept preferred terms using ELMo, BERT, and Sentence BERT models. We used BioELMo and Clinical ELMo. We used Ontology Knowledge Free (OKF) models like PubMedBERT, BioBERT, BioClinicalBERT, and Ontology Knowledge Injected (OKI) models like SapBERT, CoderBERT, KbBERT, and UmlsBERT. We trained all the BERT models using Siamese network on …
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)（美国国立卫生研究院国家医学图书馆国家生物技术信息中心）
Sentence embeddings have become an essential part of today's natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for biomedical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarki…
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)（美国国家生物技术信息中心（NCBI）、美国国家医学图书馆（NLM）、美国国立卫生研究院（NIH））
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical text-mining approaches typically formulate the problem as a cross-sentence n-ary relation-extraction task that detects relations among n entities across multiple sentences, and use either a graph neural network (GNN) with long short-term memory (LSTM) or an attention mechanism. Recently, Transformer has been shown to outperform LSTM on many natural language…
In recent years, summarizers that incorporate domain knowledge into the process of text summarization have outperformed generic methods, especially for summarization of biomedical texts. However, construction and maintenance of domain knowledge bases are resource-intense tasks requiring significant manual annotation. In this paper, we demonstrate that contextualized representations extracted from the pre-trained deep language model BERT, can be effectively used to measure the similarity between sentences and to quantify the informative content. The results show that our BERT-based summarizer c…
We present a simple document alignment method that incorporates sentence order information in both candidate generation and candidate re-scoring. Our method results in 61% relative reduction in error compared to the best previously published result on the WMT16 document alignment shared task. Our method improves downstream MT performance on web-scraped Sinhala--English documents from ParaCrawl, outperforming the document alignment method used in the most recent ParaCrawl release. It also outperforms a comparable corpora method which uses the same multilingual embeddings, demonstrating that exp…
Sentence Bag Graph Formulation for Biomedical Distant Supervision Relation Extraction
School of Computer Science and Technology, Harbin Institute of Technology（哈尔滨工业大学计算机科学与技术学院）；University of Rochester（罗切斯特大学）；School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture（北京建筑大学电气与信息工程学院）；Beijing Key Laboratory of Intelligent Processing for Building Big Data, Beijing University of Civil Engineering and Architecture（北京建筑大学北京市建筑大数据智能处理重点实验室）
Harbin Institute of Technology（哈尔滨工业大学）；Microsoft Research（微软研究院）
Sentence scoring and sentence selection are two main steps in extractive document summarization systems. However, previous works treat them as two separated subtasks. In this paper, we present a novel end-to-end neural network framework for extractive document summarization by jointly learning to score and select sentences. It first reads the document sentences with a hierarchical encoder to obtain the representation of sentences. Then it builds the output summary by extracting sentences one by one. Different from previous methods, our approach integrates the selection strategy into the scorin…
The goal of sentence and document modeling is to accurately represent the meaning of sentences and documents for various Natural Language Processing tasks. In this work, we present Dependency Sensitive Convolutional Neural Networks (DSCNN) as a general-purpose classification system for both sentences and documents. DSCNN hierarchically builds textual representations by processing pretrained word embeddings via Long Short-Term Memory networks and subsequently extracting features with convolution operators. Compared with existing recursive neural models with tree structures, DSCNN does not rely …
Department of Engineering, University of Cambridge（剑桥大学工程系）
The 2020 WMT Biomedical translation task evaluated Medline abstract translations. This is a small-domain translation task, meaning limited relevant training data with very distinct style and vocabulary. Models trained on such data are susceptible to exposure bias effects, particularly when training sentence pairs are imperfect translations of each other. This can result in poor behaviour during inference if the model learns to neglect the source sentence. The UNICAM entry addresses this problem during fine-tuning using a robust variant on Minimum Risk Training. We contrast this approach with d…
Tsinghua University（清华大学）；Microsoft Research Asia（微软亚洲研究院）
Transformer is important for text modeling. However, it has difficulty in handling long documents due to the quadratic complexity with input text length. In order to handle this problem, we propose a hierarchical interactive Transformer (Hi-Transformer) for efficient and effective long document modeling. Hi-Transformer models documents in a hierarchical way, i.e., first learns sentence representations and then learns document representations. It can effectively reduce the complexity and meanwhile capture global document context in the modeling of each sentence. More specifically, we first use …
Harbin Institute of Technology（哈尔滨工业大学）；University of Alberta（阿尔伯塔大学）
Document-level relation extraction (DocRE) aims to determine the relation between two entities from a document of multiple sentences. Recent studies typically represent the entire document by sequence- or graph-based models to predict the relations of all entity pairs. However, we find that such a model is not robust and exhibits bizarre behaviors: it predicts correctly when an entire test document is fed as input, but errs when non-evidence sentences are removed. To this end, we propose a Sentence Importance Estimation and Focusing (SIEF) framework for DocRE, where we design a sentence import…
Stony Brook University（石溪大学）；Delft University of Technology（代尔夫特理工大学）；University of Arizona（亚利桑那大学）
Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g., a protein or a chemical) affects another in a biological context. The abstracts of these publications often include a focused set of sentences that present relevant supporting statements regarding such relationships, associated experimental evidence, and a concluding sentence that summarizes the mechanism underlying the relationship. We leverage this struct…
Peking University（北京大学）；Wangxuan Institute of Computer Technology, Peking University（北京大学王选计算机研究所）；The MOE Key Laboratory of Computational Linguistics, Peking University（北京大学计算语言学教育部重点实验室）
Document-level Relation Extraction (RE) is a more challenging task than sentence RE as it often requires reasoning over multiple sentences. Yet, human annotators usually use a small number of sentences to identify the relationship between a given entity pair. In this paper, we present an embarrassingly simple but effective method to heuristically select evidence sentences for document-level RE, which can be easily combined with BiLSTM to achieve good performance on benchmark datasets, even better than fancy graph neural network based methods. We have released our code at https://github.com/And…
The summarization literature focuses on the summarization of news articles. The news articles in the CNN-DailyMail are relatively short documents with about 30 sentences per document on average. We introduce SciBERTSUM, our summarization framework designed for the summarization of long documents like scientific papers with more than 500 sentences. SciBERTSUM extends BERTSUM to long documents by 1) adding a section embedding layer to include section information in the sentence vector and 2) applying a sparse attention mechanism where each sentences will attend locally to nearby sentences and on…
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated with biochemical events. We describe the properties of an annotated corpus of context-event relations and present and evaluate several classifiers for context-event association trained on syntactic, distance and frequency features.
Electronics Research Institute（电子研究所）；Faculty of Computers and Information, Benha University（班哈大学计算机与信息学院）
Current multi-document summarization systems can successfully extract summary sentences, however with many limitations including: low coverage, inaccurate extraction to important sentences, redundancy and poor coherence among the selected sentences. The present study introduces a new concept of centroid approach and reports new techniques for extracting summary sentences for multi-document. In both techniques keyphrases are used to weigh sentences and documents. The first summarization technique (Sen-Rich) prefers maximum richness sentences. While the second (Doc-Rich), prefers sentences from …
Multilingual sentence representations pose a great advantage for low-resource languages that do not have enough data to build monolingual models on their own. These multilingual sentence representations have been separately exploited by few research for document and sentence alignment. However, most of the low-resource languages are under-represented in these pre-trained models. Thus, in the context of low-resource languages, these models have to be fine-tuned for the task at hand, using additional data sources. This paper presents a weighting mechanism that makes use of available small-scale …
The Hong Kong Polytechnic University（香港理工大学）；Peking University（北京大学）
Unsupervised extractive summarization aims to extract salient sentences from a document as the summary without labeled data. Recent literatures mostly research how to leverage sentence similarity to rank sentences in the order of salience. However, sentence similarity estimation using pre-trained language models mostly takes little account of document-level information and has a weak correlation with sentence salience ranking. In this paper, we proposed two novel strategies to improve sentence similarity estimation for unsupervised extractive summarization. We use contrastive learning to optim…
University of Chinese Academy of Sciences（中国科学院大学）；Institute of Software, Chinese Academy of Sciences（中国科学院软件研究所）
Distant supervision (DS) is a promising approach for relation extraction but often suffers from the noisy label problem. Traditional DS methods usually represent an entity pair as a bag of sentences and denoise labels using multi-instance learning techniques. The bag-based paradigm, however, fails to leverage the inter-sentence-level and the entity-level evidence for relation extraction, and their denoising algorithms are often specialized and complicated. In this paper, we propose a new DS paradigm--document-based distant supervision, which models relation extraction as a document-based machi…
In this paper, we establish Fog Index (FI) as a text filter to locate the sentences in texts that contain connected biomedical concepts of interest. To do so, we have used 24 random papers each containing four pairs of connected concepts. For each pair, we categorize sentences based on whether they contain both, any or none of the concepts. We then use FI to measure difficulty of the sentences of each category and find that sentences containing both of the concepts have low readability. We rank sentences of a text according to their FI and select 30 percent of the most difficult sentences. We …
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Amazon Alexa AI（亚马逊Alexa人工智能部门）
Providing conversation models with background knowledge has been shown to make open-domain dialogues more informative and engaging. Existing models treat knowledge selection as a sentence ranking or classification problem where each sentence is handled individually, ignoring the internal semantic connection among sentences in the background document. In this work, we propose to automatically convert the background knowledge documents into document semantic graphs and then perform knowledge selection over such graphs. Our document semantic graphs preserve sentence-level information through the …
The Pennsylvania State University（宾夕法尼亚州立大学）；QCRI（卡塔尔计算研究所）；National University of Singapore（新加坡国立大学）
Abstractive summarization is an ideal form of summarization since it can synthesize information from multiple documents to create concise informative summaries. In this work, we aim at developing an abstractive summarizer. First, our proposed approach identifies the most important document in the multi-document set. The sentences in the most important document are aligned to sentences in other documents to generate clusters of similar sentences. Second, we generate K-shortest paths from the sentences in each cluster using a word-graph structure. Finally, we select sentences from the set of sho…
In recent years, many methods have been developed to identify important portions of text documents. Summarization tools can utilize these methods to extract summaries from large volumes of textual information. However, to identify concepts representing central ideas within a text document and to extract the most informative sentences that best convey those concepts still remain two crucial tasks in summarization methods. In this paper, we introduce a graph-based method to address these two challenges in the context of biomedical text summarization. We show that how a summarizer can discover me…
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆国家生物技术信息中心）
Capturing sentence semantics plays a vital role in a range of text mining applications. Despite continuous efforts on the development of related datasets and models in the general domain, both datasets and models are limited in biomedical and clinical domains. The BioCreative/OHNLP organizers have made the first attempt to annotate 1,068 sentence pairs from clinical notes and have called for a community effort to tackle the Semantic Textual Similarity (BioCreative/OHNLP STS) challenge. We developed models using traditional machine learning and deep learning approaches. For the post challenge, …
