The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC
NRC "Kurchatov institute"（国家研究中心“库尔恰托夫研究所”）；MEPhI National Research Nuclear University（莫斯科工程物理学院国家核研究大学）；I.M. Sechenov First Moscow State Medical University (Sechenov University)（谢切诺夫第一莫斯科国立医科大学（谢切诺夫大学））
We present the full-size Russian complexly NER-labeled corpus of Internet user reviews, along with an evaluation of accuracy levels reached on this corpus by a set of advanced deep learning neural networks to extract the pharmacologically meaningful entities from Russian texts. The corpus annotation includes mentions of the following entities: Medication (33005 mentions), Adverse Drug Reaction (1778), Disease (17403), and Note (4490). Two of them - Medication and Disease - comprise a set of attributes. A part of the corpus has the coreference annotation with 1560 coreference chains in 300 docu…
This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training, our models demonstrate state-of-the-art results on RuMedBench - Russian medical language understanding benchmark that covers a diverse set of tasks, including text classification, question answering, natural language inference, and named entity recognition.
A.P. Ershov Institute of Informatics Systems SB RAS（俄罗斯科学院西伯利亚分院A.P.叶尔绍夫信息系统研究所）；Novosibirsk State University（新西伯利亚国立大学）
This paper is devoted to the study of methods for information extraction (entity recognition and relation classification) from scientific texts on information technology. Scientific publications provide valuable information into cutting-edge scientific advances, but efficient processing of increasing amounts of data is a time-consuming task. In this paper, several modifications of methods for the Russian language are proposed. It also includes the results of experiments comparing a keyword extraction method, vocabulary method, and some methods based on neural networks. Text collections for the…
We present a new corpus with coreference annotation, Russian Coreference Corpus (RuCoCo). The goal of RuCoCo is to obtain a large number of annotated texts while maintaining high inter-annotator agreement. RuCoCo contains news texts in Russian, part of which were annotated from scratch, and for the rest the machine-generated annotations were refined by human annotators. The size of our corpus is one million words and around 150,000 mentions. We make the corpus publicly available.
University of Chicago（芝加哥大学）；Argonne National Laboratory（阿贡国家实验室）；Globus
Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of coronavirus research. We report here on a project that leverages both human and artificial intelligence to detect references to drug-like molecules in free text. We engage non-expert humans to create a corpus of labeled text, use this labeled corpus to train a named enti…
Saint Petersburg State University（圣彼得堡国立大学）；CraftTalk
The article is focused on automatic development and ranking of a large corpus for Russian paraphrase generation which proves to be the first corpus of such type in Russian computational linguistics. Existing manually annotated paraphrase datasets for Russian are limited to small-sized ParaPhraser corpus and ParaPlag which are suitable for a set of NLP tasks, such as paraphrase and plagiarism detection, sentence similarity and relatedness estimation, etc. Due to size restrictions, these datasets can hardly be applied in end-to-end text generation solutions. Meanwhile, paraphrase generation requ…
Paris University（巴黎大学）；AP-HP（巴黎公共援助医院）；LIMSI（法国计算机科学与自动化研究所）；CNRS（法国国家科学研究中心）；Univ. Paris-Sud（巴黎南大学）；Université Paris-Saclay（巴黎萨克雷大学）；Sorbonne Université（索邦大学）；Inserm（法国国家健康与医学研究院）；Univ Paris 13（巴黎第十三大学）；LIMICS（医学信息学与电子健康知识工程实验室）
We aimed to enhance the performance of a supervised model for clinical named-entity recognition (NER) using medical terminologies. In order to evaluate our system in French, we built a corpus for 5 types of clinical entities. We used a terminology-based system as baseline, built upon UMLS and SNOMED. Then, we evaluated a biGRU-CRF, and an hybrid system using the prediction of the terminology-based system as feature for the biGRU-CRF. In English, we evaluated the NER systems on the i2b2-2009 Medication Challenge for Drug name recognition, which contained 8,573 entities for 268 documents. In Fre…
ABBYY（ABBYY公司）；Charles University（查理大学）；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Sberbank（俄罗斯联邦储蓄银行）；National Research University Higher School of Economics（国家研究型高等经济大学）
This paper provides a comprehensive overview of the gapping dataset for Russian that consists of 7.5k sentences with gapping (as well as 15k relevant negative sentences) and comprises data from various genres: news, fiction, social media and technical texts. The dataset was prepared for the Automatic Gapping Resolution Shared Task for Russian (AGRR-2019) - a competition aimed at stimulating the development of NLP tools and methods for processing of ellipsis. In this paper, we pay special attention to the gapping resolution methods that were introduced within the shared task as well as an alter…
University of Kentucky（肯塔基大学）；National Library of Medicine（美国国家医学图书馆）
Preventable adverse events as a result of medical errors present a growing concern in the healthcare system. As drug-drug interactions (DDIs) may lead to preventable adverse events, being able to extract DDIs from drug labels into a machine-processable form is an important step toward effective dissemination of drug safety information. In this study, we tackle the problem of jointly extracting drugs and their interactions, including interaction outcome, from drug labels. Our deep learning approach entails composing various intermediate representations including sequence and graph based context…
University of Oslo（奥斯陆大学）；University of Tyumen（秋明大学）
In this paper, we present a distributional word embedding model trained on one of the largest available Russian corpora: Araneum Russicum Maximum (over 10 billion words crawled from the web). We compare this model to the model trained on the Russian National Corpus (RNC). The two corpora are much different in their size and compilation procedures. We test these differences by evaluating the trained models against the Russian part of the Multilingual SimLex999 semantic similarity dataset. We detect and describe numerous issues in this dataset and publish a new corrected version. Aside from the …
School of Computer Science, The University of Manchester（曼彻斯特大学计算机学院）；Health eResearch Center, The University of Manchester（曼彻斯特大学健康电子研究中心）；The Alan Turing Institute（艾伦·图灵研究所）
Monitoring the administration of drugs and adverse drug reactions are key parts of pharmacovigilance. In this paper, we explore the extraction of drug mentions and drug-related information (reason for taking a drug, route, frequency, dosage, strength, form, duration, and adverse events) from hospital discharge summaries through deep learning that relies on various representations for clinical named entity recognition. This work was officially part of the 2018 n2c2 shared task, and we use the data supplied as part of the task. We developed two deep learning architecture based on recurrent neura…
The most studied and most successful language models were developed and evaluated mainly for English and other close European languages, such as French, German, etc. It is important to study applicability of these models to other languages. The use of vector space models for Russian was recently studied for multiple corpora, such as Wikipedia, RuWac, lib.ru. These models were evaluated against word semantic similarity task. For our knowledge Twitter was not considered as a corpus for this task, with this work we fill the gap. Results for vectors trained on Twitter corpus are comparable in accu…
Unidata；Saint-Petersburg State University（圣彼得堡国立大学）
Corpora that contain tabular data such as WebTables are a vital resource for the academic community. Essentially, they are the backbone of any modern research in information management. They are used for various tasks of data extraction, knowledge base construction, question answering, column semantic type detection and many other. Such corpora are useful not only as a source of data, but also as a base for building test datasets. So far, there were no such corpora for the Russian language and this seriously hindered research in the aforementioned areas. In this paper, we present the first cor…
Motivation: The proliferation of Biomedical research articles has made the task of information retrieval more important than ever. Scientists and Researchers are having difficulty in finding articles that contain information relevant to them. Proper extraction of biomedical entities like Disease, Drug/chem, Species, Gene/protein, can considerably improve the filtering of articles resulting in better extraction of relevant information. Performance on BioNer benchmarks has progressively improved because of progression in transformers-based models like BERT, XLNet, OpenAI, GPT2, etc. These models…
RuCoLA: Russian Corpus of Linguistic Acceptability
SberDevices；ABBYY；HSE University（高等经济大学）；Yandex；Huawei Noah’s Ark Lab（华为诺亚方舟实验室）；Center for Information and Language Processing (CIS), MaiNLP lab, LMU Munich（慕尼黑大学信息与语言处理中心（CIS）MaiNLP实验室）
University of Notre Dame（圣母大学）；HLTCOE, JHU（约翰斯·霍普金斯大学自然语言处理中心（HLTCOE））；UMBC, HLTCOE（马里兰大学巴尔的摩分校（UMBC）自然语言处理中心（HLTCOE））
The goal of this work is to improve the performance of a neural named entity recognition system by adding input features that indicate a word is part of a name included in a gazetteer. This article describes how to generate gazetteers from the Wikidata knowledge graph as well as how to integrate the information into a neural NER system. Experiments reveal that the approach yields performance gains in two distinct languages: a high-resource, word-based language, English and a high-resource, character-based language, Chinese. Experiments were also performed in a low-resource language, Russian on…
Institution of the Russian Academy of Sciences St.Petersburg Institute for Informatics and Automation RAS（俄罗斯科学院圣彼得堡信息与自动化研究所）；Saint-Petersburg State University（圣彼得堡国立大学）；Institute of Applied Mathematical Research of the Karelian Research Centre of the Russian Academy of Sciences（俄罗斯科学院卡累利阿研究中心应用数学研究所）
The quantitative evaluation of quotations in the Russian Wiktionary was performed using the developed Wiktionary parser. It was found that the number of quotations in the dictionary is growing fast (51.5 thousands in 2011, 62 thousands in 2012). These quotations were extracted and saved in the relational database of a machine-readable dictionary. For this database, tables related to the quotations were designed. A histogram of distribution of quotations of literary works written in different years was built. It was made an attempt to explain the characteristics of the histogram by associating …
CHU Necker, AP-HP（巴黎公共医疗救助机构内克尔大学医院）；INSERM UMR-S 872（法国国家健康与医学研究院 UMR-S 872）；Sorbonne Paris Cité, Faculté de Médecine（索邦巴黎西岱大学医学院）；Université de Paris（巴黎大学）
In this study, we evaluated the RNNG, a neural top-down transition based parser, for medication information extraction in clinical texts. We evaluated this model on a French clinical corpus. The task was to extract the name of a drug (or a drug class), as well as attributes informing its administration: frequency, dosage, duration, condition and route of administration. We compared the RNNG model that jointly identifies entities, events and their relations with separate BiLSTMs models for entities, events and relations as baselines. We call seq-BiLSTMs the baseline models for relations extract…
Artificial Intelligence Research Institute (AIRI)（人工智能研究院（AIRI））；SberDevices
The General QA field has been developing the methodology referencing the Stanford Question answering dataset (SQuAD) as the significant benchmark. However, compiling factual questions is accompanied by time- and labour-consuming annotation, limiting the training data's potential size. We present the WikiOmnia dataset, a new publicly available set of QA-pairs and corresponding Russian Wikipedia article summary sections, composed with a fully automated generative pipeline. The dataset includes every available article from Wikipedia for the Russian language. The WikiOmnia pipeline is available op…
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools
Humboldt-Universität zu Berlin（柏林洪堡大学）；Ludwig Maximilian University Munich（慕尼黑大学）；Research Industrial Systems Engineering (RISE) Forschungs-, Entwicklungs- und Großprojektberatung GmbH（RISE工业系统工程研究开发及大型项目咨询有限责任公司）
National Research University Higher School of Economics（国家研究型高等经济学院）
In this study we address the problem of automated word stress detection in Russian using character level models and no part-speech-taggers. We use a simple bidirectional RNN with LSTM nodes and achieve the accuracy of 90% or higher. We experiment with two training datasets and show that using the data from an annotated corpus is much more efficient than using a dictionary, since it allows us to take into account word frequencies and the morphological context of the word.
Domain adaptation of Russian ModernBERT for long legal documents
Independent Researcher（独立研究者）；National Research Nuclear University MEPhI（国立核研究大学 MEPhI）；Moscow Center for Advanced Studies（莫斯科高级研究中心）；University of Waterloo（滑铁卢大学）
Universitas Indonesia（印度尼西亚大学）；Universitas Mercu Buana（默库布阿纳大学）
One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text is special and has unique characteristics. In addition, the medical text mining poses more challenges, e.g., more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug. The mining is even more challenging due to the lack of labeled dataset sources and external knowledge, as well as multiple token representations for a single drug name that is more common in the real application s…
Eye-SpatialNet: Spatial Information Extraction from Ophthalmology Notes
McWilliams School of Biomedical Informatics, UTHealth Houston（德克萨斯大学休斯顿健康科学中心麦克威廉姆斯生物医学信息学院）；McGovern Medical School, UTHealth Houston（德克萨斯大学休斯顿健康科学中心麦戈文医学院）
National Research University Higher School of Economics（俄罗斯国家研究型高等经济大学）；Mail.ru Group（Mail.ru集团）
Distributed vector representations for natural language vocabulary get a lot of attention in contemporary computational linguistics. This paper summarizes the experience of applying neural network language models to the task of calculating semantic similarity for Russian. The experiments were performed in the course of Russian Semantic Similarity Evaluation track, where our models took from the 2nd to the 5th position, depending on the task. We introduce the tools and corpora used, comment on the nature of the shared task and describe the achieved results. It was found out that Continuous Skip…
Traditional biomedical version of embeddings obtained from pre-trained language models have recently shown state-of-the-art results for relation extraction (RE) tasks in the medical domain. In this paper, we explore how to incorporate domain knowledge, available in the form of molecular structure of drugs, for predicting Drug-Drug Interaction from textual corpus. We propose a method, BERTChem-DDI, to efficiently combine drug embeddings obtained from the rich chemical structure of drugs along with off-the-shelf domain-specific BioBERT embedding-based RE architecture. Experiments conducted on th…
University of Oslo（奥斯陆大学）；University of Helsinki（赫尔辛基大学）；National Research University Higher School of Economics（国立研究型大学高等经济学院）
We present our experience in applying distributional semantics (neural word embeddings) to the problem of representing and clustering documents in a bilingual comparable corpus. Our data is a collection of Russian and Ukrainian academic texts, for which topics are their academic fields. In order to build language-independent semantic representations of these documents, we train neural distributional models on monolingual corpora and learn the optimal linear transformation of vectors from one language to another. The resulting vectors are then used to produce `semantic fingerprints' of document…
Developing predictive modeling in medicine requires additional features from unstructured clinical texts. In Russia, there are no instruments for natural language processing to cope with problems of medical records. This paper is devoted to a module of negation detection. The corpus-free machine learning method is based on gradient boosting classifier is used to detect whether a disease is denied, not mentioned or presented in the text. The detector classifies negations for five diseases and shows average F-score from 0.81 to 0.93. The benefits of negation detection have been demonstrated by p…
This paper accompanies the release of Opusparcus, a new paraphrase corpus for six European languages: German, English, Finnish, French, Russian, and Swedish. The corpus consists of paraphrases, that is, pairs of sentences in the same language that mean approximately the same thing. The paraphrases are extracted from the OpenSubtitles2016 corpus, which contains subtitles from movies and TV shows. The informal and colloquial genre that occurs in subtitles makes such data a very interesting language resource, for instance, from the perspective of computer assisted language learning. For each targ…
Artificial Intelligence Institute, University of South Carolina（南卡罗来纳大学人工智能研究所）
With strong marketing advocacy of the benefits of cannabis use for improved mental health, cannabis legalization is a priority among legislators. However, preliminary scientific research does not conclusively associate cannabis with improved mental health. In this study, we explore the relationship between depression and consumption of cannabis in a targeted social media corpus involving personal use of cannabis with the intent to derive its potential mental health benefit. We use tweets that contain an association among three categories annotated by domain experts - Reason, Effect, and Addict…
The CMU Wilderness Multilingual Speech Dataset (Black, 2019) is a newly published multilingual speech dataset based on recorded readings of the New Testament. It provides data to build Automatic Speech Recognition (ASR) and Text-to-Speech (TTS) models for potentially 700 languages. However, the fact that the source content (the Bible) is the same for all the languages is not exploited to date.Therefore, this article proposes to add multilingual links between speech segments in different languages, and shares a large and clean dataset of 8,130 parallel spoken utterances across 8 languages (56 l…
A Dataset for Pharmacovigilance in German, French, and Japanese: Annotating Adverse Drug Reactions across Languages
BIFOLD；TU Berlin（柏林工业大学）；German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心（DFKI））；Université Paris-Saclay（巴黎萨克雷大学）；Nara Institute of Science and Technology（奈良科学技术研究所）；RIKEN（理化学研究所）
Skolkovo Institute of Science and Technology (Skoltech)（斯科尔科沃科学技术研究院（Skoltech））；Meta AI
We present the first neural machine translation system for translation between the endangered Erzya language and Russian and the dataset collected by us to train and evaluate it. The BLEU scores are 17 and 19 for translation to Erzya and Russian respectively, and more than half of the translations are rated as acceptable by native speakers. We also adapt our model to translate between Erzya and 10 other languages, but without additional parallel data, the quality on these directions remains low. We release the translation models along with the collected text corpus, a new language identificati…
In the absence of sufficient medication for COVID patients due to the increased demand, disused drugs have been employed or the doses of those available were modified by hospital pharmacists. Some evidences for the use of alternative drugs can be found in the existing scientific literature that could assist in such decisions. However, exploiting large corpus of documents in an efficient manner is not easy, since drugs may not appear explicitly related in the texts and could be mentioned under different brand names. Drugs4Covid combines word embedding techniques and semantic web technologies to…
Skolkovo Institute of Science and Technology（斯科尔科沃科技学院）
Toxicity on the Internet, such as hate speech, offenses towards particular users or groups of people, or the use of obscene words, is an acknowledged problem. However, there also exist other types of inappropriate messages which are usually not viewed as toxic, e.g. as they do not contain explicit offences. Such messages can contain covered toxicity or generalizations, incite harmful actions (crime, suicide, drug use), provoke "heated" discussions. Such messages are often related to particular sensitive topics, e.g. on politics, sexual minorities, social injustice which more often than other t…
City University of Hong Kong（香港城市大学）；Hong Kong Institute for Data Science, City University of Hong Kong（香港城市大学香港数据科学研究院）；Jilin University（吉林大学）
The rapid growth in literature accumulates diverse and yet comprehensive biomedical knowledge hidden to be mined such as drug interactions. However, it is difficult to extract the heterogeneous knowledge to retrieve or even discover the latest and novel knowledge in an efficient manner. To address such a problem, we propose EGFI for extracting and consolidating drug interactions from large-scale medical literature text data. Specifically, EGFI consists of two parts: classification and generation. In the classification part, EGFI encompasses the language model BioBERT which has been comprehensi…
In this paper, we present a study of neologisms and loan words frequently occurring in Facebook user posts. We have analyzed a dataset of several million publically available posts written during 2006-2013 by Russian-speaking Facebook users. From these, we have built a vocabulary of most frequent lemmatized words missing from the OpenCorpora dictionary the assumption being that many such words have entered common use only recently. This assumption is certainly not true for all the words extracted in this way; for that reason, we manually filtered the automatically obtained list in order to exc…
In this work, we present the first corpus for German Adverse Drug Reaction (ADR) detection in patient-generated content. The data consists of 4,169 binary annotated documents from a German patient forum, where users talk about health issues and get advice from medical doctors. As is common in social media data in this domain, the class labels of the corpus are very imbalanced. This and a high topic imbalance make it a very challenging dataset, since often, the same symptom can have several causes and is not always related to a medication intake. We aim to encourage further multi-lingual effort…
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification
Kazan Federal University（喀山联邦大学）；Lomonosov Moscow State University（莫斯科罗蒙诺索夫国立大学）；Sber AI；National Research University Higher School of Economics（国立研究型大学高等经济学院）
National Research University Higher School of Economics（俄罗斯国家研究型高等经济大学）；Novosibirsk State University（新西伯利亚国立大学）；A.P. Ershov Institute of Informatics Systems SB RAS（俄罗斯科学院西伯利亚分院A.P.埃尔肖夫信息系统研究所）；Kazan Federal University（喀山联邦大学）；ABBYY（ABBYY公司）；Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Innopolis University（因诺波利斯大学）
In this paper we present a corpus of Russian strategic planning documents, RuREBus. This project is grounded both from language technology and e-government perspectives. Not only new language sources and tools are being developed, but also their applications to e-goverment research. We demonstrate the pipeline for creating a text corpus from scratch. First, the annotation schema is designed. Next texts are marked up using human-in-the-loop strategy, so that preliminary annotations are derived from a machine learning model and are manually corrected. The amount of annotated texts is large enoug…
Bauman Moscow State Technical University（鲍曼莫斯科国立技术大学）；Lomonosov Moscow State University（罗蒙诺索夫莫斯科国立大学）
In the sentiment attitude extraction task, the aim is to identify <<attitudes>> -- sentiment relations between entities mentioned in text. In this paper, we provide a study on attention-based context encoders in the sentiment attitude extraction task. For this task, we adapt attentive context encoders of two types: (1) feature-based; (2) self-based. In our study, we utilize the corpus of Russian analytical texts RuSentRel and automatically constructed news collection RuAttitudes for enriching the training set. We consider the problem of attitude extraction as two-class (positive, negative) and…
