Modern biomedical concept representations are mostly trained on synonymous concept names from a biomedical knowledge base, ignoring the inter-concept interactions and a concept’s local neighborhood in a knowledge base graph. In this paper, we introduce Biomedical Entity Representation with a Graph-Augmented Multi-Objective Transformer (BERGAMOT), which adopts the power of pre-trained language models (LMs) and graph neural networks to capture both inter-concept and intra-concept interactions from the multilingual UMLS graph. To obtain fine-grained graph representations, we introduce two additional graph-based objectives: (i) a node-level contrastive objective and (ii) the Deep Graph Infomax (DGI) loss, which maximizes the mutual information between a local subgraph and a high-level graph summary. We apply contrastive loss on textual and graph representations to make them less sensitive to surface forms and enable intermodal knowledge exchange. BERGAMOT achieves state-of-the-art results in zero-shot entity linking without task-specific supervision on 4 of 5 languages of the Mantra corpus and on 8 of 10 languages of the XL-BEL benchmark.

We present a new manually annotated dataset of PubMed abstracts for concept normalization in Russian. It contains over 23,641 entity mentions in 756 documents linked to 4,544 unique concepts from the UMLS ontology. Compared to existing corpora, we explore two novel annotation characteristics: the nestedness of named entities and the incompleteness of the Russian medical terminology in UMLS. 4,424 entity mentions are linked to 1,535 unique English concepts absent in the Russian part of the UMLS ontology. We present several baselines for normalization over nested named entities obtained with state-of-the-art models such as SapBERT. Our experimental results show that models pre-trained on graph structural data from UMLS achieve superior performance in a zero-shot setting on bilingual terminology.

This paper presents a system developed for the Clinical NLP 2024 Shared Task, focusing on reliable text-to-SQL modeling on Electronic Health Records (EHRs). The goal is to create a model that accurately generates SQL queries for answerable questions while avoiding incorrect responses and handling unanswerable queries. Our approach comprises three main components: a query correspondence model, a text-to-SQL model, and an SQL verifier.For the query correspondence model, we trained a logistic regression model using hand-crafted features to distinguish between answerable and unanswerable queries. As for the text-to-SQL model, we utilized T5-3B as a pretrained language model, further fine-tuned on pairs of natural language questions and corresponding SQL queries. Finally, we applied the SQL verifier to inspect the resulting SQL queries.During the evaluation stage of the shared task, our system achieved an accuracy of 68.9 % (metric version without penalty), positioning it at the fifth-place ranking. While our approach did not surpass solutions based on large language models (LMMs) like ChatGPT, it demonstrates the promising potential of domain-specific specialized models that are more resource-efficient. The code is publicly available at https://github.com/runnerup96/EHRSQL-text2sql-solution.

This paper presents our LLM-based system designed for the MEDIQA-CORR @ NAACL-ClinicalNLP 2024 Shared Task 3, focusing on medical error detection and correction in medical records. Our approach consists of three key components: entity extraction, prompt engineering, and ensemble. First, we automatically extract biomedical entities such as therapies, diagnoses, and biological species. Next, we explore few-shot learning techniques and incorporate graph information from the MeSH database for the identified entities. Finally, we investigate two methods for ensembling: (i) combining the predictions of three previous LLMs using an AND strategy within a prompt and (ii) integrating the previous predictions into the prompt as separate ‘expert’ solutions, accompanied by trust scores representing their performance. The latter system ranked second with a BERTScore score of 0.8059 and third with an aggregated score of 0.7806 out of the 15 teams’ solutions in the shared task.

This paper describes the results of the Knowledge Graph Question Answering (KGQA) shared task that was co-located with the TextGraphs 2024 workshop. In this task, given a textual question and a list of entities with the corresponding KG subgraphs, the participating system should choose the entity that correctly answers the question. Our competition attracted thirty teams, four of which outperformed our strong ChatGPT-based zero-shot baseline. In this paper, we overview the participating systems and analyze their performance according to a large-scale automatic evaluation. To the best of our knowledge, this is the first competition aimed at the KGQA problem using the interaction between large language models (LLMs) and knowledge graphs.

Semantic parsing plays a pivotal role in advancing the accessibility of human-computer interaction on a large scale. Spider, a widely recognized dataset for text2SQL, contains a wide range of natural language (NL) questions in English and corresponding SQL queries. Original splits of Spider and its adapted to Russian language and improved version, PAUQ, assume independence and identical distribution of training and testing data (i.i.d split). In this work, we propose a target length split and multilingual i.i.d split to measure compositionality and cross-language generalization. We present experimental results of popular text2SQL models on original, multilingual, and target length splits. We also construct a context-free grammar for the evaluation of compositionality in text2SQL in an out-of-distribution setting. We make the splits publicly available on HuggingFace hub via https://huggingface.co/datasets/composite/pauq

The development of state-of-the-art systems in different applied areas of machine learning (ML) is driven by benchmarks, which have shaped the paradigm of evaluating generalisation capabilities from multiple perspectives. Although the paradigm is shifting towards more fine-grained evaluation across diverse tasks, the delicate question of how to aggregate the performances has received particular interest in the community. In general, benchmarks follow the unspoken utilitarian principles, where the systems are ranked based on their mean average score over task-specific metrics. Such aggregation procedure has been viewed as a sub-optimal evaluation protocol, which may have created the illusion of progress. This paper proposes Vote’n’Rank, a framework for ranking systems in multi-task benchmarks under the principles of the social choice theory. We demonstrate that our approach can be efficiently utilised to draw new insights on benchmarking in several ML sub-fields and identify the best-performing systems in research and development case studies. The Vote’n’Rank’s procedures are more robust than the mean average while being able to handle missing performance scores and determine conditions under which the system becomes the winner.

Medical data annotation requires highly qualified expertise. Despite the efforts devoted to medical entity linking in different languages, available data is very sparse in terms of both data volume and languages. In this work, we establish benchmarks for cross-lingual medical entity linking using clinical reports, clinical guidelines, and medical research papers. We present a test set filtering procedure designed to analyze the “hard cases” of entity linking approaching zero-shot cross-lingual transfer learning, evaluate state-of-the-art models, and draw several interesting conclusions based on our evaluation results.

In this paper, we describe entity linking annotation over nested named entities in the recently released Russian NEREL dataset for information extraction. The NEREL collection is currently the largest Russian dataset annotated with entities and relations. It includes 933 news texts with annotation of 29 entity types and 49 relation types. The paper describes the main design principles behind NEREL’s entity linking annotation, provides its statistics, and reports evaluation results for several entity linking baselines. To date, 38,152 entity mentions in 933 documents are linked to Wikidata. The NEREL dataset is publicly available.

Biomedical information retrieval has often been studied as a task of detecting whether a system correctly detects entity spans and links these entities to concepts from a given terminology. Most academic research has focused on evaluation of named entity recognition (NER) and entity linking (EL) models which are key components to recognizing diseases and genes in PubMed abstracts. In this work, we perform a fine-grained evaluation intended to understand the efficiency of state-of-the-art BERT-based information extraction (IE) architecture as a biomedical search engine. We present a novel manually annotated dataset of abstracts for disease and gene search. The dataset contains 23K query-abstract pairs, where 152 queries are selected from logs of our target discovery platform and PubMed abstracts annotated with relevance judgments. Specifically, the query list also includes a subset of concepts with at least one ambiguous concept name. As a baseline, we use off-she-shelf Elasticsearch with BM25. Our experiments on NER, EL, and retrieval in a zero-shot setup show the neural IE architecture shows superior performance for both disease and gene concept queries.

Taxonomy is a graph of terms organized hierarchically using is-a (hypernymy) relations. We suggest novel candidate-free task formulation for the taxonomy enrichment task. To solve the task, we leverage lexical knowledge from the pre-trained models to predict new words missing in the taxonomic resource. We propose a method that combines graph-, and text-based contextualized representations from transformer networks to predict new entries to the taxonomy. We have evaluated the method suggested for this task against text-only baselines based on BERT and fastText representations. The results demonstrate that incorporation of graph embedding is beneficial in the task of hyponym prediction using contextualized models. We hope the new challenging task will foster further research in automatic text graph construction methods.

We present RuCCoN, a new dataset for clinical concept normalization in Russian manually annotated by medical professionals. It contains over 16,028 entity mentions manually linked to over 2,409 unique concepts from the Russian language part of the UMLS ontology. We provide train/test splits for different settings (stratified, zero-shot, and CUI-less) and present strong baselines obtained with state-of-the-art models such as SapBERT. At present, Russian medical NLP is lacking in both datasets and trained models, and we view this work as an important step towards filling this gap. Our dataset and annotation guidelines are available at https://github.com/sberbank-ai-lab/RuCCoN.

Semantic parsing is an important task that allows to democratize human-computer interaction. One of the most popular text-to-SQL datasets with complex and diverse natural language (NL) questions and SQL queries is Spider. We construct and complement a Spider dataset for Russian, thus creating the first publicly available text-to-SQL dataset for this language. While examining its components - NL questions, SQL queries and databases content - we identify limitations of the existing database structure, fill out missing values for tables and add new requests for underrepresented categories. We select thirty functional test sets with different features that can be used for the evaluation of neural models’ abilities. To conduct the experiments, we adapt baseline architectures RAT-SQL and BRIDGE and provide in-depth query component analysis. On the target language, both models demonstrate strong results with monolingual training and improved accuracy in multilingual scenario. In this paper, we also study trade-offs between machine-translated and manually-created NL queries. At present, Russian text-to-SQL is lacking in datasets as well as trained models, and we view this work as an important step towards filling this gap.

This paper is an organizers’ report of the competition on argument mining systems dealing with English tweets about COVID-19 health mandates. This competition was held within the framework of the SMM4H 2022 shared tasks. During the competition, the participants were offered two subtasks: stance detection and premise classification. We present a manually annotated corpus containing 6,156 short posts from Twitter on three topics related to the COVID-19 pandemic: school closures, stay-at-home orders, and wearing masks. We hope the prepared dataset will support further research on argument mining in the health field.

For the past seven years, the Social Media Mining for Health Applications (#SMM4H) shared tasks have promoted the community-driven development and evaluation of advanced natural language processing systems to detect, extract, and normalize health-related information in public, user-generated content. This seventh iteration consists of ten tasks that include English and Spanish posts on Twitter, Reddit, and WebMD. Interest in the #SMM4H shared tasks continues to grow, with 117 teams that registered and 54 teams that participated in at least one task—a 17.5% and 35% increase in registration and participation, respectively, over the last iteration. This paper provides an overview of the tasks and participants’ systems. The data sets remain available upon request, and new systems can be evaluated through the post-evaluation phase on CodaLab.

The global growth of social media usage over the past decade has opened research avenues for mining health related information that can ultimately be used to improve public health. The Social Media Mining for Health Applications (#SMM4H) shared tasks in its sixth iteration sought to advance the use of social media texts such as Twitter for pharmacovigilance, disease tracking and patient centered outcomes. #SMM4H 2021 hosted a total of eight tasks that included reruns of adverse drug effect extraction in English and Russian and newer tasks such as detecting medication non-adherence from Twitter and WebMD forum, detecting self-reported adverse pregnancy outcomes, detecting cases and symptoms of COVID-19, identifying occupations mentioned in Spanish by Twitter users, and detecting self-reported breast cancer diagnosis. The eight tasks included a total of 12 individual subtasks spanning three languages requiring methods for binary classification, multi-class classification, named entity recognition and entity normalization. With a total of 97 registering teams and 40 teams submitting predictions, the interest in the shared tasks grew by 70% and participation grew by 38% compared to the previous iteration.

This paper describes neural models developed for the Social Media Mining for Health (SMM4H) 2021 Shared Task. We participated in two tasks on classification of tweets that mention an adverse drug effect (ADE) (Tasks 1a & 2) and two tasks on extraction of ADE concepts (Tasks 1b & 1c). For classification, we investigate the impact of joint use of BERTbased language models and drug embeddings obtained by chemical structure BERT-based encoder. The BERT-based multimodal models ranked first and second on classification of Russian (Task 2) and English tweets (Task 1a) with the F1 scores of 57% and 61%, respectively. For Task 1b and 1c, we utilized the previous year’s best solution based on the EnDR-BERT model with additional corpora. Our model achieved the best results in Task 1c, obtaining an F1 of 29%.

In this paper, we present NEREL, a Russian dataset for named entity recognition and relation extraction. NEREL is significantly larger than existing Russian datasets: to date it contains 56K annotated named entities and 39K annotated relations. Its important difference from previous datasets is annotation of nested named entities, as well as relations within nested entities and at the discourse level. NEREL can facilitate development of novel models that can extract relations between nested named entities, as well as relations on both sentence and document levels. NEREL also contains the annotation of events involving named entities and their roles in the events. The NEREL collection is available via https://github.com/nerel-ds/NEREL.

This work is devoted to semantic role labeling (SRL) task in Russian. We investigate the role of transfer learning strategies between English FrameNet and Russian FrameBank corpora. We perform experiments with embeddings obtained from various types of multilingual language models, including BERT, XLM-R, MUSE, and LASER. For evaluation, we use a Russian FrameBank dataset. As source data for transfer learning, we experimented with the full version of FrameNet and the reduced dataset with a smaller number of semantic roles identical to FrameBank. Evaluation results demonstrate that BERT embeddings show the best transfer capabilities. The model with pretraining on the reduced English SRL data and fine-tuning on the Russian SRL data show macro-averaged F1-measure of 79.8%, which is above our baseline of 78.4%.

Understanding image advertisements is a challenging task, often requiring non-literal interpretation. We argue that standard image-based predictions are insufficient for symbolism prediction. Following the intuition that texts and images are complementary in advertising, we introduce a multimodal ensemble of a state of the art image-based classifier, a classifier based on an object detection architecture, and a fine-tuned language model applied to texts extracted from ads by OCR. The resulting system establishes a new state of the art in symbolism prediction.

Linking of biomedical entity mentions to various terminologies of chemicals, diseases, genes, adverse drug reactions is a challenging task, often requiring non-syntactic interpretation. A large number of biomedical corpora and state-of-the-art models have been introduced in the past five years. However, there are no general guidelines regarding the evaluation of models on these corpora in single- and cross-terminology settings. In this work, we perform a comparative evaluation of various benchmarks and study the efficiency of state-of-the-art neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) for linking of three entity types across three domains: research abstracts, drug labels, and user-generated texts on drug therapy in English. We have made the source code and results available at https://github.com/insilicomedicine/Fair-Evaluation-BERT.

The vast amount of data on social media presents significant opportunities and challenges for utilizing it as a resource for health informatics. The fifth iteration of the Social Media Mining for Health Applications (#SMM4H) shared tasks sought to advance the use of Twitter data (tweets) for pharmacovigilance, toxicovigilance, and epidemiology of birth defects. In addition to re-runs of three tasks, #SMM4H 2020 included new tasks for detecting adverse effects of medications in French and Russian tweets, characterizing chatter related to prescription medication abuse, and detecting self reports of birth defect pregnancy outcomes. The five tasks required methods for binary classification, multi-class classification, and named entity recognition (NER). With 29 teams and a total of 130 system submissions, participation in the #SMM4H shared tasks continues to grow.

This paper describes neural models developed for the Social Media Mining for Health (SMM4H) 2020 shared tasks. Specifically, we participated in two tasks. We investigate the use of a language representation model BERT pretrained on a large-scale corpus of 5 million health-related user reviews in English and Russian. The ensemble of neural networks for extraction and normalization of adverse drug reactions ranked first among 7 teams at the SMM4H 2020 Task 3 and obtained a relaxed F1 of 46%. The BERT-based multilingual model for classification of English and Russian tweets that report adverse reactions ranked second among 16 and 7 teams at two first subtasks of the SMM4H 2019 Task 2 and obtained a relaxed F1 of 58% on English tweets and 51% on Russian tweets.

In this work, we consider the medical concept normalization problem, i.e., the problem of mapping a health-related entity mention in a free-form text to a concept in a controlled vocabulary, usually to the standard thesaurus in the Unified Medical Language System (UMLS). This is a challenging task since medical terminology is very different when coming from health care professionals or from the general public in the form of social media texts. We approach it as a sequence learning problem with powerful neural networks such as recurrent neural networks and contextualized word representation models trained to obtain semantic representations of social media expressions. Our experimental evaluation over three different benchmarks shows that neural architectures leverage the semantic meaning of the entity mention and significantly outperform existing state of the art models.

Detection of adverse drug reactions in postapproval periods is a crucial challenge for pharmacology. Social media and electronic clinical reports are becoming increasingly popular as a source for obtaining health related information. In this work, we focus on extraction information of adverse drug reactions from various sources of biomedical textbased information, including biomedical literature and social media. We formulate the problem as a binary classification task and compare the performance of four state-of-the-art attention-based neural networks in terms of the F-measure. We show the effectiveness of these methods on four different benchmarks.

News articles often convey attitudes between the mentioned subjects, which is essential for understanding the described situation. In this paper, we describe a new approach to distant supervision for extracting sentiment attitudes between named entities mentioned in texts. Two factors (pair-based and frame-based) were used to automatically label an extensive news collection, dubbed as RuAttitudes. The latter became a basis for adaptation and training convolutional architectures, including piecewise max pooling and full use of information across different sentences. The results show that models, trained with RuAttitudes, outperform ones that were trained with only supervised learning approach and achieve 13.4% increase in F1-score on RuSentRel collection.

This paper describes a system developed for the Social Media Mining for Health (SMM4H) 2019 shared tasks. Specifically, we participated in three tasks. The goals of the first two tasks are to classify whether a tweet contains mentions of adverse drug reactions (ADR) and extract these mentions, respectively. The objective of the third task is to build an end-to-end solution: first, detect ADR mentions and then map these entities to concepts in a controlled vocabulary. We investigate the use of a language representation model BERT trained to obtain semantic representations of social media texts. Our experiments on a dataset of user reviews showed that BERT is superior to state-of-the-art models based on recurrent neural networks. The BERT-based system for Task 1 obtained an F1 of 57.38%, with improvements up to +7.19% F1 over a score averaged across all 43 submissions. The ensemble of neural networks with a voting scheme for named entity recognition ranked first among 9 teams at the SMM4H 2019 Task 2 and obtained a relaxed F1 of 65.8%. The end-to-end model based on BERT for ADR normalization ranked first at the SMM4H 2019 Task 3 and obtained a relaxed F1 of 43.2%.

We propose a novel Aspect-based Rating Prediction model (AspeRa) that estimates user rating based on review texts for the items. It is based on aspect extraction with neural networks and combines the advantages of deep learning and topic modeling. It is mainly designed for recommendations, but an important secondary goal of AspeRa is to discover coherent aspects of reviews that can be used to explain predictions or for user profiling. We conduct a comprehensive empirical study of AspeRa, showing that it outperforms state-of-the-art models in terms of recommendation quality and produces interpretable aspects. This paper is an abridged version of our work (Nikolenko et al., 2019)

This paper presents our experimental work on exploring the potential of neural network models developed for aspect-based sentiment analysis for entity-level adverse drug reaction (ADR) classification. Our goal is to explore how to represent local context around ADR mentions and learn an entity representation, interacting with its context. We conducted extensive experiments on various sources of text-based information, including social media, electronic health records, and abstracts of scientific articles from PubMed. The results show that Interactive Attention Neural Network (IAN) outperformed other models on four corpora in terms of macro F-measure. This work is an abridged version of our recent paper accepted to Programming and Computer Software journal in 2019.