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Biomedical Information Extraction from scientific literature presents two unique and non-trivial challenges.
First, compared with general natural language texts, sentences from scientific papers usually possess wider contexts between knowledge elements. Moreover, comprehending the fine-grained scientific entities and events urgently requires domain-specific background knowledge. In this paper, we propose a novel biomedical Information Extraction (IE) model to tackle these two challenges and extract scientific entities and events from English research papers. We perform Abstract Meaning Representation (AMR) to compress the wide context to uncover a clear semantic structure for each complex sentence. Besides, we construct the sentence-level knowledge graph from an external knowledge base and use it to enrich the AMR graph to improve the model&#39;s understanding of complex scientific concepts. We use an edge-conditioned graph attention network to encode the knowledge-enriched AMR graph for biomedical IE tasks.
Experiments on the GENIA 2011 dataset show that the AMR and external knowledge have contributed 1.8% and 3.0% absolute F-score gains respectively. In order to evaluate the impact of our approach on real-world problems that involve topic-specific fine-grained knowledge elements, we have also created a new ontology and annotated corpus for entity and event extraction for the COVID-19 scientific literature, which can serve as a new benchmark for the biomedical IE community.

IJCNLP-AACL 2021

Fine-grained Information Extraction from Biomedical Literature based on Knowledge-enriched Abstract Meaning Representation

external knowledge graph

biomedical event extraction

abstract meaning representation

**Welcome to ACL-IJCNLP 2021!**

The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP). 

As in previous years, the program of the conference includes a poster session, tutorials, workshops and demonstrations in addition to the main conference.


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The great event is jointly organized by the Association for Computational Linguistics (ACL) and Asian Federation of Natural Language Processing (AFNLP).

Biomedical Information Extraction from scientific literature presents two unique and non-trivial challenges.
First, compared with general natural language texts, sentences from scientific papers usually possess wider contexts between knowledge elements. Moreover, comprehending the fine-grained scientific entities and events urgently requires domain-specific background knowledge. In this paper, we propose a novel biomedical Information Extraction (IE) model to tackle these two challenges and extract scientific entities and events from English research papers. We perform Abstract Meaning Representation (AMR) to compress the wide context to uncover a clear semantic structure for each complex sentence. Besides, we construct the sentence-level knowledge graph from an external knowledge base and use it to enrich the AMR graph to improve the model's understanding of complex scientific concepts. We use an edge-conditioned graph attention network to encode the knowledge-enriched AMR graph for biomedical IE tasks.
Experiments on the GENIA 2011 dataset show that the AMR and external knowledge have contributed 1.8% and 3.0% absolute F-score gains respectively. In order to evaluate the impact of our approach on real-world problems that involve topic-specific fine-grained knowledge elements, we have also created a new ontology and annotated corpus for entity and event extraction for the COVID-19 scientific literature, which can serve as a new benchmark for the biomedical IE community.

poster

Distant supervision for relation extraction provides uniform bag labels for each sentence inside the bag, while accurate sentence labels are important for downstream applications that need the exact relation type. Directly using bag labels for sentence-level training will introduce much noise, thus severely degrading performance. In this work, we propose the use of negative training (NT), in which a model is trained using complementary labels regarding that ``the instance does not belong to these complementary labels". Since the probability of selecting a true label as a complementary label is low, NT provides less noisy information. Furthermore, the model trained with NT is able to separate the noisy data from the training data. Based on NT, we propose a sentence-level framework, SENT, for distant relation extraction. SENT not only filters the noisy data to construct a cleaner dataset, but also performs a re-labeling process to transform the noisy data into useful training data, thus further benefiting the model's performance. Experimental results show the significant improvement of the proposed method over previous methods on sentence-level evaluation and de-noise effect.

SENT: Sentence-level Distant Relation Extraction via Negative Training

Medical named entity recognition (NER) and normalization (NEN) are fundamental for constructing knowledge graphs and building QA systems. Existing implementations for medical NER and NEN are suffered from the error propagation between the two tasks. The mispredicted mentions from NER will directly influence the results of NEN. Therefore, the NER module is the bottleneck of the whole system. Besides, the learnable features for both tasks are beneficial to improving the model performance. To avoid the disadvantages of existing models and exploit the generalized representation across the two tasks, we design an end-to-end progressive multi-task learning model for jointly modeling medical NER and NEN in an effective way. There are three level tasks with progressive difficulty in the framework. The progressive tasks can reduce the error propagation with the incremental task settings which implies the lower level tasks gain the supervised signals other than errors from the higher level tasks to improve their performances. Besides, the context features are exploited to enrich the semantic information of entity mentions extracted by NER. The performance of NEN profits from the enhanced entity mention features. The standard entities from knowledge bases are introduced into the NER module for extracting corresponding entity mentions correctly. The empirical results on two publicly available medical literature datasets demonstrate the superiority of our method over nine typical methods.

An End-to-End Progressive Multi-Task Learning Framework for Medical Named Entity Recognition and Normalization

Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential growth of biomedical publications, models that do not go beyond their fixed set of parameters will likely fall behind. Inspired by how humans look up relevant information to comprehend a scientific text, we present a novel framework that utilizes external knowledge for joint entity and relation extraction named KECI (Knowledge-Enhanced Collective Inference). Given an input text, KECI first constructs an initial span graph representing its initial understanding of the text. It then uses an entity linker to form a knowledge graph containing relevant background knowledge for the the entity mentions in the text. To make the final predictions, KECI fuses the initial span graph and the knowledge graph into a more refined graph using an attention mechanism. KECI takes a collective approach to link mention spans to entities by integrating global relational information into local representations using graph convolutional networks. Our experimental results show that the framework is highly effective, achieving new state-of-the-art results in two different benchmark datasets: BioRelEx (binding interaction detection) and ADE (adverse drug event extraction). For example, KECI achieves absolute improvements of 4.59% and 4.91% in F1 scores over the state-of-the-art on the BioRelEx entity and relation extraction tasks

Joint Biomedical Entity and Relation Extraction with Knowledge-Enhanced Collective Inference

Few-shot relation extraction (FSRE) is of great importance in long-tail distribution problem, especially in special domain with low-resource data. Most existing FSRE algorithms fail to accurately classify the relations merely based on the information of the sentences together with the recognized entity pairs, due to limited samples and lack of knowledge. To address this problem, in this paper, we proposed a novel entity CONCEPT-enhanced FEw-shot Relation Extraction scheme (ConceptFERE), which introduces the inherent concepts of entities to provide clues for relation prediction and boost the relations classification performance. Firstly, a concept-sentence attention module is developed to select the most appropriate concept from multiple concepts of each entity by calculating the semantic similarity between sentences and concepts. Secondly, a self-attention based fusion module is presented to bridge the gap of concept embedding and sentence embedding from different semantic spaces. Extensive experiments on the FSRE benchmark dataset FewRel have demonstrated the effectiveness and the superiority of the proposed ConceptFERE scheme as compared to the state-of-the-art baselines. Code is available at https://github.com/LittleGuoKe/ConceptFERE.

Entity Concept-enhanced Few-shot Relation Extraction

This paper presents the Source-Free Domain Adaptation shared task held within SemEval-2021. The aim of the task was to explore adaptation of machine-learning models in the face of data sharing constraints. Specifically, we consider the scenario where annotations exist for a domain but cannot be shared. Instead, participants are provided with models trained on that (source) data. Participants also receive some labeled data from a new (development) domain on which to explore domain adaptation algorithms. Participants are then tested on data representing a new (target) domain. We explored this scenario with two different semantic tasks: negation detection (a text classification task) and time expression recognition (a sequence tagging task).

SemEval-2021 Task 10: Source-Free Domain Adaptationfor Semantic Processing

There is currently a gap between the natural language expression of scholarly publications and their structured semantic content modeling to enable intelligent content search. With the volume of research growing exponentially every year, a search feature operating over semantically structured content is compelling. The SemEval-2021 Shared Task NLPContributionGraph (a.k.a. 'the NCG task') tasks participants to develop automated systems that structure contributions from NLP scholarly articles in the English language. Being the first-of-its-kind in the SemEval series, the task released structured data from NLP scholarly articles at three levels of information granularity, i.e. at sentence-level, phrase-level, and phrases organized as triples toward Knowledge Graph (KG) building. The sentence-level annotations comprised the few sentences about the article's contribution. The phrase-level annotations were scientific term and predicate phrases from the contribution sentences. Finally, the triples constituted the research overview KG. For the Shared Task, participating systems were then expected to automatically classify contribution sentences, extract scientific terms and relations from the sentences, and organize them as KG triples.

Overall, the task drew a strong participation demographic of seven teams and 27 participants. The best end-to-end task system classified contribution sentences at 57.27% F1, phrases at 46.41% F1, and triples at 22.28% F1. While the absolute performance to generate triples remains low, in the conclusion of this article, the difficulty of producing such data and as a consequence of modeling it is highlighted.

SemEval-2021 Task 11: NLPContributionGraph - Structuring Scholarly NLP Contributions for a Research Knowledge Graph

In this presentation, we introduce the first SemEval task on Multilingual and Cross-Lingual Word-in-Context disambiguation (MCL-WiC). This task allows the largely under-investigated inherent ability of systems to discriminate between word senses within and across languages to be evaluated, dropping the requirement of a fixed sense inventory.

Multilingual and Cross-lingual Word-in-Context Disambiguation (MCL-WiC)

This paper presents the results and main findings of SemEval-2021 Task 1 - Lexical Complexity Prediction. We provided participants with an augmented version of the CompLex Corpus \cite{shardlow-etal-2020-complex}. CompLex is an English multi-domain corpus in which words and multi-word expressions (MWEs) were annotated with respect to their complexity using a five point Likert scale. SemEval-2021 Task 1 featured two Sub-tasks: Sub-task 1 focused on single words and Sub-task 2 focused on MWEs. The competition attracted 198 teams in total, of which 54 teams submitted official runs on the test data to Sub-task 1 and 37 to Sub-task 2.

SemEval-2021 Task 1: Lexical Complexity Prediction

We describe SemEval-2021 task 6 on Detection of Persuasion Techniques in Texts and Images: the data, the annotation guidelines, the evaluation setup, the results, and the participating systems. The task focused on memes and had three subtasks: (i) detecting the techniques in the text, (ii) detecting the text spans where the techniques are used, and (iii) detecting techniques in the entire meme, i.e., both in the text and in the image. It was a popular task, attracting 71 registrations, and 22 teams that eventually made an official submission on the test set. The evaluation results for the third subtask confirmed the importance of both modalities, the text and the image. Moreover, some teams reported benefits when not just combining the two modalities, e.g., by using early or late fusion, but rather modeling the interaction between them in a joint model.

SemEval-2021 Task 6: Detection of Persuasion Techniques in Texts and Images

Disagreement between coders is ubiquitous in virtually all datasets annotated with human judgements in both natural language processing and computer vision. However, most supervised machine learning methods assumethat a single preferred interpretation exists for each item, which is at best an idealization. The aim of the SemEval-2021 shared task on Learning with Disagreements (Le-wi-Di) wasto provide a unified testing framework for methods for learning from data containing multiple and possibly contradictory annotations covering the best-known datasets containing information about disagreements for interpreting language and classifying images. In this paper we describe the shared task and its results.

Fine-grained Information Extraction from Biomedical Literature based on Knowledge-enriched Abstract Meaning Representation

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