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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

IJCNLP-AACL 2021

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

entity extraction

relation extraction

information extraction

**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). 

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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).

poster

Recently multimodal transformer models have gained popularity because their performance on language and vision tasks suggest they learn rich visual-linguistic representations. Focusing on zero-shot image retrieval tasks, we study three important factors which can impact the quality of learned representations: pretraining data, the attention mechanism, and loss functions. By pretraining models on six datasets, we observe that dataset noise and language similarity to our downstream task are important indicators of model performance. Through architectural analysis, we learn that models with a multimodal attention mechanism can outperform deeper models with modality specific attention mechanisms. Finally, we show that successful contrastive losses used in the self-supervised learning literature do not yield similar performance gains when used in multimodal transformers.

Decoupling the Role of Data, Attention, and Losses in Multimodal Transformers

We study the problem of learning a named entity recognition (NER) tagger using noisy labels from multiple weak supervision sources. Though cheap to obtain, the labels from weak supervision sources are often incomplete, inaccurate, and contradictory, making it difficult to learn an accurate NER model. To address this challenge, we propose a conditional hidden Markov model (CHMM), which can effectively infer true labels from multi-source noisy labels in an unsupervised way. CHMM enhances the classic hidden Markov model with the contextual representation power of pre-trained language models. Specifically, CHMM learns token-wise transition and emission probabilities from the BERT embeddings of the input tokens to infer the latent true labels from noisy observations. We further refine CHMM with an alternate-training approach (CHMM-ALT). It fine-tunes a BERT-NER model with the labels inferred by CHMM, and this BERT-NER's output is regarded as an additional weak source to train the CHMM in return. Experiments on four NER benchmarks from various domains show that our method outperforms state-of-the-art weakly supervised NER models by wide margins.

BERTifying the Hidden Markov Model for Multi-Source Weakly Supervised Named Entity Recognition

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

In this task, we applied a two-phase training on RoBERTa model. Phase One pre-trains RoBERTa on LIME labeled Reddit Comments. Phase Two fine-tunes the model on organizer-provided data (Gold Dataset)

Investigating Toxic Span Detection Using RoBERTa Pre-training

We describe MeasEval, a SemEval task of extracting counts, measurements, and related context from scientific documents, which is of significant importance to the creation of Knowledge Graphs that distill information from the scientific literature. This is a new task in 2021, for which over 75 submissions from 25 participants were received. We expect the data developed for this task and the findings reported to be valuable to the scientific knowledge extraction, metrology, and automated knowledge base construction communities.

SemEval-2021 Task 8: MeasEval – Extracting Counts and Measurements and their Related Contexts

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.

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

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