Ireland

This paper proposes novel drug-protein relation extraction models that indirectly utilize distant supervision data. Concretely, instead of adding distant supervision data to the manually annotated training data, our models incorporate distantly supervised models that are relation extraction models trained with distant supervision data. Distantly supervised learning has been proposed to generate a large amount of pseudo-training data at low cost. However, there is still a problem of low prediction performance due to the inclusion of mislabeled data. Therefore, several methods have been proposed to suppress the effects of noisy cases by utilizing some manually annotated training data. However, their performance is lower than that of supervised learning on manually annotated data because mislabeled data that cannot be fully suppressed becomes noise when training the model. To overcome this issue, our methods indirectly utilize distant supervision data with manually annotated training data. The experimental results on the DrugProt corpus in the BioCreative VII Track 1 showed that our proposed model can consistently improve the supervised models in different settings.

ACL 2022

Improving Supervised Drug-Protein Relation Extraction with Distantly Supervised Models

bioinfomatics

relation extraction

distant supervision

# Welcome everyone to ACL 2022!

The 60th Annual Meeting of the Association for Computational Linguistics is taking place May 22-27, 2022 as a hybrid event, in Dublin and online. We are happy to welcome all of you to this anniversary edition with an almost 50-50 in-person and virtual participation. 
The main conference program features oral presentations, in-person and virtual posters and demo sessions, a plenary session for our best paper presentations and awards, three amazing keynote events and two new initiatives of invited talks: Spotlight Talks for Young Rising Stars (STIRS) and The Next Big Idea Talks. Posters (including Findings of ACL 2022) and demos are grouped by areas for both the in-person and the virtual sessions. For the virtual component, the talks will be on Zoom and the posters and the demos will be in GatherTown. The Student Research Workshop will have an oral session and a poster session as part of Poster Session 1. The program also features eight Tutorials and 28 Workshops. 

 
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The Association for Computational Linguistics (ACL) is the premier international scientific and professional society for people working on computational problems involving human language, a field often referred to as either computational linguistics or natural language processing (NLP). 

workshop paper

Cancer immunology research involves several important cell and protein factors. Extracting the information of such cells and proteins and the interactions between them from text are crucial in text mining for cancer immunology research. However, there are few available datasets for these entities, and the amount of annotated documents is not sufficient compared with other major named entity types. In this work, we introduce our automatically annotated dataset of key named entities, i.e., T-cells, cytokines, and transcription factors, which engages the recent cancer immunotherapy. The entities are annotated based on the UniProtKB knowledge base using dictionary matching. We build a neural named entity recognition (NER) model to be trained on this dataset and evaluate it on a manually-annotated data. Experimental results show that we can achieve a promising NER performance even though our data is automatically annotated. Our dataset also enhances the NER performance when combined with existing data, especially gaining improvement in yet investigated named entities such as cytokines and transcription factors.

Named Entity Recognition for Cancer Immunology Research Using Distant Supervision

In this presentation, we propose the two-stage method with cross-modal fusion using the pre-trained language model. We report the performance of our model compared with baselines on the test set in monomodal and multimodal settings. The experimental results show that our method obtains the best performance on the seen test set and unseen official test set, which proves that our method is effective. Finally, we ranked the Top-1 in this shared task 1 of the BioNLP.


VPAI Lab at MedVidQA 2022: A Two Stage Cross-modal Fusion Method for Medical Instructional Video Classification

In this paper, we present an overview of the MedVidQA 2022 shared task, collocated with the 21st BioNLP workshop at ACL 2022. The shared task addressed two of the challenges faced by medical video question answering: (i) a video classification task that explores new approaches to medical video understanding (labeling), and (ii) a visual answer localization task. Visual answer localization refers to the identification of the relevant temporal segments (start and end timestamps) in the video where the answer to the medical question is being shown or illustrated. A total of thirteen teams participated in the shared task challenges, with eleven system descriptions submitted to the workshop. The descriptions present monomodal and multi-modal approaches developed for medical video classification and visual answer localization. This paper describes the tasks, the datasets, evaluation metrics, and baseline systems for both tasks. Finally, the paper summarizes the techniques and results of the evaluation of the various approaches explored by the participating teams.

Overview of the MedVidQA 2022 Shared Task on Medical Video Question-Answering

Algorithmic oppression is an urgent and persistent problem in speech and language technologies. Considering power relations embedded in datasets before compiling or using them to train or test speech and language technologies is essential to designing less harmful, more just technologies. This paper presents a reflective exercise to recognise and challenge gaps and the power relations they reveal in speech and language datasets by applying principles of Data Feminism and Design Justice, and building on work on dataset documentation and sociolinguistics.

Mind the data gap(s): Investigating power in speech and language datasets

Current language technology is ubiquitous and directly influences individuals' lives worldwide. Given the recent trend in AI on training and constantly releasing new and powerful large language models (LLMs), there is a need to assess their biases and potential concrete consequences. While some studies have highlighted the shortcomings of these models, there is only little on the negative impact of LLMs on LGBTQIA+ individuals. In this paper, we investigated a state-of-the-art template-based approach for measuring the harmfulness of English LLMs sentence completion when the subjects belong to the LGBTQIA+ community. Our findings show that, on average, the most likely LLM-generated completion is an identity attack 13% of the time. Our results raise serious concerns about the applicability of these models in production environments.

Measuring Harmful Sentence Completion in Language Models for LGBTQIA+ Individuals

Deaf and hard of hearing individuals regularly rely on captioning while watching live TV. Live TV captioning is evaluated by regulatory agencies using various caption evaluation metrics. However, caption evaluation metrics are often not informed by preferences of DHH users or how meaningful the captions are. There is a need to construct caption evaluation metrics that take the relative importance of words in a transcript into account. We conducted correlation analysis between two types of word embeddings and human-annotated labeled word-importance scores in existing corpus. We found that normalized contextualized word embeddings generated using BERT correlated better with manually annotated importance scores than word2vec-based word embeddings. We make available a pairing of word embeddings and their human-annotated importance scores. We also provide proof-of-concept utility by training word importance models, achieving an F1-score of 0.57 in the 6-class word importance classification task.

Using BERT Embeddings to Model Word Importance in Conversational Transcripts for Deaf and Hard of Hearing Users

This paper presents a new method for automatic detection of gendered terms in large-scale language datasets. Currently, the evaluation of gender bias in natural language processing relies on the use of manually compiled lexicons of gendered expressions, such as pronouns and words that imply gender. However, manual compilation of lists with lexical gender can lead to static information if lists are not periodically updated and often involve value judgements by individual annotators and researchers. Moreover, terms not included in the lexicons fall out of the range of analysis. To address these issues, we devised a scalable dictionary-based method to automatically detect lexical gender that can provide a dynamic, up-to-date analysis with high coverage. Our approach reaches over 80% accuracy in determining the lexical gender of words retrieved randomly from a Wikipedia sample and when testing on a list of gendered words used in previous research.

Inferring Gender: A Scalable Methodology for Gender Detection with Online Lexical Databases

An explosion in the popularity of transformer-based language models (such as GPT-3, BERT, RoBERTa, and ALBERT) has opened the doors to new machine learning applications involving language modeling, text generation, and more. However, recent scrutiny reveals that these language models contain inherent biases towards certain demographics reflected in their training data. While research has tried mitigating this problem, existing approaches either fail to remove the bias completely, degrade performance ("catastrophic forgetting"), or are costly to execute. This work examines how to reduce gender bias in a GPT-2 language model by fine-tuning less than 1% of its parameters. Through quantitative benchmarks, we show that this is a viable way to reduce prejudice in pre-trained language models while remaining cost-effective at scale.

Debiasing Pre-Trained Language Models via Efficient Fine-Tuning


Many datasets contain personally identifiable information, or PII, which poses privacy risks to individuals. PII masking is commonly used to redact personal information such as names, addresses, and phone numbers from text data. Most modern PII masking pipelines involve machine learning algorithms. However, these systems may vary in performance, such that individuals from particular demographic groups bear a higher risk for having their personal information exposed. In this paper, we evaluate the performance of three off-the-shelf PII masking systems on name detection and redaction. We generate data using names and templates from the customer service domain. We find that an open-source RoBERTa-based system shows fewer disparities than the commercial models we test. However, all systems demon- strate significant differences in error rate based on demographics. In particular, the highest error rates occurred for names associated with Black and Asian/Pacific Islander individuals.

Behind the Mask: Demographic bias in name detection for PII masking

As natural language processing systems become more widespread, it is necessary to address fairness issues in their implementation and deployment to ensure that their negative impacts on society are understood and minimized. However, there is limited work that studies fairness using a multilingual and intersectional framework or on downstream tasks. In this paper, we introduce four multilingual Equity Evaluation Corpora, supplementary test sets designed to measure social biases, and a novel statistical framework for studying unisectional and intersectional social biases in natural language processing. We use these tools to measure gender, racial, ethnic, and intersectional social biases across five models trained on emotion regression tasks in English, Spanish, and Arabic. We find that many systems demonstrate statistically significant unisectional and intersectional social biases.

Improving Supervised Drug-Protein Relation Extraction with Distantly Supervised Models

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Named Entity Recognition for Cancer Immunology Research Using Distant Supervision

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Improving Supervised Drug-Protein Relation Extraction with Distantly Supervised Models

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Next from ACL 2022

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A sequence-to-sequence approach for document-level relation extraction

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Downloads