arXiv subjects

Jaewoo Kang

Publications and source records attributed to Jaewoo Kang.

At least 91 records · Page 5Linked to original sources

arXiv2022

Sequence tagging for biomedical extractive question answering

Current studies in extractive question answering (EQA) have modeled the single-span extraction setting, where a single answer span is a label to predict for a given question-passage pair. This setting is natural for general domain EQA as the majority of the questions in the general domain can be answered with a single span. Following general domain EQA models, current biomedical EQA (BioEQA) models utilize the single-span extraction setting with post-processing steps. In this article, we investigate the question distribution across the general and biomedical domains and discover biomedical questions are more likely to require list-type answers (multiple answers) than factoid-type answers (single answer). This necessitates the models capable of producing multiple answers for a question. Based on this preliminary study, we propose a sequence tagging approach for BioEQA, which is a multi-span extraction setting. Our approach directly tackles questions with a variable number of phrases as their answer and can learn to decide the number of answers for a question from training data. Our experimental results on the BioASQ 7b and 8b list-type questions outperformed the best-performing existing models without requiring post-processing steps. Source codes and resources are freely available for download at https://github.com/dmis-lab/SeqTagQA

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arXiv2022

Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction

Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and graph classification. However, since GNNs heavily rely on smoothed node features rather than graph structure, they often show poor performance than simple heuristic methods in link prediction where the structural information, e.g., overlapped neighborhoods, degrees, and shortest paths, is crucial. To address this limitation, we propose Neighborhood Overlap-aware Graph Neural Networks (Neo-GNNs) that learn useful structural features from an adjacency matrix and estimate overlapped neighborhoods for link prediction. Our Neo-GNNs generalize neighborhood overlap-based heuristic methods and handle overlapped multi-hop neighborhoods. Our extensive experiments on Open Graph Benchmark datasets (OGB) demonstrate that Neo-GNNs consistently achieve state-of-the-art performance in link prediction. Our code is publicly available at https://github.com/seongjunyun/Neo_GNNs.

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arXiv2022

Lack of Fluency is Hurting Your Translation Model

Many machine translation models are trained on bilingual corpus, which consist of aligned sentence pairs from two different languages with same semantic. However, there is a qualitative discrepancy between train and test set in bilingual corpus. While the most train sentences are created via automatic techniques such as crawling and sentence-alignment methods, the test sentences are annotated with the consideration of fluency by human. We suppose this discrepancy in training corpus will yield performance drop of translation model. In this work, we define \textit{fluency noise} to determine which parts of train sentences cause them to seem unnatural. We show that \textit{fluency noise} can be detected by simple gradient-based method with pre-trained classifier. By removing \textit{fluency noise} in train sentences, our final model outperforms the baseline on WMT-14 DE$\rightarrow$EN and RU$\rightarrow$EN. We also show the compatibility with back-translation augmentation, which has been commonly used to improve the fluency of the translation model. At last, the qualitative analysis of \textit{fluency noise} provides the insight of what points we should focus on.

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arXiv2022

Consistency Training with Virtual Adversarial Discrete Perturbation

Consistency training regularizes a model by enforcing predictions of original and perturbed inputs to be similar. Previous studies have proposed various augmentation methods for the perturbation but are limited in that they are agnostic to the training model. Thus, the perturbed samples may not aid in regularization due to their ease of classification from the model. In this context, we propose an augmentation method of adding a discrete noise that would incur the highest divergence between predictions. This virtual adversarial discrete noise obtained by replacing a small portion of tokens while keeping original semantics as much as possible efficiently pushes a training model's decision boundary. Experimental results show that our proposed method outperforms other consistency training baselines with text editing, paraphrasing, or a continuous noise on semi-supervised text classification tasks and a robustness benchmark

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arXiv2022

FaVIQ: FAct Verification from Information-seeking Questions

Despite significant interest in developing general purpose fact checking models, it is challenging to construct a large-scale fact verification dataset with realistic real-world claims. Existing claims are either authored by crowdworkers, thereby introducing subtle biases that are difficult to control for, or manually verified by professional fact checkers, causing them to be expensive and limited in scale. In this paper, we construct a large-scale challenging fact verification dataset called FAVIQ, consisting of 188k claims derived from an existing corpus of ambiguous information-seeking questions. The ambiguities in the questions enable automatically constructing true and false claims that reflect user confusions (e.g., the year of the movie being filmed vs. being released). Claims in FAVIQ are verified to be natural, contain little lexical bias, and require a complete understanding of the evidence for verification. Our experiments show that the state-of-the-art models are far from solving our new task. Moreover, training on our data helps in professional fact-checking, outperforming models trained on the widely used dataset FEVER or in-domain data by up to 17% absolute. Altogether, our data will serve as a challenging benchmark for natural language understanding and support future progress in professional fact checking.

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arXiv2022

How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?

The number of biomedical literature on new biomedical concepts is rapidly increasing, which necessitates a reliable biomedical named entity recognition (BioNER) model for identifying new and unseen entity mentions. However, it is questionable whether existing models can effectively handle them. In this work, we systematically analyze the three types of recognition abilities of BioNER models: memorization, synonym generalization, and concept generalization. We find that although current best models achieve state-of-the-art performance on benchmarks based on overall performance, they have limitations in identifying synonyms and new biomedical concepts, indicating they are overestimated in terms of their generalization abilities. We also investigate failure cases of models and identify several difficulties in recognizing unseen mentions in biomedical literature as follows: (1) models tend to exploit dataset biases, which hinders the models' abilities to generalize, and (2) several biomedical names have novel morphological patterns with weak name regularity, and models fail to recognize them. We apply a statistics-based debiasing method to our problem as a simple remedy and show the improvement in generalization to unseen mentions. We hope that our analyses and findings would be able to facilitate further research into the generalization capabilities of NER models in a domain where their reliability is of utmost importance.

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arXiv2022

Regularization for Long Named Entity Recognition

When performing named entity recognition (NER), entity length is variable and dependent on a specific domain or dataset. Pre-trained language models (PLMs) are used to solve NER tasks and tend to be biased toward dataset patterns such as length statistics, surface form, and skewed class distribution. These biases hinder the generalization ability of PLMs, which is necessary to address many unseen mentions in real-world situations. We propose a novel debiasing method RegLER to improve predictions for entities of varying lengths. To close the gap between evaluation and real-world situations, we evaluated PLMs on partitioned benchmark datasets containing unseen mention sets. Here, RegLER shows significant improvement over long-named entities that can predict through debiasing on conjunction or special characters within entities. Furthermore, there is a severe class imbalance in most NER datasets, causing easy-negative examples to dominate during training, such as "The". Our approach alleviates skewed class distribution by reducing the influence of easy-negative examples. Extensive experiments on the biomedical and general domains demonstrated the generalization capabilities of our method. To facilitate reproducibility and future work, we release our code."https://github.com/minstar/RegLER"

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arXiv2021

Improving Tagging Consistency and Entity Coverage for Chemical Identification in Full-text Articles

This paper is a technical report on our system submitted to the chemical identification task of the BioCreative VII Track 2 challenge. The main feature of this challenge is that the data consists of full-text articles, while current datasets usually consist of only titles and abstracts. To effectively address the problem, we aim to improve tagging consistency and entity coverage using various methods such as majority voting within the same articles for named entity recognition (NER) and a hybrid approach that combines a dictionary and a neural model for normalization. In the experiments on the NLM-Chem dataset, we show that our methods improve models' performance, particularly in terms of recall. Finally, in the official evaluation of the challenge, our system was ranked 1st in NER by significantly outperforming the baseline model and more than 80 submissions from 16 teams.

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arXiv2021

Pandemics are catalysts of scientific novelty: Evidence from COVID-19

Scientific novelty drives the efforts to invent new vaccines and solutions during the pandemic. First-time collaboration and international collaboration are two pivotal channels to expand teams' search activities for a broader scope of resources required to address the global challenge, which might facilitate the generation of novel ideas. Our analysis of 98,981 coronavirus papers suggests that scientific novelty measured by the BioBERT model that is pre-trained on 29 million PubMed articles, and first-time collaboration increased after the outbreak of COVID-19, and international collaboration witnessed a sudden decrease. During COVID-19, papers with more first-time collaboration were found to be more novel and international collaboration did not hamper novelty as it had done in the normal periods. The findings suggest the necessity of reaching out for distant resources and the importance of maintaining a collaborative scientific community beyond nationalism during a pandemic.

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arXiv2021

Can Language Models be Biomedical Knowledge Bases?

Pre-trained language models (LMs) have become ubiquitous in solving various natural language processing (NLP) tasks. There has been increasing interest in what knowledge these LMs contain and how we can extract that knowledge, treating LMs as knowledge bases (KBs). While there has been much work on probing LMs in the general domain, there has been little attention to whether these powerful LMs can be used as domain-specific KBs. To this end, we create the BioLAMA benchmark, which is comprised of 49K biomedical factual knowledge triples for probing biomedical LMs. We find that biomedical LMs with recently proposed probing methods can achieve up to 18.51% Acc@5 on retrieving biomedical knowledge. Although this seems promising given the task difficulty, our detailed analyses reveal that most predictions are highly correlated with prompt templates without any subjects, hence producing similar results on each relation and hindering their capabilities to be used as domain-specific KBs. We hope that BioLAMA can serve as a challenging benchmark for biomedical factual probing.

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arXiv2021

Learn to Resolve Conversational Dependency: A Consistency Training Framework for Conversational Question Answering

One of the main challenges in conversational question answering (CQA) is to resolve the conversational dependency, such as anaphora and ellipsis. However, existing approaches do not explicitly train QA models on how to resolve the dependency, and thus these models are limited in understanding human dialogues. In this paper, we propose a novel framework, ExCorD (Explicit guidance on how to resolve Conversational Dependency) to enhance the abilities of QA models in comprehending conversational context. ExCorD first generates self-contained questions that can be understood without the conversation history, then trains a QA model with the pairs of original and self-contained questions using a consistency-based regularizer. In our experiments, we demonstrate that ExCorD significantly improves the QA models' performance by up to 1.2 F1 on QuAC, and 5.2 F1 on CANARD, while addressing the limitations of the existing approaches.

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arXiv2021

Graph Transformer Networks: Learning Meta-path Graphs to Improve GNNs

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed and homogeneous graphs. The limitations especially become problematic when learning representations on a misspecified graph or a heterogeneous graph that consists of various types of nodes and edges. To address this limitations, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which preclude noisy connections and include useful connections (e.g., meta-paths) for tasks, while learning effective node representations on the new graphs in an end-to-end fashion. We further propose enhanced version of GTNs, Fast Graph Transformer Networks (FastGTNs), that improve scalability of graph transformations. Compared to GTNs, FastGTNs are 230x faster and use 100x less memory while allowing the identical graph transformations as GTNs. In addition, we extend graph transformations to the semantic proximity of nodes allowing non-local operations beyond meta-paths. Extensive experiments on both homogeneous graphs and heterogeneous graphs show that GTNs and FastGTNs with non-local operations achieve the state-of-the-art performance for node classification tasks. The code is available: https://github.com/seongjunyun/Graph_Transformer_Networks

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arXiv2021

Learning by Semantic Similarity Makes Abstractive Summarization Better

By harnessing pre-trained language models, summarization models had rapid progress recently. However, the models are mainly assessed by automatic evaluation metrics such as ROUGE. Although ROUGE is known for having a positive correlation with human evaluation scores, it has been criticized for its vulnerability and the gap between actual qualities. In this paper, we compare the generated summaries from recent LM, BART, and the reference summaries from a benchmark dataset, CNN/DM, using a crowd-sourced human evaluation metric. Interestingly, model-generated summaries receive higher scores relative to reference summaries. Stemming from our experimental results, we first argue the intrinsic characteristics of the CNN/DM dataset, the progress of pre-trained language models, and their ability to generalize on the training data. Finally, we share our insights into the model-generated summaries and presents our thought on learning methods for abstractive summarization.

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arXiv2021

Learning Dense Representations of Phrases at Scale

Open-domain question answering can be reformulated as a phrase retrieval problem, without the need for processing documents on-demand during inference (Seo et al., 2019). However, current phrase retrieval models heavily depend on sparse representations and still underperform retriever-reader approaches. In this work, we show for the first time that we can learn dense representations of phrases alone that achieve much stronger performance in open-domain QA. We present an effective method to learn phrase representations from the supervision of reading comprehension tasks, coupled with novel negative sampling methods. We also propose a query-side fine-tuning strategy, which can support transfer learning and reduce the discrepancy between training and inference. On five popular open-domain QA datasets, our model DensePhrases improves over previous phrase retrieval models by 15%-25% absolute accuracy and matches the performance of state-of-the-art retriever-reader models. Our model is easy to parallelize due to pure dense representations and processes more than 10 questions per second on CPUs. Finally, we directly use our pre-indexed dense phrase representations for two slot filling tasks, showing the promise of utilizing DensePhrases as a dense knowledge base for downstream tasks.

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arXiv2021

HOTR: End-to-End Human-Object Interaction Detection with Transformers

Human-Object Interaction (HOI) detection is a task of identifying "a set of interactions" in an image, which involves the i) localization of the subject (i.e., humans) and target (i.e., objects) of interaction, and ii) the classification of the interaction labels. Most existing methods have indirectly addressed this task by detecting human and object instances and individually inferring every pair of the detected instances. In this paper, we present a novel framework, referred to by HOTR, which directly predicts a set of triplets from an image based on a transformer encoder-decoder architecture. Through the set prediction, our method effectively exploits the inherent semantic relationships in an image and does not require time-consuming post-processing which is the main bottleneck of existing methods. Our proposed algorithm achieves the state-of-the-art performance in two HOI detection benchmarks with an inference time under 1 ms after object detection.

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arXiv2021

Look at the First Sentence: Position Bias in Question Answering

Many extractive question answering models are trained to predict start and end positions of answers. The choice of predicting answers as positions is mainly due to its simplicity and effectiveness. In this study, we hypothesize that when the distribution of the answer positions is highly skewed in the training set (e.g., answers lie only in the k-th sentence of each passage), QA models predicting answers as positions can learn spurious positional cues and fail to give answers in different positions. We first illustrate this position bias in popular extractive QA models such as BiDAF and BERT and thoroughly examine how position bias propagates through each layer of BERT. To safely deliver position information without position bias, we train models with various de-biasing methods including entropy regularization and bias ensembling. Among them, we found that using the prior distribution of answer positions as a bias model is very effective at reducing position bias, recovering the performance of BERT from 37.48% to 81.64% when trained on a biased SQuAD dataset.

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arXiv2021

Transferability of Natural Language Inference to Biomedical Question Answering

Biomedical question answering (QA) is a challenging task due to the scarcity of data and the requirement of domain expertise. Pre-trained language models have been used to address these issues. Recently, learning relationships between sentence pairs has been proved to improve performance in general QA. In this paper, we focus on applying BioBERT to transfer the knowledge of natural language inference (NLI) to biomedical QA. We observe that BioBERT trained on the NLI dataset obtains better performance on Yes/No (+5.59%), Factoid (+0.53%), List type (+13.58%) questions compared to performance obtained in a previous challenge (BioASQ 7B Phase B). We present a sequential transfer learning method that significantly performed well in the 8th BioASQ Challenge (Phase B). In sequential transfer learning, the order in which tasks are fine-tuned is important. We measure an unanswerable rate of the extractive QA setting when the formats of factoid and list type questions are converted to the format of the Stanford Question Answering Dataset (SQuAD).

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arXiv2021

"Killing Me" Is Not a Spoiler: Spoiler Detection Model using Graph Neural Networks with Dependency Relation-Aware Attention Mechanism

Several machine learning-based spoiler detection models have been proposed recently to protect users from spoilers on review websites. Although dependency relations between context words are important for detecting spoilers, current attention-based spoiler detection models are insufficient for utilizing dependency relations. To address this problem, we propose a new spoiler detection model called SDGNN that is based on syntax-aware graph neural networks. In the experiments on two real-world benchmark datasets, we show that our SDGNN outperforms the existing spoiler detection models.

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