arXiv subjects

Hyunjae Kim

Publications and source records attributed to Hyunjae Kim.

At least 37 records · Page 2Linked to original sources

arXiv2024

Augmenting Biomedical Named Entity Recognition with General-domain Resources

Training a neural network-based biomedical named entity recognition (BioNER) model usually requires extensive and costly human annotations. While several studies have employed multi-task learning with multiple BioNER datasets to reduce human effort, this approach does not consistently yield performance improvements and may introduce label ambiguity in different biomedical corpora. We aim to tackle those challenges through transfer learning from easily accessible resources with fewer concept overlaps with biomedical datasets. We proposed GERBERA, a simple-yet-effective method that utilized general-domain NER datasets for training. We performed multi-task learning to train a pre-trained biomedical language model with both the target BioNER dataset and the general-domain dataset. Subsequently, we fine-tuned the models specifically for the BioNER dataset. We systematically evaluated GERBERA on five datasets of eight entity types, collectively consisting of 81,410 instances. Despite using fewer biomedical resources, our models demonstrated superior performance compared to baseline models trained with additional BioNER datasets. Specifically, our models consistently outperformed the baseline models in six out of eight entity types, achieving an average improvement of 0.9% over the best baseline performance across eight entities. Our method was especially effective in amplifying performance on BioNER datasets characterized by limited data, with a 4.7% improvement in F1 scores on the JNLPBA-RNA dataset. This study introduces a new training method that leverages cost-effective general-domain NER datasets to augment BioNER models. This approach significantly improves BioNER model performance, making it a valuable asset for scenarios with scarce or costly biomedical datasets.

cs.CL↗

arXiv2024

Small Language Models Learn Enhanced Reasoning Skills from Medical Textbooks

While recent advancements in commercial large language models (LM) have shown promising results in medical tasks, their closed-source nature poses significant privacy and security concerns, hindering their widespread use in the medical field. Despite efforts to create open-source models, their limited parameters often result in insufficient multi-step reasoning capabilities required for solving complex medical problems. To address this, we introduce Meerkat, a new family of medical AI systems ranging from 7 to 70 billion parameters. The models were trained using our new synthetic dataset consisting of high-quality chain-of-thought reasoning paths sourced from 18 medical textbooks, along with diverse instruction-following datasets. Our systems achieved remarkable accuracy across six medical benchmarks, surpassing the previous best models such as MediTron and BioMistral, and GPT-3.5 by a large margin. Notably, Meerkat-7B surpassed the passing threshold of the United States Medical Licensing Examination (USMLE) for the first time for a 7B-parameter model, while Meerkat-70B outperformed GPT-4 by an average of 1.3%. Additionally, Meerkat-70B correctly diagnosed 21 out of 38 complex clinical cases, outperforming humans' 13.8 and closely matching GPT-4's 21.8. Our systems offered more detailed free-form responses to clinical queries compared to existing small models, approaching the performance level of large commercial models. This significantly narrows the performance gap with large LMs, showcasing its effectiveness in addressing complex medical challenges.

cs.CL↗

arXiv2024

CookingSense: A Culinary Knowledgebase with Multidisciplinary Assertions

This paper introduces CookingSense, a descriptive collection of knowledge assertions in the culinary domain extracted from various sources, including web data, scientific papers, and recipes, from which knowledge covering a broad range of aspects is acquired. CookingSense is constructed through a series of dictionary-based filtering and language model-based semantic filtering techniques, which results in a rich knowledgebase of multidisciplinary food-related assertions. Additionally, we present FoodBench, a novel benchmark to evaluate culinary decision support systems. From evaluations with FoodBench, we empirically prove that CookingSense improves the performance of retrieval augmented language models. We also validate the quality and variety of assertions in CookingSense through qualitative analysis.

cs.AI↗

arXiv2024

Fine-tuning CLIP Text Encoders with Two-step Paraphrasing

Contrastive language-image pre-training (CLIP) models have demonstrated considerable success across various vision-language tasks, such as text-to-image retrieval, where the model is required to effectively process natural language input to produce an accurate visual output. However, current models still face limitations in dealing with linguistic variations in input queries, such as paraphrases, making it challenging to handle a broad range of user queries in real-world applications. In this study, we introduce a straightforward fine-tuning approach to enhance the representations of CLIP models for paraphrases. Our approach involves a two-step paraphrase generation process, where we automatically create two categories of paraphrases from web-scale image captions by leveraging large language models. Subsequently, we fine-tune the CLIP text encoder using these generated paraphrases while freezing the image encoder. Our resulting model, which we call ParaCLIP, exhibits significant improvements over baseline CLIP models across various tasks, including paraphrased retrieval (with rank similarity scores improved by up to 2.0% and 5.6%), Visual Genome Relation and Attribution, as well as seven semantic textual similarity tasks.

cs.CV↗

arXiv2023

KU-DMIS-MSRA at RadSum23: Pre-trained Vision-Language Model for Radiology Report Summarization

In this paper, we introduce CheXOFA, a new pre-trained vision-language model (VLM) for the chest X-ray domain. Our model is initially pre-trained on various multimodal datasets within the general domain before being transferred to the chest X-ray domain. Following a prominent VLM, we unify various domain-specific tasks into a simple sequence-to-sequence schema. It enables the model to effectively learn the required knowledge and skills from limited resources in the domain. Demonstrating superior performance on the benchmark datasets provided by the BioNLP shared task, our model benefits from its training across multiple tasks and domains. With subtle techniques including ensemble and factual calibration, our system achieves first place on the RadSum23 leaderboard for the hidden test set.

cs.CL↗

arXiv2023

Automatic Creation of Named Entity Recognition Datasets by Querying Phrase Representations

Most weakly supervised named entity recognition (NER) models rely on domain-specific dictionaries provided by experts. This approach is infeasible in many domains where dictionaries do not exist. While a phrase retrieval model was used to construct pseudo-dictionaries with entities retrieved from Wikipedia automatically in a recent study, these dictionaries often have limited coverage because the retriever is likely to retrieve popular entities rather than rare ones. In this study, we present a novel framework, HighGEN, that generates NER datasets with high-coverage pseudo-dictionaries. Specifically, we create entity-rich dictionaries with a novel search method, called phrase embedding search, which encourages the retriever to search a space densely populated with various entities. In addition, we use a new verification process based on the embedding distance between candidate entity mentions and entity types to reduce the false-positive noise in weak labels generated by high-coverage dictionaries. We demonstrate that HighGEN outperforms the previous best model by an average F1 score of 4.7 across five NER benchmark datasets.

cs.CL↗

arXiv2023

LIQUID: A Framework for List Question Answering Dataset Generation

Question answering (QA) models often rely on large-scale training datasets, which necessitates the development of a data generation framework to reduce the cost of manual annotations. Although several recent studies have aimed to generate synthetic questions with single-span answers, no study has been conducted on the creation of list questions with multiple, non-contiguous spans as answers. To address this gap, we propose LIQUID, an automated framework for generating list QA datasets from unlabeled corpora. We first convert a passage from Wikipedia or PubMed into a summary and extract named entities from the summarized text as candidate answers. This allows us to select answers that are semantically correlated in context and is, therefore, suitable for constructing list questions. We then create questions using an off-the-shelf question generator with the extracted entities and original passage. Finally, iterative filtering and answer expansion are performed to ensure the accuracy and completeness of the answers. Using our synthetic data, we significantly improve the performance of the previous best list QA models by exact-match F1 scores of 5.0 on MultiSpanQA, 1.9 on Quoref, and 2.8 averaged across three BioASQ benchmarks.

cs.CL↗

arXiv2022

Simple Questions Generate Named Entity Recognition Datasets

Recent named entity recognition (NER) models often rely on human-annotated datasets, requiring the significant engagement of professional knowledge on the target domain and entities. This research introduces an ask-to-generate approach that automatically generates NER datasets by asking questions in simple natural language to an open-domain question answering system (e.g., "Which disease?"). Despite using fewer in-domain resources, our models, solely trained on the generated datasets, largely outperform strong low-resource models by an average F1 score of 19.4 for six popular NER benchmarks. Furthermore, our models provide competitive performance with rich-resource models that additionally leverage in-domain dictionaries provided by domain experts. In few-shot NER, we outperform the previous best model by an F1 score of 5.2 on three benchmarks and achieve new state-of-the-art performance.

cs.CL↗

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.

cs.CL↗

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.

cs.CL↗

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.

cs.CL↗

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.

cs.CL↗

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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arXiv2020

Exploring The Spatial Reasoning Ability of Neural Models in Human IQ Tests

Although neural models have performed impressively well on various tasks such as image recognition and question answering, their reasoning ability has been measured in only few studies. In this work, we focus on spatial reasoning and explore the spatial understanding of neural models. First, we describe the following two spatial reasoning IQ tests: rotation and shape composition. Using well-defined rules, we constructed datasets that consist of various complexity levels. We designed a variety of experiments in terms of generalization, and evaluated six different baseline models on the newly generated datasets. We provide an analysis of the results and factors that affect the generalization abilities of models. Also, we analyze how neural models solve spatial reasoning tests with visual aids. Our findings would provide valuable insights into understanding a machine and the difference between a machine and human.

cs.AI↗

arXiv2020

Fast frequency discrimination and phoneme recognition using a biomimetic membrane coupled to a neural network

In the human ear, the basilar membrane plays a central role in sound recognition. When excited by sound, this membrane responds with a frequency-dependent displacement pattern that is detected and identified by the auditory hair cells combined with the human neural system. Inspired by this structure, we designed and fabricated an artificial membrane that produces a spatial displacement pattern in response to an audible signal, which we used to train a convolutional neural network (CNN). When trained with single frequency tones, this system can unambiguously distinguish tones closely spaced in frequency. When instead trained to recognize spoken vowels, this system outperforms existing methods for phoneme recognition, including the discrete Fourier transform (DFT), zoom FFT and chirp z-transform, especially when tested in short time windows. This sound recognition scheme therefore promises significant benefits in fast and accurate sound identification compared to existing methods.

eess.AS↗

arXiv2019

Predicting Multiple Demographic Attributes with Task Specific Embedding Transformation and Attention Network

Most companies utilize demographic information to develop their strategy in a market. However, such information is not available to most retail companies. Several studies have been conducted to predict the demographic attributes of users from their transaction histories, but they have some limitations. First, they focused on parameter sharing to predict all attributes but capturing task-specific features is also important in multi-task learning. Second, they assumed that all transactions are equally important in predicting demographic attributes. However, some transactions are more useful than others for predicting a certain attribute. Furthermore, decision making process of models cannot be interpreted as they work in a black-box manner. To address the limitations, we propose an Embedding Transformation Network with Attention (ETNA) model which shares representations at the bottom of the model structure and transforms them to task-specific representations using a simple linear transformation method. In addition, we can obtain more informative transactions for predicting certain attributes using the attention mechanism. The experimental results show that our model outperforms the previous models on all tasks. In our qualitative analysis, we show the visualization of attention weights, which provides business managers with some useful insights.

cs.LG↗

arXiv2018

Ranking Paragraphs for Improving Answer Recall in Open-Domain Question Answering

Recently, open-domain question answering (QA) has been combined with machine comprehension models to find answers in a large knowledge source. As open-domain QA requires retrieving relevant documents from text corpora to answer questions, its performance largely depends on the performance of document retrievers. However, since traditional information retrieval systems are not effective in obtaining documents with a high probability of containing answers, they lower the performance of QA systems. Simply extracting more documents increases the number of irrelevant documents, which also degrades the performance of QA systems. In this paper, we introduce Paragraph Ranker which ranks paragraphs of retrieved documents for a higher answer recall with less noise. We show that ranking paragraphs and aggregating answers using Paragraph Ranker improves performance of open-domain QA pipeline on the four open-domain QA datasets by 7.8% on average.

cs.CL↗

arXiv2018

Liver Lesion Detection from Weakly-labeled Multi-phase CT Volumes with a Grouped Single Shot MultiBox Detector

We present a focal liver lesion detection model leveraged by custom-designed multi-phase computed tomography (CT) volumes, which reflects real-world clinical lesion detection practice using a Single Shot MultiBox Detector (SSD). We show that grouped convolutions effectively harness richer information of the multi-phase data for the object detection model, while a naive application of SSD suffers from a generalization gap. We trained and evaluated the modified SSD model and recently proposed variants with our CT dataset of 64 subjects by five-fold cross validation. Our model achieved a 53.3% average precision score and ran in under three seconds per volume, outperforming the original model and state-of-the-art variants. Results show that the one-stage object detection model is a practical solution, which runs in near real-time and can learn an unbiased feature representation from a large-volume real-world detection dataset, which requires less tedious and time consuming construction of the weak phase-level bounding box labels.

cs.CV↗