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Researcher profile

Jaewoo Kang

Jaewoo Kang contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computation and LanguageArtificial IntelligenceMachine LearningComputational Engineering, Finance, and ScienceDigital LibrariesInformation RetrievalMultiagent SystemsSocial and Information Networks

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Trust 21 - EmergingVerification L1Unclaimed author
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Published work

18 published item(s)

preprint2026arXiv

MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Teaching Language Models to Think in Code

Tool-integrated reasoning (TIR) has emerged as a dominant paradigm for mathematical problem solving in language models, combining natural language (NL) reasoning with code execution. However, this interleaved setup has three key limitations: code often acts as a post-hoc verifier, intermediate NL computations are error-prone, and NL and code play overlapping rather than clearly distinct roles. We propose ThinC (Thinking in Code), a framework in which code itself serves as the reasoner rather than as a tool invoked by NL. A ThinC trajectory begins with a brief NL planning step, after which all reasoning unfolds through code blocks connected only by their execution outputs. We distill 12.2k code-centric trajectories from a teacher model and train ThinC-1.7B and ThinC-4B with supervised fine-tuning followed by reinforcement learning. ThinC-4B consistently outperforms every TIR baseline on five competition-level math benchmarks and even surpasses the much larger Qwen3-235B-A22B-Thinking. Further analysis shows that ThinC reasons through code: 99.2% of its final answers are grounded in interpreter output, and the model recovers reliably from code execution failures without intermediate NL reasoning. Our code and models will be released soon.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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"

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

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

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

"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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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).

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Biomedical Entity Representations with Synonym Marginalization

Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very challenging. In this paper, we focus on learning representations of biomedical entities solely based on the synonyms of entities. To learn from the incomplete synonyms, we use a model-based candidate selection and maximize the marginal likelihood of the synonyms present in top candidates. Our model-based candidates are iteratively updated to contain more difficult negative samples as our model evolves. In this way, we avoid the explicit pre-selection of negative samples from more than 400K candidates. On four biomedical entity normalization datasets having three different entity types (disease, chemical, adverse reaction), our model BioSyn consistently outperforms previous state-of-the-art models almost reaching the upper bound on each dataset.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Building a PubMed knowledge graph

PubMed is an essential resource for the medical domain, but useful concepts are either difficult to extract or are ambiguated, which has significantly hindered knowledge discovery. To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National Institutes of Health (NIH) ExPORTER, collecting affiliation history and educational background of authors from ORCID, and identifying fine-grained affiliation data from MapAffil. Through the integration of the credible multi-source data, we could create connections among the bio-entities, authors, articles, affiliations, and funding. Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation (AND) achieving a F1 score of 98.09%. PKG can trigger broader innovations, not only enabling us to measure scholarly impact, knowledge usage, and knowledge transfer, but also assisting us in profiling authors and organizations based on their connections with bio-entities. The PKG is freely available on Figshare (https://figshare.com/s/6327a55355fc2c99f3a2, simplified version that exclude PubMed raw data) and TACC website (http://er.tacc.utexas.edu/datasets/ped, full version).

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Contextualized Sparse Representations for Real-Time Open-Domain Question Answering

Open-domain question answering can be formulated as a phrase retrieval problem, in which we can expect huge scalability and speed benefit but often suffer from low accuracy due to the limitation of existing phrase representation models. In this paper, we aim to improve the quality of each phrase embedding by augmenting it with a contextualized sparse representation (Sparc). Unlike previous sparse vectors that are term-frequency-based (e.g., tf-idf) or directly learned (only few thousand dimensions), we leverage rectified self-attention to indirectly learn sparse vectors in n-gram vocabulary space. By augmenting the previous phrase retrieval model (Seo et al., 2019) with Sparc, we show 4%+ improvement in CuratedTREC and SQuAD-Open. Our CuratedTREC score is even better than the best known retrieve & read model with at least 45x faster inference speed.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Graph Transformer Networks

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, 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. In this paper, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which involve identifying useful connections between unconnected nodes on the original graph, while learning effective node representation on the new graphs in an end-to-end fashion. Graph Transformer layer, a core layer of GTNs, learns a soft selection of edge types and composite relations for generating useful multi-hop connections so-called meta-paths. Our experiments show that GTNs learn new graph structures, based on data and tasks without domain knowledge, and yield powerful node representation via convolution on the new graphs. Without domain-specific graph preprocessing, GTNs achieved the best performance in all three benchmark node classification tasks against the state-of-the-art methods that require pre-defined meta-paths from domain knowledge.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Learning User Preferences and Understanding Calendar Contexts for Event Scheduling

With online calendar services gaining popularity worldwide, calendar data has become one of the richest context sources for understanding human behavior. However, event scheduling is still time-consuming even with the development of online calendars. Although machine learning based event scheduling models have automated scheduling processes to some extent, they often fail to understand subtle user preferences and complex calendar contexts with event titles written in natural language. In this paper, we propose Neural Event Scheduling Assistant (NESA) which learns user preferences and understands calendar contexts, directly from raw online calendars for fully automated and highly effective event scheduling. We leverage over 593K calendar events for NESA to learn scheduling personal events, and we further utilize NESA for multi-attendee event scheduling. NESA successfully incorporates deep neural networks such as Bidirectional Long Short-Term Memory, Convolutional Neural Network, and Highway Network for learning the preferences of each user and understanding calendar context based on natural languages. The experimental results show that NESA significantly outperforms previous baseline models in terms of various evaluation metrics on both personal and multi-attendee event scheduling tasks. Our qualitative analysis demonstrates the effectiveness of each layer in NESA and learned user preferences.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

MAPS: Multi-agent Reinforcement Learning-based Portfolio Management System

Generating an investment strategy using advanced deep learning methods in stock markets has recently been a topic of interest. Most existing deep learning methods focus on proposing an optimal model or network architecture by maximizing return. However, these models often fail to consider and adapt to the continuously changing market conditions. In this paper, we propose the Multi-Agent reinforcement learning-based Portfolio management System (MAPS). MAPS is a cooperative system in which each agent is an independent "investor" creating its own portfolio. In the training procedure, each agent is guided to act as diversely as possible while maximizing its own return with a carefully designed loss function. As a result, MAPS as a system ends up with a diversified portfolio. Experiment results with 12 years of US market data show that MAPS outperforms most of the baselines in terms of Sharpe ratio. Furthermore, our results show that adding more agents to our system would allow us to get a higher Sharpe ratio by lowering risk with a more diversified portfolio.

0 citations0 reviewsNo code linkedOpen access