arXiv subjects

Jaewoo Kang

Publications and source records attributed to Jaewoo Kang.

At least 73 records · Page 4Linked to original sources

arXiv2024

MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints

Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel pre-training framework that employs masked graph contrastive learning in understanding the underlying decomposable parts inmolecules that implicate their core structure and peripheral R-groups. Furthermore, we formulate an additional framework that grants MolPLA the ability to help chemists find replaceable R-groups in lead optimization scenarios. Experimental results on molecular property prediction show that MolPLA exhibits predictability comparable to current state-of-the-art models. Qualitative analysis implicate that MolPLA is capable of distinguishing core and R-group sub-structures, identifying decomposable regions in molecules and contributing to lead optimization scenarios by rationally suggesting R-group replacements given various query core templates. The code implementation for MolPLA and its pre-trained model checkpoint is available at https://github.com/dmis-lab/MolPLA

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arXiv2023

UnionDet: Union-Level Detector Towards Real-Time Human-Object Interaction Detection

Recent advances in deep neural networks have achieved significant progress in detecting individual objects from an image. However, object detection is not sufficient to fully understand a visual scene. Towards a deeper visual understanding, the interactions between objects, especially humans and objects are essential. Most prior works have obtained this information with a bottom-up approach, where the objects are first detected and the interactions are predicted sequentially by pairing the objects. This is a major bottleneck in HOI detection inference time. To tackle this problem, we propose UnionDet, a one-stage meta-architecture for HOI detection powered by a novel union-level detector that eliminates this additional inference stage by directly capturing the region of interaction. Our one-stage detector for human-object interaction shows a significant reduction in interaction prediction time 4x~14x while outperforming state-of-the-art methods on two public datasets: V-COCO and HICO-DET.

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arXiv2023

Tree of Clarifications: Answering Ambiguous Questions with Retrieval-Augmented Large Language Models

Questions in open-domain question answering are often ambiguous, allowing multiple interpretations. One approach to handling them is to identify all possible interpretations of the ambiguous question (AQ) and to generate a long-form answer addressing them all, as suggested by Stelmakh et al., (2022). While it provides a comprehensive response without bothering the user for clarification, considering multiple dimensions of ambiguity and gathering corresponding knowledge remains a challenge. To cope with the challenge, we propose a novel framework, Tree of Clarifications (ToC): It recursively constructs a tree of disambiguations for the AQ -- via few-shot prompting leveraging external knowledge -- and uses it to generate a long-form answer. ToC outperforms existing baselines on ASQA in a few-shot setup across the metrics, while surpassing fully-supervised baselines trained on the whole training set in terms of Disambig-F1 and Disambig-ROUGE. Code is available at https://github.com/gankim/tree-of-clarifications.

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arXiv2023

Co-attention Graph Pooling for Efficient Pairwise Graph Interaction Learning

Graph Neural Networks (GNNs) have proven to be effective in processing and learning from graph-structured data. However, previous works mainly focused on understanding single graph inputs while many real-world applications require pair-wise analysis for graph-structured data (e.g., scene graph matching, code searching, and drug-drug interaction prediction). To this end, recent works have shifted their focus to learning the interaction between pairs of graphs. Despite their improved performance, these works were still limited in that the interactions were considered at the node-level, resulting in high computational costs and suboptimal performance. To address this issue, we propose a novel and efficient graph-level approach for extracting interaction representations using co-attention in graph pooling. Our method, Co-Attention Graph Pooling (CAGPool), exhibits competitive performance relative to existing methods in both classification and regression tasks using real-world datasets, while maintaining lower computational complexity.

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arXiv2023

ELVIS: Empowering Locality of Vision Language Pre-training with Intra-modal Similarity

Deep learning has shown great potential in assisting radiologists in reading chest X-ray (CXR) images, but its need for expensive annotations for improving performance prevents widespread clinical application. Visual language pre-training (VLP) can alleviate the burden and cost of annotation by leveraging routinely generated reports for radiographs, which exist in large quantities as well as in paired form (image-text pairs). Additionally, extensions to localization-aware VLPs are being proposed to address the needs for accurate localization of abnormalities for computer-aided diagnosis (CAD) in CXR. However, we find that the formulation proposed by locality-aware VLP literature actually leads to a loss in spatial relationships required for downstream localization tasks. Therefore, we propose Empowering Locality of VLP with Intra-modal Similarity, ELVIS, a VLP aware of intra-modal locality, to better preserve the locality within radiographs or reports, which enhances the ability to comprehend location references in text reports. Our locality-aware VLP method significantly outperforms state-of-the art baselines in multiple segmentation tasks and the MS-CXR phrase grounding task. Qualitatively, we show that ELVIS focuses well on regions of interest described in the report text compared to prior approaches, allowing for enhanced interpretability.

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arXiv2023

Towards Flexible Time-to-event Modeling: Optimizing Neural Networks via Rank Regression

Time-to-event analysis, also known as survival analysis, aims to predict the time of occurrence of an event, given a set of features. One of the major challenges in this area is dealing with censored data, which can make learning algorithms more complex. Traditional methods such as Cox's proportional hazards model and the accelerated failure time (AFT) model have been popular in this field, but they often require assumptions such as proportional hazards and linearity. In particular, the AFT models often require pre-specified parametric distributional assumptions. To improve predictive performance and alleviate strict assumptions, there have been many deep learning approaches for hazard-based models in recent years. However, representation learning for AFT has not been widely explored in the neural network literature, despite its simplicity and interpretability in comparison to hazard-focused methods. In this work, we introduce the Deep AFT Rank-regression model for Time-to-event prediction (DART). This model uses an objective function based on Gehan's rank statistic, which is efficient and reliable for representation learning. On top of eliminating the requirement to establish a baseline event time distribution, DART retains the advantages of directly predicting event time in standard AFT models. The proposed method is a semiparametric approach to AFT modeling that does not impose any distributional assumptions on the survival time distribution. This also eliminates the need for additional hyperparameters or complex model architectures, unlike existing neural network-based AFT models. Through quantitative analysis on various benchmark datasets, we have shown that DART has significant potential for modeling high-throughput censored time-to-event data.

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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.

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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.

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arXiv2023

Optimizing Test-Time Query Representations for Dense Retrieval

Recent developments of dense retrieval rely on quality representations of queries and contexts from pre-trained query and context encoders. In this paper, we introduce TOUR (Test-Time Optimization of Query Representations), which further optimizes instance-level query representations guided by signals from test-time retrieval results. We leverage a cross-encoder re-ranker to provide fine-grained pseudo labels over retrieval results and iteratively optimize query representations with gradient descent. Our theoretical analysis reveals that TOUR can be viewed as a generalization of the classical Rocchio algorithm for pseudo relevance feedback, and we present two variants that leverage pseudo-labels as hard binary or soft continuous labels. We first apply TOUR on phrase retrieval with our proposed phrase re-ranker, and also evaluate its effectiveness on passage retrieval with an off-the-shelf re-ranker. TOUR greatly improves end-to-end open-domain question answering accuracy, as well as passage retrieval performance. TOUR also consistently improves direct re-ranking by up to 2.0% while running 1.3-2.4x faster with an efficient implementation.

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arXiv2023

KitchenScale: Learning to predict ingredient quantities from recipe contexts

Determining proper quantities for ingredients is an essential part of cooking practice from the perspective of enriching tastiness and promoting healthiness. We introduce KitchenScale, a fine-tuned Pre-trained Language Model (PLM) that predicts a target ingredient's quantity and measurement unit given its recipe context. To effectively train our KitchenScale model, we formulate an ingredient quantity prediction task that consists of three sub-tasks which are ingredient measurement type classification, unit classification, and quantity regression task. Furthermore, we utilized transfer learning of cooking knowledge from recipe texts to PLMs. We adopted the Discrete Latent Exponent (DExp) method to cope with high variance of numerical scales in recipe corpora. Experiments with our newly constructed dataset and recommendation examples demonstrate KitchenScale's understanding of various recipe contexts and generalizability in predicting ingredient quantities. We implemented a web application for KitchenScale to demonstrate its functionality in recommending ingredient quantities expressed in numerals (e.g., 2) with units (e.g., ounce).

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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.

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arXiv2022

Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework

In order to assist the drug discovery/development process, pharmaceutical companies often apply biomedical NER and linking techniques over internal and public corpora. Decades of study of the field of BioNLP has produced a plethora of algorithms, systems and datasets. However, our experience has been that no single open source system meets all the requirements of a modern pharmaceutical company. In this work, we describe these requirements according to our experience of the industry, and present Kazu, a highly extensible, scalable open source framework designed to support BioNLP for the pharmaceutical sector. Kazu is a built around a computationally efficient version of the BERN2 NER model (TinyBERN2), and subsequently wraps several other BioNLP technologies into one coherent system. KAZU framework is open-sourced: https://github.com/AstraZeneca/KAZU

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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.

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arXiv2022

Generating Information-Seeking Conversations from Unlabeled Documents

In this paper, we introduce a novel framework, SIMSEEK, (Simulating information-Seeking conversation from unlabeled documents), and compare its two variants. In our baseline SIMSEEK-SYM, a questioner generates follow-up questions upon the predetermined answer by an answerer. On the contrary, SIMSEEK-ASYM first generates the question and then finds its corresponding answer under the conversational context. Our experiments show that they can synthesize effective training resources for CQA and conversational search tasks. As a result, conversations from SIMSEEK-ASYM not only make more improvements in our experiments but also are favorably reviewed in a human evaluation. We finally release a large-scale resource of synthetic conversations, WIKI-SIMSEEK, containing 2 million CQA pairs built upon Wikipedia documents. With the dataset, our CQA model achieves state-of-the-art performance on a recent CQA benchmark, QuAC.

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arXiv2022

Enhancing Label Consistency on Document-level Named Entity Recognition

Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although existing document NER models show consistent predictions, they still do not meet our expectations. We investigated whether the adjectives and prepositions within an entity cause a low label consistency, which results in inconsistent predictions. In this paper, we present our method, ConNER, which enhances the label dependency of modifiers (e.g., adjectives and prepositions) to achieve higher label agreement. ConNER refines the draft labels of the modifiers to improve the output representations of biomedical entities. The effectiveness of our method is demonstrated on four popular biomedical NER datasets; in particular, its efficacy is proved on two datasets with 7.5-8.6% absolute improvements in the F1 score. We interpret that our ConNER method is effective on datasets that have intrinsically low label consistency. In the qualitative analysis, we demonstrate how our approach makes the NER model generate consistent predictions. Our code and resources are available at https://github.com/dmis-lab/ConNER/.

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arXiv2022

RecipeMind: Guiding Ingredient Choices from Food Pairing to Recipe Completion using Cascaded Set Transformer

We propose a computational approach for recipe ideation, a downstream task that helps users select and gather ingredients for creating dishes. To perform this task, we developed RecipeMind, a food affinity score prediction model that quantifies the suitability of adding an ingredient to set of other ingredients. We constructed a large-scale dataset containing ingredient co-occurrence based scores to train and evaluate RecipeMind on food affinity score prediction. Deployed in recipe ideation, RecipeMind helps the user expand an initial set of ingredients by suggesting additional ingredients. Experiments and qualitative analysis show RecipeMind's potential in fulfilling its assistive role in cuisine domain.

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arXiv2022

BERN2: an advanced neural biomedical named entity recognition and normalization tool

In biomedical natural language processing, named entity recognition (NER) and named entity normalization (NEN) are key tasks that enable the automatic extraction of biomedical entities (e.g. diseases and drugs) from the ever-growing biomedical literature. In this article, we present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by employing a multi-task NER model and neural network-based NEN models to achieve much faster and more accurate inference. We hope that our tool can help annotate large-scale biomedical texts for various tasks such as biomedical knowledge graph construction.

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arXiv2022

Deformable Graph Transformer

Transformer-based models have recently shown success in representation learning on graph-structured data beyond natural language processing and computer vision. However, the success is limited to small-scale graphs due to the drawbacks of full dot-product attention on graphs such as the quadratic complexity with respect to the number of nodes and message aggregation from enormous irrelevant nodes. To address these issues, we propose Deformable Graph Transformer (DGT) that performs sparse attention via dynamically sampled relevant nodes for efficiently handling large-scale graphs with a linear complexity in the number of nodes. Specifically, our framework first constructs multiple node sequences with various criteria to consider both structural and semantic proximity. Then, combining with our learnable Katz Positional Encodings, the sparse attention is applied to the node sequences for learning node representations with a significantly reduced computational cost. Extensive experiments demonstrate that our DGT achieves state-of-the-art performance on 7 graph benchmark datasets with 2.5 - 449 times less computational cost compared to transformer-based graph models with full attention.

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