Junhyun Lee

Seongjun Yun, Seoyoon Kim, Junhyun Lee et al.

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.

Seungheun Baek, Soyon Park, Yan Ting Chok et al.

Predicting cellular responses to various perturbations is a critical focus in drug discovery and personalized therapeutics, with deep learning models playing a significant role in this endeavor. Single-cell datasets contain technical artifacts that may hinder the predictability of such models, which poses quality control issues highly regarded in this area. To address this, we propose CRADLE-VAE, a causal generative framework tailored for single-cell gene perturbation modeling, enhanced with counterfactual reasoning-based artifact disentanglement. Throughout training, CRADLE-VAE models the underlying latent distribution of technical artifacts and perturbation effects present in single-cell datasets. It employs counterfactual reasoning to effectively disentangle such artifacts by modulating the latent basal spaces and learns robust features for generating cellular response data with improved quality. Experimental results demonstrate that this approach improves not only treatment effect estimation performance but also generative quality as well. The CRADLE-VAE codebase is publicly available at https://github.com/dmis-lab/CRADLE-VAE.

Bumsoo Kim, Jonghwan Mun, Kyoung-Woon On et al.

Human-Object Interaction (HOI) detection is the task of identifying a set of <human, object, interaction> triplets from an image. Recent work proposed transformer encoder-decoder architectures that successfully eliminated the need for many hand-designed components in HOI detection through end-to-end training. However, they are limited to single-scale feature resolution, providing suboptimal performance in scenes containing humans, objects and their interactions with vastly different scales and distances. To tackle this problem, we propose a Multi-Scale TRansformer (MSTR) for HOI detection powered by two novel HOI-aware deformable attention modules called Dual-Entity attention and Entity-conditioned Context attention. While existing deformable attention comes at a huge cost in HOI detection performance, our proposed attention modules of MSTR learn to effectively attend to sampling points that are essential to identify interactions. In experiments, we achieve the new state-of-the-art performance on two HOI detection benchmarks.

Junhyun Lee, Bumsoo Kim, Minji Jeon et al.

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.

Hyunjun Lee, Junhyun Lee, Taehwa Choi et al.

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.

Junhyun Lee, Veronika Thost, Bumsoo Kim et al.

Message Passing Neural Networks (MPNNs) hold a key position in machine learning on graphs, but they struggle with unintended behaviors, such as over-smoothing and over-squashing, due to irregular data structures. The observation and formulation of these limitations have become foundational in constructing more informative graph representations. In this paper, we delve into the limitations of MPNNs, focusing on aspects that have previously been overlooked. Our observations reveal that even within a single layer, the information specific to an individual node can become significantly diluted. To delve into this phenomenon in depth, we present the concept of Over-dilution and formulate it with two dilution factors: intra-node dilution for attribute-level and inter-node dilution for node-level representations. We also introduce a transformer-based solution that alleviates over-dilution and complements existing node embedding methods like MPNNs. Our findings provide new insights and contribute to the development of informative representations. The implementation and supplementary materials are publicly available at https://github.com/LeeJunHyun/NATR.

Mogan Gim, Jueon Park, Soyon Park et al.

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

Seokeon Choi, Junhyun Lee, Yunsung Lee et al.

We propose an improved discriminative model prediction method for robust long-term tracking based on a pre-trained short-term tracker. The baseline pre-trained short-term tracker is SuperDiMP which combines the bounding-box regressor of PrDiMP with the standard DiMP classifier. Our tracker RLT-DiMP improves SuperDiMP in the following three aspects: (1) Uncertainty reduction using random erasing: To make our model robust, we exploit an agreement from multiple images after erasing random small rectangular areas as a certainty. And then, we correct the tracking state of our model accordingly. (2) Random search with spatio-temporal constraints: we propose a robust random search method with a score penalty applied to prevent the problem of sudden detection at a distance. (3) Background augmentation for more discriminative feature learning: We augment various backgrounds that are not included in the search area to train a more robust model in the background clutter. In experiments on the VOT-LT2020 benchmark dataset, the proposed method achieves comparable performance to the state-of-the-art long-term trackers. The source code is available at: https://github.com/bismex/RLT-DIMP.

Yonggyu Park, Junhyun Lee, Yookyung Koh et al.

The mood of a text and the intention of the writer can be reflected in the typeface. However, in designing a typeface, it is difficult to keep the style of various characters consistent, especially for languages with lots of morphological variations such as Chinese. In this paper, we propose a Typeface Completion Network (TCN) which takes one character as an input, and automatically completes the entire set of characters in the same style as the input characters. Unlike existing models proposed for image-to-image translation, TCN embeds a character image into two separate vectors representing typeface and content. Combined with a reconstruction loss from the latent space, and with other various losses, TCN overcomes the inherent difficulty in designing a typeface. Also, compared to previous image-to-image translation models, TCN generates high quality character images of the same typeface with a much smaller number of model parameters. We validate our proposed model on the Chinese and English character datasets, which is paired data, and the CelebA dataset, which is unpaired data. In these datasets, TCN outperforms recently proposed state-of-the-art models for image-to-image translation. The source code of our model is available at https://github.com/yongqyu/TCN.

Junhyun Lee, Wooseong Yang, Jaewoo Kang

In the evolving landscape of machine learning, the adaptation of pre-trained models through prompt tuning has become increasingly prominent. This trend is particularly observable in the graph domain, where diverse pre-training strategies present unique challenges in developing effective prompt-based tuning methods for graph neural networks. Previous approaches have been limited, focusing on specialized prompting functions tailored to models with edge prediction pre-training tasks. These methods, however, suffer from a lack of generalizability across different pre-training strategies. Recently, a simple prompt tuning method has been designed for any pre-training strategy, functioning within the input graph's feature space. This allows it to theoretically emulate any type of prompting function, thereby significantly increasing its versatility for a range of downstream applications. Nevertheless, the capacity of such simple prompts to fully grasp the complex contexts found in graphs remains an open question, necessitating further investigation. Addressing this challenge, our work introduces the Subgraph-level Universal Prompt Tuning (SUPT) approach, focusing on the detailed context within subgraphs. In SUPT, prompt features are assigned at the subgraph-level, preserving the method's universal capability. This requires extremely fewer tuning parameters than fine-tuning-based methods, outperforming them in 42 out of 45 full-shot scenario experiments with an average improvement of over 2.5%. In few-shot scenarios, it excels in 41 out of 45 experiments, achieving an average performance increase of more than 6.6%.

Junseon Park, Junhyun Lee, Hyeongon Park

In South Korea, power grid is currently operated based on the static line rating (SLR) method, where the transmission line capacity is determined based on extreme weather conditions. However, with global warming, there is a concern that the temperatures during summer may exceed the SLR criteria, posing safety risks. On the other hand, the conservative estimates used for winter conditions limit the utilization of renewable energy. Proposals to install new lines face significant financial and environmental hurdles, complicating efforts to adapt to these changing conditions. Dynamic Line Rating (DLR) offers a real-time solution but requires extensive weather monitoring and complex integration. This paper proposes a novel method that improves on SLR by analyzing historical data to refine line rating criteria on a monthly, seasonal, and semi-annual basis. Through simulations, we show our approach significantly enhances cost effectiveness and reliability of the power system, achieving efficiencies close to DLR with existing infrastructure. This method offers a practical alternative to overcome the limitations of SLR and the implementation challenges of DLR.

Kiwoong Yoo, Owen Oertell, Junhyun Lee et al.

Navigating the vast chemical space of druggable compounds is a formidable challenge in drug discovery, where generative models are increasingly employed to identify viable candidates. Conditional 3D structure-based drug design (3D-SBDD) models, which take into account complex three-dimensional interactions and molecular geometries, are particularly promising. Scaffold hopping is an efficient strategy that facilitates the identification of similar active compounds by strategically modifying the core structure of molecules, effectively narrowing the wide chemical space and enhancing the discovery of drug-like products. However, the practical application of 3D-SBDD generative models is hampered by their slow processing speeds. To address this bottleneck, we introduce TurboHopp, an accelerated pocket-conditioned 3D scaffold hopping model that merges the strategic effectiveness of traditional scaffold hopping with rapid generation capabilities of consistency models. This synergy not only enhances efficiency but also significantly boosts generation speeds, achieving up to 30 times faster inference speed as well as superior generation quality compared to existing diffusion-based models, establishing TurboHopp as a powerful tool in drug discovery. Supported by faster inference speed, we further optimize our model, using Reinforcement Learning for Consistency Models (RLCM), to output desirable molecules. We demonstrate the broad applicability of TurboHopp across multiple drug discovery scenarios, underscoring its potential in diverse molecular settings.

Seoha Song, Junhyun Lee, Hyeonmok Ko

Despite the great success of large language models (LLMs), efficiently controlling the length of the output sequence still remains a challenge. In this paper, we propose Hansel, an efficient framework for length control in LLMs without affecting its generation ability. Hansel utilizes periodically outputted hidden special tokens to keep track of the remaining target length of the output sequence. Together with techniques to avoid abrupt termination of the output, this seemingly simple method proved to be efficient and versatile, while not harming the coherency and fluency of the generated text. The framework can be applied to any pre-trained LLMs during the finetuning stage of the model, regardless of its original positional encoding method. We demonstrate this by finetuning four different LLMs with Hansel and show that the mean absolute error of the output sequence decreases significantly in every model and dataset compared to the prompt-based length control finetuning. Moreover, the framework showed a substantially improved ability to extrapolate to target lengths unseen during finetuning, such as long dialog responses or extremely short summaries. This indicates that the model learns the general means of length control, rather than learning to match output lengths to those seen during training.

Dhananjaya Gowda, Seoha Song, Harshith Goka et al.

Large language models (LLMs) are increasingly deployed with task-specific adapters catering to multiple downstream applications. In such a scenario, the additional compute associated with these apparently insignificant number of adapter parameters (typically less than 1% of the base model) turns out to be disproportionately significant during inference time (upto 2.5x times that of the base model). In this paper, we propose a new zero-latency fused low-rank adapter (zFLoRA) that introduces zero or negligible latency overhead on top of the base model. Experimental results on LLMs of size 1B, 3B and 7B show that zFLoRA compares favorably against the popular supervised fine-tuning benchmarks including low-rank adapters (LoRA) as well as full fine-tuning (FFT). Experiments are conducted on 18 different tasks across three different categories namely commonsense reasoning, math reasoning and summary-dialogue. Latency measurements made on NPU (Samsung Galaxy S25+) as well as GPU (NVIDIA H100) platforms show that the proposed zFLoRA adapters introduce zero to negligible latency overhead.

Dhananjaya Gowda, Seoha Song, Junhyun Lee et al.

As the large language models (LLMs) grow in size each day, efficient training and fine-tuning has never been as important as nowadays. This resulted in the great interest in parameter efficient fine-tuning (PEFT), and effective methods including low-rank adapters (LoRA) has emerged. Although the various PEFT methods have been studied extensively in the recent years, the greater part of the subject remains unexplored with the huge degree of freedom. In this paper, we propose FLoRA, a family of fused forward-backward adapters (FFBA) for parameter-efficient fine-tuning of LLMs on downstream tasks. The FFBA combine ideas from the popular LoRA and parallel adapters to improve the overall fine-tuning accuracies. At the same time, latencies are minimized by fusing the forward and backward adapters into existing projection layers of the base model. Experimental results show that the proposed FFB adapters perform significantly better than the popularly used LoRA in both accuracy and latency for a similar parameter budget.

JungHo Jung, Junhyun Lee

End-to-end speech-to-text translation typically suffers from the scarcity of paired speech-text data. One way to overcome this shortcoming is to utilize the bitext data from the Machine Translation (MT) task and perform Multi-Task Learning (MTL). In this paper, we formulate MTL from a regularization perspective and explore how sequences can be regularized within and across modalities. By thoroughly investigating the effect of consistency regularization (different modality) and R-drop (same modality), we show how they respectively contribute to the total regularization. We also demonstrate that the coefficient of MT loss serves as another source of regularization in the MTL setting. With these three sources of regularization, we introduce the optimal regularization contour in the high-dimensional space, called the regularization horizon. Experiments show that tuning the hyperparameters within the regularization horizon achieves near state-of-the-art performance on the MuST-C dataset.

Yan Ting Chok, Soyon Park, Seungheun Baek et al.

Medication recommendation is a crucial task for assisting physicians in making timely decisions from longitudinal patient medical records. However, real-world EHR data present significant challenges due to the presence of rarely observed medical entities and incomplete records that may not fully capture the clinical ground truth. While data-driven models trained on longitudinal Electronic Health Records often achieve strong empirical performance, they struggle to generalize under missing or novel conditions, largely due to their reliance on observed co-occurrence patterns. To address these issues, we propose Hierarchical Ontology and Network Refinement for Robust Medication Recommendation (HiRef), a unified framework that combines two complementary structures: (i) the hierarchical semantics encoded in curated medical ontologies, and (ii) refined co-occurrence patterns derived from real-world EHRs. We embed ontology entities in hyperbolic space, which naturally captures tree-like relationships and enables knowledge transfer through shared ancestors, thereby improving generalizability to unseen codes. To further improve robustness, we introduce a prior-guided sparse regularization scheme that refines the EHR co-occurrence graph by suppressing spurious edges while preserving clinically meaningful associations. Our model achieves strong performance on EHR benchmarks (MIMIC-III and MIMIC-IV) and maintains high accuracy under simulated unseen-code settings. Extensive experiments with comprehensive ablation studies demonstrate HiRef's resilience to unseen medical codes, supported by in-depth analyses of the learned sparsified graph structure and medical code embeddings.

Junhyun Lee, Harshith Goka, Hyeonmok Ko

Hallucination refers to the inaccurate, irrelevant, and inconsistent text generated from large language models (LLMs). While the LLMs have shown great promise in a variety of tasks, the issue of hallucination still remains a major challenge for many practical uses. In this paper, we tackle the issue of hallucination in abstract text summarization by mitigating exposure bias. Existing models targeted for exposure bias mitigation, namely BRIO, aim for better summarization quality in the ROUGE score. We propose a model that uses a similar exposure bias mitigation strategy but with a goal that is aligned with less hallucination. We conjecture that among a group of candidate outputs, ones with hallucinations will comprise the minority of the whole group. That is, candidates with less similarity with others will have a higher chance of containing hallucinated content. Our method uses this aspect and utilizes contrastive learning, incentivizing candidates with high inter-candidate ROUGE scores. We performed experiments on the XSum and CNN/DM summarization datasets, and our method showed 6.25% and 3.82% improvement, respectively, on the consistency G-Eval score over BRIO.

Bumsoo Kim, Junhyun Lee, Jaewoo Kang et al.

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 <human, object, interaction> 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.

Junhyun Lee, Inyeop Lee, Jaewoo Kang

Advanced methods of applying deep learning to structured data such as graphs have been proposed in recent years. In particular, studies have focused on generalizing convolutional neural networks to graph data, which includes redefining the convolution and the downsampling (pooling) operations for graphs. The method of generalizing the convolution operation to graphs has been proven to improve performance and is widely used. However, the method of applying downsampling to graphs is still difficult to perform and has room for improvement. In this paper, we propose a graph pooling method based on self-attention. Self-attention using graph convolution allows our pooling method to consider both node features and graph topology. To ensure a fair comparison, the same training procedures and model architectures were used for the existing pooling methods and our method. The experimental results demonstrate that our method achieves superior graph classification performance on the benchmark datasets using a reasonable number of parameters.