Taewon Kim

Taesik Gong, Jongheon Jeong, Taewon Kim et al.

Test-time adaptation (TTA) is an emerging paradigm that addresses distributional shifts between training and testing phases without additional data acquisition or labeling cost; only unlabeled test data streams are used for continual model adaptation. Previous TTA schemes assume that the test samples are independent and identically distributed (i.i.d.), even though they are often temporally correlated (non-i.i.d.) in application scenarios, e.g., autonomous driving. We discover that most existing TTA methods fail dramatically under such scenarios. Motivated by this, we present a new test-time adaptation scheme that is robust against non-i.i.d. test data streams. Our novelty is mainly two-fold: (a) Instance-Aware Batch Normalization (IABN) that corrects normalization for out-of-distribution samples, and (b) Prediction-balanced Reservoir Sampling (PBRS) that simulates i.i.d. data stream from non-i.i.d. stream in a class-balanced manner. Our evaluation with various datasets, including real-world non-i.i.d. streams, demonstrates that the proposed robust TTA not only outperforms state-of-the-art TTA algorithms in the non-i.i.d. setting, but also achieves comparable performance to those algorithms under the i.i.d. assumption. Code is available at https://github.com/TaesikGong/NOTE.

Hyosoon Jang, Hyunjin Seo, Honghui Kim et al.

Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue of such supervision by exposing models to atom-level ligand-protein interactions, raising the question of whether co-folding models can yield strong small-molecule representations. We study this question using Boltz2, a modern co-folding model, by transferring its atom-level ligand representations to standalone small-molecule tasks. Through systematic probing and distillation, we show that Boltz2 representations match or outperform existing models on the ADMET benchmark, accelerate molecular generative modeling, and improve sample efficiency in structure-guided ligand optimization. We further find that Boltz2 representations are complementary to those learned from conventional standalone molecular supervision, including 3D conformers, bioassay labels, and quantum-chemical properties. Finally, we extend representation alignment to reinforcement learning, showing that dense representation-level supervision can complement scalar rewards in molecular discovery. These results identify protein-ligand co-folding as a promising pretraining paradigm for small-molecule representation learning and position Boltz2 as a strong, off-the-shelf molecular foundation model.

Taewon Kim, Jihwan Shin, Hyomin Kim et al.

DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making fixed tokenizations a brittle design choice under shifts, indels, and local repeats. We introduce DNAChunker, a masked DNA language model that incorporates a learnable adaptive segmentation module to produce context-dependent, variable-length units. Building on a dynamic segmentation procedure, DNAChunker learns to allocate finer granularity to functionally enriched regions while compressing repetitive or redundant sequence. We pretrain DNAChunker on the human reference genome and evaluate it across five benchmarks, where it consistently improves over strong fixed-tokenization baselines. Further analyses and ablations indicate that unlike fixed tokenizations, segmentation is learned in a biologically-informed, mutation-resilient manner.

Taewon Kim, Hyosoon Jang, Hyunjin Seo et al.

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotation. We propose TriProRep, a structure-aware pretraining method that jointly models three aligned residue-level views: amino-acid identity, backbone geometry, and local full-atom geometry, discretely encoded via VQ-VAE tokenizers. By pretraining to recover original tokens from generator-corrupted views, TriProRep learns to distinguish plausible but incorrect cross-view augmentations from the original protein. We further introduce RepSP, a benchmark for evaluating protein representations in structure-predictive settings. RepSP tests three uses of representations: homodimer co-folding from apo-chain representations, residue-level prediction of homodimer-derived interaction properties, and representation-aligned monomer structure prediction. Across these tasks, TriProRep improves over sequence-only and prior structure-aware representation models, while maintaining competitive performance on conventional benchmarks.

Changhun Kim, Taewon Kim, Seungyeon Woo et al.

In real-world scenarios, tabular data often suffer from distribution shifts that threaten the performance of machine learning models. Despite its prevalence and importance, handling distribution shifts in the tabular domain remains underexplored due to the inherent challenges within the tabular data itself. In this sense, test-time adaptation (TTA) offers a promising solution by adapting models to target data without accessing source data, crucial for privacy-sensitive tabular domains. However, existing TTA methods either 1) overlook the nature of tabular distribution shifts, often involving label distribution shifts, or 2) impose architectural constraints on the model, leading to a lack of applicability. To this end, we propose AdapTable, a novel TTA framework for tabular data. AdapTable operates in two stages: 1) calibrating model predictions using a shift-aware uncertainty calibrator, and 2) adjusting these predictions to match the target label distribution with a label distribution handler. We validate the effectiveness of AdapTable through theoretical analysis and extensive experiments on various distribution shift scenarios. Our results demonstrate AdapTable's ability to handle various real-world distribution shifts, achieving up to a 16% improvement on the HELOC dataset.

Gilhyun Nam, Taewon Kim, Joonhyun Jeong et al.

Test-time adaptation (TTA) enables efficient adaptation of deployed models, yet it often leads to poorly calibrated predictive uncertainty - a critical issue in high-stakes domains such as autonomous driving, finance, and healthcare. Existing calibration methods typically assume fixed models or static distributions, resulting in degraded performance under real-world, dynamic test conditions. To address these challenges, we introduce Style Invariance as a Correctness Likelihood (SICL), a framework that leverages style-invariance for robust uncertainty estimation. SICL estimates instance-wise correctness likelihood by measuring prediction consistency across style-altered variants, requiring only the model's forward pass. This makes it a plug-and-play, backpropagation-free calibration module compatible with any TTA method. Comprehensive evaluations across four baselines, five TTA methods, and two realistic scenarios with three model architecture demonstrate that SICL reduces calibration error by an average of 13 percentage points compared to conventional calibration approaches.

Hyunjin Seo, Taewon Kim, Sihyun Yu et al.

Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that naively applying standards MDMs severely degrades the performance. We identify the critical cause of this issue as a state-clashing problem-where the forward diffusion of distinct molecules collapse into a common state, resulting in a mixture of reconstruction targets that cannot be learned using typical reverse diffusion process with unimodal predictions. To mitigate this, we propose Masked Element-wise Learnable Diffusion (MELD) that orchestrates per-element corruption trajectories to avoid collision between distinct molecular graphs. This is achieved through a parameterized noise scheduling network that assigns distinct corruption rates to individual graph elements, i.e., atoms and bonds. Extensive experiments on diverse molecular benchmarks reveal that MELD markedly enhances overall generation quality compared to element-agnostic noise scheduling, increasing the chemical validity of vanilla MDMs on ZINC250K from 15% to 93%, Furthermore, it achieves state-of-the-art property alignment in conditional generation tasks.

Seunghyeok Back, Joosoon Lee, Taewon Kim et al.

Instance-aware segmentation of unseen objects is essential for a robotic system in an unstructured environment. Although previous works achieved encouraging results, they were limited to segmenting the only visible regions of unseen objects. For robotic manipulation in a cluttered scene, amodal perception is required to handle the occluded objects behind others. This paper addresses Unseen Object Amodal Instance Segmentation (UOAIS) to detect 1) visible masks, 2) amodal masks, and 3) occlusions on unseen object instances. For this, we propose a Hierarchical Occlusion Modeling (HOM) scheme designed to reason about the occlusion by assigning a hierarchy to a feature fusion and prediction order. We evaluated our method on three benchmarks (tabletop, indoors, and bin environments) and achieved state-of-the-art (SOTA) performance. Robot demos for picking up occluded objects, codes, and datasets are available at https://sites.google.com/view/uoais

Taewon Kim, Yeseong Park, Youngbin Park et al.

For a robotic grasping task in which diverse unseen target objects exist in a cluttered environment, some deep learning-based methods have achieved state-of-the-art results using visual input directly. In contrast, actor-critic deep reinforcement learning (RL) methods typically perform very poorly when grasping diverse objects, especially when learning from raw images and sparse rewards. To make these RL techniques feasible for vision-based grasping tasks, we employ state representation learning (SRL), where we encode essential information first for subsequent use in RL. However, typical representation learning procedures are unsuitable for extracting pertinent information for learning the grasping skill, because the visual inputs for representation learning, where a robot attempts to grasp a target object in clutter, are extremely complex. We found that preprocessing based on the disentanglement of a raw input image is the key to effectively capturing a compact representation. This enables deep RL to learn robotic grasping skills from highly varied and diverse visual inputs. We demonstrate the effectiveness of this approach with varying levels of disentanglement in a realistic simulated environment.