Chanyoung Park

Gyoung S. Na, Chanyoung Park

Various representation learning methods for molecular structures have been devised to accelerate data-driven chemistry. However, the representation capabilities of existing methods are essentially limited to atom-level information, which is not sufficient to describe real-world molecular physics. Although electron-level information can provide fundamental knowledge about chemical compounds beyond the atom-level information, obtaining the electron-level information in real-world molecules is computationally impractical and sometimes infeasible. We propose a method for learning electron-informed molecular representations without additional computation costs by transferring readily accessible electron-level information about small molecules to large molecules of our interest. The proposed method achieved state-of-the-art prediction accuracy on extensive benchmark datasets containing experimentally observed molecular physics. The source code for HEDMoL is available at https://github.com/ngs00/HEDMoL.

Wonjoong Kim, Sangwu Park, Yeonjun In et al.

Although recent tool-augmented benchmarks incorporate complex user requests and diverse tools, the evaluation methods for most of them remain limited to answer matching. However, as the number of steps required to resolve a user request increases, a proper evaluation of an agent's performance must go beyond the final answer to also assess the problem-solving trajectory, including previously ignored aspects such as efficiency, hallucination, and adaptivity. The most straightforward method for evaluating these aspects is to compare an agent's trajectory with the ground-truth trajectory, but this approach is fundamentally limited since annotating all valid ground-truth trajectories is prohibitively expensive. However, a simple LLM-based evaluator struggles to assess trajectories in detail without ground truth. To effectively evaluate the agents in this manner, we introduce TRACE, a framework for the multi-dimensional evaluation of tool-augmented LLM agent performance. By incorporating an evidence bank, which accumulates knowledge gathered from preceding reasoning steps, TRACE enables a multi-faceted analysis and evaluation of an agent's reasoning trajectory effectively. To validate our framework, we develop a new meta-evaluation dataset by augmenting existing benchmarks with diverse and flawed trajectories, each labeled with multi-faceted performance scores. Our results confirm that TRACE accurately evaluates these complex behaviors in a scalable and cost-effective manner, even with small open-source LLMs. Furthermore, we apply our method to evaluate the trajectories that agents produce while solving tool-augmented tasks, presenting previously unreported observations and their corresponding insights.

Namkyeong Lee, Yunhak Oh, Heewoong Noh et al.

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, earlier MRL approaches are limited to using only the 2D topological structure of molecules, as obtaining the 3D interaction geometry remains prohibitively expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the limitations of costly traditional quantum mechanical calculation methods. With the constructed 3D virtual interaction environment, 3DMRL trains 2D MRL model to learn the global and local 3D geometric information of molecular interaction. Extensive experiments on various tasks using real-world datasets, including out-of-distribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, showing up to a 24.93% improvement in performance across 40 tasks. Our code is publicly available at https://github.com/Namkyeong/3DMRL.

Namwoo Kim, Takahiro Yabe, Chanyoung Park et al.

Recently, learning effective representations of urban regions has gained significant attention as a key approach to understanding urban dynamics and advancing smarter cities. Existing approaches have demonstrated the potential of leveraging mobility data to generate latent representations, providing valuable insights into the intrinsic characteristics of urban areas. However, incorporating the temporal dynamics and detailed semantics inherent in human mobility patterns remains underexplored. To address this gap, we propose a novel urban region representation learning model, Mobility Time Series Contrastive Learning for Urban Region Representations (MobiCLR), designed to capture semantically meaningful embeddings from inflow and outflow mobility patterns. MobiCLR uses contrastive learning to enhance the discriminative power of its representations, applying an instance-wise contrastive loss to capture distinct flow-specific characteristics. Additionally, we develop a regularizer to align output features with these flow-specific representations, enabling a more comprehensive understanding of mobility dynamics. To validate our model, we conduct extensive experiments in Chicago, New York, and Washington, D.C. to predict income, educational attainment, and social vulnerability. The results demonstrate that our model outperforms state-of-the-art models.