Gyoung S. Na

Namkyeong Lee, Dongmin Hyun, Gyoung S. Na et al.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Namkyeong Lee, Heewoong Noh, Gyoung S. Na et al.

Machine learning (ML) has seen promising developments in materials science, yet its efficacy largely depends on detailed crystal structural data, which are often complex and hard to obtain, limiting their applicability in real-world material synthesis processes. An alternative, using compositional descriptors, offers a simpler approach by indicating the elemental ratios of compounds without detailed structural insights. However, accurately representing materials solely with compositional descriptors presents challenges due to polymorphism, where a single composition can correspond to various structural arrangements, creating ambiguities in its representation. To this end, we introduce PCRL, a novel approach that employs probabilistic modeling of composition to capture the diverse polymorphs from available structural information. Extensive evaluations on sixteen datasets demonstrate the effectiveness of PCRL in learning compositional representation, and our analysis highlights its potential applicability of PCRL in material discovery. The source code for PCRL is available at https://github.com/Namkyeong/PCRL.

Namkyeong Lee, Heewoong Noh, Sungwon Kim et al.

The density of states (DOS) is a spectral property of materials, which provides fundamental insights on various characteristics of materials. In this paper, we propose a model to predict the DOS by reflecting the nature of DOS: DOS determines the general distribution of states as a function of energy. Specifically, we integrate the heterogeneous information obtained from the crystal structure and the energies via multi-modal transformer, thereby modeling the complex relationships between the atoms in the crystal structure, and various energy levels. Extensive experiments on two types of DOS, i.e., Phonon DOS and Electron DOS, with various real-world scenarios demonstrate the superiority of DOSTransformer. The source code for DOSTransformer is available at https://github.com/HeewoongNoh/DOSTransformer.

Namkyeong Lee, Heewoong Noh, Sungwon Kim et al.

The density of states (DOS) is a spectral property of crystalline materials, which provides fundamental insights into various characteristics of the materials. While previous works mainly focus on obtaining high-quality representations of crystalline materials for DOS prediction, we focus on predicting the DOS from the obtained representations by reflecting the nature of DOS: DOS determines the general distribution of states as a function of energy. That is, DOS is not solely determined by the crystalline material but also by the energy levels, which has been neglected in previous works. In this paper, we propose to integrate heterogeneous information obtained from the crystalline materials and the energies via a multi-modal transformer, thereby modeling the complex relationships between the atoms in the crystalline materials and various energy levels for DOS prediction. Moreover, we propose to utilize prompts to guide the model to learn the crystal structural system-specific interactions between crystalline materials and energies. Extensive experiments on two types of DOS, i.e., Phonon DOS and Electron DOS, with various real-world scenarios demonstrate the superiority of DOSTransformer. The source code for DOSTransformer is available at https://github.com/HeewoongNoh/DOSTransformer.

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.

Heewoong Noh, Namkyeong Lee, Gyoung S. Na et al.

While inorganic retrosynthesis planning is essential in the field of chemical science, the application of machine learning in this area has been notably less explored compared to organic retrosynthesis planning. In this paper, we propose Retrieval-Retro for inorganic retrosynthesis planning, which implicitly extracts the precursor information of reference materials that are retrieved from the knowledge base regarding domain expertise in the field. Specifically, instead of directly employing the precursor information of reference materials, we propose implicitly extracting it with various attention layers, which enables the model to learn novel synthesis recipes more effectively. Moreover, during retrieval, we consider the thermodynamic relationship between target material and precursors, which is essential domain expertise in identifying the most probable precursor set among various options. Extensive experiments demonstrate the superiority of Retrieval-Retro in retrosynthesis planning, especially in discovering novel synthesis recipes, which is crucial for materials discovery. The source code for Retrieval-Retro is available at https://github.com/HeewoongNoh/Retrieval-Retro.

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.

Namkyeong Lee, Kanghoon Yoon, Gyoung S. Na et al.

Recently, molecular relational learning, whose goal is to predict the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. In this work, we propose CMRL that is robust to the distributional shift in molecular relational learning by detecting the core substructure that is causally related to chemical reactions. To do so, we first assume a causal relationship based on the domain knowledge of molecular sciences and construct a structural causal model (SCM) that reveals the relationship between variables. Based on the SCM, we introduce a novel conditional intervention framework whose intervention is conditioned on the paired molecule. With the conditional intervention framework, our model successfully learns from the causal substructure and alleviates the confounding effect of shortcut substructures that are spuriously correlated to chemical reactions. Extensive experiments on various tasks with real-world and synthetic datasets demonstrate the superiority of CMRL over state-of-the-art baseline models. Our code is available at https://github.com/Namkyeong/CMRL.

Gyoung S. Na, Chanyoung Park

Deriving governing equations from empirical observations is a longstanding challenge in science. Although artificial intelligence (AI) has demonstrated substantial capabilities in function approximation, the discovery of explainable and extrapolatable equations remains a fundamental limitation of modern AI, posing a central bottleneck for AI-driven scientific discovery. Here, we present machine collective intelligence, a unified paradigm that integrates two fundamental yet distinct traditions in computational intelligence--symbolism and metaheuristics--to enable autonomous and evolutionary discovery of governing equations. It orchestrates multiple reasoning agents to evolve their symbolic hypotheses through coordinated generation, evaluation, critique, and consolidation, enabling scientific discovery beyond single-agent inference. Across scientific systems governed by deterministic, stochastic, or previously uncharacterized dynamics, machine collective intelligence autonomously recovered the underlying governing equations without relying on hand-crafted domain knowledge. Furthermore, the resulting equations reduced extrapolation error by up to six orders of magnitude relative to deep neural networks, while condensing 0.5-1 million model parameters into just 5-40 interpretable parameters. This study marks an important shift in AI toward the autonomous discovery of principled scientific equations.

Heewoong Noh, Namkyeong Lee, Gyoung S. Na et al.

Spectral analysis provides crucial clues for the elucidation of unknown materials. Among various techniques, infrared spectroscopy (IR) plays an important role in laboratory settings due to its high accessibility and low cost. However, existing approaches often fail to reflect expert analytical processes and lack flexibility in incorporating diverse types of chemical knowledge, which is essential in real-world analytical scenarios. In this paper, we propose IR-Agent, a novel multi-agent framework for molecular structure elucidation from IR spectra. The framework is designed to emulate expert-driven IR analysis procedures and is inherently extensible. Each agent specializes in a specific aspect of IR interpretation, and their complementary roles enable integrated reasoning, thereby improving the overall accuracy of structure elucidation. Through extensive experiments, we demonstrate that IR-Agent not only improves baseline performance on experimental IR spectra but also shows strong adaptability to various forms of chemical information.