arXiv subjects

Jeonghee Jo

Publications and source records attributed to Jeonghee Jo.

8 recordsLinked to original sources

arXiv2026

Hessian-based molecular conformation augmentation for a scalable and efficient strategy of machine learning interatomic potentials

While machine-learning interatomic potentials (MLIPs) have successfully learned potential energy surfaces (PES) and atomic forces, many practical applications, such as vibrational analysis and transition state search, rely heavily on the PES Hessian. Yet, standard MLIPs tend to be trained on energy and forces alone, leaving Hessian information largely unexploited. Meanwhile, existing methods that explicitly incorporate the Hessian into training objectives require architectural modifications and introduce significant computational and memory overheads due to higher-order backpropagation. To address these limitations, we propose two Hessian-derived data augmentation schemes: isotropic Gaussian displacement (\textbf{UniAug}) and normal mode-weighted displacement (\textbf{ModeAug}). Both methods utilize simple Taylor expansions, achieving effective augmentation without altering training objectives or extending the autograd graph. This allows seamless, plug-and-play integration with existing architectures and training pipelines. Comprehensive evaluations across non-equilibrium and equilibrium datasets demonstrate that our approach enhances model accuracy while providing practical, task-specific guidelines.

cs.LG↗

arXiv2024

A More Accurate Approximation of Activation Function with Few Spikes Neurons

Recent deep neural networks (DNNs), such as diffusion models [1], have faced high computational demands. Thus, spiking neural networks (SNNs) have attracted lots of attention as energy-efficient neural networks. However, conventional spiking neurons, such as leaky integrate-and-fire neurons, cannot accurately represent complex non-linear activation functions, such as Swish [2]. To approximate activation functions with spiking neurons, few spikes (FS) neurons were proposed [3], but the approximation performance was limited due to the lack of training methods considering the neurons. Thus, we propose tendency-based parameter initialization (TBPI) to enhance the approximation of activation function with FS neurons, exploiting temporal dependencies initializing the training parameters.

cs.NE↗

arXiv2024

Neural Polarization: Toward Electron Density for Molecules by Extending Equivariant Networks

Recent SO(3)-equivariant models embedded a molecule as a set of single atoms fixed in the three-dimensional space, which is analogous to a ball-and-stick view. This perspective provides a concise view of atom arrangements, however, the surrounding electron density cannot be represented and its polarization effects may be underestimated. To overcome this limitation, we propose \textit{Neural Polarization}, a novel method extending equivariant network by embedding each atom as a pair of fixed and moving points. Motivated by density functional theory, Neural Polarization represents molecules as a space-filling view which includes an electron density, in contrast with a ball-and-stick view. Neural Polarization can flexibly be applied to most type of existing equivariant models. We showed that Neural Polarization can improve prediction performances of existing models over a wide range of targets. Finally, we verified that our method can improve the expressiveness and equivariance in terms of mathematical aspects.

physics.chem-ph↗

arXiv2023

Gradient Scaling on Deep Spiking Neural Networks with Spike-Dependent Local Information

Deep spiking neural networks (SNNs) are promising neural networks for their model capacity from deep neural network architecture and energy efficiency from SNNs' operations. To train deep SNNs, recently, spatio-temporal backpropagation (STBP) with surrogate gradient was proposed. Although deep SNNs have been successfully trained with STBP, they cannot fully utilize spike information. In this work, we proposed gradient scaling with local spike information, which is the relation between pre- and post-synaptic spikes. Considering the causality between spikes, we could enhance the training performance of deep SNNs. According to our experiments, we could achieve higher accuracy with lower spikes by adopting the gradient scaling on image classification tasks, such as CIFAR10 and CIFAR100.

cs.NE↗

arXiv2023

Mass Spectra Prediction with Structural Motif-based Graph Neural Networks

Mass spectra, which are agglomerations of ionized fragments from targeted molecules, play a crucial role across various fields for the identification of molecular structures. A prevalent analysis method involves spectral library searches,where unknown spectra are cross-referenced with a database. The effectiveness of such search-based approaches, however, is restricted by the scope of the existing mass spectra database, underscoring the need to expand the database via mass spectra prediction. In this research, we propose the Motif-based Mass Spectrum Prediction Network (MoMS-Net), a system that predicts mass spectra using the information derived from structural motifs and the implementation of Graph Neural Networks (GNNs). We have tested our model across diverse mass spectra and have observed its superiority over other existing models. MoMS-Net considers substructure at the graph level, which facilitates the incorporation of long-range dependencies while using less memory compared to the graph transformer model.

cs.LG↗

arXiv2022

E2V-SDE: From Asynchronous Events to Fast and Continuous Video Reconstruction via Neural Stochastic Differential Equations

Event cameras respond to brightness changes in the scene asynchronously and independently for every pixel. Due to the properties, these cameras have distinct features: high dynamic range (HDR), high temporal resolution, and low power consumption. However, the results of event cameras should be processed into an alternative representation for computer vision tasks. Also, they are usually noisy and cause poor performance in areas with few events. In recent years, numerous researchers have attempted to reconstruct videos from events. However, they do not provide good quality videos due to a lack of temporal information from irregular and discontinuous data. To overcome these difficulties, we introduce an E2V-SDE whose dynamics are governed in a latent space by Stochastic differential equations (SDE). Therefore, E2V-SDE can rapidly reconstruct images at arbitrary time steps and make realistic predictions on unseen data. In addition, we successfully adopted a variety of image composition techniques for improving image clarity and temporal consistency. By conducting extensive experiments on simulated and real-scene datasets, we verify that our model outperforms state-of-the-art approaches under various video reconstruction settings. In terms of image quality, the LPIPS score improves by up to 12% and the reconstruction speed is 87% higher than that of ET-Net.

cs.CV↗

arXiv2021

GeoT: A Geometry-aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning

In recent years, molecular representation learning has emerged as a key area of focus in various chemical tasks. However, many existing models fail to fully consider the geometric information of molecular structures, resulting in less intuitive representations. Moreover, the widely used message-passing mechanism is limited to provide the interpretation of experimental results from a chemical perspective. To address these challenges, we introduce a novel Transformer-based framework for molecular representation learning, named the Geometry-aware Transformer (GeoT). GeoT learns molecular graph structures through attention-based mechanisms specifically designed to offer reliable interpretability, as well as molecular property prediction. Consequently, GeoT can generate attention maps of interatomic relationships associated with training objectives. In addition, GeoT demonstrates comparable performance to MPNN-based models while achieving reduced computational complexity. Our comprehensive experiments, including an empirical simulation, reveal that GeoT effectively learns the chemical insights into molecular structures, bridging the gap between artificial intelligence and molecular sciences.

cs.LG↗

arXiv2021

Flexible dual-branched message passing neural network for quantum mechanical property prediction with molecular conformation

A molecule is a complex of heterogeneous components, and the spatial arrangements of these components determine the whole molecular properties and characteristics. With the advent of deep learning in computational chemistry, several studies have focused on how to predict molecular properties based on molecular configurations. Message passing neural network provides an effective framework for capturing molecular geometric features with the perspective of a molecule as a graph. However, most of these studies assumed that all heterogeneous molecular features, such as atomic charge, bond length, or other geometric features always contribute equivalently to the target prediction, regardless of the task type. In this study, we propose a dual-branched neural network for molecular property prediction based on message-passing framework. Our model learns heterogeneous molecular features with different scales, which are trained flexibly according to each prediction target. In addition, we introduce a discrete branch to learn single atom features without local aggregation, apart from message-passing steps. We verify that this novel structure can improve the model performance with faster convergence in most targets. The proposed model outperforms other recent models with sparser representations. Our experimental results indicate that in the chemical property prediction tasks, the diverse chemical nature of targets should be carefully considered for both model performance and generalizability.

cs.LG↗