arXiv subjects

Seungyeon Choi

Publications and source records attributed to Seungyeon Choi.

3 recordsLinked to original sources

arXiv2026

LatentTune: Efficient Tuning of High Dimensional Database Parameters via Latent Representation Learning

As data volumes continue to grow, optimizing database performance has become increasingly critical, making the implementation of effective tuning methods essential. Among various approaches, database parameter tuning has proven to be a highly effective means of enhancing performance. Recent studies have shown that machine learning techniques can successfully optimize database parameters, leading to significant performance improvements. However, existing methods still face several limitations. First, they require substantial time to generate large training datasets. Second, to cope with the challenges of highdimensional optimization, they typically optimize only a subset of parameters rather than the full configuration space. Third, they often rely on information from similar workloads instead of directly leveraging information from the target workload. To address these limitations, we propose LatentTune, a novel approach that differs fundamentally from traditional methods. To reduce the time required for data generation, LatentTune incorporates a data augmentation strategy. Furthermore, it constructs a latent space that compresses information from all database parameters, enabling the optimization of the full configuration space. In addition, LatentTune integrates external metric information into the latent space, allowing for precise tuning tailored to the actual target workload. Experimental results demonstrate that LatentTune outperforms baseline models across four workloads on MySQL and RocksDB, achieving up to 1332% improvement for RocksDB and 11.82% throughput gain with 46.01% latency reduction for MySQL.

cs.DB↗

arXiv2025

Controllable 3D Molecular Generation for Structure-Based Drug Design Through Bayesian Flow Networks and Gradient Integration

Recent advances in Structure-based Drug Design (SBDD) have leveraged generative models for 3D molecular generation, predominantly evaluating model performance by binding affinity to target proteins. However, practical drug discovery necessitates high binding affinity along with synthetic feasibility and selectivity, critical properties that were largely neglected in previous evaluations. To address this gap, we identify fundamental limitations of conventional diffusion-based generative models in effectively guiding molecule generation toward these diverse pharmacological properties. We propose CByG, a novel framework extending Bayesian Flow Network into a gradient-based conditional generative model that robustly integrates property-specific guidance. Additionally, we introduce a comprehensive evaluation scheme incorporating practical benchmarks for binding affinity, synthetic feasibility, and selectivity, overcoming the limitations of conventional evaluation methods. Extensive experiments demonstrate that our proposed CByG framework significantly outperforms baseline models across multiple essential evaluation criteria, highlighting its effectiveness and practicality for real-world drug discovery applications.

cs.LG↗

arXiv2024

SPIN: SE(3)-Invariant Physics Informed Network for Binding Affinity Prediction

Accurate prediction of protein-ligand binding affinity is crucial for rapid and efficient drug development. Recently, the importance of predicting binding affinity has led to increased attention on research that models the three-dimensional structure of protein-ligand complexes using graph neural networks to predict binding affinity. However, traditional methods often fail to accurately model the complex's spatial information or rely solely on geometric features, neglecting the principles of protein-ligand binding. This can lead to overfitting, resulting in models that perform poorly on independent datasets and ultimately reducing their usefulness in real drug development. To address this issue, we propose SPIN, a model designed to achieve superior generalization by incorporating various inductive biases applicable to this task, beyond merely training on empirical data from datasets. For prediction, we defined two types of inductive biases: a geometric perspective that maintains consistent binding affinity predictions regardless of the complexs rotations and translations, and a physicochemical perspective that necessitates minimal binding free energy along their reaction coordinate for effective protein-ligand binding. These prior knowledge inputs enable the SPIN to outperform comparative models in benchmark sets such as CASF-2016 and CSAR HiQ. Furthermore, we demonstrated the practicality of our model through virtual screening experiments and validated the reliability and potential of our proposed model based on experiments assessing its interpretability.

cs.LG↗