10 papers
Blending experimental electron density information to protein-ligand interaction
Seonghyun Park, Shuan Chen, Jun Jin Choong +6
Machine learning models for protein-ligand interactions commonly rely on atomic coordinates, which are constructed by fitting molecular models to experimental electron-density maps…
scTrilemma: Balancing Identity, Invariance, and Fidelity in Single-Cell Representation Learning
Yunhak Oh, Yoonho Lee, Junseok Lee +9
Single-cell RNA-seq representation learning is fundamentally label-free: cell identities, states, and contexts are not fixed training targets, so what constitutes signal or nuisanc…
Co-folding with a Soup of Representations
Hyosoon Jang, Taewon Kim, Sungsoo Ahn
Co-folding models such as AlphaFold3, Protenix, ESMFold2, and OpenDDE have advanced rapidly, yet no single model consistently performs best across all biomolecular complexes. In th…
Atom-level Protein Representation Learning Improves Protein Structure Prediction
Taewon Kim, Hyosoon Jang, Hyunjin Seo +6
Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protei…
VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
Hyunjin Seo, Hongjoon Ahn, Jimin Park +16
Protein design aims to compose amino-acid sequences that fold into stable three-dimensional structures while satisfying targeted functional properties. The field is increasingly sh…
Multimodal Crystal Flow: Any-to-Any Modality Generation for Unified Crystal Modeling
Kiyoung Seong, Sungsoo Ahn, Sehui Han +1
Crystal modeling spans a family of conditional and unconditional generation tasks, including crystal structure prediction (CSP) and de novo generation (DNG). While recent deep gene…
Learning Adaptive Perturbation-Conditioned Contexts for Robust Transcriptional Response Prediction
Yinhua Piao, Hyomin Kim, Seonghwan Kim +7
Predicting high-dimensional transcriptional responses to genetic perturbations is challenging because signals are sparse and experimental noise is severe. Existing methods often su…
DNACHUNKER: Learnable Tokenization for DNA Language Models
Taewon Kim, Jihwan Shin, Hyomin Kim +5
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 n…
Learning Flexible Forward Trajectories for Masked Molecular Diffusion
Hyunjin Seo, Taewon Kim, Sihyun Yu +1
Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explo…
REBIND: Enhancing ground-state molecular conformation via force-based graph rewiring
Taewon Kim, Hyunjin Seo, Sungsoo Ahn +1
Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep lear…