Genome analysis through image processing with deep learning models

Y Zhang, S Imoto - Journal of Human Genetics, 2024 - nature.com
Genomic sequences are traditionally represented as strings of characters: A (adenine), C
(cytosine), G (guanine), and T (thymine). However, an alternative approach involves …

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

J **a, L Zhang, Y Liu, Y Liu, W Du… - Advances in …, 2025 - proceedings.neurips.cc
Molecular relational learning (MRL) is crucial for understanding the interaction behaviors
between molecular pairs, a critical aspect of drug discovery and development. However, the …

Mixed graph contrastive network for semi-supervised node classification

X Yang, Y Wang, Y Liu, Y Wen, L Meng… - ACM Transactions on …, 2024 - dl.acm.org
Graph Neural Networks (GNNs) have achieved promising performance in semi-supervised
node classification in recent years. However, the problem of insufficient supervision …

Human-in-the-loop active learning for goal-oriented molecule generation

Y Nahal, J Menke, J Martinelli, M Heinonen… - Journal of …, 2024 - Springer
Machine learning (ML) systems have enabled the modelling of quantitative structure–
property relationships (QSPR) and structure-activity relationships (QSAR) using existing …

Molx: Enhancing large language models for molecular learning with a multi-modal extension

K Le, Z Guo, K Dong, X Huang, B Nan, R Iyer… - arxiv preprint arxiv …, 2024 - arxiv.org
Large Language Models (LLMs) with their strong task-handling capabilities have shown
remarkable advancements across a spectrum of fields, moving beyond natural language …

Atomas: Hierarchical alignment on molecule-text for unified molecule understanding and generation

Y Zhang, G Ye, C Yuan, B Han, LK Huang… - arxiv preprint arxiv …, 2024 - arxiv.org
Molecule-and-text cross-modal representation learning has emerged as a promising
direction for enhancing the quality of molecular representation, thereby improving …

MIFS: An adaptive multipath information fused self-supervised framework for drug discovery

X Gong, Q Liu, R Han, Y Guo, G Wang - Neural Networks, 2025 - Elsevier
The production of expressive molecular representations with scarce labeled data is
challenging for AI-driven drug discovery. Mainstream studies often follow a pipeline that pre …

Metaenzyme: Meta pan-enzyme learning for task-adaptive redesign

J Zheng, H Zhang, Q Xu, AP Zeng, SZ Li - Proceedings of the 32nd ACM …, 2024 - dl.acm.org
Enzyme design plays a crucial role in both industrial production and biology. However, this
field faces challenges due to the lack of comprehensive benchmarks and the complexity of …

Atomas: Hierarchical Adaptive Alignment on Molecule-Text for Unified Molecule Understanding and Generation

Y Zhang, G Ye, C Yuan, B Han, LK Huang… - The Thirteenth …, 2025 - openreview.net
Molecule-and-text cross-modal representation learning has emerged as a promising
direction for enhancing the quality of molecular representation, thereby improving …

Representing molecules as random walks over interpretable grammars

M Sun, M Guo, W Yuan, V Thost, CE Owens… - arxiv preprint arxiv …, 2024 - arxiv.org
Recent research in molecular discovery has primarily been devoted to small, drug-like
molecules, leaving many similarly important applications in material design without …