5 papers
Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials
Alex Morehead, Miruna Cretu, Antonia Panescu +14
General-purpose 3D modeling in chemistry encompasses molecules and materials, requiring both generative and predictive capabilities. However, most existing AI approaches are optimi…
Remember to Forget: Gated Adaptive Positional Encoding
Riccardo Ali, Alessio Borgi, Christopher Irwin +2
Rotary Positional Encoding (RoPE) is widely used in modern large language models. However, when sequences are extended beyond the range seen during training, rotary phases can ente…
Many Needles in a Haystack: Active Hit Discovery for Perturbation Experiments
Andrea Rubbi, Arpit Merchant, Samuel Ogden +4
High-throughput gene perturbation experiments can test several genetic interventions in parallel, yet experimental budgets remain limited. A central goal is hit discovery: identify…
Molecular Representations in Implicit Functional Space via Hyper-Networks
Zehong Wang, Xiaolong Han, Qi Yang +10
Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipel…
Graph Foundation Models: A Comprehensive Survey
Zehong Wang, Zheyuan Liu, Tianyi Ma +16
Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural lang…