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Drug discovery frequently loses momentum when data, expertise, and tools are scattered, slowing design cycles. To shorten this loop we built a hierarchical, tool using agent framework that automates molecular optimisation. A Principal…

Machine Learning · Computer Science 2025-08-06 Atabey Ünlü , Phil Rohr , Ahmet Celebi

We evaluate the impact of pretraining Graph Transformer architectures on atom-level quantum-mechanical features for the modeling of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of drug-like compounds. We…

Multi-task imitation learning (MTIL) has shown significant potential in robotic manipulation by enabling agents to perform various tasks using a single policy. This simplifies the policy deployment and enhances the agent's adaptability…

Robotics · Computer Science 2025-03-27 Litao Liu , Wentao Wang , Yifan Han , Zhuoli Xie , Pengfei Yi , Junyan Li , Yi Qin , Wenzhao Lian

The growing demand for Large Language Models (LLMs) in applications such as content generation, intelligent chatbots, and sentiment analysis poses considerable challenges for LLM service providers. To efficiently use GPU resources and boost…

Machine Learning · Computer Science 2024-04-17 Yilong Zhao , Chien-Yu Lin , Kan Zhu , Zihao Ye , Lequn Chen , Size Zheng , Luis Ceze , Arvind Krishnamurthy , Tianqi Chen , Baris Kasikci

Simulations of biological macromolecules play an important role in understanding the physical basis of a number of complex processes such as protein folding. Even with increasing computational power and evolution of specialized…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-09-18 Hyungro Lee , Heng Ma , Matteo Turilli , Debsindhu Bhowmik , Shantenu Jha , Arvind Ramanathan

Machine-learning models in chemistry - when based on descriptors of atoms embedded within molecules - face essential challenges in transferring the quality of predictions of local electronic structures and their associated properties across…

Chemical Physics · Physics 2024-09-27 Frederik Ø. Kjeldal , Janus J. Eriksen

All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…

Soft Condensed Matter · Physics 2018-04-20 Davide Bochicchio , Giovanni M. Pavan

Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…

Chemical Physics · Physics 2018-12-20 Michael Gastegger , Philipp Marquetand

Accurate simulations of molecules require high-level electronic-structure theory in combination with rigorous methods for approximating the quantum dynamics. Machine-learning approaches can significantly reduce the computational expense of…

Chemical Physics · Physics 2026-02-24 Valerii Andreichev , Jindra Dušek , Markus Meuwly , Jeremy O. Richardson

Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required…

Chemical Physics · Physics 2024-09-19 Yi-Fan Hou , Lina Zhang , Quanhao Zhang , Fuchun Ge , Pavlo O. Dral

Recent works have shown the promise of learning pre-trained models for 3D molecular representation. However, existing pre-training models focus predominantly on equilibrium data and largely overlook off-equilibrium conformations. It is…

Chemical Physics · Physics 2023-08-30 Rui Feng , Qi Zhu , Huan Tran , Binghong Chen , Aubrey Toland , Rampi Ramprasad , Chao Zhang

Molecular optimization is a crucial yet complex and time-intensive process that often acts as a bottleneck for drug development. Traditional methods rely heavily on trial and error, making multi-objective optimization both time-consuming…

Biomolecules · Quantitative Biology 2025-03-06 Jiajun Yu , Yizhen Zheng , Huan Yee Koh , Shirui Pan , Tianyue Wang , Haishuai Wang

Molecular representation learning has become a central approach in AI-driven drug discovery, yet existing molecular tokenizations such as SMILES remain largely syntactic and do not naturally align with chemically meaningful substructures.…

Machine Learning · Computer Science 2026-05-19 Takayuki Kimura

Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on…

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds…

Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…

Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…

Building general-purpose embodied agents across diverse hardware remains a central challenge in robotics, often framed as the ''one-brain, many-forms'' paradigm. Progress is hindered by fragmented data, inconsistent representations, and…

Computer Vision and Pattern Recognition · Computer Science 2026-04-15 Yandan Yang , Shuang Zeng , Tong Lin , Xinyuan Chang , Dekang Qi , Junjin Xiao , Haoyun Liu , Ronghan Chen , Yuzhi Chen , Dongjie Huo , Feng Xiong , Xing Wei , Zhiheng Ma , Mu Xu

Despite recent progress in time-series foundation models, challenges persist in improving representation learning and adapting to diverse downstream tasks. We introduce a General Time-series Model (GTM), which advances representation…

Machine Learning · Computer Science 2026-03-13 Cheng He , Xu Huang , Gangwei Jiang , Zhaoyi Li , Defu Lian , Hong Xie , Enhong Chen , Xijie Liang , Zengrong Zheng , Patrick P. C. Lee

Accurate and efficient prediction of electronic wavefunctions is central to ab initio molecular dynamics (AIMD) and electronic structure theory. However, conventional ab initio methods require self-consistent optimization of electronic…

Chemical Physics · Physics 2025-11-12 Yanxian Tao , Lingyun Wan , Xiongzhi Zeng , Yingdi Jin , Jie Liu , Zhenyu Li , Jinlong Yang