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Protein representation learning is critical in various tasks in biology, such as drug design and protein structure or function prediction, which has primarily benefited from protein language models and graph neural networks. These models…

生物大分子 · 定量生物学 2024-02-16 Bozhen Hu , Zelin Zang , Cheng Tan , Stan Z. Li

A major obstacle to the realization of novel inorganic materials with desirable properties is the inability to perform efficient optimization across both materials properties and synthesis of those materials. In this work, we propose a…

材料科学 · 物理学 2022-10-24 Elton Pan , Christopher Karpovich , Elsa Olivetti

Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

生物大分子 · 定量生物学 2025-12-01 Filippo Stocco , Maria Artigues-Lleixa , Andrea Hunklinger , Talal Widatalla , Marc Guell , Noelia Ferruz

With the growing demand for novel materials, machine learning-driven inverse design methods face significant challenges in reconciling the high-dimensional materials composition space with limited experimental data. Existing approaches…

机器学习 · 计算机科学 2025-07-02 Yeyong Yu , Xilei Bian , Jie Xiong , Xing Wu , Quan Qian

While backpropagation and automatic differentiation have driven deep learning's success, the physical limits of chip manufacturing and rising environmental costs of deep learning motivate alternative learning paradigms such as physical…

机器学习 · 计算机科学 2026-04-21 Yaqi Guo , Fabian Braun , Bastiaan Ketelaar , Stephanie Tan , Richard Norte , Siddhant Kumar

A promising way to improve the sample efficiency of reinforcement learning is model-based methods, in which many explorations and evaluations can happen in the learned models to save real-world samples. However, when the learned model has a…

机器学习 · 计算机科学 2022-09-14 Haoxin Lin , Yihao Sun , Jiaji Zhang , Yang Yu

While DeepMind has tentatively solved protein folding, its inverse problem -- protein design which predicts protein sequences from their 3D structures -- still faces significant challenges. Particularly, the lack of large-scale standardized…

定量方法 · 定量生物学 2022-02-15 Zhangyang Gao , Cheng Tan , Stan Z. Li

Design of process control scheme is critical for quality assurance to reduce variations in manufacturing systems. Taking semiconductor manufacturing as an example, extensive literature focuses on control optimization based on certain…

机器学习 · 计算机科学 2023-09-19 Yanrong Li , Juan Du , Wei Jiang

Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints,…

机器学习 · 计算机科学 2025-10-29 Joohwan Ko , Aristofanis Rontogiannis , Yih-En Andrew Ban , Axel Elaldi , Nicholas Franklin

Zero-shot reinforcement learning (RL) promises to provide agents that can perform any task in an environment after an offline, reward-free pre-training phase. Methods leveraging successor measures and successor features have shown strong…

机器学习 · 计算机科学 2024-10-31 Scott Jeen , Tom Bewley , Jonathan M. Cullen

Quantum sensors offer control flexibility during estimation by allowing manipulation by the experimenter across various parameters. For each sensing platform, pinpointing the optimal controls to enhance the sensor's precision remains a…

量子物理 · 物理学 2024-12-11 Federico Belliardo , Fabio Zoratti , Florian Marquardt , Vittorio Giovannetti

The aim of Reinforcement Learning (RL) in real-world applications is to create systems capable of making autonomous decisions by learning from their environment through trial and error. This paper emphasizes the importance of reward…

机器学习 · 计算机科学 2024-12-31 Sinan Ibrahim , Mostafa Mostafa , Ali Jnadi , Hadi Salloum , Pavel Osinenko

Zero Reinforcement Learning (Zero-RL) has proven to be an effective approach for enhancing the reasoning capabilities of large language models (LLMs) by directly applying reinforcement learning with verifiable rewards on pretrained models,…

人工智能 · 计算机科学 2025-10-30 Yuyuan Zeng , Yufei Huang , Can Xu , Qingfeng Sun , Jianfeng Yan , Guanghui Xu , Tao Yang , Fengzong Lian

Tools like Tamarin and ProVerif have achieved notable success in analyzing and verifying complex real-world protocols such as EMV, 5G, and WPA2, even detecting zero-day exploits. Despite these successes, verifying such protocols remains a…

密码学与安全 · 计算机科学 2026-05-25 Matthias Cosler , Cas Cremers , Bernd Finkbeiner , Mohamed Ghanem , Niklas Medinger

Quantum computers have the potential to outperform classical computers in important tasks such as optimization and number factoring. They are characterized by limited connectivity, which necessitates the routing of their computational bits,…

量子物理 · 物理学 2024-10-08 Wei Tang , Yiheng Duan , Yaroslav Kharkov , Rasool Fakoor , Eric Kessler , Yunong Shi

The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…

生物大分子 · 定量生物学 2018-11-07 Joe G Greener , Lewis Moffat , David T Jones

The AlphaZero/MuZero (A/MZ) family of algorithms has achieved remarkable success across various challenging domains by integrating Monte Carlo Tree Search (MCTS) with learned models. Learned models introduce epistemic uncertainty, which is…

机器学习 · 计算机科学 2026-05-18 Yaniv Oren , Viliam Vadocz , Matthijs T. J. Spaan , Wendelin Böhmer

Automating molecular design using deep reinforcement learning (RL) holds the promise of accelerating the discovery of new chemical compounds. Existing approaches work with molecular graphs and thus ignore the location of atoms in space,…

机器学习 · 统计学 2021-03-02 Gregor N. C. Simm , Robert Pinsler , José Miguel Hernández-Lobato

Prediction of protein structures using computational approaches has been explored for over two decades, paving a way for more focused research and development of algorithms in comparative modelling, ab intio modelling and structure…

定量方法 · 定量生物学 2020-05-19 Surbhi Dhingra , Ramanathan Sowdhamini , Frédéric Cadet , Bernard Offmann

Monte-Carlo planning and Reinforcement Learning (RL) are essential to sequential decision making. The recent AlphaGo and AlphaZero algorithms have shown how to successfully combine these two paradigms in order to solve large scale…

机器学习 · 计算机科学 2021-02-17 Tuan Dam , Carlo D'Eramo , Jan Peters , Joni Pajarinen