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 nature machine intelligence


Multi-Agent Design Assistant for the Simulation of Inertial Fusion Energy

Shachar, Meir H., Sterbentz, Dane M., Menon, Harshitha, Jekel, Charles F., Fernández-Godino, M. Giselle, Brown, Nathan K., Boureima, Ismael D., Hao, Yue, Korner, Kevin, Rieben, Robert, White, Daniel A., Schill, William J., Belof, Jonathan L.

arXiv.org Artificial Intelligence

Inertial fusion energy promises nearly unlimited, clean power if it can be achieved. However, the design and engineering of fusion systems requires controlling and manipulating matter at extreme energies and timescales; the shock physics and radiation transport governing the physical behavior under these conditions are complex requiring the development, calibration, and use of predictive multiphysics codes to navigate the highly nonlinear and multi-faceted design landscape. We hypothesize that artificial intelligence reasoning models can be combined with physics codes and emulators to autonomously design fusion fuel capsules. In this article, we construct a multi-agent system where natural language is utilized to explore the complex physics regimes around fusion energy. The agentic system is capable of executing a high-order multiphysics inertial fusion computational code. We demonstrate the capacity of the multi-agent design assistant to both collaboratively and autonomously manipulate, navigate, and optimize capsule geometry while accounting for high fidelity physics that ultimately achieve simulated ignition via inverse design.


Neural Brain: A Neuroscience-inspired Framework for Embodied Agents

Liu, Jian, Shi, Xiongtao, Nguyen, Thai Duy, Zhang, Haitian, Zhang, Tianxiang, Sun, Wei, Li, Yanjie, Vasilakos, Athanasios V., Iacca, Giovanni, Khan, Arshad Ali, Kumar, Arvind, Cho, Jae Won, Mian, Ajmal, Xie, Lihua, Cambria, Erik, Wang, Lin

arXiv.org Artificial Intelligence

The rapid evolution of artificial intelligence (AI) has shifted from static, data-driven models to dynamic systems capable of perceiving and interacting with real-world environments. Despite advancements in pattern recognition and symbolic reasoning, current AI systems, such as large language models, remain disembodied, unable to physically engage with the world. This limitation has driven the rise of embodied AI, where autonomous agents, such as humanoid robots, must navigate and manipulate unstructured environments with human-like adaptability. At the core of this challenge lies the concept of Neural Brain, a central intelligence system designed to drive embodied agents with human-like adaptability. A Neural Brain must seamlessly integrate multimodal sensing and perception with cognitive capabilities. Achieving this also requires an adaptive memory system and energy-efficient hardware-software co-design, enabling real-time action in dynamic environments. This paper introduces a unified framework for the Neural Brain of embodied agents, addressing two fundamental challenges: (1) defining the core components of Neural Brain and (2) bridging the gap between static AI models and the dynamic adaptability required for real-world deployment. To this end, we propose a biologically inspired architecture that integrates multimodal active sensing, perception-cognition-action function, neuroplasticity-based memory storage and updating, and neuromorphic hardware/software optimization. Furthermore, we also review the latest research on embodied agents across these four aspects and analyze the gap between current AI systems and human intelligence. By synthesizing insights from neuroscience, we outline a roadmap towards the development of generalizable, autonomous agents capable of human-level intelligence in real-world scenarios.


Experience Scaling: Post-Deployment Evolution For Large Language Models

Yin, Xingkun, Huang, Kaibin, Kim, Dong In, Du, Hongyang

arXiv.org Artificial Intelligence

Scaling model size, training data, and compute power have driven advances in large language models (LLMs), but these approaches are reaching saturation as human-generated text is exhausted and further gains diminish. We propose experience scaling, a framework for continuous post-deployment evolution for LLMs through autonomous interaction with the environment and collaborative sharing of accumulated experience. The framework captures raw interactions, distills them into compact, reusable knowledge, and periodically refines stored content to preserve relevance and efficiency. We validate the framework in simulated real-world scenarios involving generalization to previously unseen but related tasks, repetitive queries, and over-saturated knowledge stores. Across all settings, experience scaling improves accuracy, sustains performance over time, and maintains gains when applied to novel situations. These results demonstrate that structured post-deployment learning can extend LLM capabilities beyond the limits of static human-generated data, offering a scalable path for continued intelligence progress.


Graph Foundation Models: A Comprehensive Survey

Wang, Zehong, Liu, Zheyuan, Ma, Tianyi, Li, Jiazheng, Zhang, Zheyuan, Fu, Xingbo, Li, Yiyang, Yuan, Zhengqing, Song, Wei, Ma, Yijun, Zeng, Qingkai, Chen, Xiusi, Zhao, Jianan, Li, Jundong, Jiang, Meng, Lio, Pietro, Chawla, Nitesh, Zhang, Chuxu, Ye, Yanfang

arXiv.org Artificial Intelligence

Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.


Barriers for the performance of graph neural networks (GNN) in discrete random structures. A comment on~\cite{schuetz2022combinatorial},\cite{angelini2023modern},\cite{schuetz2023reply}

Gamarnik, David

arXiv.org Artificial Intelligence

Recently graph neural network (GNN) based algorithms were proposed to solve a variety of combinatorial optimization problems, including Maximum Cut problem, Maximum Independent Set problem and similar other problems~\cite{schuetz2022combinatorial},\cite{schuetz2022graph}. The publication~\cite{schuetz2022combinatorial} stirred a debate whether GNN based method was adequately benchmarked against best prior methods. In particular, critical commentaries~\cite{angelini2023modern} and~\cite{boettcher2023inability} point out that simple greedy algorithm performs better than GNN in the setting of random graphs, and in fact stronger algorithmic performance can be reached with more sophisticated methods. A response from the authors~\cite{schuetz2023reply} pointed out that GNN performance can be improved further by tuning up the parameters better. We do not intend to discuss the merits of arguments and counter-arguments in~\cite{schuetz2022combinatorial},\cite{angelini2023modern},\cite{boettcher2023inability},\cite{schuetz2023reply}. Rather in this note we establish a fundamental limitation for running GNN on random graphs considered in these references, for a broad range of choices of GNN architecture. These limitations arise from the presence of the Overlap Gap Property (OGP) phase transition, which is a barrier for many algorithms, both classical and quantum. As we demonstrate in this paper, it is also a barrier to GNN due to its local structure. We note that at the same time known algorithms ranging from simple greedy algorithms to more sophisticated algorithms based on message passing, provide best results for these problems \emph{up to} the OGP phase transition. This leaves very little space for GNN to outperform the known algorithms, and based on this we side with the conclusions made in~\cite{angelini2023modern} and~\cite{boettcher2023inability}.


Synthetic data for AI outperform real data in robot-assisted surgery

#artificialintelligence

While artificial intelligence continues to transform health care, the tech has an Achilles heel: training AI systems to perform specific tasks requires a great deal of annotated data that engineers sometimes just don't have or cannot get. In a perfect world, researchers would be able to digitally generate the exact data they need when they need it, unlocking new capabilities of AI. In reality, however, even digitally generating this data is tricky because real-world data, especially in medicine, is complex and multi-faceted. But solutions are in the pipeline. Researchers in the Whiting School of Engineering's Laboratory for Computational Sensing and Robotics have created software to realistically simulate the data necessary for developing AI algorithms that perform important tasks in surgery, such as X-ray image analysis.


New AI model transforms understanding of metal-organic frameworks

#artificialintelligence

How does an iPhone predict the next word you're going to type in your messages? The technology behind this, and also at the core of many AI applications, is called a transformer; a deep-learning algorithm that detects patterns in datasets. Now, researchers at EPFL and KAIST have created a transformer for Metal-Organic Frameworks (MOFs), a class of porous crystalline materials. By combining organic linkers with metal nodes, chemists can synthesize millions of different materials with potential applications in energy storage and gas separation. The "MOFtransformer" is designed to be the ChatGPT for researchers that study MOFs.


AI could speed up discovery of new medicines

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Artificial intelligence that could reduce the cost and speed-up the discovery of new medicines has been developed as part of a collaboration between researchers at the University of Sheffield and AstraZeneca. The new technology, developed by Professor Haiping Lu and his Ph.D. student Peizhen Bai from Sheffield's Department of Computer Science, with Dr. Filip Miljković and Dr. Bino John from AstraZeneca, is described in a new study published in Nature Machine Intelligence. The study demonstrates that the AI, called DrugBAN, can predict whether a candidate drug will interact with its intended target protein molecules inside the human body. AI that can predict whether drugs will reach their intended targets already exists, but the technology developed by the researchers at Sheffield and AstraZeneca can do this with greater accuracy and also provide useful insights to help scientists understand how drugs engage with their protein partners at a molecular level, according to the paper published on February 2, 2023. AI has the potential to inform whether a drug will successfully engage an intended cancer-related protein, or whether a candidate drug will bind to unintended targets in the body and lead to undesirable side-effects for patients.


How AI can help people be more empathetic about mental health

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Empathy is critical to having supportive conversations about mental health. But this skill can be tricky to learn, especially in the moment when a person is sharing something hard. A team led by researchers at the University of Washington studied how artificial intelligence could help people on the platform TalkLife, where people give each other mental health support. The researchers developed an AI system that suggested changes to participants' responses to make them more empathetic. The system helped people communicate empathy more effectively than traditional training did.


Predicting unseen antibodies' neutralizability via adaptive graph neural networks - Nature Machine Intelligence

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Most natural and synthetic antibodies are ‘unseen’. That is, the demonstration of their neutralization effects with any antigen requires laborious and costly wet-lab experiments. The existing methods that learn antibody representations from known antibody–antigen interactions are unsuitable for unseen antibodies owing to the absence of interaction instances. The DeepAAI method proposed herein learns unseen antibody representations by constructing two adaptive relation graphs among antibodies and antigens and applying Laplacian smoothing between unseen and seen antibodies’ representations. Rather than using static protein descriptors, DeepAAI learns representations and relation graphs ‘dynamically’, optimized towards the downstream tasks of neutralization prediction and 50% inhibition concentration estimation. The performance of DeepAAI is demonstrated on human immunodeficiency virus, severe acute respiratory syndrome coronavirus 2, influenza and dengue. Moreover, the relation graphs have rich interpretability. The antibody relation graph implies similarity in antibody neutralization reactions, and the antigen relation graph indicates the relation among a virus’s different variants. We accordingly recommend probable broad-spectrum antibodies against new variants of these viruses. The effects of novel antibodies are hard to predict owing to the complex interactions between antibodies and antigens. Zhang and colleagues use a graph-based method to learn a dynamic representation that allows for predictions of neutralization activity and demonstrate the method by recommending probable antibodies for human immunodeficiency virus, severe acute respiratory syndrome coronavirus 2, influenza and dengue.