Hengjie Yu

Hengjie Yu, Dan Luo, Sam F. Y. Li et al.

Crops are constantly challenged by different environmental conditions. Seed treatment by nanomaterials is a cost-effective and environmentally-friendly solution for environmental stress mitigation in crop plants. Here, 56 seed nanopriming treatments are used to alleviate environmental stresses in maize. Seven selected nanopriming treatments significantly increase the stress resistance index (SRI) by 13.9% and 12.6% under salinity stress and combined heat-drought stress, respectively. Metabolomics data reveals that ZnO nanopriming treatment, with the highest SRI value, mainly regulates the pathways of amino acid metabolism, secondary metabolite synthesis, carbohydrate metabolism, and translation. Understanding the mechanism of seed nanopriming is still difficult due to the variety of nanomaterials and the complexity of interactions between nanomaterials and plants. Using the nanopriming data, we present an interpretable structure-activity relationship (ISAR) approach based on interpretable machine learning for predicting and understanding its stress mitigation effects. The post hoc and model-based interpretation approaches of machine learning are combined to provide complementary benefits and give researchers or policymakers more illuminating or trustworthy results. The concentration, size, and zeta potential of nanoparticles are identified as dominant factors for correlating root dry weight under salinity stress, and their effects and interactions are explained. Additionally, a web-based interactive tool is developed for offering prediction-level interpretation and gathering more details about specific nanopriming treatments. This work offers a promising framework for accelerating the agricultural applications of nanomaterials and may profoundly contribute to nanosafety assessment.

Hengjie Yu, Kenneth A. Dawson, Haiyun Yang et al.

Unlocking the potential of nanomaterials in medicine and environmental science hinges on understanding their interactions with proteins, a complex decision space where AI is poised to make a transformative impact. However, progress has been hindered by limited datasets and the restricted generalizability of existing models. Here, we propose NanoPro-3M, the largest nanomaterial-protein interaction dataset to date, comprising over 3.2 million samples and 37,000 unique proteins. Leveraging this, we present NanoProFormer, a foundational model that predicts nanomaterial-protein affinities through multimodal representation learning, demonstrating strong generalization, handling missing features, and unseen nanomaterials or proteins. We show that multimodal modeling significantly outperforms single-modality approaches and identifies key determinants of corona formation. Furthermore, we demonstrate its applicability to a range of downstream tasks through zero-shot inference and fine-tuning. Together, this work establishes a solid foundation for high-performance and generalized prediction of nanomaterial-protein interaction endpoints, reducing experimental reliance and accelerating various in vitro applications.

Yingchao Yu, Yaochu Jin, Kuangrong Hao et al.

Learning-to-learn (L2L), defined as progressively faster learning across similar tasks, is fundamental to both neuroscience and artificial intelligence. However, its neural basis remains elusive, as most studies emphasize neural population dynamics induced by synaptic plasticity while overlooking adaptations driven by intrinsic neuronal plasticity, which point-neuron models cannot capture. To address the above issue, we develop a recurrent spiking neural network with bi-level intrinsic plasticity (IP$^{2}$-RSNN). First, based on task demands, a slow meta-intrinsic plasticity determines which intrinsic neuronal properties are learnable, which is preserved throughout subsequent task learning once configured. Second, a fast intrinsic plasticity fine-tunes those learnable properties within each task. Our results indicate that the proposed bi-level intrinsic plasticity plays a critical role in enabling L2L in RSNNs and show that IP$^{2}$-RSNNs outperform point-neuron recurrent neural networks and self-attention models. Furthermore, our analysis of multi-scale neural dynamics reveals that the bi-level intrinsic plasticity is essential to task-type-specific adaptations at both the neuronal and network levels during L2L, while such adaptations cannot be captured by point-neuron models. Our results suggest that intrinsic plasticity provides significant computational advantages in L2L, shedding light on the design of brain-inspired deep learning models and algorithms.