arXiv subjects

Hengjie Yu

Publications and source records attributed to Hengjie Yu.

4 recordsLinked to original sources

arXiv2025

Curriculum-guided multimodal representation learning enables generalizable prediction of nanomaterial-protein interactions

Nanomaterial-protein interactions (NPI) are pivotal to realizing the therapeutic and diagnostic potential of nanomaterials. Although AI promises to accelerate mechanistic understanding and enable rational nanomaterial design, robust generalization to unseen nanomaterials or proteins remains unresolved. Here, we present CuMMI (curriculum-guided multimodal interaction model), a generalizable, explainable, and transferable model designed to infer NPI across complex biological settings. CuMMI leverages a self-constructed million-scale NPI dataset and adopts a multi-stage curriculum centered on human plasma, with progressively broader biofluid exposure to enhance data coverage and generalizability. By integrating protein sequence, structure, and a text-encoded experimental context of 37 features, CuMMI captures complementary material-specific, biochemical, and environmental information. Sample-level quality weights are assigned to ensure full utilization of available data while mitigating low-confidence and sparsely recorded entries. Ablation studies highlight the most influential tabular features, clarifying their contribution to the prediction. Through rigorous external validation across independence-preserving temporal, nanomaterial-held-out, and protein-held-out evaluations, our framework consistently achieves good performance (mean of five classification metrics exceeding 0.75), highlighting its robustness and generalizability to unseen data. Furthermore, fine-tuning on independent gold-nanoparticle data and a held-out protein subset further delivers better performance than training from scratch with substantially fewer samples. Together, our approach enables generalizable and transferable NPI prediction and may accelerate in vitro research and applications of nanomaterials.

cs.LG↗

arXiv2025

Position Paper: Unlocking the Potential of AI Researchers in Scientific Discovery-What Is Missing?

The potential of AI researchers in scientific discovery remains largely untapped. Over the past decade, AI for Science (AI4Science) publications in 145 Nature Index journals have increased fifteen-fold, yet they still account for less than 3% of the total publications. Drawing upon the Diffusion of Innovation theory, we project AI4Science's share of total publications to rise from 2.72% in 2024 to approximately 20% by 2050. Achieving this shift requires fully harnessing the potential of AI researchers, as nearly 95% of AI-driven research in these journals is led by experimental scientists. To facilitate this, we propose structured workflows and strategic interventions to position AI researchers at the forefront of scientific discovery. Specifically, we identify three critical pathways: equipping experimental scientists with accessible AI tools to amplify the impact of AI researchers, bridging cognitive and methodological gaps to enable more direct involvement in scientific discovery, and proactively fostering a thriving AI-driven scientific ecosystem. By addressing these challenges, we aim to empower AI researchers as key drivers of future scientific breakthroughs.

cs.CY↗

arXiv2025

IP$^{2}$-RSNN: Bi-level Intrinsic Plasticity Enables Learning-to-learn in Recurrent Spiking Neural Networks

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.

cs.NE↗

arXiv2023

Interpretable machine learning-accelerated seed treatment by nanomaterials for environmental stress alleviation

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.

cs.LG↗