#01Jul 22, 2026
q-bio.QM
Plausibility-Driven Prioritization of Candidate Biomedical Annotations
Emanuele Cavalleri, Miad Alavinezhad, Dario Malchiodi and 1 more
The rapid growth of biomedical knowledge has made the validation of automatically generated biological annotations a major bottleneck in biomedical curation. While computational methods can rapidly produce large numbers of candidate annotations, determining which are biologically valid still requires costly expert review. Prioritizing these candidates before manual curation has therefore become a fundamental challenge. Machine learning techniques can support this process by exploiting biomedical knowledge graphs (bioKGs), which capture biological entities and their functional associations. In this work, we propose a framework that leverages bioKGs to estimate the plausibility of candidate annotations and guide expert curation. Starting from knowledge graph embeddings, we train relation-specific binary classifiers using a community-based negative sampling strategy to obtain reliable confidence estimates. We then introduce a family of plausibility measures that combine classifier confidence, classifier reliability, and the semantic context provided by alternative relationships involving the same pair of biological entities. Unlike conventional confidence estimation, the proposed approach explicitly accounts for multiple biologically meaningful relations that may coexist between the same entities. Experimental results on five large bioKGs demonstrate that the proposed negative sampling strategy consistently improves classifier robustness, increasing balanced accuracy by an average of 5.8%. Moreover, the plausibility measures outperform classifier confidence alone, enabling more effective prioritization of candidate annotations for expert review. Overall, our results show that the use of bioKGs improves the efficiency of AI-assisted biomedical curation while preserving expert control over the final annotation assessment.
#02Jul 22, 2026
physics.flu-dyn
Label-Free Finite-Volume-Residual Training of Attention Graph Neural Networks for Coupled Thermo-Fluid Fields
Tianyu Li, Zhiwei Cao, Qingang Zhang and 3 more
Neural surrogates are widely used in scientific machine learning for fast prediction of three-dimensional (3D) thermo-fluid fields. However, generating training data using conventional numerical solvers often incurs substantial computational and storage costs. We propose to train an attention graph neural network by minimizing the finite-volume method (FVM) residuals of the governing equations. These residuals are evaluated directly on the mesh, requiring no labeled data. We evaluate the trained surrogates against computational fluid dynamics (CFD) references and a data-supervised baseline across four scenarios. On the two steady-state benchmarks, the FVM-loss model achieves an all-field normalized root-mean-square error (nRMSE) of 2.3-2.8%. It demonstrates close agreement with the CFD references, including the buoyancy-energy coupling. On the two parametric transient cases, the FVM-loss model outperforms the supervised baseline in terms of accuracy, while avoiding the data-generation cost entirely. These results indicate that the FVM loss can provide a practical training signal for neural surrogates and reduce the model development cost.
#03Jul 22, 2026
cs.LG
The Blessing of Dimensionality: How Near-Orthogonality in High-Dimensional Spaces Explains Temporal Portability
Abigail Woodring, Adrian Chan, Rana Muhammad Shahroz Khan and 3 more
Fine-tuning has been widely used to adapt large language models (LLMs) for domain-specific tasks. Parameter efficient fine-tuning (PEFT) methods such as low-rank adaptation (LoRA) are frequently used to reduce computational costs. PortLLM is a training-free and data-free scheme used to adapt LLMs after continual pretraining. Although the initial PortLLM results show that LoRA patches exhibit short-term temporal portability, the long-term performance of PortLLM across several updates of continual pretraining remains underexplored. Furthermore, the intriguing effectiveness of PortLLM is not well understood from a theoretical standpoint. We address these two open questions by (1) performing an extensive empirical study of the long-term temporal portability of PortLLM patches across 10 continual pretraining steps using base models Mistral, Gemma, and Qwen; and (2) offering two theoretical analyses to explain our observation that the simple PortLLM method achieves competitive performance. We find empirically that the portability persists across longer time duration, indicating that repeated fine-tuning is not required when the base model is periodically updated. We find theoretically that near-orthogonality of high-dimensional vectors is a key justification for temporal portability. Our analyses also demonstrate a geometric perspective of the loss landscape in facilitating the theoretical comparison of different adaptation options.
#04Jul 22, 2026
cs.LG
Classical Hardware Acceleration of Quantum Autoencoders for Real-Time Anomaly Detection in Collider Experiments
Ivan Ge, Sagar Addepalli, Abhilasha Dave and 1 more
Quantum machine learning (QML) algorithms in high energy physics (HEP) can efficiently represent and leverage long-range, high-order correlations in high-dimensional collider data, potentially with fewer parameters and favorable scaling relative to classical models. Deployment of QML in real-time collider applications such as trigger systems requires the ability to emulate and compile quantum circuits classically, then synthesize the resulting quantum gates onto low-latency hardware accelerators, namely field-programmable gate arrays (FPGAs). We present a study of variational quantum autoencoder models for real-time anomaly detection triggers in modern collider experiments. The models achieve performance comparable to state-of-the-art classical approaches and, after FPGA synthesis, satisfy resource usage and timing constraints consistent with trigger applications in future colliders. This work provides one of the first FPGA implementations of QML models for HEP triggers, enabling higher-capability models in today's classical data acquisition pipelines while advancing quantum readiness of collider experiment infrastructure.
#05Jul 22, 2026
cs.LG
Self-organizing Architecture of Receptron Units: a Hardware-Aware Framework for Edge Intelligence
Stefano Radice, Ludovico Casaccia, Riccaro Emanuele Beccalli and 2 more
The growing demand for intelligent processing at the edge of IoT networks is constrained by the severe computational and memory limitations of microcontroller units, which render impractical conventional deep learning approaches. We propose a neuromorphicinspired classifier based on the Receptron model, a single-unit architecture capable of implementing non-linearly separable decision boundaries, without resorting to multi-layer networks. The model is designed for direct deployment on mid-range MCUs, while supporting continuous on-device adaptation. Experimental evaluation on basic dataset benchmarks yields cross-validated accuracies compatible with standard machine learning method baselines. These results position the Receptron as a viable and interpretable alternative for resource-constrained neuromorphic edge systems operating in dynamic, non-stationary environments.