Residue-Level Attributions in Protein Language Models Do Not Recover Allergen Epitopes

Deep allergenicity classifiers are increasingly used in safety screening of novel foods, and recent protein language models have substantially improved protein-level allergenicity prediction. However, whether their explanations capture biologically meaningful information remains unclear. We introduce an epitope-grounded residue-level benchmark for quantitatively evaluating attribution faithfulness in protein allergenicity models. Across frozen ESM-2, multi-task ESM-2, and DeepPlantAllergy, protein-level classification was robust, yet classification-head explanation signals did not significantly exceed random in their residue-level alignment with annotated epitopes across AUROC, AUPRC, and Precision@k. Integrated Gradients identified residues that were functionally important to the model, but not overlapping annotated epitopes. Saturation mutagenesis further suggested classifiers may rely on physicochemical and compositional sequence features rather than epitope-specific mechanisms. Residue-level importance signals should therefore not be interpreted as immunological explanations for safety screening or hypoallergen design without quantitative validation. Code available: https://github.com/Jeffateth/XAllergen2.0-paper

Personalized Spiking Neural Networks with Ferroelectric Synapses for EEG Signal Processing

Electroencephalography (EEG)-based brain-computer interfaces (BCIs) are strongly affected by non-stationary neural signals that vary across sessions and individuals, limiting the generalization of subject-agnostic models and motivating adaptive and personalized learning on resource-constrained platforms. Programmable memristive hardware offers a promising substrate for such post-deployment adaptation; however, practical realization is challenged by limited weight resolution, device variability, nonlinear programming dynamics, and finite device endurance. In this work, we show that spiking neural networks (SNNs) can be deployed on ferroelectric memristive synaptic devices for adaptive EEG-based motor imagery decoding under realistic device constraints. We fabricate, characterize, and model ferroelectric synapses. We evaluate a convolutional-recurrent SNN architecture under two complementary deployment strategies: (i) device-aware training using a ferroelectric synapse model, and (ii) transfer of software-trained weights followed by low-overhead on-device re-tuning. To enable efficient adaptation, we introduce a device-aware weight-update strategy in which gradient-based updates are accumulated digitally and converted into discrete programming events only when a threshold is exceeded, emulating nonlinear, state-dependent programming dynamics while reducing programming frequency. Both deployment strategies achieve classification performance comparable to state-of-the-art software-based SNNs. Furthermore, subject-specific transfer learning achieved by retraining only the final network layers improves classification accuracy. These results demonstrate that programmable ferroelectric hardware can support robust, low-overhead adaptation in spiking neural networks, opening a practical path toward personalized neuromorphic processing of neural signals.